diff --git a/.gitignore b/.gitignore index 1fb8c951..013ab917 100644 --- a/.gitignore +++ b/.gitignore @@ -77,11 +77,7 @@ mmif/vocabulary ./VERSION* .hypothesis - -# sphinx/autodoc files -documentation/_build/ - -/VERSION -_issues - +# Documentation build artifacts documentation/cli_help.rst +documentation/whatsnew.rst +docs-test diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 00000000..0c7f166b --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,47 @@ +# Contributing to mmif-python + +## Documentation + +The documentation for `mmif-python` is built using Sphinx and published to the [CLAMS documentation hub](https://github.com/clamsproject/website-test). + +### Building Documentation Locally + +To build the documentation for the current checkout: + +```bash +make doc +# OR +python3 build-tools/docs.py +``` + +The output will be in `documentation/_build/html`. + +### Building Documentation for Old Versions + +To build documentation for a specific historical version (e.g., `v1.0.0`): + +```bash +make doc-version +# OR +python3 build-tools/docs.py --build-ver v1.0.0 +``` + +This runs the build in a sandboxed temporary directory. The output will be in `docs-test/`. + +### Troubleshooting Old Version Builds + +**Important:** The build script (`build-tools/docs.py`) uses a "Modern Environment, Legacy Source" strategy. It checks out the old source code but installs **modern** build dependencies (Sphinx 7.x, Furo) to ensure the build works on current systems (including Python 3.13). + +If an old version fails to build because a dependency is missing (e.g., it was removed from `requirements.txt` in later versions but the old `setup.py` needs it), **do not try to fix the old `setup.py`**. + +Instead, manually add the missing dependency to the `run_pip` call in `build-tools/docs.py`: + +```python +# In build-tools/docs.py +def build_versioned_docs(...): + # ... + # Add the missing dependency here + env.run_pip("install", "jsonschema", "requests", "pyyaml", "deepdiff<7", "YOUR_MISSING_DEP", cwd=source_path) +``` + +This "overlay" strategy ensures we can build old docs without modifying historical git tags. diff --git a/Makefile b/Makefile index 3b6fe22e..ec63ccf1 100644 --- a/Makefile +++ b/Makefile @@ -35,19 +35,18 @@ publish: distclean version package test $(generatedcode): dist/$(sdistname)*.tar.gz -docs: latest := $(shell git tag | sort -t. -k 1,1nr -k 2,2nr -k 3,3nr -k 4,4nr | head -n 1) -docs: VERSION $(generatedcode) - rm -rf docs - pip install --upgrade -r requirements.txt - pip install --upgrade -r requirements.old - sphinx-multiversion documentation docs -b html -a - touch docs/.nojekyll - ln -sf $(latest) docs/latest - echo " Redirect to latest version " > docs/index.html - -doc: VERSION $(generatedcode) # for single version sphinx - only use when developing - rm -rf docs - sphinx-build documentation docs -b html -a +docs: + @echo "WARNING: The 'docs' target is deprecated and will be removed." + @echo "The 'docs' directory is no longer used. Documentation is now hosted in the central CLAMS documentation hub." + @echo "Use 'make doc' for local builds or 'make doc-version' for specific versions." + @echo "Nothing is done." + +doc: # for single version sphinx - builds current source + python3 build-tools/docs.py + +doc-version: # interactive build for specific version + @read -p "Enter version/tag to build (e.g., v1.0.0): " ver; \ + [ -n "$$ver" ] && python3 build-tools/docs.py --build-ver $$ver package: VERSION dist/$(sdistname)*.tar.gz diff --git a/README.md b/README.md index b3e8f98a..1cd1070a 100644 --- a/README.md +++ b/README.md @@ -16,3 +16,6 @@ including ; * [Version history and patch notes](https://github.com/clamsproject/mmif-python/blob/main/CHANGELOG.md) * [MMIF Python API documentation](https://clamsproject.github.io/mmif-python) * [MMIF JSON specification and schema](https://clamsproject.github.io/mmif) + +## For devs ... +* Build documentation: `python build-tools/docs.py --help` diff --git a/build-tools/docs.py b/build-tools/docs.py new file mode 100644 index 00000000..ee5d4550 --- /dev/null +++ b/build-tools/docs.py @@ -0,0 +1,323 @@ +import argparse +import shutil +import subprocess +import sys +import tempfile +import venv +from pathlib import Path + + +def run_command(command, cwd=None, check=True, env=None): + """Helper to run a shell command.""" + print(f"Running: {' '.join(str(c) for c in command)}") + result = subprocess.run(command, cwd=cwd, env=env) + if check and result.returncode != 0: + print(f"Error: Command failed with exit code {result.returncode}") + sys.exit(result.returncode) + return result + + +class Venv: + """A helper class to manage a virtual environment.""" + + def __init__(self, venv_dir): + self.venv_dir = Path(venv_dir) + self.python = self.venv_dir / "bin" / "python" + self.pip = self.venv_dir / "bin" / "pip" + self.sphinx_build = self.venv_dir / "bin" / "sphinx-build" + + def create(self): + print(f"Creating virtual environment in: {self.venv_dir}") + venv.create(self.venv_dir, with_pip=True) + + def run_pip(self, *args, cwd=None): + run_command([self.pip, *args], cwd=cwd) + + def run_python(self, *args, cwd=None): + run_command([self.python, *args], cwd=cwd) + + def run_sphinx_build(self, *args, cwd=None, check=True): + return run_command([self.sphinx_build, *args], cwd=cwd, check=check) + + +def build_docs_local(source_dir: Path, output_dir: Path): + """ + Builds documentation for the provided source directory. + Assumes it's running in an environment with necessary tools. + """ + print("--- Running in Local Build Mode ---") + + # 1. Generate source code and install in editable mode. + print("\n--- Step 1: Generating source code and installing in editable mode ---") + try: + run_command([sys.executable, "-m", "pip", "install", "-e", "."], cwd=source_dir) + except SystemExit: + print("Warning: 'pip install -e .' failed. This might be due to an externally managed environment.") + print("Attempting to proceed with documentation build assuming dependencies are met...") + + + # 2. Install documentation-specific dependencies. + print("\n--- Step 2: Installing documentation dependencies ---") + doc_reqs = Path.cwd() / "build-tools" / "requirements.docs.txt" + if not doc_reqs.exists(): + print(f"Error: Documentation requirements not found at {doc_reqs}") + sys.exit(1) + try: + run_command([sys.executable, "-m", "pip", "install", "-r", str(doc_reqs)]) + except SystemExit: + print("Warning: Failed to install documentation dependencies.") + # Check if sphinx-build is available + if shutil.which("sphinx-build") is None: + print("Error: 'sphinx-build' not found and installation failed.") + print("Please install dependencies manually or run this script inside a virtual environment.") + sys.exit(1) + print("Assuming dependencies are already installed...") + + # 3. Build the documentation using Sphinx. + print("\n--- Step 3: Building Sphinx documentation ---") + docs_source_dir = source_dir / "documentation" + docs_build_dir = output_dir / "develop" + sphinx_command = [ + "sphinx-build", + str(docs_source_dir), + str(docs_build_dir), + "-b", "html", # build html + "-a", # write all files (rebuild everything) + "-E", # don't use a saved environment, reread all files + ] + run_command(sphinx_command) + + print(f"\nDocumentation build complete. Output in: {docs_build_dir}") + return docs_build_dir + + +def build_versioned_docs(env: Venv, source_path: Path, version: str): + """ + Build documentation for a specific version with unified furo theme. + Works for all versions (old and new) with consistent visual output. + """ + print(f"\n--- Building documentation for version {version} ---") + + # Skip old pinned requirements.txt as they have Python 3.13 incompatible deps + # Instead, install modern versions of core dependencies + # Pin deepdiff<7 for compatibility with orderly-set 5.3.x (required by older versions) + print("\n--- Installing modern compatible dependencies ---") + env.run_pip("install", "jsonschema", "requests", "pyyaml", "deepdiff<7", cwd=source_path) + + # Install sphinx 7.x (Python 3.13 compatible), furo theme, and m2r2 + print("\n--- Installing sphinx and furo theme ---") + env.run_pip("install", "sphinx>=7.0,<8.0", "furo", "m2r2", cwd=source_path) + + # Write VERSION file (needed for setup.py and sphinx) + version_file = source_path / "VERSION" + version_file.write_text(version) + + # Inject linkcode_resolve function into conf.py for GitHub source links + # because some old version of conf.py may not have it + print("\n--- Injecting linkcode_resolve into conf.py ---") + conf_py = source_path / "documentation" / "conf.py" + if conf_py.exists(): + linkcode_snippet = f''' + +# -- Injected linkcode configuration for GitHub source links -- +import inspect +import os +import sys +from pathlib import Path + +def linkcode_resolve(domain, info): + if domain != 'py' or not info.get('module'): + return None + try: + obj = sys.modules.get(info['module']) + if obj is None: return None + for part in info['fullname'].split('.'): + obj = getattr(obj, part) + unwrapped_obj = inspect.unwrap(obj) + filename = inspect.getsourcefile(unwrapped_obj) + if not filename: return None + lines, start_lineno = inspect.getsourcelines(unwrapped_obj) + end_lineno = start_lineno + len(lines) - 1 + repo_root = Path(__file__).parent.parent + rel_path = Path(filename).relative_to(repo_root) + return f"https://github.com/clamsproject/mmif-python/blob/{version}/{{rel_path}}#L{{start_lineno}}-L{{end_lineno}}" + except Exception: + return None +''' + with open(conf_py, "a") as f: + f.write(linkcode_snippet) + + # Install package in develop mode to generate code (ver, res, vocabulary) + # Uses setup.py develop for compatibility with all versions + print("\n--- Installing package in develop mode ---") + env.run_python("setup.py", "develop", cwd=source_path) + + # Build documentation with sphinx-build + print("\n--- Building Sphinx documentation ---") + docs_source_dir = source_path / "documentation" + docs_build_dir = docs_source_dir / "_build" / "html" + + # Run sphinx-build with unified parameters for visual consistency + result = env.run_sphinx_build( + str(docs_source_dir), + str(docs_build_dir), + "-b", "html", + "-D", f"project=mmif-python-{version}", + "-D", f"version={version}", + "-D", "extensions=sphinx.ext.autodoc,sphinx.ext.linkcode,m2r2", + "-D", "html_theme=furo", + "-a", # write all files + "-E", # don't use saved environment + "--keep-going", # continue past errors + cwd=source_path, + check=False + ) + + # Verify output was created + index_html = docs_build_dir / "index.html" + if not index_html.exists(): + print(f"Error: Documentation build failed - no index.html created") + sys.exit(1) + + if result.returncode != 0: + print(f"Warning: Sphinx build had errors (exit code {result.returncode}), but output was created") + + return docs_build_dir + + +def build_docs_for_version(version: str, output_base_dir: Path, repo_path: Path = None): + """ + Builds docs for a specific version in a sandbox. + Uses local repo copy instead of cloning for efficiency. + + Args: + version: Git tag/ref to build + output_base_dir: Directory to output built docs + repo_path: Path to local repo to copy from (defaults to cwd) + """ + print(f"--- Running in Version Build Mode for version: {version} ---") + + if repo_path is None: + repo_path = Path.cwd() + + with tempfile.TemporaryDirectory() as tmpdir: + tmp_path = Path(tmpdir) + source_path = tmp_path / "source" + venv_path = tmp_path / "venv" + + print(f"\n--- Step 1: Copying local repository to temporary directory ---") + shutil.copytree(repo_path, source_path, symlinks=True) + # Reset to clean state and checkout the target version + run_command(["git", "checkout", "."], cwd=source_path) + run_command(["git", "clean", "-fdx"], cwd=source_path) + run_command(["git", "checkout", version], cwd=source_path) + + print(f"\n--- Step 2: Creating and setting up virtual environment ---") + env = Venv(venv_path) + env.create() + # Use setuptools<80 for compatibility with older setup.py files + # that use the old import structure + env.run_pip("install", "--upgrade", "pip", "setuptools<80", "wheel") + + print(f"\n--- Step 3: Building documentation ---") + built_docs_path = build_versioned_docs(env, source_path, version) + + print(f"\n--- Step 4: Copying built artifacts to output directory ---") + version_output_dir = output_base_dir / version + if version_output_dir.exists(): + print(f"Removing existing directory: {version_output_dir}") + shutil.rmtree(version_output_dir) + shutil.copytree(built_docs_path, version_output_dir) + + print(f"\nDocumentation for {version} built successfully in: {version_output_dir}") + + +def get_all_tags(): + """Get all git tags sorted by version.""" + result = subprocess.run( + ["git", "tag", "--sort=version:refname"], + capture_output=True, text=True, check=True + ) + return [tag.strip() for tag in result.stdout.strip().split('\n') if tag.strip()] + + +def get_tags_since(since_version: str): + """Get all tags >= since_version.""" + all_tags = get_all_tags() + try: + start_idx = all_tags.index(since_version) + return all_tags[start_idx:] + except ValueError: + print(f"Warning: Version {since_version} not found in tags.") + return [] + + +def main(): + parser = argparse.ArgumentParser( + description="Build documentation for the mmif-python project. " + "Can build for the current directory or a specific git version in a sandbox." + ) + parser.add_argument( + "--build-ver", + metavar="", + help="Build docs for a specific git ref (tag/branch) in a temporary, sandboxed environment." + ) + parser.add_argument( + "--build-all-since", + metavar="", + help="Build docs for all versions since (and including) the specified version." + ) + parser.add_argument( + "--output-dir", + metavar="", + default="docs-test", + help="The base directory for versioned documentation output (default: docs-test). For non-versioned builds, this is ignored, and the artifacts are placed in the local documentation _build/html directory." + ) + parser.add_argument( + "--list-versions", + action="store_true", + help="List all available versions and exit." + ) + args = parser.parse_args() + + if args.list_versions: + tags = get_all_tags() + print("Available versions:") + for tag in tags: + print(f" {tag}") + return + + output_dir = Path(args.output_dir) + output_dir.mkdir(exist_ok=True) + if args.build_all_since: + versions = get_tags_since(args.build_all_since) + print(f"Building documentation for {len(versions)} versions: {versions}") + failed = [] + for i, version in enumerate(versions, 1): + print(f"\n{'=' * 60}") + print(f"Building version {version} ({i}/{len(versions)})") + print(f"{'=' * 60}") + try: + build_docs_for_version(version, output_dir) + except Exception as e: + print(f"ERROR building {version}: {e}") + failed.append((version, str(e))) + + print(f"\n{'=' * 60}") + print(f"BUILD SUMMARY") + print(f"{'=' * 60}") + print(f"Total versions: {len(versions)}") + print(f"Successful: {len(versions) - len(failed)}") + print(f"Failed: {len(failed)}") + if failed: + print("\nFailed versions:") + for version, error in failed: + print(f" {version}: {error}") + elif args.build_ver: + build_docs_for_version(args.build_ver, output_dir) + else: + build_docs_local(Path.cwd(), output_dir) + + +if __name__ == "__main__": + main() diff --git a/build-tools/requirements.docs.txt b/build-tools/requirements.docs.txt new file mode 100644 index 00000000..8d9ee33d --- /dev/null +++ b/build-tools/requirements.docs.txt @@ -0,0 +1,3 @@ +sphinx>=7.0,<8.0 +furo +m2r2 diff --git a/docs/.nojekyll b/docs/.nojekyll deleted file mode 100644 index e69de29b..00000000 diff --git a/docs/0.3.0/.buildinfo b/docs/0.3.0/.buildinfo deleted file mode 100644 index 80f4bb3c..00000000 --- a/docs/0.3.0/.buildinfo +++ /dev/null @@ -1,4 +0,0 @@ -# Sphinx build info version 1 -# This file records the configuration used when building these files. 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The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the `appliance documentation `_ to learn more about the appliance. - -MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance. - -#. The code must be hosted on a public git repository (e.g. Github, Gitlab, ...) -#. Must listen to ``5000`` port. -#. Must expose ``/display`` route . -#. ``/display`` router should response to ``GET`` requests. -#. In the ``GET`` request, a public URL of the input MMIF file is passed via ``file`` URL parameter. -#. On the codebase root, there must be a ``Dockerfile`` that can build a `docker `_ image that runs the web app. - -We provide an example consumer at https://github.com/clamsproject/mmif-visualizer. diff --git a/docs/0.3.0/_sources/index.rst.txt b/docs/0.3.0/_sources/index.rst.txt deleted file mode 100644 index 6146286d..00000000 --- a/docs/0.3.0/_sources/index.rst.txt +++ /dev/null @@ -1,25 +0,0 @@ -Welcome to mmif-python's documentation! -======================================= - -.. mdinclude:: ../README.md - -.. toctree:: - :maxdepth: 2 - :caption: Contents - - introduction - consumer-tutorial - -.. toctree:: - :maxdepth: 2 - :caption: API documentation: - - modules - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/docs/0.3.0/_sources/introduction.rst.txt b/docs/0.3.0/_sources/introduction.rst.txt deleted file mode 100644 index 6af8cd61..00000000 --- a/docs/0.3.0/_sources/introduction.rst.txt +++ /dev/null @@ -1,75 +0,0 @@ -.. _instroduction: - -Getting Started -=============== - - -Overview ---------- - -MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF wbesite `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports de-/serialization of MMIF objects, as well as many navigation and manipulation helpers for MMIF objects. - -Prerequisites -------------- - -* `Python `_: ``mmif-python`` requires Python 3.6 or newer. We have no plan to support `Python 2.7 `_. - -Installation ---------------- - -Package ``mmif-python`` is distributed via the official PyPI. Users are supposed to pip-install to get latest release. - -.. code-block:: bash - - pip install mmif-python - -This will install a package `mmif` to local python. -The MMIF format and specification is evolving over time, and ``mmif-python`` package will be updated along with the changes in MMIF format. Note that MMIF format is not always backward-compatible. To find out more about relations between MMIF versions and ``mmif-python`` versions, and which supports which, please take time to read our decision on the subject `here `_. - -MMIF Serialization ---------------------------- - -:class:`mmif.serialize.mmif.Mmif` represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of :class:`mmif.serialize.model.MmifObject`, including the :class:`mmif.serialize.mmif.Mmif`. To start with an existing MMIF :class:`str`, simple initiate a new ``Mmif`` object with the file. - -.. code-block:: python - - import mmif - from mmif import Mmif - - mmif_str = """{ - "metadata": { - "mmif": "http://mmif.clams.ai/0.2.0" - }, - "documents": [ - { - "@type": "http://mmif.clams.ai/0.2.0/vocabulary/VideoDocument", - "properties": { - "id": "m1", - "mime": "video/mp4", - "location": "file:///var/archive/video-0012.mp4" - } - }, - { - "@type": "http://mmif.clams.ai/0.2.0/vocabulary/TextDocument", - "properties": { - "id": "m2", - "mime": "text/plain", - "location": "file:///var/archive/video-0012-transcript.txt" - } - } - ], - "views": []}""" - mmif_obj = Mmif(mmif_str) - - -Few notes; - -#. MMIF does not carry the primary source files in it. -#. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version ``mmif-python`` implementation of the MMIF might not be able to load an unsupported version of MMIF string. - -When serializing back to :class:`str`, call ``.serialize()`` (:meth:`mmif.serialize.model.MmifObject.serialize`) on the object. - -To get subcomponents, you can use various getters implemented in subclasses. For more details, the API documentation (:ref:`apidoc`) will help. - diff --git a/docs/0.3.0/_sources/modules.rst.txt b/docs/0.3.0/_sources/modules.rst.txt deleted file mode 100644 index e4269c6d..00000000 --- a/docs/0.3.0/_sources/modules.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _apidoc: - -mmif package -============ - -.. toctree:: - :maxdepth: 4 - - autodoc/mmif.serialize - autodoc/mmif.vocabulary diff --git a/docs/0.3.0/_static/_sphinx_javascript_frameworks_compat.js b/docs/0.3.0/_static/_sphinx_javascript_frameworks_compat.js deleted file mode 100644 index 81415803..00000000 --- a/docs/0.3.0/_static/_sphinx_javascript_frameworks_compat.js +++ /dev/null @@ -1,123 +0,0 @@ -/* Compatability shim for jQuery and underscores.js. - * - * Copyright Sphinx contributors - * Released under the two clause BSD licence - */ - -/** - * small helper function to urldecode strings - * - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL - */ -jQuery.urldecode = function(x) { - if (!x) { - return x - } - return decodeURIComponent(x.replace(/\+/g, ' ')); -}; - -/** - * small helper function to urlencode strings - */ -jQuery.urlencode = encodeURIComponent; - -/** - * This function returns the parsed url parameters of the - * current request. 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- -/** - * Simple result scoring code. - */ -if (typeof Scorer === "undefined") { - var Scorer = { - // Implement the following function to further tweak the score for each result - // The function takes a result array [docname, title, anchor, descr, score, filename] - // and returns the new score. - /* - score: result => { - const [docname, title, anchor, descr, score, filename, kind] = result - return score - }, - */ - - // query matches the full name of an object - objNameMatch: 11, - // or matches in the last dotted part of the object name - objPartialMatch: 6, - // Additive scores depending on the priority of the object - objPrio: { - 0: 15, // used to be importantResults - 1: 5, // used to be objectResults - 2: -5, // used to be unimportantResults - }, - // Used when the priority is not in the mapping. - objPrioDefault: 0, - - // query found in title - title: 15, - partialTitle: 7, - // query found in terms - term: 5, - partialTerm: 2, - }; -} - -// Global search result kind enum, used by themes to style search results. -class SearchResultKind { - static get index() { return "index"; } - static get object() { return "object"; } - static get text() { return "text"; } - static get title() { return "title"; } -} - -const _removeChildren = (element) => { - while (element && element.lastChild) element.removeChild(element.lastChild); -}; - -/** - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping - */ -const _escapeRegExp = (string) => - string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string - -const _displayItem = (item, searchTerms, highlightTerms) => { - const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; - const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; - const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; - const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; - const contentRoot = document.documentElement.dataset.content_root; - - const [docName, title, anchor, descr, score, _filename, kind] = item; - - let listItem = document.createElement("li"); - // Add a class representing the item's type: - // can be used by a theme's CSS selector for styling - // See SearchResultKind for the class names. - listItem.classList.add(`kind-${kind}`); - let requestUrl; - let linkUrl; - if (docBuilder === "dirhtml") { - // dirhtml builder - let dirname = docName + "/"; - if (dirname.match(/\/index\/$/)) - dirname = dirname.substring(0, dirname.length - 6); - else if (dirname === "index/") dirname = ""; - requestUrl = contentRoot + dirname; - linkUrl = requestUrl; - } else { - // normal html builders - requestUrl = contentRoot + docName + docFileSuffix; - linkUrl = docName + docLinkSuffix; - } - let linkEl = listItem.appendChild(document.createElement("a")); - linkEl.href = linkUrl + anchor; - linkEl.dataset.score = score; - linkEl.innerHTML = title; - if (descr) { - listItem.appendChild(document.createElement("span")).innerHTML = - " (" + descr + ")"; - // highlight search terms in the description - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - } - else if (showSearchSummary) - fetch(requestUrl) - .then((responseData) => responseData.text()) - .then((data) => { - if (data) - listItem.appendChild( - Search.makeSearchSummary(data, searchTerms, anchor) - ); - // highlight search terms in the summary - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - }); - Search.output.appendChild(listItem); -}; -const _finishSearch = (resultCount) => { - Search.stopPulse(); - Search.title.innerText = _("Search Results"); - if (!resultCount) - Search.status.innerText = Documentation.gettext( - "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." - ); - else - Search.status.innerText = Documentation.ngettext( - "Search finished, found one page matching the search query.", - "Search finished, found ${resultCount} pages matching the search query.", - resultCount, - ).replace('${resultCount}', resultCount); -}; -const _displayNextItem = ( - results, - resultCount, - searchTerms, - highlightTerms, -) => { - // results left, load the summary and display it - // this is intended to be dynamic (don't sub resultsCount) - if (results.length) { - _displayItem(results.pop(), searchTerms, highlightTerms); - setTimeout( - () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), - 5 - ); - } - // search finished, update title and status message - else _finishSearch(resultCount); -}; -// Helper function used by query() to order search results. -// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. -// Order the results by score (in opposite order of appearance, since the -// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. -const _orderResultsByScoreThenName = (a, b) => { - const leftScore = a[4]; - const rightScore = b[4]; - if (leftScore === rightScore) { - // same score: sort alphabetically - const leftTitle = a[1].toLowerCase(); - const rightTitle = b[1].toLowerCase(); - if (leftTitle === rightTitle) return 0; - return leftTitle > rightTitle ? -1 : 1; // inverted is intentional - } - return leftScore > rightScore ? 1 : -1; -}; - -/** - * Default splitQuery function. Can be overridden in ``sphinx.search`` with a - * custom function per language. - * - * The regular expression works by splitting the string on consecutive characters - * that are not Unicode letters, numbers, underscores, or emoji characters. - * This is the same as ``\W+`` in Python, preserving the surrogate pair area. - */ -if (typeof splitQuery === "undefined") { - var splitQuery = (query) => query - .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) - .filter(term => term) // remove remaining empty strings -} - -/** - * Search Module - */ -const Search = { - _index: null, - _queued_query: null, - _pulse_status: -1, - - htmlToText: (htmlString, anchor) => { - const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - for (const removalQuery of [".headerlink", "script", "style"]) { - htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); - } - if (anchor) { - const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); - if (anchorContent) return anchorContent.textContent; - - console.warn( - `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` - ); - } - - // if anchor not specified or not found, fall back to main content - const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent) return docContent.textContent; - - console.warn( - "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." - ); - return ""; - }, - - init: () => { - const query = new URLSearchParams(window.location.search).get("q"); - document - .querySelectorAll('input[name="q"]') - .forEach((el) => (el.value = query)); - if (query) Search.performSearch(query); - }, - - loadIndex: (url) => - (document.body.appendChild(document.createElement("script")).src = url), - - setIndex: (index) => { - Search._index = index; - if (Search._queued_query !== null) { - const query = Search._queued_query; - Search._queued_query = null; - Search.query(query); - } - }, - - hasIndex: () => Search._index !== null, - - deferQuery: (query) => (Search._queued_query = query), - - stopPulse: () => (Search._pulse_status = -1), - - startPulse: () => { - if (Search._pulse_status >= 0) return; - - const pulse = () => { - Search._pulse_status = (Search._pulse_status + 1) % 4; - Search.dots.innerText = ".".repeat(Search._pulse_status); - if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); - }; - pulse(); - }, - - /** - * perform a search for something (or wait until index is loaded) - */ - performSearch: (query) => { - // create the required interface elements - const searchText = document.createElement("h2"); - searchText.textContent = _("Searching"); - const searchSummary = document.createElement("p"); - searchSummary.classList.add("search-summary"); - searchSummary.innerText = ""; - const searchList = document.createElement("ul"); - searchList.setAttribute("role", "list"); - searchList.classList.add("search"); - - const out = document.getElementById("search-results"); - Search.title = out.appendChild(searchText); - Search.dots = Search.title.appendChild(document.createElement("span")); - Search.status = out.appendChild(searchSummary); - Search.output = out.appendChild(searchList); - - const searchProgress = document.getElementById("search-progress"); - // Some themes don't use the search progress node - if (searchProgress) { - searchProgress.innerText = _("Preparing search..."); - } - Search.startPulse(); - - // index already loaded, the browser was quick! - if (Search.hasIndex()) Search.query(query); - else Search.deferQuery(query); - }, - - _parseQuery: (query) => { - // stem the search terms and add them to the correct list - const stemmer = new Stemmer(); - const searchTerms = new Set(); - const excludedTerms = new Set(); - const highlightTerms = new Set(); - const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); - splitQuery(query.trim()).forEach((queryTerm) => { - const queryTermLower = queryTerm.toLowerCase(); - - // maybe skip this "word" - // stopwords array is from language_data.js - if ( - stopwords.indexOf(queryTermLower) !== -1 || - queryTerm.match(/^\d+$/) - ) - return; - - // stem the word - let word = stemmer.stemWord(queryTermLower); - // select the correct list - if (word[0] === "-") excludedTerms.add(word.substr(1)); - else { - searchTerms.add(word); - highlightTerms.add(queryTermLower); - } - }); - - if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js - localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) - } - - // console.debug("SEARCH: searching for:"); - // console.info("required: ", [...searchTerms]); - // console.info("excluded: ", [...excludedTerms]); - - return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; - }, - - /** - * execute search (requires search index to be loaded) - */ - _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - - // Collect multiple result groups to be sorted separately and then ordered. - // Each is an array of [docname, title, anchor, descr, score, filename, kind]. - const normalResults = []; - const nonMainIndexResults = []; - - _removeChildren(document.getElementById("search-progress")); - - const queryLower = query.toLowerCase().trim(); - for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { - for (const [file, id] of foundTitles) { - const score = Math.round(Scorer.title * queryLower.length / title.length); - const boost = titles[file] === title ? 1 : 0; // add a boost for document titles - normalResults.push([ - docNames[file], - titles[file] !== title ? `${titles[file]} > ${title}` : title, - id !== null ? "#" + id : "", - null, - score + boost, - filenames[file], - SearchResultKind.title, - ]); - } - } - } - - // search for explicit entries in index directives - for (const [entry, foundEntries] of Object.entries(indexEntries)) { - if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id, isMain] of foundEntries) { - const score = Math.round(100 * queryLower.length / entry.length); - const result = [ - docNames[file], - titles[file], - id ? "#" + id : "", - null, - score, - filenames[file], - SearchResultKind.index, - ]; - if (isMain) { - normalResults.push(result); - } else { - nonMainIndexResults.push(result); - } - } - } - } - - // lookup as object - objectTerms.forEach((term) => - normalResults.push(...Search.performObjectSearch(term, objectTerms)) - ); - - // lookup as search terms in fulltext - normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); - - // let the scorer override scores with a custom scoring function - if (Scorer.score) { - normalResults.forEach((item) => (item[4] = Scorer.score(item))); - nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); - } - - // Sort each group of results by score and then alphabetically by name. - normalResults.sort(_orderResultsByScoreThenName); - nonMainIndexResults.sort(_orderResultsByScoreThenName); - - // Combine the result groups in (reverse) order. - // Non-main index entries are typically arbitrary cross-references, - // so display them after other results. - let results = [...nonMainIndexResults, ...normalResults]; - - // remove duplicate search results - // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept - let seen = new Set(); - results = results.reverse().reduce((acc, result) => { - let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); - if (!seen.has(resultStr)) { - acc.push(result); - seen.add(resultStr); - } - return acc; - }, []); - - return results.reverse(); - }, - - query: (query) => { - const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); - const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); - - // for debugging - //Search.lastresults = results.slice(); // a copy - // console.info("search results:", Search.lastresults); - - // print the results - _displayNextItem(results, results.length, searchTerms, highlightTerms); - }, - - /** - * search for object names - */ - performObjectSearch: (object, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const objects = Search._index.objects; - const objNames = Search._index.objnames; - const titles = Search._index.titles; - - const results = []; - - const objectSearchCallback = (prefix, match) => { - const name = match[4] - const fullname = (prefix ? prefix + "." : "") + name; - const fullnameLower = fullname.toLowerCase(); - if (fullnameLower.indexOf(object) < 0) return; - - let score = 0; - const parts = fullnameLower.split("."); - - // check for different match types: exact matches of full name or - // "last name" (i.e. last dotted part) - if (fullnameLower === object || parts.slice(-1)[0] === object) - score += Scorer.objNameMatch; - else if (parts.slice(-1)[0].indexOf(object) > -1) - score += Scorer.objPartialMatch; // matches in last name - - const objName = objNames[match[1]][2]; - const title = titles[match[0]]; - - // If more than one term searched for, we require other words to be - // found in the name/title/description - const otherTerms = new Set(objectTerms); - otherTerms.delete(object); - if (otherTerms.size > 0) { - const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); - if ( - [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) - ) - return; - } - - let anchor = match[3]; - if (anchor === "") anchor = fullname; - else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; - - const descr = objName + _(", in ") + title; - - // add custom score for some objects according to scorer - if (Scorer.objPrio.hasOwnProperty(match[2])) - score += Scorer.objPrio[match[2]]; - else score += Scorer.objPrioDefault; - - results.push([ - docNames[match[0]], - fullname, - "#" + anchor, - descr, - score, - filenames[match[0]], - SearchResultKind.object, - ]); - }; - Object.keys(objects).forEach((prefix) => - objects[prefix].forEach((array) => - objectSearchCallback(prefix, array) - ) - ); - return results; - }, - - /** - * search for full-text terms in the index - */ - performTermsSearch: (searchTerms, excludedTerms) => { - // prepare search - const terms = Search._index.terms; - const titleTerms = Search._index.titleterms; - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - - const scoreMap = new Map(); - const fileMap = new Map(); - - // perform the search on the required terms - searchTerms.forEach((word) => { - const files = []; - const arr = [ - { files: terms[word], score: Scorer.term }, - { files: titleTerms[word], score: Scorer.title }, - ]; - // add support for partial matches - if (word.length > 2) { - const escapedWord = _escapeRegExp(word); - if (!terms.hasOwnProperty(word)) { - Object.keys(terms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: terms[term], score: Scorer.partialTerm }); - }); - } - if (!titleTerms.hasOwnProperty(word)) { - Object.keys(titleTerms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); - }); - } - } - - // no match but word was a required one - if (arr.every((record) => record.files === undefined)) return; - - // found search word in contents - arr.forEach((record) => { - if (record.files === undefined) return; - - let recordFiles = record.files; - if (recordFiles.length === undefined) recordFiles = [recordFiles]; - files.push(...recordFiles); - - // set score for the word in each file - recordFiles.forEach((file) => { - if (!scoreMap.has(file)) scoreMap.set(file, {}); - scoreMap.get(file)[word] = record.score; - }); - }); - - // create the mapping - files.forEach((file) => { - if (!fileMap.has(file)) fileMap.set(file, [word]); - else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); - }); - }); - - // now check if the files don't contain excluded terms - const results = []; - for (const [file, wordList] of fileMap) { - // check if all requirements are matched - - // as search terms with length < 3 are discarded - const filteredTermCount = [...searchTerms].filter( - (term) => term.length > 2 - ).length; - if ( - wordList.length !== searchTerms.size && - wordList.length !== filteredTermCount - ) - continue; - - // ensure that none of the excluded terms is in the search result - if ( - [...excludedTerms].some( - (term) => - terms[term] === file || - titleTerms[term] === file || - (terms[term] || []).includes(file) || - (titleTerms[term] || []).includes(file) - ) - ) - break; - - // select one (max) score for the file. - const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); - // add result to the result list - results.push([ - docNames[file], - titles[file], - "", - null, - score, - filenames[file], - SearchResultKind.text, - ]); - } - return results; - }, - - /** - * helper function to return a node containing the - * search summary for a given text. keywords is a list - * of stemmed words. - */ - makeSearchSummary: (htmlText, keywords, anchor) => { - const text = Search.htmlToText(htmlText, anchor); - if (text === "") return null; - - const textLower = text.toLowerCase(); - const actualStartPosition = [...keywords] - .map((k) => textLower.indexOf(k.toLowerCase())) - .filter((i) => i > -1) - .slice(-1)[0]; - const startWithContext = Math.max(actualStartPosition - 120, 0); - - const top = startWithContext === 0 ? "" : "..."; - const tail = startWithContext + 240 < text.length ? "..." : ""; - - let summary = document.createElement("p"); - summary.classList.add("context"); - summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; - - return summary; - }, -}; - -_ready(Search.init); diff --git a/docs/0.3.0/_static/sphinx_highlight.js b/docs/0.3.0/_static/sphinx_highlight.js deleted file mode 100644 index 8a96c69a..00000000 --- a/docs/0.3.0/_static/sphinx_highlight.js +++ /dev/null @@ -1,154 +0,0 @@ -/* Highlighting utilities for Sphinx HTML documentation. */ -"use strict"; - -const SPHINX_HIGHLIGHT_ENABLED = true - -/** - * highlight a given string on a node by wrapping it in - * span elements with the given class name. - */ -const _highlight = (node, addItems, text, className) => { - if (node.nodeType === Node.TEXT_NODE) { - const val = node.nodeValue; - const parent = node.parentNode; - const pos = val.toLowerCase().indexOf(text); - if ( - pos >= 0 && - !parent.classList.contains(className) && - !parent.classList.contains("nohighlight") - ) { - let span; - - const closestNode = parent.closest("body, svg, foreignObject"); - const isInSVG = closestNode && closestNode.matches("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.classList.add(className); - } - - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - const rest = document.createTextNode(val.substr(pos + text.length)); - parent.insertBefore( - span, - parent.insertBefore( - rest, - node.nextSibling - ) - ); - node.nodeValue = val.substr(0, pos); - /* There may be more occurrences of search term in this node. So call this - * function recursively on the remaining fragment. - */ - _highlight(rest, addItems, text, className); - - if (isInSVG) { - const rect = document.createElementNS( - "http://www.w3.org/2000/svg", - "rect" - ); - const bbox = parent.getBBox(); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute("class", className); - addItems.push({ parent: parent, target: rect }); - } - } - } else if (node.matches && !node.matches("button, select, textarea")) { - node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); - } -}; -const _highlightText = (thisNode, text, className) => { - let addItems = []; - _highlight(thisNode, addItems, text, className); - addItems.forEach((obj) => - obj.parent.insertAdjacentElement("beforebegin", obj.target) - ); -}; - -/** - * Small JavaScript module for the documentation. - */ -const SphinxHighlight = { - - /** - * highlight the search words provided in localstorage in the text - */ - highlightSearchWords: () => { - if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight - - // get and clear terms from localstorage - const url = new URL(window.location); - const highlight = - localStorage.getItem("sphinx_highlight_terms") - || url.searchParams.get("highlight") - || ""; - localStorage.removeItem("sphinx_highlight_terms") - url.searchParams.delete("highlight"); - window.history.replaceState({}, "", url); - - // get individual terms from highlight string - const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); - if (terms.length === 0) return; // nothing to do - - // There should never be more than one element matching "div.body" - const divBody = document.querySelectorAll("div.body"); - const body = divBody.length ? divBody[0] : document.querySelector("body"); - window.setTimeout(() => { - terms.forEach((term) => _highlightText(body, term, "highlighted")); - }, 10); - - const searchBox = document.getElementById("searchbox"); - if (searchBox === null) return; - searchBox.appendChild( - document - .createRange() - .createContextualFragment( - '

' + - '' + - _("Hide Search Matches") + - "

" - ) - ); - }, - - /** - * helper function to hide the search marks again - */ - hideSearchWords: () => { - document - .querySelectorAll("#searchbox .highlight-link") - .forEach((el) => el.remove()); - document - .querySelectorAll("span.highlighted") - .forEach((el) => el.classList.remove("highlighted")); - localStorage.removeItem("sphinx_highlight_terms") - }, - - initEscapeListener: () => { - // only install a listener if it is really needed - if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; - - document.addEventListener("keydown", (event) => { - // bail for input elements - if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; - // bail with special keys - if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; - if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { - SphinxHighlight.hideSearchWords(); - event.preventDefault(); - } - }); - }, -}; - -_ready(() => { - /* Do not call highlightSearchWords() when we are on the search page. - * It will highlight words from the *previous* search query. - */ - if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); - SphinxHighlight.initEscapeListener(); -}); diff --git a/docs/0.3.0/autodoc/mmif.serialize.html b/docs/0.3.0/autodoc/mmif.serialize.html deleted file mode 100644 index 827f8d56..00000000 --- a/docs/0.3.0/autodoc/mmif.serialize.html +++ /dev/null @@ -1,369 +0,0 @@ - - - - - - - - - mmif.serialize module — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.serialize module

-
-

mmif.serialize.model module

-
-
-

mmif.serialize.mmif module

-
-
-

mmif.serialize.view module

-
-
-

mmif.serialize.annotation module

-

The annotation module contains the classes used to represent a -MMIF annotation as a live Python object.

-

In MMIF, annotations are created by apps in a pipeline as a part -of a view. For documentation on how views are represented, see -mmif.serialize.view.

-
-
-class mmif.serialize.annotation.Annotation(anno_obj: bytes | str | dict | None = None)[source]
-

Bases: FreezableMmifObject

-

MmifObject that represents an annotation in a MMIF view.

-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]]) → None[source]
-

Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

-
- -
-
-property at_type: str | ThingTypesBase[source]
-
- -
-
-property id: str[source]
-
- -
-
-is_document()[source]
-
- -
-
-is_type(type: str | ThingTypesBase) → bool[source]
-

Check if the @type of this object matches.

-
- -
- -
-
-class mmif.serialize.annotation.AnnotationProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: FreezableMmifObject

-

AnnotationProperties object that represents the -properties object within a MMIF annotation.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
- -
-
-class mmif.serialize.annotation.Document(doc_obj: bytes | str | dict | None = None)[source]
-

Bases: Annotation

-

Document object that represents a single document in a MMIF file.

-

A document is identified by an ID, and contains certain attributes -and potentially contains the contents of the document itself, -metadata about how the document was created, and/or a list of -subdocuments grouped together logically.

-

If document_obj is not provided, an empty Document will be generated.

-
-
Parameters:
-

document_obj – the JSON data that defines the document

-
-
-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None]) → None[source]
-

Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

-
- -
-
-property location: str[source]
-
- -
-
-location_address() → str[source]
-
- -
-
-location_path() → str[source]
-
- -
-
-location_scheme() → str[source]
-
- -
-
-property parent: str[source]
-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.DocumentProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: AnnotationProperties

-

DocumentProperties object that represents the -properties object within a MMIF document.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
-
-property location: str[source]
-
- -
-
-location_address() → str[source]
-
- -
-
-location_path() → str[source]
-
- -
-
-location_scheme() → str[source]
-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.Text(text_obj: bytes | str | dict | None = None)[source]
-

Bases: FreezableMmifObject

-
-
-property lang: str[source]
-
- -
-
-property value: str[source]
-
- -
- -
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.3.0 - - -
-
- -
0.3.0
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0.3.1
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0.3.2
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0.3.3
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0.3.4
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0.3.5
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0.4.1
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0.4.2
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0.4.3
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- - - \ No newline at end of file diff --git a/docs/0.3.0/autodoc/mmif.vocabulary.html b/docs/0.3.0/autodoc/mmif.vocabulary.html deleted file mode 100644 index 564a1848..00000000 --- a/docs/0.3.0/autodoc/mmif.vocabulary.html +++ /dev/null @@ -1,306 +0,0 @@ - - - - - - - - - mmif.vocabulary module — mmif-python documentation - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.vocabulary module

-
-

mmif.vocabulary.annotation_types module

-
-
-class mmif.vocabulary.annotation_types.AnnotationTypes(value)[source]
-

Bases: AnnotationTypesBase

-

This enum contains the URIs for the MMIF annotation types defined in the spec version 0.3.1. -Use this to quickly get the correct URIs for those types, or use the objects themselves in your -code and they will serialize to the strings.

-
-
-Alignment = 'http://mmif.clams.ai/0.3.1/vocabulary/Alignment'[source]
-
- -
-
-Annotation = 'http://mmif.clams.ai/0.3.1/vocabulary/Annotation'[source]
-
- -
-
-BoundingBox = 'http://mmif.clams.ai/0.3.1/vocabulary/BoundingBox'[source]
-
- -
-
-Chapter = 'http://mmif.clams.ai/0.3.1/vocabulary/Chapter'[source]
-
- -
-
-Interval = 'http://mmif.clams.ai/0.3.1/vocabulary/Interval'[source]
-
- -
-
-Polygon = 'http://mmif.clams.ai/0.3.1/vocabulary/Polygon'[source]
-
- -
-
-Region = 'http://mmif.clams.ai/0.3.1/vocabulary/Region'[source]
-
- -
-
-Relation = 'http://mmif.clams.ai/0.3.1/vocabulary/Relation'[source]
-
- -
-
-Span = 'http://mmif.clams.ai/0.3.1/vocabulary/Span'[source]
-
- -
-
-TimeFrame = 'http://mmif.clams.ai/0.3.1/vocabulary/TimeFrame'[source]
-
- -
-
-TimePoint = 'http://mmif.clams.ai/0.3.1/vocabulary/TimePoint'[source]
-
- -
-
-VideoObject = 'http://mmif.clams.ai/0.3.1/vocabulary/VideoObject'[source]
-
- -
- -
-
-class mmif.vocabulary.annotation_types.AnnotationTypesBase(value)[source]
-

Bases: ThingTypesBase

-

Inherit from this class to build your own custom annotation -vocabularies. Each member’s name should be the name of the -type, and each member’s value should be the URI of that type.

-
- -
-
-

mmif.vocabulary.media_types module

-
-
-class mmif.vocabulary.document_types.DocumentTypes(value)[source]
-

Bases: DocumentTypesBase

-

This enum contains the URIs for the MMIF document types defined in the spec version 0.3.1. -Use this to quickly get the correct URIs for those types, or use the objects themselves in your -code and they will serialize to the strings.

-
-
-AudioDocument = 'http://mmif.clams.ai/0.3.1/vocabulary/AudioDocument'[source]
-
- -
-
-Document = 'http://mmif.clams.ai/0.3.1/vocabulary/Document'[source]
-
- -
-
-ImageDocument = 'http://mmif.clams.ai/0.3.1/vocabulary/ImageDocument'[source]
-
- -
-
-TextDocument = 'http://mmif.clams.ai/0.3.1/vocabulary/TextDocument'[source]
-
- -
-
-VideoDocument = 'http://mmif.clams.ai/0.3.1/vocabulary/VideoDocument'[source]
-
- -
- -
-
-class mmif.vocabulary.document_types.DocumentTypesBase(value)[source]
-

Bases: ThingTypesBase

-

Inherit from this class to build your own custom document -vocabularies. Each member’s name should be the name of the -type, and each member’s value should be the URI of that type.

-
- -
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.3.0 - - -
-
- -
0.3.0
-
0.3.1
-
0.3.2
-
0.3.3
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0.3.4
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0.3.5
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0.4.0
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0.4.1
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0.4.8
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- - - \ No newline at end of file diff --git a/docs/0.3.0/consumer-tutorial.html b/docs/0.3.0/consumer-tutorial.html deleted file mode 100644 index 9a2e3344..00000000 --- a/docs/0.3.0/consumer-tutorial.html +++ /dev/null @@ -1,175 +0,0 @@ - - - - - - - - - MMIF consumer — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • MMIF consumer
    • -
  • -
    • -
-
-
-
-
- -
-

MMIF consumer

-

A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the appliance documentation to learn more about the appliance.

-

MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance.

-
    -

  1. The code must be hosted on a public git repository (e.g. Github, Gitlab, …)

    2. -

  2. Must listen to 5000 port.

    3. -

  3. Must expose /display route .

    4. -

  4. /display router should response to GET requests.

    5. -

  5. In the GET request, a public URL of the input MMIF file is passed via file URL parameter.

    6. -

  6. On the codebase root, there must be a Dockerfile that can build a docker image that runs the web app.

    7. -
-

We provide an example consumer at https://github.com/clamsproject/mmif-visualizer.

-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.3.0 - - -
-
- -
0.3.0
-
0.3.1
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0.3.2
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0.3.3
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0.3.4
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0.3.5
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0.4.0
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0.4.1
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0.4.2
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- - - \ No newline at end of file diff --git a/docs/0.3.0/genindex.html b/docs/0.3.0/genindex.html deleted file mode 100644 index f1d0660f..00000000 --- a/docs/0.3.0/genindex.html +++ /dev/null @@ -1,407 +0,0 @@ - - - - - - - - Index — mmif-python documentation - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • Index
    • -
  • -
    • -
-
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- - -

Index

- -
- A - | B - | C - | D - | I - | L - | M - | P - | R - | S - | T - | V - -
-

A

- - - -
- -

B

- - -
- -

C

- - -
- -

D

- - - -
- -

I

- - - -
- -

L

- - - -
- -

M

- - - -
    -
  • - mmif.serialize.annotation - -
    • -
  • - mmif.vocabulary.annotation_types - -
    • -
  • - mmif.vocabulary.document_types - -
    • -
- -

P

- - - -
- -

R

- - - -
- -

S

- - -
- -

T

- - - -
- -

V

- - - -
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- - Other Versions - v: 0.3.0 - - -
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0.3.0
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0.3.1
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0.3.2
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0.3.3
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0.3.4
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0.3.5
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0.4.0
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0.4.1
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0.4.2
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0.4.3
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0.4.4
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0.4.6
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0.4.8
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0.5.2
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1.0.12
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- - - \ No newline at end of file diff --git a/docs/0.3.0/index.html b/docs/0.3.0/index.html deleted file mode 100644 index 2804fb5f..00000000 --- a/docs/0.3.0/index.html +++ /dev/null @@ -1,201 +0,0 @@ - - - - - - - - - Welcome to mmif-python’s documentation! — mmif-python documentation - - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • Welcome to mmif-python’s documentation!
    • -
  • -
    • -
-
-
-
-
- -
-

Welcome to mmif-python’s documentation!

-
-
-

MMIF for python

-

NOTE that this project is in pre-alpha and being actively developed. Nothing is guaranteed to reliably work for the moment and developer need to be very careful when using APIs implemented here. Please use the issue track to report bugs and malfunctions.

-
-

MultiMedia Interchange Format

-

MMIF is a JSON(-LD)-based data format designed for transferring annotation data between computational analysis applications in CLAMS project.

-
-

Contents

- -
-
-

API documentation:

- -
-
-
-
-

Indices and tables

- -
- - -
-
- -
-
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-
- -
- - Other Versions - v: 0.3.0 - - -
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0.3.2
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0.3.3
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0.3.4
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- - - \ No newline at end of file diff --git a/docs/0.3.0/introduction.html b/docs/0.3.0/introduction.html deleted file mode 100644 index 6ec68815..00000000 --- a/docs/0.3.0/introduction.html +++ /dev/null @@ -1,231 +0,0 @@ - - - - - - - - - Getting Started — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
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  • Getting Started
    • -
  • -
    • -
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- -
-

Getting Started

-
-

Overview

-

MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF wbesite. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports de-/serialization of MMIF objects, as well as many navigation and manipulation helpers for MMIF objects.

-
-
-

Prerequisites

-
    -

  • Python: mmif-python requires Python 3.6 or newer. We have no plan to support Python 2.7.

    • -
-
-
-

Installation

-

Package mmif-python is distributed via the official PyPI. Users are supposed to pip-install to get latest release.

-
pip install mmif-python
-
-
-

This will install a package mmif to local python. -The MMIF format and specification is evolving over time, and mmif-python package will be updated along with the changes in MMIF format. Note that MMIF format is not always backward-compatible. To find out more about relations between MMIF versions and mmif-python versions, and which supports which, please take time to read our decision on the subject here.

-
-
-

MMIF Serialization

-

mmif.serialize.mmif.Mmif represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of mmif.serialize.model.MmifObject, including the mmif.serialize.mmif.Mmif. To start with an existing MMIF str, simple initiate a new Mmif object with the file.

-
import mmif
-from mmif import Mmif
-
-mmif_str = """{
-"metadata": {
-  "mmif": "http://mmif.clams.ai/0.2.0"
-},
-"documents": [
-  {
-    "@type": "http://mmif.clams.ai/0.2.0/vocabulary/VideoDocument",
-    "properties": {
-      "id": "m1",
-      "mime": "video/mp4",
-      "location": "file:///var/archive/video-0012.mp4"
-    }
-  },
-  {
-    "@type": "http://mmif.clams.ai/0.2.0/vocabulary/TextDocument",
-    "properties": {
-      "id": "m2",
-      "mime": "text/plain",
-      "location": "file:///var/archive/video-0012-transcript.txt"
-    }
-  }
-],
-"views": []}"""
-mmif_obj = Mmif(mmif_str)
-
-
-

Few notes;

-
    -

  1. MMIF does not carry the primary source files in it.

    2. -

  2. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version mmif-python implementation of the MMIF might not be able to load an unsupported version of MMIF string.

    3. -
-

When serializing back to str, call .serialize() (mmif.serialize.model.MmifObject.serialize()) on the object.

-

To get subcomponents, you can use various getters implemented in subclasses. For more details, the API documentation (mmif package) will help.

-
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.3.0 - - -
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- -
0.3.0
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0.3.1
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0.3.2
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0.3.3
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0.3.4
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0.3.5
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0.4.0
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0.4.1
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0.4.2
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0.4.3
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- - - \ No newline at end of file diff --git a/docs/0.3.0/modules.html b/docs/0.3.0/modules.html deleted file mode 100644 index 69519e6f..00000000 --- a/docs/0.3.0/modules.html +++ /dev/null @@ -1,249 +0,0 @@ - - - - - - - - - mmif package — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
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  • mmif package
    • -
  • -
    • -
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mmif package

-
- -
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0.3.0
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The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the `appliance documentation `_ to learn more about the appliance. - -MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance. - -#. The code must be hosted on a public git repository (e.g. Github, Gitlab, ...) -#. Must listen to ``5000`` port. -#. Must expose ``/display`` route . -#. ``/display`` router should response to ``GET`` requests. -#. In the ``GET`` request, a public URL of the input MMIF file is passed via ``file`` URL parameter. -#. On the codebase root, there must be a ``Dockerfile`` that can build a `docker `_ image that runs the web app. - -We provide an example consumer at https://github.com/clamsproject/mmif-visualizer. diff --git a/docs/0.3.1/_sources/index.rst.txt b/docs/0.3.1/_sources/index.rst.txt deleted file mode 100644 index 6146286d..00000000 --- a/docs/0.3.1/_sources/index.rst.txt +++ /dev/null @@ -1,25 +0,0 @@ -Welcome to mmif-python's documentation! -======================================= - -.. mdinclude:: ../README.md - -.. toctree:: - :maxdepth: 2 - :caption: Contents - - introduction - consumer-tutorial - -.. toctree:: - :maxdepth: 2 - :caption: API documentation: - - modules - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/docs/0.3.1/_sources/introduction.rst.txt b/docs/0.3.1/_sources/introduction.rst.txt deleted file mode 100644 index 6af8cd61..00000000 --- a/docs/0.3.1/_sources/introduction.rst.txt +++ /dev/null @@ -1,75 +0,0 @@ -.. _instroduction: - -Getting Started -=============== - - -Overview ---------- - -MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF wbesite `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports de-/serialization of MMIF objects, as well as many navigation and manipulation helpers for MMIF objects. - -Prerequisites -------------- - -* `Python `_: ``mmif-python`` requires Python 3.6 or newer. We have no plan to support `Python 2.7 `_. - -Installation ---------------- - -Package ``mmif-python`` is distributed via the official PyPI. Users are supposed to pip-install to get latest release. - -.. code-block:: bash - - pip install mmif-python - -This will install a package `mmif` to local python. -The MMIF format and specification is evolving over time, and ``mmif-python`` package will be updated along with the changes in MMIF format. Note that MMIF format is not always backward-compatible. To find out more about relations between MMIF versions and ``mmif-python`` versions, and which supports which, please take time to read our decision on the subject `here `_. - -MMIF Serialization ---------------------------- - -:class:`mmif.serialize.mmif.Mmif` represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of :class:`mmif.serialize.model.MmifObject`, including the :class:`mmif.serialize.mmif.Mmif`. To start with an existing MMIF :class:`str`, simple initiate a new ``Mmif`` object with the file. - -.. code-block:: python - - import mmif - from mmif import Mmif - - mmif_str = """{ - "metadata": { - "mmif": "http://mmif.clams.ai/0.2.0" - }, - "documents": [ - { - "@type": "http://mmif.clams.ai/0.2.0/vocabulary/VideoDocument", - "properties": { - "id": "m1", - "mime": "video/mp4", - "location": "file:///var/archive/video-0012.mp4" - } - }, - { - "@type": "http://mmif.clams.ai/0.2.0/vocabulary/TextDocument", - "properties": { - "id": "m2", - "mime": "text/plain", - "location": "file:///var/archive/video-0012-transcript.txt" - } - } - ], - "views": []}""" - mmif_obj = Mmif(mmif_str) - - -Few notes; - -#. MMIF does not carry the primary source files in it. -#. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version ``mmif-python`` implementation of the MMIF might not be able to load an unsupported version of MMIF string. - -When serializing back to :class:`str`, call ``.serialize()`` (:meth:`mmif.serialize.model.MmifObject.serialize`) on the object. - -To get subcomponents, you can use various getters implemented in subclasses. For more details, the API documentation (:ref:`apidoc`) will help. - diff --git a/docs/0.3.1/_sources/modules.rst.txt b/docs/0.3.1/_sources/modules.rst.txt deleted file mode 100644 index e4269c6d..00000000 --- a/docs/0.3.1/_sources/modules.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _apidoc: - -mmif package -============ - -.. toctree:: - :maxdepth: 4 - - autodoc/mmif.serialize - autodoc/mmif.vocabulary diff --git a/docs/0.3.1/_static/_sphinx_javascript_frameworks_compat.js b/docs/0.3.1/_static/_sphinx_javascript_frameworks_compat.js deleted file mode 100644 index 81415803..00000000 --- a/docs/0.3.1/_static/_sphinx_javascript_frameworks_compat.js +++ /dev/null @@ -1,123 +0,0 @@ -/* Compatability shim for jQuery and underscores.js. - * - * Copyright Sphinx contributors - * Released under the two clause BSD licence - */ - -/** - * small helper function to urldecode strings - * - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL - */ -jQuery.urldecode = function(x) { - if (!x) { - return x - } - return decodeURIComponent(x.replace(/\+/g, ' ')); -}; - -/** - * small helper function to urlencode strings - */ -jQuery.urlencode = encodeURIComponent; - -/** - * This function returns the parsed url parameters of the - * current request. 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- -/** - * Simple result scoring code. - */ -if (typeof Scorer === "undefined") { - var Scorer = { - // Implement the following function to further tweak the score for each result - // The function takes a result array [docname, title, anchor, descr, score, filename] - // and returns the new score. - /* - score: result => { - const [docname, title, anchor, descr, score, filename, kind] = result - return score - }, - */ - - // query matches the full name of an object - objNameMatch: 11, - // or matches in the last dotted part of the object name - objPartialMatch: 6, - // Additive scores depending on the priority of the object - objPrio: { - 0: 15, // used to be importantResults - 1: 5, // used to be objectResults - 2: -5, // used to be unimportantResults - }, - // Used when the priority is not in the mapping. - objPrioDefault: 0, - - // query found in title - title: 15, - partialTitle: 7, - // query found in terms - term: 5, - partialTerm: 2, - }; -} - -// Global search result kind enum, used by themes to style search results. -class SearchResultKind { - static get index() { return "index"; } - static get object() { return "object"; } - static get text() { return "text"; } - static get title() { return "title"; } -} - -const _removeChildren = (element) => { - while (element && element.lastChild) element.removeChild(element.lastChild); -}; - -/** - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping - */ -const _escapeRegExp = (string) => - string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string - -const _displayItem = (item, searchTerms, highlightTerms) => { - const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; - const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; - const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; - const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; - const contentRoot = document.documentElement.dataset.content_root; - - const [docName, title, anchor, descr, score, _filename, kind] = item; - - let listItem = document.createElement("li"); - // Add a class representing the item's type: - // can be used by a theme's CSS selector for styling - // See SearchResultKind for the class names. - listItem.classList.add(`kind-${kind}`); - let requestUrl; - let linkUrl; - if (docBuilder === "dirhtml") { - // dirhtml builder - let dirname = docName + "/"; - if (dirname.match(/\/index\/$/)) - dirname = dirname.substring(0, dirname.length - 6); - else if (dirname === "index/") dirname = ""; - requestUrl = contentRoot + dirname; - linkUrl = requestUrl; - } else { - // normal html builders - requestUrl = contentRoot + docName + docFileSuffix; - linkUrl = docName + docLinkSuffix; - } - let linkEl = listItem.appendChild(document.createElement("a")); - linkEl.href = linkUrl + anchor; - linkEl.dataset.score = score; - linkEl.innerHTML = title; - if (descr) { - listItem.appendChild(document.createElement("span")).innerHTML = - " (" + descr + ")"; - // highlight search terms in the description - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - } - else if (showSearchSummary) - fetch(requestUrl) - .then((responseData) => responseData.text()) - .then((data) => { - if (data) - listItem.appendChild( - Search.makeSearchSummary(data, searchTerms, anchor) - ); - // highlight search terms in the summary - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - }); - Search.output.appendChild(listItem); -}; -const _finishSearch = (resultCount) => { - Search.stopPulse(); - Search.title.innerText = _("Search Results"); - if (!resultCount) - Search.status.innerText = Documentation.gettext( - "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." - ); - else - Search.status.innerText = Documentation.ngettext( - "Search finished, found one page matching the search query.", - "Search finished, found ${resultCount} pages matching the search query.", - resultCount, - ).replace('${resultCount}', resultCount); -}; -const _displayNextItem = ( - results, - resultCount, - searchTerms, - highlightTerms, -) => { - // results left, load the summary and display it - // this is intended to be dynamic (don't sub resultsCount) - if (results.length) { - _displayItem(results.pop(), searchTerms, highlightTerms); - setTimeout( - () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), - 5 - ); - } - // search finished, update title and status message - else _finishSearch(resultCount); -}; -// Helper function used by query() to order search results. -// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. -// Order the results by score (in opposite order of appearance, since the -// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. -const _orderResultsByScoreThenName = (a, b) => { - const leftScore = a[4]; - const rightScore = b[4]; - if (leftScore === rightScore) { - // same score: sort alphabetically - const leftTitle = a[1].toLowerCase(); - const rightTitle = b[1].toLowerCase(); - if (leftTitle === rightTitle) return 0; - return leftTitle > rightTitle ? -1 : 1; // inverted is intentional - } - return leftScore > rightScore ? 1 : -1; -}; - -/** - * Default splitQuery function. Can be overridden in ``sphinx.search`` with a - * custom function per language. - * - * The regular expression works by splitting the string on consecutive characters - * that are not Unicode letters, numbers, underscores, or emoji characters. - * This is the same as ``\W+`` in Python, preserving the surrogate pair area. - */ -if (typeof splitQuery === "undefined") { - var splitQuery = (query) => query - .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) - .filter(term => term) // remove remaining empty strings -} - -/** - * Search Module - */ -const Search = { - _index: null, - _queued_query: null, - _pulse_status: -1, - - htmlToText: (htmlString, anchor) => { - const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - for (const removalQuery of [".headerlink", "script", "style"]) { - htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); - } - if (anchor) { - const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); - if (anchorContent) return anchorContent.textContent; - - console.warn( - `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` - ); - } - - // if anchor not specified or not found, fall back to main content - const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent) return docContent.textContent; - - console.warn( - "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." - ); - return ""; - }, - - init: () => { - const query = new URLSearchParams(window.location.search).get("q"); - document - .querySelectorAll('input[name="q"]') - .forEach((el) => (el.value = query)); - if (query) Search.performSearch(query); - }, - - loadIndex: (url) => - (document.body.appendChild(document.createElement("script")).src = url), - - setIndex: (index) => { - Search._index = index; - if (Search._queued_query !== null) { - const query = Search._queued_query; - Search._queued_query = null; - Search.query(query); - } - }, - - hasIndex: () => Search._index !== null, - - deferQuery: (query) => (Search._queued_query = query), - - stopPulse: () => (Search._pulse_status = -1), - - startPulse: () => { - if (Search._pulse_status >= 0) return; - - const pulse = () => { - Search._pulse_status = (Search._pulse_status + 1) % 4; - Search.dots.innerText = ".".repeat(Search._pulse_status); - if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); - }; - pulse(); - }, - - /** - * perform a search for something (or wait until index is loaded) - */ - performSearch: (query) => { - // create the required interface elements - const searchText = document.createElement("h2"); - searchText.textContent = _("Searching"); - const searchSummary = document.createElement("p"); - searchSummary.classList.add("search-summary"); - searchSummary.innerText = ""; - const searchList = document.createElement("ul"); - searchList.setAttribute("role", "list"); - searchList.classList.add("search"); - - const out = document.getElementById("search-results"); - Search.title = out.appendChild(searchText); - Search.dots = Search.title.appendChild(document.createElement("span")); - Search.status = out.appendChild(searchSummary); - Search.output = out.appendChild(searchList); - - const searchProgress = document.getElementById("search-progress"); - // Some themes don't use the search progress node - if (searchProgress) { - searchProgress.innerText = _("Preparing search..."); - } - Search.startPulse(); - - // index already loaded, the browser was quick! - if (Search.hasIndex()) Search.query(query); - else Search.deferQuery(query); - }, - - _parseQuery: (query) => { - // stem the search terms and add them to the correct list - const stemmer = new Stemmer(); - const searchTerms = new Set(); - const excludedTerms = new Set(); - const highlightTerms = new Set(); - const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); - splitQuery(query.trim()).forEach((queryTerm) => { - const queryTermLower = queryTerm.toLowerCase(); - - // maybe skip this "word" - // stopwords array is from language_data.js - if ( - stopwords.indexOf(queryTermLower) !== -1 || - queryTerm.match(/^\d+$/) - ) - return; - - // stem the word - let word = stemmer.stemWord(queryTermLower); - // select the correct list - if (word[0] === "-") excludedTerms.add(word.substr(1)); - else { - searchTerms.add(word); - highlightTerms.add(queryTermLower); - } - }); - - if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js - localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) - } - - // console.debug("SEARCH: searching for:"); - // console.info("required: ", [...searchTerms]); - // console.info("excluded: ", [...excludedTerms]); - - return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; - }, - - /** - * execute search (requires search index to be loaded) - */ - _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - - // Collect multiple result groups to be sorted separately and then ordered. - // Each is an array of [docname, title, anchor, descr, score, filename, kind]. - const normalResults = []; - const nonMainIndexResults = []; - - _removeChildren(document.getElementById("search-progress")); - - const queryLower = query.toLowerCase().trim(); - for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { - for (const [file, id] of foundTitles) { - const score = Math.round(Scorer.title * queryLower.length / title.length); - const boost = titles[file] === title ? 1 : 0; // add a boost for document titles - normalResults.push([ - docNames[file], - titles[file] !== title ? `${titles[file]} > ${title}` : title, - id !== null ? "#" + id : "", - null, - score + boost, - filenames[file], - SearchResultKind.title, - ]); - } - } - } - - // search for explicit entries in index directives - for (const [entry, foundEntries] of Object.entries(indexEntries)) { - if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id, isMain] of foundEntries) { - const score = Math.round(100 * queryLower.length / entry.length); - const result = [ - docNames[file], - titles[file], - id ? "#" + id : "", - null, - score, - filenames[file], - SearchResultKind.index, - ]; - if (isMain) { - normalResults.push(result); - } else { - nonMainIndexResults.push(result); - } - } - } - } - - // lookup as object - objectTerms.forEach((term) => - normalResults.push(...Search.performObjectSearch(term, objectTerms)) - ); - - // lookup as search terms in fulltext - normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); - - // let the scorer override scores with a custom scoring function - if (Scorer.score) { - normalResults.forEach((item) => (item[4] = Scorer.score(item))); - nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); - } - - // Sort each group of results by score and then alphabetically by name. - normalResults.sort(_orderResultsByScoreThenName); - nonMainIndexResults.sort(_orderResultsByScoreThenName); - - // Combine the result groups in (reverse) order. - // Non-main index entries are typically arbitrary cross-references, - // so display them after other results. - let results = [...nonMainIndexResults, ...normalResults]; - - // remove duplicate search results - // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept - let seen = new Set(); - results = results.reverse().reduce((acc, result) => { - let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); - if (!seen.has(resultStr)) { - acc.push(result); - seen.add(resultStr); - } - return acc; - }, []); - - return results.reverse(); - }, - - query: (query) => { - const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); - const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); - - // for debugging - //Search.lastresults = results.slice(); // a copy - // console.info("search results:", Search.lastresults); - - // print the results - _displayNextItem(results, results.length, searchTerms, highlightTerms); - }, - - /** - * search for object names - */ - performObjectSearch: (object, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const objects = Search._index.objects; - const objNames = Search._index.objnames; - const titles = Search._index.titles; - - const results = []; - - const objectSearchCallback = (prefix, match) => { - const name = match[4] - const fullname = (prefix ? prefix + "." : "") + name; - const fullnameLower = fullname.toLowerCase(); - if (fullnameLower.indexOf(object) < 0) return; - - let score = 0; - const parts = fullnameLower.split("."); - - // check for different match types: exact matches of full name or - // "last name" (i.e. last dotted part) - if (fullnameLower === object || parts.slice(-1)[0] === object) - score += Scorer.objNameMatch; - else if (parts.slice(-1)[0].indexOf(object) > -1) - score += Scorer.objPartialMatch; // matches in last name - - const objName = objNames[match[1]][2]; - const title = titles[match[0]]; - - // If more than one term searched for, we require other words to be - // found in the name/title/description - const otherTerms = new Set(objectTerms); - otherTerms.delete(object); - if (otherTerms.size > 0) { - const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); - if ( - [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) - ) - return; - } - - let anchor = match[3]; - if (anchor === "") anchor = fullname; - else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; - - const descr = objName + _(", in ") + title; - - // add custom score for some objects according to scorer - if (Scorer.objPrio.hasOwnProperty(match[2])) - score += Scorer.objPrio[match[2]]; - else score += Scorer.objPrioDefault; - - results.push([ - docNames[match[0]], - fullname, - "#" + anchor, - descr, - score, - filenames[match[0]], - SearchResultKind.object, - ]); - }; - Object.keys(objects).forEach((prefix) => - objects[prefix].forEach((array) => - objectSearchCallback(prefix, array) - ) - ); - return results; - }, - - /** - * search for full-text terms in the index - */ - performTermsSearch: (searchTerms, excludedTerms) => { - // prepare search - const terms = Search._index.terms; - const titleTerms = Search._index.titleterms; - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - - const scoreMap = new Map(); - const fileMap = new Map(); - - // perform the search on the required terms - searchTerms.forEach((word) => { - const files = []; - const arr = [ - { files: terms[word], score: Scorer.term }, - { files: titleTerms[word], score: Scorer.title }, - ]; - // add support for partial matches - if (word.length > 2) { - const escapedWord = _escapeRegExp(word); - if (!terms.hasOwnProperty(word)) { - Object.keys(terms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: terms[term], score: Scorer.partialTerm }); - }); - } - if (!titleTerms.hasOwnProperty(word)) { - Object.keys(titleTerms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); - }); - } - } - - // no match but word was a required one - if (arr.every((record) => record.files === undefined)) return; - - // found search word in contents - arr.forEach((record) => { - if (record.files === undefined) return; - - let recordFiles = record.files; - if (recordFiles.length === undefined) recordFiles = [recordFiles]; - files.push(...recordFiles); - - // set score for the word in each file - recordFiles.forEach((file) => { - if (!scoreMap.has(file)) scoreMap.set(file, {}); - scoreMap.get(file)[word] = record.score; - }); - }); - - // create the mapping - files.forEach((file) => { - if (!fileMap.has(file)) fileMap.set(file, [word]); - else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); - }); - }); - - // now check if the files don't contain excluded terms - const results = []; - for (const [file, wordList] of fileMap) { - // check if all requirements are matched - - // as search terms with length < 3 are discarded - const filteredTermCount = [...searchTerms].filter( - (term) => term.length > 2 - ).length; - if ( - wordList.length !== searchTerms.size && - wordList.length !== filteredTermCount - ) - continue; - - // ensure that none of the excluded terms is in the search result - if ( - [...excludedTerms].some( - (term) => - terms[term] === file || - titleTerms[term] === file || - (terms[term] || []).includes(file) || - (titleTerms[term] || []).includes(file) - ) - ) - break; - - // select one (max) score for the file. - const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); - // add result to the result list - results.push([ - docNames[file], - titles[file], - "", - null, - score, - filenames[file], - SearchResultKind.text, - ]); - } - return results; - }, - - /** - * helper function to return a node containing the - * search summary for a given text. keywords is a list - * of stemmed words. - */ - makeSearchSummary: (htmlText, keywords, anchor) => { - const text = Search.htmlToText(htmlText, anchor); - if (text === "") return null; - - const textLower = text.toLowerCase(); - const actualStartPosition = [...keywords] - .map((k) => textLower.indexOf(k.toLowerCase())) - .filter((i) => i > -1) - .slice(-1)[0]; - const startWithContext = Math.max(actualStartPosition - 120, 0); - - const top = startWithContext === 0 ? "" : "..."; - const tail = startWithContext + 240 < text.length ? "..." : ""; - - let summary = document.createElement("p"); - summary.classList.add("context"); - summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; - - return summary; - }, -}; - -_ready(Search.init); diff --git a/docs/0.3.1/_static/sphinx_highlight.js b/docs/0.3.1/_static/sphinx_highlight.js deleted file mode 100644 index 8a96c69a..00000000 --- a/docs/0.3.1/_static/sphinx_highlight.js +++ /dev/null @@ -1,154 +0,0 @@ -/* Highlighting utilities for Sphinx HTML documentation. */ -"use strict"; - -const SPHINX_HIGHLIGHT_ENABLED = true - -/** - * highlight a given string on a node by wrapping it in - * span elements with the given class name. - */ -const _highlight = (node, addItems, text, className) => { - if (node.nodeType === Node.TEXT_NODE) { - const val = node.nodeValue; - const parent = node.parentNode; - const pos = val.toLowerCase().indexOf(text); - if ( - pos >= 0 && - !parent.classList.contains(className) && - !parent.classList.contains("nohighlight") - ) { - let span; - - const closestNode = parent.closest("body, svg, foreignObject"); - const isInSVG = closestNode && closestNode.matches("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.classList.add(className); - } - - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - const rest = document.createTextNode(val.substr(pos + text.length)); - parent.insertBefore( - span, - parent.insertBefore( - rest, - node.nextSibling - ) - ); - node.nodeValue = val.substr(0, pos); - /* There may be more occurrences of search term in this node. So call this - * function recursively on the remaining fragment. - */ - _highlight(rest, addItems, text, className); - - if (isInSVG) { - const rect = document.createElementNS( - "http://www.w3.org/2000/svg", - "rect" - ); - const bbox = parent.getBBox(); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute("class", className); - addItems.push({ parent: parent, target: rect }); - } - } - } else if (node.matches && !node.matches("button, select, textarea")) { - node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); - } -}; -const _highlightText = (thisNode, text, className) => { - let addItems = []; - _highlight(thisNode, addItems, text, className); - addItems.forEach((obj) => - obj.parent.insertAdjacentElement("beforebegin", obj.target) - ); -}; - -/** - * Small JavaScript module for the documentation. - */ -const SphinxHighlight = { - - /** - * highlight the search words provided in localstorage in the text - */ - highlightSearchWords: () => { - if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight - - // get and clear terms from localstorage - const url = new URL(window.location); - const highlight = - localStorage.getItem("sphinx_highlight_terms") - || url.searchParams.get("highlight") - || ""; - localStorage.removeItem("sphinx_highlight_terms") - url.searchParams.delete("highlight"); - window.history.replaceState({}, "", url); - - // get individual terms from highlight string - const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); - if (terms.length === 0) return; // nothing to do - - // There should never be more than one element matching "div.body" - const divBody = document.querySelectorAll("div.body"); - const body = divBody.length ? divBody[0] : document.querySelector("body"); - window.setTimeout(() => { - terms.forEach((term) => _highlightText(body, term, "highlighted")); - }, 10); - - const searchBox = document.getElementById("searchbox"); - if (searchBox === null) return; - searchBox.appendChild( - document - .createRange() - .createContextualFragment( - '

' + - '' + - _("Hide Search Matches") + - "

" - ) - ); - }, - - /** - * helper function to hide the search marks again - */ - hideSearchWords: () => { - document - .querySelectorAll("#searchbox .highlight-link") - .forEach((el) => el.remove()); - document - .querySelectorAll("span.highlighted") - .forEach((el) => el.classList.remove("highlighted")); - localStorage.removeItem("sphinx_highlight_terms") - }, - - initEscapeListener: () => { - // only install a listener if it is really needed - if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; - - document.addEventListener("keydown", (event) => { - // bail for input elements - if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; - // bail with special keys - if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; - if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { - SphinxHighlight.hideSearchWords(); - event.preventDefault(); - } - }); - }, -}; - -_ready(() => { - /* Do not call highlightSearchWords() when we are on the search page. - * It will highlight words from the *previous* search query. - */ - if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); - SphinxHighlight.initEscapeListener(); -}); diff --git a/docs/0.3.1/autodoc/mmif.serialize.html b/docs/0.3.1/autodoc/mmif.serialize.html deleted file mode 100644 index 47ad5a23..00000000 --- a/docs/0.3.1/autodoc/mmif.serialize.html +++ /dev/null @@ -1,369 +0,0 @@ - - - - - - - - - mmif.serialize module — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.serialize module

-
-

mmif.serialize.model module

-
-
-

mmif.serialize.mmif module

-
-
-

mmif.serialize.view module

-
-
-

mmif.serialize.annotation module

-

The annotation module contains the classes used to represent a -MMIF annotation as a live Python object.

-

In MMIF, annotations are created by apps in a pipeline as a part -of a view. For documentation on how views are represented, see -mmif.serialize.view.

-
-
-class mmif.serialize.annotation.Annotation(anno_obj: bytes | str | dict | None = None)[source]
-

Bases: FreezableMmifObject

-

MmifObject that represents an annotation in a MMIF view.

-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]]) → None[source]
-

Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

-
- -
-
-property at_type: str | ThingTypesBase[source]
-
- -
-
-property id: str[source]
-
- -
-
-is_document()[source]
-
- -
-
-is_type(type: str | ThingTypesBase) → bool[source]
-

Check if the @type of this object matches.

-
- -
- -
-
-class mmif.serialize.annotation.AnnotationProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: FreezableMmifObject

-

AnnotationProperties object that represents the -properties object within a MMIF annotation.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
- -
-
-class mmif.serialize.annotation.Document(doc_obj: bytes | str | dict | None = None)[source]
-

Bases: Annotation

-

Document object that represents a single document in a MMIF file.

-

A document is identified by an ID, and contains certain attributes -and potentially contains the contents of the document itself, -metadata about how the document was created, and/or a list of -subdocuments grouped together logically.

-

If document_obj is not provided, an empty Document will be generated.

-
-
Parameters:
-

document_obj – the JSON data that defines the document

-
-
-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None]) → None[source]
-

Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

-
- -
-
-property location: str[source]
-
- -
-
-location_address() → str[source]
-
- -
-
-location_path() → str[source]
-
- -
-
-location_scheme() → str[source]
-
- -
-
-property parent: str[source]
-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.DocumentProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: AnnotationProperties

-

DocumentProperties object that represents the -properties object within a MMIF document.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
-
-property location: str[source]
-
- -
-
-location_address() → str[source]
-
- -
-
-location_path() → str[source]
-
- -
-
-location_scheme() → str[source]
-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.Text(text_obj: bytes | str | dict | None = None)[source]
-

Bases: FreezableMmifObject

-
-
-property lang: str[source]
-
- -
-
-property value: str[source]
-
- -
- -
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.3.1 - - -
-
- -
0.3.0
-
0.3.1
-
0.3.2
-
0.3.3
-
0.3.4
-
0.3.5
-
0.4.0
-
0.4.1
-
0.4.2
-
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-
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-
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-
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-
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-
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-
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-
1.1.0
-
-
-
- - - \ No newline at end of file diff --git a/docs/0.3.1/autodoc/mmif.vocabulary.html b/docs/0.3.1/autodoc/mmif.vocabulary.html deleted file mode 100644 index 4f6cdb55..00000000 --- a/docs/0.3.1/autodoc/mmif.vocabulary.html +++ /dev/null @@ -1,306 +0,0 @@ - - - - - - - - - mmif.vocabulary module — mmif-python documentation - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.vocabulary module

-
-

mmif.vocabulary.annotation_types module

-
-
-class mmif.vocabulary.annotation_types.AnnotationTypes(value)[source]
-

Bases: AnnotationTypesBase

-

This enum contains the URIs for the MMIF annotation types defined in the spec version 0.3.1. -Use this to quickly get the correct URIs for those types, or use the objects themselves in your -code and they will serialize to the strings.

-
-
-Alignment = 'http://mmif.clams.ai/0.3.1/vocabulary/Alignment'[source]
-
- -
-
-Annotation = 'http://mmif.clams.ai/0.3.1/vocabulary/Annotation'[source]
-
- -
-
-BoundingBox = 'http://mmif.clams.ai/0.3.1/vocabulary/BoundingBox'[source]
-
- -
-
-Chapter = 'http://mmif.clams.ai/0.3.1/vocabulary/Chapter'[source]
-
- -
-
-Interval = 'http://mmif.clams.ai/0.3.1/vocabulary/Interval'[source]
-
- -
-
-Polygon = 'http://mmif.clams.ai/0.3.1/vocabulary/Polygon'[source]
-
- -
-
-Region = 'http://mmif.clams.ai/0.3.1/vocabulary/Region'[source]
-
- -
-
-Relation = 'http://mmif.clams.ai/0.3.1/vocabulary/Relation'[source]
-
- -
-
-Span = 'http://mmif.clams.ai/0.3.1/vocabulary/Span'[source]
-
- -
-
-TimeFrame = 'http://mmif.clams.ai/0.3.1/vocabulary/TimeFrame'[source]
-
- -
-
-TimePoint = 'http://mmif.clams.ai/0.3.1/vocabulary/TimePoint'[source]
-
- -
-
-VideoObject = 'http://mmif.clams.ai/0.3.1/vocabulary/VideoObject'[source]
-
- -
- -
-
-class mmif.vocabulary.annotation_types.AnnotationTypesBase(value)[source]
-

Bases: ThingTypesBase

-

Inherit from this class to build your own custom annotation -vocabularies. Each member’s name should be the name of the -type, and each member’s value should be the URI of that type.

-
- -
-
-

mmif.vocabulary.media_types module

-
-
-class mmif.vocabulary.document_types.DocumentTypes(value)[source]
-

Bases: DocumentTypesBase

-

This enum contains the URIs for the MMIF document types defined in the spec version 0.3.1. -Use this to quickly get the correct URIs for those types, or use the objects themselves in your -code and they will serialize to the strings.

-
-
-AudioDocument = 'http://mmif.clams.ai/0.3.1/vocabulary/AudioDocument'[source]
-
- -
-
-Document = 'http://mmif.clams.ai/0.3.1/vocabulary/Document'[source]
-
- -
-
-ImageDocument = 'http://mmif.clams.ai/0.3.1/vocabulary/ImageDocument'[source]
-
- -
-
-TextDocument = 'http://mmif.clams.ai/0.3.1/vocabulary/TextDocument'[source]
-
- -
-
-VideoDocument = 'http://mmif.clams.ai/0.3.1/vocabulary/VideoDocument'[source]
-
- -
- -
-
-class mmif.vocabulary.document_types.DocumentTypesBase(value)[source]
-

Bases: ThingTypesBase

-

Inherit from this class to build your own custom document -vocabularies. Each member’s name should be the name of the -type, and each member’s value should be the URI of that type.

-
- -
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.3.1 - - -
-
- -
0.3.0
-
0.3.1
-
0.3.2
-
0.3.3
-
0.3.4
-
0.3.5
-
0.4.0
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0.4.1
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0.4.2
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0.4.3
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0.4.4
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0.4.5
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0.4.6
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0.4.7
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0.4.8
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0.5.1
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0.5.2
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1.0.6
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1.0.7
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1.0.8
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1.0.9
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1.1.0
-
-
-
- - - \ No newline at end of file diff --git a/docs/0.3.1/consumer-tutorial.html b/docs/0.3.1/consumer-tutorial.html deleted file mode 100644 index cfa15487..00000000 --- a/docs/0.3.1/consumer-tutorial.html +++ /dev/null @@ -1,175 +0,0 @@ - - - - - - - - - MMIF consumer — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • MMIF consumer
    • -
  • -
    • -
-
-
-
-
- -
-

MMIF consumer

-

A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the appliance documentation to learn more about the appliance.

-

MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance.

-
    -

  1. The code must be hosted on a public git repository (e.g. Github, Gitlab, …)

    2. -

  2. Must listen to 5000 port.

    3. -

  3. Must expose /display route .

    4. -

  4. /display router should response to GET requests.

    5. -

  5. In the GET request, a public URL of the input MMIF file is passed via file URL parameter.

    6. -

  6. On the codebase root, there must be a Dockerfile that can build a docker image that runs the web app.

    7. -
-

We provide an example consumer at https://github.com/clamsproject/mmif-visualizer.

-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.3.1 - - -
-
- -
0.3.0
-
0.3.1
-
0.3.2
-
0.3.3
-
0.3.4
-
0.3.5
-
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-
0.4.1
-
0.4.2
-
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- - - \ No newline at end of file diff --git a/docs/0.3.1/genindex.html b/docs/0.3.1/genindex.html deleted file mode 100644 index 5db488af..00000000 --- a/docs/0.3.1/genindex.html +++ /dev/null @@ -1,407 +0,0 @@ - - - - - - - - Index — mmif-python documentation - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • Index
    • -
  • -
    • -
-
-
-
-
- - -

Index

- -
- A - | B - | C - | D - | I - | L - | M - | P - | R - | S - | T - | V - -
-

A

- - - -
- -

B

- - -
- -

C

- - -
- -

D

- - - -
- -

I

- - - -
- -

L

- - - -
- -

M

- - - -
    -
  • - mmif.serialize.annotation - -
    • -
  • - mmif.vocabulary.annotation_types - -
    • -
  • - mmif.vocabulary.document_types - -
    • -
- -

P

- - - -
- -

R

- - - -
- -

S

- - -
- -

T

- - - -
- -

V

- - - -
- - - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.3.1 - - -
-
- -
0.3.0
-
0.3.1
-
0.3.2
-
0.3.3
-
0.3.4
-
0.3.5
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0.4.0
-
0.4.1
-
0.4.2
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0.4.3
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0.4.4
-
0.4.5
-
0.4.6
-
0.4.7
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0.4.8
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0.5.0
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0.5.1
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0.5.2
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1.0.0
-
1.0.1
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1.0.10
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1.0.11
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1.0.12
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1.0.13
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1.0.14
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1.0.15
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1.0.16
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1.0.17
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1.0.18
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1.0.19
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1.0.2
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1.0.3
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1.0.4
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1.0.5
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1.0.6
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1.0.7
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1.0.8
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1.0.9
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1.1.0
-
-
-
- - - \ No newline at end of file diff --git a/docs/0.3.1/index.html b/docs/0.3.1/index.html deleted file mode 100644 index dcfd71ba..00000000 --- a/docs/0.3.1/index.html +++ /dev/null @@ -1,201 +0,0 @@ - - - - - - - - - Welcome to mmif-python’s documentation! — mmif-python documentation - - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • Welcome to mmif-python’s documentation!
    • -
  • -
    • -
-
-
-
-
- -
-

Welcome to mmif-python’s documentation!

-
-
-

MMIF for python

-

NOTE that this project is in pre-alpha and being actively developed. Nothing is guaranteed to reliably work for the moment and developer need to be very careful when using APIs implemented here. Please use the issue track to report bugs and malfunctions.

-
-

MultiMedia Interchange Format

-

MMIF is a JSON(-LD)-based data format designed for transferring annotation data between computational analysis applications in CLAMS project.

-
-

Contents

- -
-
-

API documentation:

- -
-
-
-
-

Indices and tables

- -
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.3.1 - - -
-
- -
0.3.0
-
0.3.1
-
0.3.2
-
0.3.3
-
0.3.4
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0.3.5
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0.4.0
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0.4.1
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0.4.2
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0.4.3
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0.4.4
-
0.4.5
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0.4.6
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0.4.7
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0.4.8
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0.5.0
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0.5.1
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0.5.2
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1.0.0
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1.0.1
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1.0.10
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1.0.11
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1.0.12
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1.0.13
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1.0.14
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1.0.16
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- - - \ No newline at end of file diff --git a/docs/0.3.1/introduction.html b/docs/0.3.1/introduction.html deleted file mode 100644 index c05e1095..00000000 --- a/docs/0.3.1/introduction.html +++ /dev/null @@ -1,231 +0,0 @@ - - - - - - - - - Getting Started — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • Getting Started
    • -
  • -
    • -
-
-
-
-
- -
-

Getting Started

-
-

Overview

-

MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF wbesite. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports de-/serialization of MMIF objects, as well as many navigation and manipulation helpers for MMIF objects.

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Prerequisites

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  • Python: mmif-python requires Python 3.6 or newer. We have no plan to support Python 2.7.

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Installation

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Package mmif-python is distributed via the official PyPI. Users are supposed to pip-install to get latest release.

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pip install mmif-python
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This will install a package mmif to local python. -The MMIF format and specification is evolving over time, and mmif-python package will be updated along with the changes in MMIF format. Note that MMIF format is not always backward-compatible. To find out more about relations between MMIF versions and mmif-python versions, and which supports which, please take time to read our decision on the subject here.

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MMIF Serialization

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mmif.serialize.mmif.Mmif represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of mmif.serialize.model.MmifObject, including the mmif.serialize.mmif.Mmif. To start with an existing MMIF str, simple initiate a new Mmif object with the file.

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import mmif
-from mmif import Mmif
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-mmif_str = """{
-"metadata": {
-  "mmif": "http://mmif.clams.ai/0.2.0"
-},
-"documents": [
-  {
-    "@type": "http://mmif.clams.ai/0.2.0/vocabulary/VideoDocument",
-    "properties": {
-      "id": "m1",
-      "mime": "video/mp4",
-      "location": "file:///var/archive/video-0012.mp4"
-    }
-  },
-  {
-    "@type": "http://mmif.clams.ai/0.2.0/vocabulary/TextDocument",
-    "properties": {
-      "id": "m2",
-      "mime": "text/plain",
-      "location": "file:///var/archive/video-0012-transcript.txt"
-    }
-  }
-],
-"views": []}"""
-mmif_obj = Mmif(mmif_str)
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Few notes;

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  1. MMIF does not carry the primary source files in it.

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  2. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version mmif-python implementation of the MMIF might not be able to load an unsupported version of MMIF string.

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When serializing back to str, call .serialize() (mmif.serialize.model.MmifObject.serialize()) on the object.

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To get subcomponents, you can use various getters implemented in subclasses. For more details, the API documentation (mmif package) will help.

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The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the `appliance documentation `_ to learn more about the appliance. - -MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance. - -#. The code must be hosted on a public git repository (e.g. Github, Gitlab, ...) -#. Must listen to ``5000`` port. -#. Must expose ``/display`` route . -#. ``/display`` router should response to ``GET`` requests. -#. In the ``GET`` request, a public URL of the input MMIF file is passed via ``file`` URL parameter. -#. On the codebase root, there must be a ``Dockerfile`` that can build a `docker `_ image that runs the web app. - -We provide an example consumer at https://github.com/clamsproject/mmif-visualizer. diff --git a/docs/0.3.2/_sources/index.rst.txt b/docs/0.3.2/_sources/index.rst.txt deleted file mode 100644 index 6146286d..00000000 --- a/docs/0.3.2/_sources/index.rst.txt +++ /dev/null @@ -1,25 +0,0 @@ -Welcome to mmif-python's documentation! -======================================= - -.. mdinclude:: ../README.md - -.. toctree:: - :maxdepth: 2 - :caption: Contents - - introduction - consumer-tutorial - -.. toctree:: - :maxdepth: 2 - :caption: API documentation: - - modules - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/docs/0.3.2/_sources/introduction.rst.txt b/docs/0.3.2/_sources/introduction.rst.txt deleted file mode 100644 index 6af8cd61..00000000 --- a/docs/0.3.2/_sources/introduction.rst.txt +++ /dev/null @@ -1,75 +0,0 @@ -.. _instroduction: - -Getting Started -=============== - - -Overview ---------- - -MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF wbesite `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports de-/serialization of MMIF objects, as well as many navigation and manipulation helpers for MMIF objects. - -Prerequisites -------------- - -* `Python `_: ``mmif-python`` requires Python 3.6 or newer. We have no plan to support `Python 2.7 `_. - -Installation ---------------- - -Package ``mmif-python`` is distributed via the official PyPI. Users are supposed to pip-install to get latest release. - -.. code-block:: bash - - pip install mmif-python - -This will install a package `mmif` to local python. -The MMIF format and specification is evolving over time, and ``mmif-python`` package will be updated along with the changes in MMIF format. Note that MMIF format is not always backward-compatible. To find out more about relations between MMIF versions and ``mmif-python`` versions, and which supports which, please take time to read our decision on the subject `here `_. - -MMIF Serialization ---------------------------- - -:class:`mmif.serialize.mmif.Mmif` represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of :class:`mmif.serialize.model.MmifObject`, including the :class:`mmif.serialize.mmif.Mmif`. To start with an existing MMIF :class:`str`, simple initiate a new ``Mmif`` object with the file. - -.. code-block:: python - - import mmif - from mmif import Mmif - - mmif_str = """{ - "metadata": { - "mmif": "http://mmif.clams.ai/0.2.0" - }, - "documents": [ - { - "@type": "http://mmif.clams.ai/0.2.0/vocabulary/VideoDocument", - "properties": { - "id": "m1", - "mime": "video/mp4", - "location": "file:///var/archive/video-0012.mp4" - } - }, - { - "@type": "http://mmif.clams.ai/0.2.0/vocabulary/TextDocument", - "properties": { - "id": "m2", - "mime": "text/plain", - "location": "file:///var/archive/video-0012-transcript.txt" - } - } - ], - "views": []}""" - mmif_obj = Mmif(mmif_str) - - -Few notes; - -#. MMIF does not carry the primary source files in it. -#. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version ``mmif-python`` implementation of the MMIF might not be able to load an unsupported version of MMIF string. - -When serializing back to :class:`str`, call ``.serialize()`` (:meth:`mmif.serialize.model.MmifObject.serialize`) on the object. - -To get subcomponents, you can use various getters implemented in subclasses. 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- -/** - * Simple result scoring code. - */ -if (typeof Scorer === "undefined") { - var Scorer = { - // Implement the following function to further tweak the score for each result - // The function takes a result array [docname, title, anchor, descr, score, filename] - // and returns the new score. - /* - score: result => { - const [docname, title, anchor, descr, score, filename, kind] = result - return score - }, - */ - - // query matches the full name of an object - objNameMatch: 11, - // or matches in the last dotted part of the object name - objPartialMatch: 6, - // Additive scores depending on the priority of the object - objPrio: { - 0: 15, // used to be importantResults - 1: 5, // used to be objectResults - 2: -5, // used to be unimportantResults - }, - // Used when the priority is not in the mapping. - objPrioDefault: 0, - - // query found in title - title: 15, - partialTitle: 7, - // query found in terms - term: 5, - partialTerm: 2, - }; -} - -// Global search result kind enum, used by themes to style search results. -class SearchResultKind { - static get index() { return "index"; } - static get object() { return "object"; } - static get text() { return "text"; } - static get title() { return "title"; } -} - -const _removeChildren = (element) => { - while (element && element.lastChild) element.removeChild(element.lastChild); -}; - -/** - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping - */ -const _escapeRegExp = (string) => - string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string - -const _displayItem = (item, searchTerms, highlightTerms) => { - const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; - const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; - const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; - const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; - const contentRoot = document.documentElement.dataset.content_root; - - const [docName, title, anchor, descr, score, _filename, kind] = item; - - let listItem = document.createElement("li"); - // Add a class representing the item's type: - // can be used by a theme's CSS selector for styling - // See SearchResultKind for the class names. - listItem.classList.add(`kind-${kind}`); - let requestUrl; - let linkUrl; - if (docBuilder === "dirhtml") { - // dirhtml builder - let dirname = docName + "/"; - if (dirname.match(/\/index\/$/)) - dirname = dirname.substring(0, dirname.length - 6); - else if (dirname === "index/") dirname = ""; - requestUrl = contentRoot + dirname; - linkUrl = requestUrl; - } else { - // normal html builders - requestUrl = contentRoot + docName + docFileSuffix; - linkUrl = docName + docLinkSuffix; - } - let linkEl = listItem.appendChild(document.createElement("a")); - linkEl.href = linkUrl + anchor; - linkEl.dataset.score = score; - linkEl.innerHTML = title; - if (descr) { - listItem.appendChild(document.createElement("span")).innerHTML = - " (" + descr + ")"; - // highlight search terms in the description - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - } - else if (showSearchSummary) - fetch(requestUrl) - .then((responseData) => responseData.text()) - .then((data) => { - if (data) - listItem.appendChild( - Search.makeSearchSummary(data, searchTerms, anchor) - ); - // highlight search terms in the summary - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - }); - Search.output.appendChild(listItem); -}; -const _finishSearch = (resultCount) => { - Search.stopPulse(); - Search.title.innerText = _("Search Results"); - if (!resultCount) - Search.status.innerText = Documentation.gettext( - "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." - ); - else - Search.status.innerText = Documentation.ngettext( - "Search finished, found one page matching the search query.", - "Search finished, found ${resultCount} pages matching the search query.", - resultCount, - ).replace('${resultCount}', resultCount); -}; -const _displayNextItem = ( - results, - resultCount, - searchTerms, - highlightTerms, -) => { - // results left, load the summary and display it - // this is intended to be dynamic (don't sub resultsCount) - if (results.length) { - _displayItem(results.pop(), searchTerms, highlightTerms); - setTimeout( - () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), - 5 - ); - } - // search finished, update title and status message - else _finishSearch(resultCount); -}; -// Helper function used by query() to order search results. -// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. -// Order the results by score (in opposite order of appearance, since the -// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. -const _orderResultsByScoreThenName = (a, b) => { - const leftScore = a[4]; - const rightScore = b[4]; - if (leftScore === rightScore) { - // same score: sort alphabetically - const leftTitle = a[1].toLowerCase(); - const rightTitle = b[1].toLowerCase(); - if (leftTitle === rightTitle) return 0; - return leftTitle > rightTitle ? -1 : 1; // inverted is intentional - } - return leftScore > rightScore ? 1 : -1; -}; - -/** - * Default splitQuery function. Can be overridden in ``sphinx.search`` with a - * custom function per language. - * - * The regular expression works by splitting the string on consecutive characters - * that are not Unicode letters, numbers, underscores, or emoji characters. - * This is the same as ``\W+`` in Python, preserving the surrogate pair area. - */ -if (typeof splitQuery === "undefined") { - var splitQuery = (query) => query - .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) - .filter(term => term) // remove remaining empty strings -} - -/** - * Search Module - */ -const Search = { - _index: null, - _queued_query: null, - _pulse_status: -1, - - htmlToText: (htmlString, anchor) => { - const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - for (const removalQuery of [".headerlink", "script", "style"]) { - htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); - } - if (anchor) { - const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); - if (anchorContent) return anchorContent.textContent; - - console.warn( - `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` - ); - } - - // if anchor not specified or not found, fall back to main content - const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent) return docContent.textContent; - - console.warn( - "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." - ); - return ""; - }, - - init: () => { - const query = new URLSearchParams(window.location.search).get("q"); - document - .querySelectorAll('input[name="q"]') - .forEach((el) => (el.value = query)); - if (query) Search.performSearch(query); - }, - - loadIndex: (url) => - (document.body.appendChild(document.createElement("script")).src = url), - - setIndex: (index) => { - Search._index = index; - if (Search._queued_query !== null) { - const query = Search._queued_query; - Search._queued_query = null; - Search.query(query); - } - }, - - hasIndex: () => Search._index !== null, - - deferQuery: (query) => (Search._queued_query = query), - - stopPulse: () => (Search._pulse_status = -1), - - startPulse: () => { - if (Search._pulse_status >= 0) return; - - const pulse = () => { - Search._pulse_status = (Search._pulse_status + 1) % 4; - Search.dots.innerText = ".".repeat(Search._pulse_status); - if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); - }; - pulse(); - }, - - /** - * perform a search for something (or wait until index is loaded) - */ - performSearch: (query) => { - // create the required interface elements - const searchText = document.createElement("h2"); - searchText.textContent = _("Searching"); - const searchSummary = document.createElement("p"); - searchSummary.classList.add("search-summary"); - searchSummary.innerText = ""; - const searchList = document.createElement("ul"); - searchList.setAttribute("role", "list"); - searchList.classList.add("search"); - - const out = document.getElementById("search-results"); - Search.title = out.appendChild(searchText); - Search.dots = Search.title.appendChild(document.createElement("span")); - Search.status = out.appendChild(searchSummary); - Search.output = out.appendChild(searchList); - - const searchProgress = document.getElementById("search-progress"); - // Some themes don't use the search progress node - if (searchProgress) { - searchProgress.innerText = _("Preparing search..."); - } - Search.startPulse(); - - // index already loaded, the browser was quick! - if (Search.hasIndex()) Search.query(query); - else Search.deferQuery(query); - }, - - _parseQuery: (query) => { - // stem the search terms and add them to the correct list - const stemmer = new Stemmer(); - const searchTerms = new Set(); - const excludedTerms = new Set(); - const highlightTerms = new Set(); - const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); - splitQuery(query.trim()).forEach((queryTerm) => { - const queryTermLower = queryTerm.toLowerCase(); - - // maybe skip this "word" - // stopwords array is from language_data.js - if ( - stopwords.indexOf(queryTermLower) !== -1 || - queryTerm.match(/^\d+$/) - ) - return; - - // stem the word - let word = stemmer.stemWord(queryTermLower); - // select the correct list - if (word[0] === "-") excludedTerms.add(word.substr(1)); - else { - searchTerms.add(word); - highlightTerms.add(queryTermLower); - } - }); - - if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js - localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) - } - - // console.debug("SEARCH: searching for:"); - // console.info("required: ", [...searchTerms]); - // console.info("excluded: ", [...excludedTerms]); - - return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; - }, - - /** - * execute search (requires search index to be loaded) - */ - _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - - // Collect multiple result groups to be sorted separately and then ordered. - // Each is an array of [docname, title, anchor, descr, score, filename, kind]. - const normalResults = []; - const nonMainIndexResults = []; - - _removeChildren(document.getElementById("search-progress")); - - const queryLower = query.toLowerCase().trim(); - for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { - for (const [file, id] of foundTitles) { - const score = Math.round(Scorer.title * queryLower.length / title.length); - const boost = titles[file] === title ? 1 : 0; // add a boost for document titles - normalResults.push([ - docNames[file], - titles[file] !== title ? `${titles[file]} > ${title}` : title, - id !== null ? "#" + id : "", - null, - score + boost, - filenames[file], - SearchResultKind.title, - ]); - } - } - } - - // search for explicit entries in index directives - for (const [entry, foundEntries] of Object.entries(indexEntries)) { - if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id, isMain] of foundEntries) { - const score = Math.round(100 * queryLower.length / entry.length); - const result = [ - docNames[file], - titles[file], - id ? "#" + id : "", - null, - score, - filenames[file], - SearchResultKind.index, - ]; - if (isMain) { - normalResults.push(result); - } else { - nonMainIndexResults.push(result); - } - } - } - } - - // lookup as object - objectTerms.forEach((term) => - normalResults.push(...Search.performObjectSearch(term, objectTerms)) - ); - - // lookup as search terms in fulltext - normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); - - // let the scorer override scores with a custom scoring function - if (Scorer.score) { - normalResults.forEach((item) => (item[4] = Scorer.score(item))); - nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); - } - - // Sort each group of results by score and then alphabetically by name. - normalResults.sort(_orderResultsByScoreThenName); - nonMainIndexResults.sort(_orderResultsByScoreThenName); - - // Combine the result groups in (reverse) order. - // Non-main index entries are typically arbitrary cross-references, - // so display them after other results. - let results = [...nonMainIndexResults, ...normalResults]; - - // remove duplicate search results - // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept - let seen = new Set(); - results = results.reverse().reduce((acc, result) => { - let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); - if (!seen.has(resultStr)) { - acc.push(result); - seen.add(resultStr); - } - return acc; - }, []); - - return results.reverse(); - }, - - query: (query) => { - const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); - const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); - - // for debugging - //Search.lastresults = results.slice(); // a copy - // console.info("search results:", Search.lastresults); - - // print the results - _displayNextItem(results, results.length, searchTerms, highlightTerms); - }, - - /** - * search for object names - */ - performObjectSearch: (object, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const objects = Search._index.objects; - const objNames = Search._index.objnames; - const titles = Search._index.titles; - - const results = []; - - const objectSearchCallback = (prefix, match) => { - const name = match[4] - const fullname = (prefix ? prefix + "." : "") + name; - const fullnameLower = fullname.toLowerCase(); - if (fullnameLower.indexOf(object) < 0) return; - - let score = 0; - const parts = fullnameLower.split("."); - - // check for different match types: exact matches of full name or - // "last name" (i.e. last dotted part) - if (fullnameLower === object || parts.slice(-1)[0] === object) - score += Scorer.objNameMatch; - else if (parts.slice(-1)[0].indexOf(object) > -1) - score += Scorer.objPartialMatch; // matches in last name - - const objName = objNames[match[1]][2]; - const title = titles[match[0]]; - - // If more than one term searched for, we require other words to be - // found in the name/title/description - const otherTerms = new Set(objectTerms); - otherTerms.delete(object); - if (otherTerms.size > 0) { - const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); - if ( - [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) - ) - return; - } - - let anchor = match[3]; - if (anchor === "") anchor = fullname; - else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; - - const descr = objName + _(", in ") + title; - - // add custom score for some objects according to scorer - if (Scorer.objPrio.hasOwnProperty(match[2])) - score += Scorer.objPrio[match[2]]; - else score += Scorer.objPrioDefault; - - results.push([ - docNames[match[0]], - fullname, - "#" + anchor, - descr, - score, - filenames[match[0]], - SearchResultKind.object, - ]); - }; - Object.keys(objects).forEach((prefix) => - objects[prefix].forEach((array) => - objectSearchCallback(prefix, array) - ) - ); - return results; - }, - - /** - * search for full-text terms in the index - */ - performTermsSearch: (searchTerms, excludedTerms) => { - // prepare search - const terms = Search._index.terms; - const titleTerms = Search._index.titleterms; - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - - const scoreMap = new Map(); - const fileMap = new Map(); - - // perform the search on the required terms - searchTerms.forEach((word) => { - const files = []; - const arr = [ - { files: terms[word], score: Scorer.term }, - { files: titleTerms[word], score: Scorer.title }, - ]; - // add support for partial matches - if (word.length > 2) { - const escapedWord = _escapeRegExp(word); - if (!terms.hasOwnProperty(word)) { - Object.keys(terms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: terms[term], score: Scorer.partialTerm }); - }); - } - if (!titleTerms.hasOwnProperty(word)) { - Object.keys(titleTerms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); - }); - } - } - - // no match but word was a required one - if (arr.every((record) => record.files === undefined)) return; - - // found search word in contents - arr.forEach((record) => { - if (record.files === undefined) return; - - let recordFiles = record.files; - if (recordFiles.length === undefined) recordFiles = [recordFiles]; - files.push(...recordFiles); - - // set score for the word in each file - recordFiles.forEach((file) => { - if (!scoreMap.has(file)) scoreMap.set(file, {}); - scoreMap.get(file)[word] = record.score; - }); - }); - - // create the mapping - files.forEach((file) => { - if (!fileMap.has(file)) fileMap.set(file, [word]); - else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); - }); - }); - - // now check if the files don't contain excluded terms - const results = []; - for (const [file, wordList] of fileMap) { - // check if all requirements are matched - - // as search terms with length < 3 are discarded - const filteredTermCount = [...searchTerms].filter( - (term) => term.length > 2 - ).length; - if ( - wordList.length !== searchTerms.size && - wordList.length !== filteredTermCount - ) - continue; - - // ensure that none of the excluded terms is in the search result - if ( - [...excludedTerms].some( - (term) => - terms[term] === file || - titleTerms[term] === file || - (terms[term] || []).includes(file) || - (titleTerms[term] || []).includes(file) - ) - ) - break; - - // select one (max) score for the file. - const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); - // add result to the result list - results.push([ - docNames[file], - titles[file], - "", - null, - score, - filenames[file], - SearchResultKind.text, - ]); - } - return results; - }, - - /** - * helper function to return a node containing the - * search summary for a given text. keywords is a list - * of stemmed words. - */ - makeSearchSummary: (htmlText, keywords, anchor) => { - const text = Search.htmlToText(htmlText, anchor); - if (text === "") return null; - - const textLower = text.toLowerCase(); - const actualStartPosition = [...keywords] - .map((k) => textLower.indexOf(k.toLowerCase())) - .filter((i) => i > -1) - .slice(-1)[0]; - const startWithContext = Math.max(actualStartPosition - 120, 0); - - const top = startWithContext === 0 ? "" : "..."; - const tail = startWithContext + 240 < text.length ? "..." : ""; - - let summary = document.createElement("p"); - summary.classList.add("context"); - summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; - - return summary; - }, -}; - -_ready(Search.init); diff --git a/docs/0.3.2/_static/sphinx_highlight.js b/docs/0.3.2/_static/sphinx_highlight.js deleted file mode 100644 index 8a96c69a..00000000 --- a/docs/0.3.2/_static/sphinx_highlight.js +++ /dev/null @@ -1,154 +0,0 @@ -/* Highlighting utilities for Sphinx HTML documentation. */ -"use strict"; - -const SPHINX_HIGHLIGHT_ENABLED = true - -/** - * highlight a given string on a node by wrapping it in - * span elements with the given class name. - */ -const _highlight = (node, addItems, text, className) => { - if (node.nodeType === Node.TEXT_NODE) { - const val = node.nodeValue; - const parent = node.parentNode; - const pos = val.toLowerCase().indexOf(text); - if ( - pos >= 0 && - !parent.classList.contains(className) && - !parent.classList.contains("nohighlight") - ) { - let span; - - const closestNode = parent.closest("body, svg, foreignObject"); - const isInSVG = closestNode && closestNode.matches("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.classList.add(className); - } - - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - const rest = document.createTextNode(val.substr(pos + text.length)); - parent.insertBefore( - span, - parent.insertBefore( - rest, - node.nextSibling - ) - ); - node.nodeValue = val.substr(0, pos); - /* There may be more occurrences of search term in this node. So call this - * function recursively on the remaining fragment. - */ - _highlight(rest, addItems, text, className); - - if (isInSVG) { - const rect = document.createElementNS( - "http://www.w3.org/2000/svg", - "rect" - ); - const bbox = parent.getBBox(); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute("class", className); - addItems.push({ parent: parent, target: rect }); - } - } - } else if (node.matches && !node.matches("button, select, textarea")) { - node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); - } -}; -const _highlightText = (thisNode, text, className) => { - let addItems = []; - _highlight(thisNode, addItems, text, className); - addItems.forEach((obj) => - obj.parent.insertAdjacentElement("beforebegin", obj.target) - ); -}; - -/** - * Small JavaScript module for the documentation. - */ -const SphinxHighlight = { - - /** - * highlight the search words provided in localstorage in the text - */ - highlightSearchWords: () => { - if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight - - // get and clear terms from localstorage - const url = new URL(window.location); - const highlight = - localStorage.getItem("sphinx_highlight_terms") - || url.searchParams.get("highlight") - || ""; - localStorage.removeItem("sphinx_highlight_terms") - url.searchParams.delete("highlight"); - window.history.replaceState({}, "", url); - - // get individual terms from highlight string - const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); - if (terms.length === 0) return; // nothing to do - - // There should never be more than one element matching "div.body" - const divBody = document.querySelectorAll("div.body"); - const body = divBody.length ? divBody[0] : document.querySelector("body"); - window.setTimeout(() => { - terms.forEach((term) => _highlightText(body, term, "highlighted")); - }, 10); - - const searchBox = document.getElementById("searchbox"); - if (searchBox === null) return; - searchBox.appendChild( - document - .createRange() - .createContextualFragment( - '

' + - '' + - _("Hide Search Matches") + - "

" - ) - ); - }, - - /** - * helper function to hide the search marks again - */ - hideSearchWords: () => { - document - .querySelectorAll("#searchbox .highlight-link") - .forEach((el) => el.remove()); - document - .querySelectorAll("span.highlighted") - .forEach((el) => el.classList.remove("highlighted")); - localStorage.removeItem("sphinx_highlight_terms") - }, - - initEscapeListener: () => { - // only install a listener if it is really needed - if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; - - document.addEventListener("keydown", (event) => { - // bail for input elements - if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; - // bail with special keys - if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; - if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { - SphinxHighlight.hideSearchWords(); - event.preventDefault(); - } - }); - }, -}; - -_ready(() => { - /* Do not call highlightSearchWords() when we are on the search page. - * It will highlight words from the *previous* search query. - */ - if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); - SphinxHighlight.initEscapeListener(); -}); diff --git a/docs/0.3.2/autodoc/mmif.serialize.html b/docs/0.3.2/autodoc/mmif.serialize.html deleted file mode 100644 index 79c081f4..00000000 --- a/docs/0.3.2/autodoc/mmif.serialize.html +++ /dev/null @@ -1,369 +0,0 @@ - - - - - - - - - mmif.serialize module — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.serialize module

-
-

mmif.serialize.model module

-
-
-

mmif.serialize.mmif module

-
-
-

mmif.serialize.view module

-
-
-

mmif.serialize.annotation module

-

The annotation module contains the classes used to represent a -MMIF annotation as a live Python object.

-

In MMIF, annotations are created by apps in a pipeline as a part -of a view. For documentation on how views are represented, see -mmif.serialize.view.

-
-
-class mmif.serialize.annotation.Annotation(anno_obj: bytes | str | dict | None = None)[source]
-

Bases: FreezableMmifObject

-

MmifObject that represents an annotation in a MMIF view.

-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]]) → None[source]
-

Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

-
- -
-
-property at_type: str | ThingTypesBase[source]
-
- -
-
-property id: str[source]
-
- -
-
-is_document()[source]
-
- -
-
-is_type(type: str | ThingTypesBase) → bool[source]
-

Check if the @type of this object matches.

-
- -
- -
-
-class mmif.serialize.annotation.AnnotationProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: FreezableMmifObject

-

AnnotationProperties object that represents the -properties object within a MMIF annotation.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
- -
-
-class mmif.serialize.annotation.Document(doc_obj: bytes | str | dict | None = None)[source]
-

Bases: Annotation

-

Document object that represents a single document in a MMIF file.

-

A document is identified by an ID, and contains certain attributes -and potentially contains the contents of the document itself, -metadata about how the document was created, and/or a list of -subdocuments grouped together logically.

-

If document_obj is not provided, an empty Document will be generated.

-
-
Parameters:
-

document_obj – the JSON data that defines the document

-
-
-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None]) → None[source]
-

Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

-
- -
-
-property location: str[source]
-
- -
-
-location_address() → str[source]
-
- -
-
-location_path() → str[source]
-
- -
-
-location_scheme() → str[source]
-
- -
-
-property parent: str[source]
-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.DocumentProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: AnnotationProperties

-

DocumentProperties object that represents the -properties object within a MMIF document.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
-
-property location: str[source]
-
- -
-
-location_address() → str[source]
-
- -
-
-location_path() → str[source]
-
- -
-
-location_scheme() → str[source]
-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.Text(text_obj: bytes | str | dict | None = None)[source]
-

Bases: FreezableMmifObject

-
-
-property lang: str[source]
-
- -
-
-property value: str[source]
-
- -
- -
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.3.2 - - -
-
- -
0.3.0
-
0.3.1
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0.3.2
-
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- - - \ No newline at end of file diff --git a/docs/0.3.2/autodoc/mmif.vocabulary.html b/docs/0.3.2/autodoc/mmif.vocabulary.html deleted file mode 100644 index cbbfa172..00000000 --- a/docs/0.3.2/autodoc/mmif.vocabulary.html +++ /dev/null @@ -1,306 +0,0 @@ - - - - - - - - - mmif.vocabulary module — mmif-python documentation - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.vocabulary module

-
-

mmif.vocabulary.annotation_types module

-
-
-class mmif.vocabulary.annotation_types.AnnotationTypes(value)[source]
-

Bases: AnnotationTypesBase

-

This enum contains the URIs for the MMIF annotation types defined in the spec version 0.3.1. -Use this to quickly get the correct URIs for those types, or use the objects themselves in your -code and they will serialize to the strings.

-
-
-Alignment = 'http://mmif.clams.ai/0.3.1/vocabulary/Alignment'[source]
-
- -
-
-Annotation = 'http://mmif.clams.ai/0.3.1/vocabulary/Annotation'[source]
-
- -
-
-BoundingBox = 'http://mmif.clams.ai/0.3.1/vocabulary/BoundingBox'[source]
-
- -
-
-Chapter = 'http://mmif.clams.ai/0.3.1/vocabulary/Chapter'[source]
-
- -
-
-Interval = 'http://mmif.clams.ai/0.3.1/vocabulary/Interval'[source]
-
- -
-
-Polygon = 'http://mmif.clams.ai/0.3.1/vocabulary/Polygon'[source]
-
- -
-
-Region = 'http://mmif.clams.ai/0.3.1/vocabulary/Region'[source]
-
- -
-
-Relation = 'http://mmif.clams.ai/0.3.1/vocabulary/Relation'[source]
-
- -
-
-Span = 'http://mmif.clams.ai/0.3.1/vocabulary/Span'[source]
-
- -
-
-TimeFrame = 'http://mmif.clams.ai/0.3.1/vocabulary/TimeFrame'[source]
-
- -
-
-TimePoint = 'http://mmif.clams.ai/0.3.1/vocabulary/TimePoint'[source]
-
- -
-
-VideoObject = 'http://mmif.clams.ai/0.3.1/vocabulary/VideoObject'[source]
-
- -
- -
-
-class mmif.vocabulary.annotation_types.AnnotationTypesBase(value)[source]
-

Bases: ThingTypesBase

-

Inherit from this class to build your own custom annotation -vocabularies. Each member’s name should be the name of the -type, and each member’s value should be the URI of that type.

-
- -
-
-

mmif.vocabulary.media_types module

-
-
-class mmif.vocabulary.document_types.DocumentTypes(value)[source]
-

Bases: DocumentTypesBase

-

This enum contains the URIs for the MMIF document types defined in the spec version 0.3.1. -Use this to quickly get the correct URIs for those types, or use the objects themselves in your -code and they will serialize to the strings.

-
-
-AudioDocument = 'http://mmif.clams.ai/0.3.1/vocabulary/AudioDocument'[source]
-
- -
-
-Document = 'http://mmif.clams.ai/0.3.1/vocabulary/Document'[source]
-
- -
-
-ImageDocument = 'http://mmif.clams.ai/0.3.1/vocabulary/ImageDocument'[source]
-
- -
-
-TextDocument = 'http://mmif.clams.ai/0.3.1/vocabulary/TextDocument'[source]
-
- -
-
-VideoDocument = 'http://mmif.clams.ai/0.3.1/vocabulary/VideoDocument'[source]
-
- -
- -
-
-class mmif.vocabulary.document_types.DocumentTypesBase(value)[source]
-

Bases: ThingTypesBase

-

Inherit from this class to build your own custom document -vocabularies. Each member’s name should be the name of the -type, and each member’s value should be the URI of that type.

-
- -
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.3.2 - - -
-
- -
0.3.0
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0.3.1
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0.3.2
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- - - \ No newline at end of file diff --git a/docs/0.3.2/consumer-tutorial.html b/docs/0.3.2/consumer-tutorial.html deleted file mode 100644 index 61301732..00000000 --- a/docs/0.3.2/consumer-tutorial.html +++ /dev/null @@ -1,175 +0,0 @@ - - - - - - - - - MMIF consumer — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • MMIF consumer
    • -
  • -
    • -
-
-
-
-
- -
-

MMIF consumer

-

A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the appliance documentation to learn more about the appliance.

-

MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance.

-
    -

  1. The code must be hosted on a public git repository (e.g. Github, Gitlab, …)

    2. -

  2. Must listen to 5000 port.

    3. -

  3. Must expose /display route .

    4. -

  4. /display router should response to GET requests.

    5. -

  5. In the GET request, a public URL of the input MMIF file is passed via file URL parameter.

    6. -

  6. On the codebase root, there must be a Dockerfile that can build a docker image that runs the web app.

    7. -
-

We provide an example consumer at https://github.com/clamsproject/mmif-visualizer.

-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.3.2 - - -
-
- -
0.3.0
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0.3.1
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- - - \ No newline at end of file diff --git a/docs/0.3.2/genindex.html b/docs/0.3.2/genindex.html deleted file mode 100644 index 5431a8b8..00000000 --- a/docs/0.3.2/genindex.html +++ /dev/null @@ -1,407 +0,0 @@ - - - - - - - - Index — mmif-python documentation - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • Index
    • -
  • -
    • -
-
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- - -

Index

- -
- A - | B - | C - | D - | I - | L - | M - | P - | R - | S - | T - | V - -
-

A

- - - -
- -

B

- - -
- -

C

- - -
- -

D

- - - -
- -

I

- - - -
- -

L

- - - -
- -

M

- - - -
    -
  • - mmif.serialize.annotation - -
    • -
  • - mmif.vocabulary.annotation_types - -
    • -
  • - mmif.vocabulary.document_types - -
    • -
- -

P

- - - -
- -

R

- - - -
- -

S

- - -
- -

T

- - - -
- -

V

- - - -
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- - Other Versions - v: 0.3.2 - - -
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0.3.0
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0.3.1
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0.3.2
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0.3.3
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0.3.4
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0.3.5
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0.4.0
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0.4.1
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0.4.2
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0.4.3
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0.4.4
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0.4.5
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0.4.6
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0.4.7
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0.5.1
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0.5.2
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1.0.10
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- - - \ No newline at end of file diff --git a/docs/0.3.2/index.html b/docs/0.3.2/index.html deleted file mode 100644 index d5640eda..00000000 --- a/docs/0.3.2/index.html +++ /dev/null @@ -1,201 +0,0 @@ - - - - - - - - - Welcome to mmif-python’s documentation! — mmif-python documentation - - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • Welcome to mmif-python’s documentation!
    • -
  • -
    • -
-
-
-
-
- -
-

Welcome to mmif-python’s documentation!

-
-
-

MMIF for python

-

NOTE that this project is in pre-alpha and being actively developed. Nothing is guaranteed to reliably work for the moment and developer need to be very careful when using APIs implemented here. Please use the issue track to report bugs and malfunctions.

-
-

MultiMedia Interchange Format

-

MMIF is a JSON(-LD)-based data format designed for transferring annotation data between computational analysis applications in CLAMS project.

-
-

Contents

- -
-
-

API documentation:

- -
-
-
-
-

Indices and tables

- -
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.3.2 - - -
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0.3.0
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0.3.1
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0.3.2
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0.3.3
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0.3.4
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- - - \ No newline at end of file diff --git a/docs/0.3.2/introduction.html b/docs/0.3.2/introduction.html deleted file mode 100644 index 124a6ed9..00000000 --- a/docs/0.3.2/introduction.html +++ /dev/null @@ -1,231 +0,0 @@ - - - - - - - - - Getting Started — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
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  • Getting Started
    • -
  • -
    • -
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- -
-

Getting Started

-
-

Overview

-

MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF wbesite. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports de-/serialization of MMIF objects, as well as many navigation and manipulation helpers for MMIF objects.

-
-
-

Prerequisites

-
    -

  • Python: mmif-python requires Python 3.6 or newer. We have no plan to support Python 2.7.

    • -
-
-
-

Installation

-

Package mmif-python is distributed via the official PyPI. Users are supposed to pip-install to get latest release.

-
pip install mmif-python
-
-
-

This will install a package mmif to local python. -The MMIF format and specification is evolving over time, and mmif-python package will be updated along with the changes in MMIF format. Note that MMIF format is not always backward-compatible. To find out more about relations between MMIF versions and mmif-python versions, and which supports which, please take time to read our decision on the subject here.

-
-
-

MMIF Serialization

-

mmif.serialize.mmif.Mmif represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of mmif.serialize.model.MmifObject, including the mmif.serialize.mmif.Mmif. To start with an existing MMIF str, simple initiate a new Mmif object with the file.

-
import mmif
-from mmif import Mmif
-
-mmif_str = """{
-"metadata": {
-  "mmif": "http://mmif.clams.ai/0.2.0"
-},
-"documents": [
-  {
-    "@type": "http://mmif.clams.ai/0.2.0/vocabulary/VideoDocument",
-    "properties": {
-      "id": "m1",
-      "mime": "video/mp4",
-      "location": "file:///var/archive/video-0012.mp4"
-    }
-  },
-  {
-    "@type": "http://mmif.clams.ai/0.2.0/vocabulary/TextDocument",
-    "properties": {
-      "id": "m2",
-      "mime": "text/plain",
-      "location": "file:///var/archive/video-0012-transcript.txt"
-    }
-  }
-],
-"views": []}"""
-mmif_obj = Mmif(mmif_str)
-
-
-

Few notes;

-
    -

  1. MMIF does not carry the primary source files in it.

    2. -

  2. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version mmif-python implementation of the MMIF might not be able to load an unsupported version of MMIF string.

    3. -
-

When serializing back to str, call .serialize() (mmif.serialize.model.MmifObject.serialize()) on the object.

-

To get subcomponents, you can use various getters implemented in subclasses. For more details, the API documentation (mmif package) will help.

-
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.3.2 - - -
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0.3.0
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0.3.1
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0.4.0
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0.4.1
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0.4.2
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- - - \ No newline at end of file diff --git a/docs/0.3.2/modules.html b/docs/0.3.2/modules.html deleted file mode 100644 index 4bc3a1b5..00000000 --- a/docs/0.3.2/modules.html +++ /dev/null @@ -1,249 +0,0 @@ - - - - - - - - - mmif package — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
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  • mmif package
    • -
  • -
    • -
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-

mmif package

-
- -
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- - -
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- -
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The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the `appliance documentation `_ to learn more about the appliance. - -MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance. - -#. The code must be hosted on a public git repository (e.g. Github, Gitlab, ...) -#. Must listen to ``5000`` port. -#. Must expose ``/display`` route . -#. ``/display`` router should response to ``GET`` requests. -#. In the ``GET`` request, a public URL of the input MMIF file is passed via ``file`` URL parameter. -#. On the codebase root, there must be a ``Dockerfile`` that can build a `docker `_ image that runs the web app. - -We provide an example consumer at https://github.com/clamsproject/mmif-visualizer. diff --git a/docs/0.3.3/_sources/index.rst.txt b/docs/0.3.3/_sources/index.rst.txt deleted file mode 100644 index 6146286d..00000000 --- a/docs/0.3.3/_sources/index.rst.txt +++ /dev/null @@ -1,25 +0,0 @@ -Welcome to mmif-python's documentation! -======================================= - -.. mdinclude:: ../README.md - -.. toctree:: - :maxdepth: 2 - :caption: Contents - - introduction - consumer-tutorial - -.. toctree:: - :maxdepth: 2 - :caption: API documentation: - - modules - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/docs/0.3.3/_sources/introduction.rst.txt b/docs/0.3.3/_sources/introduction.rst.txt deleted file mode 100644 index 6af8cd61..00000000 --- a/docs/0.3.3/_sources/introduction.rst.txt +++ /dev/null @@ -1,75 +0,0 @@ -.. _instroduction: - -Getting Started -=============== - - -Overview ---------- - -MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF wbesite `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports de-/serialization of MMIF objects, as well as many navigation and manipulation helpers for MMIF objects. - -Prerequisites -------------- - -* `Python `_: ``mmif-python`` requires Python 3.6 or newer. We have no plan to support `Python 2.7 `_. - -Installation ---------------- - -Package ``mmif-python`` is distributed via the official PyPI. Users are supposed to pip-install to get latest release. - -.. code-block:: bash - - pip install mmif-python - -This will install a package `mmif` to local python. -The MMIF format and specification is evolving over time, and ``mmif-python`` package will be updated along with the changes in MMIF format. Note that MMIF format is not always backward-compatible. To find out more about relations between MMIF versions and ``mmif-python`` versions, and which supports which, please take time to read our decision on the subject `here `_. - -MMIF Serialization ---------------------------- - -:class:`mmif.serialize.mmif.Mmif` represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of :class:`mmif.serialize.model.MmifObject`, including the :class:`mmif.serialize.mmif.Mmif`. To start with an existing MMIF :class:`str`, simple initiate a new ``Mmif`` object with the file. - -.. code-block:: python - - import mmif - from mmif import Mmif - - mmif_str = """{ - "metadata": { - "mmif": "http://mmif.clams.ai/0.2.0" - }, - "documents": [ - { - "@type": "http://mmif.clams.ai/0.2.0/vocabulary/VideoDocument", - "properties": { - "id": "m1", - "mime": "video/mp4", - "location": "file:///var/archive/video-0012.mp4" - } - }, - { - "@type": "http://mmif.clams.ai/0.2.0/vocabulary/TextDocument", - "properties": { - "id": "m2", - "mime": "text/plain", - "location": "file:///var/archive/video-0012-transcript.txt" - } - } - ], - "views": []}""" - mmif_obj = Mmif(mmif_str) - - -Few notes; - -#. MMIF does not carry the primary source files in it. -#. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version ``mmif-python`` implementation of the MMIF might not be able to load an unsupported version of MMIF string. - -When serializing back to :class:`str`, call ``.serialize()`` (:meth:`mmif.serialize.model.MmifObject.serialize`) on the object. - -To get subcomponents, you can use various getters implemented in subclasses. 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- -/** - * Simple result scoring code. - */ -if (typeof Scorer === "undefined") { - var Scorer = { - // Implement the following function to further tweak the score for each result - // The function takes a result array [docname, title, anchor, descr, score, filename] - // and returns the new score. - /* - score: result => { - const [docname, title, anchor, descr, score, filename, kind] = result - return score - }, - */ - - // query matches the full name of an object - objNameMatch: 11, - // or matches in the last dotted part of the object name - objPartialMatch: 6, - // Additive scores depending on the priority of the object - objPrio: { - 0: 15, // used to be importantResults - 1: 5, // used to be objectResults - 2: -5, // used to be unimportantResults - }, - // Used when the priority is not in the mapping. - objPrioDefault: 0, - - // query found in title - title: 15, - partialTitle: 7, - // query found in terms - term: 5, - partialTerm: 2, - }; -} - -// Global search result kind enum, used by themes to style search results. -class SearchResultKind { - static get index() { return "index"; } - static get object() { return "object"; } - static get text() { return "text"; } - static get title() { return "title"; } -} - -const _removeChildren = (element) => { - while (element && element.lastChild) element.removeChild(element.lastChild); -}; - -/** - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping - */ -const _escapeRegExp = (string) => - string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string - -const _displayItem = (item, searchTerms, highlightTerms) => { - const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; - const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; - const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; - const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; - const contentRoot = document.documentElement.dataset.content_root; - - const [docName, title, anchor, descr, score, _filename, kind] = item; - - let listItem = document.createElement("li"); - // Add a class representing the item's type: - // can be used by a theme's CSS selector for styling - // See SearchResultKind for the class names. - listItem.classList.add(`kind-${kind}`); - let requestUrl; - let linkUrl; - if (docBuilder === "dirhtml") { - // dirhtml builder - let dirname = docName + "/"; - if (dirname.match(/\/index\/$/)) - dirname = dirname.substring(0, dirname.length - 6); - else if (dirname === "index/") dirname = ""; - requestUrl = contentRoot + dirname; - linkUrl = requestUrl; - } else { - // normal html builders - requestUrl = contentRoot + docName + docFileSuffix; - linkUrl = docName + docLinkSuffix; - } - let linkEl = listItem.appendChild(document.createElement("a")); - linkEl.href = linkUrl + anchor; - linkEl.dataset.score = score; - linkEl.innerHTML = title; - if (descr) { - listItem.appendChild(document.createElement("span")).innerHTML = - " (" + descr + ")"; - // highlight search terms in the description - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - } - else if (showSearchSummary) - fetch(requestUrl) - .then((responseData) => responseData.text()) - .then((data) => { - if (data) - listItem.appendChild( - Search.makeSearchSummary(data, searchTerms, anchor) - ); - // highlight search terms in the summary - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - }); - Search.output.appendChild(listItem); -}; -const _finishSearch = (resultCount) => { - Search.stopPulse(); - Search.title.innerText = _("Search Results"); - if (!resultCount) - Search.status.innerText = Documentation.gettext( - "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." - ); - else - Search.status.innerText = Documentation.ngettext( - "Search finished, found one page matching the search query.", - "Search finished, found ${resultCount} pages matching the search query.", - resultCount, - ).replace('${resultCount}', resultCount); -}; -const _displayNextItem = ( - results, - resultCount, - searchTerms, - highlightTerms, -) => { - // results left, load the summary and display it - // this is intended to be dynamic (don't sub resultsCount) - if (results.length) { - _displayItem(results.pop(), searchTerms, highlightTerms); - setTimeout( - () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), - 5 - ); - } - // search finished, update title and status message - else _finishSearch(resultCount); -}; -// Helper function used by query() to order search results. -// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. -// Order the results by score (in opposite order of appearance, since the -// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. -const _orderResultsByScoreThenName = (a, b) => { - const leftScore = a[4]; - const rightScore = b[4]; - if (leftScore === rightScore) { - // same score: sort alphabetically - const leftTitle = a[1].toLowerCase(); - const rightTitle = b[1].toLowerCase(); - if (leftTitle === rightTitle) return 0; - return leftTitle > rightTitle ? -1 : 1; // inverted is intentional - } - return leftScore > rightScore ? 1 : -1; -}; - -/** - * Default splitQuery function. Can be overridden in ``sphinx.search`` with a - * custom function per language. - * - * The regular expression works by splitting the string on consecutive characters - * that are not Unicode letters, numbers, underscores, or emoji characters. - * This is the same as ``\W+`` in Python, preserving the surrogate pair area. - */ -if (typeof splitQuery === "undefined") { - var splitQuery = (query) => query - .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) - .filter(term => term) // remove remaining empty strings -} - -/** - * Search Module - */ -const Search = { - _index: null, - _queued_query: null, - _pulse_status: -1, - - htmlToText: (htmlString, anchor) => { - const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - for (const removalQuery of [".headerlink", "script", "style"]) { - htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); - } - if (anchor) { - const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); - if (anchorContent) return anchorContent.textContent; - - console.warn( - `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` - ); - } - - // if anchor not specified or not found, fall back to main content - const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent) return docContent.textContent; - - console.warn( - "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." - ); - return ""; - }, - - init: () => { - const query = new URLSearchParams(window.location.search).get("q"); - document - .querySelectorAll('input[name="q"]') - .forEach((el) => (el.value = query)); - if (query) Search.performSearch(query); - }, - - loadIndex: (url) => - (document.body.appendChild(document.createElement("script")).src = url), - - setIndex: (index) => { - Search._index = index; - if (Search._queued_query !== null) { - const query = Search._queued_query; - Search._queued_query = null; - Search.query(query); - } - }, - - hasIndex: () => Search._index !== null, - - deferQuery: (query) => (Search._queued_query = query), - - stopPulse: () => (Search._pulse_status = -1), - - startPulse: () => { - if (Search._pulse_status >= 0) return; - - const pulse = () => { - Search._pulse_status = (Search._pulse_status + 1) % 4; - Search.dots.innerText = ".".repeat(Search._pulse_status); - if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); - }; - pulse(); - }, - - /** - * perform a search for something (or wait until index is loaded) - */ - performSearch: (query) => { - // create the required interface elements - const searchText = document.createElement("h2"); - searchText.textContent = _("Searching"); - const searchSummary = document.createElement("p"); - searchSummary.classList.add("search-summary"); - searchSummary.innerText = ""; - const searchList = document.createElement("ul"); - searchList.setAttribute("role", "list"); - searchList.classList.add("search"); - - const out = document.getElementById("search-results"); - Search.title = out.appendChild(searchText); - Search.dots = Search.title.appendChild(document.createElement("span")); - Search.status = out.appendChild(searchSummary); - Search.output = out.appendChild(searchList); - - const searchProgress = document.getElementById("search-progress"); - // Some themes don't use the search progress node - if (searchProgress) { - searchProgress.innerText = _("Preparing search..."); - } - Search.startPulse(); - - // index already loaded, the browser was quick! - if (Search.hasIndex()) Search.query(query); - else Search.deferQuery(query); - }, - - _parseQuery: (query) => { - // stem the search terms and add them to the correct list - const stemmer = new Stemmer(); - const searchTerms = new Set(); - const excludedTerms = new Set(); - const highlightTerms = new Set(); - const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); - splitQuery(query.trim()).forEach((queryTerm) => { - const queryTermLower = queryTerm.toLowerCase(); - - // maybe skip this "word" - // stopwords array is from language_data.js - if ( - stopwords.indexOf(queryTermLower) !== -1 || - queryTerm.match(/^\d+$/) - ) - return; - - // stem the word - let word = stemmer.stemWord(queryTermLower); - // select the correct list - if (word[0] === "-") excludedTerms.add(word.substr(1)); - else { - searchTerms.add(word); - highlightTerms.add(queryTermLower); - } - }); - - if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js - localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) - } - - // console.debug("SEARCH: searching for:"); - // console.info("required: ", [...searchTerms]); - // console.info("excluded: ", [...excludedTerms]); - - return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; - }, - - /** - * execute search (requires search index to be loaded) - */ - _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - - // Collect multiple result groups to be sorted separately and then ordered. - // Each is an array of [docname, title, anchor, descr, score, filename, kind]. - const normalResults = []; - const nonMainIndexResults = []; - - _removeChildren(document.getElementById("search-progress")); - - const queryLower = query.toLowerCase().trim(); - for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { - for (const [file, id] of foundTitles) { - const score = Math.round(Scorer.title * queryLower.length / title.length); - const boost = titles[file] === title ? 1 : 0; // add a boost for document titles - normalResults.push([ - docNames[file], - titles[file] !== title ? `${titles[file]} > ${title}` : title, - id !== null ? "#" + id : "", - null, - score + boost, - filenames[file], - SearchResultKind.title, - ]); - } - } - } - - // search for explicit entries in index directives - for (const [entry, foundEntries] of Object.entries(indexEntries)) { - if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id, isMain] of foundEntries) { - const score = Math.round(100 * queryLower.length / entry.length); - const result = [ - docNames[file], - titles[file], - id ? "#" + id : "", - null, - score, - filenames[file], - SearchResultKind.index, - ]; - if (isMain) { - normalResults.push(result); - } else { - nonMainIndexResults.push(result); - } - } - } - } - - // lookup as object - objectTerms.forEach((term) => - normalResults.push(...Search.performObjectSearch(term, objectTerms)) - ); - - // lookup as search terms in fulltext - normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); - - // let the scorer override scores with a custom scoring function - if (Scorer.score) { - normalResults.forEach((item) => (item[4] = Scorer.score(item))); - nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); - } - - // Sort each group of results by score and then alphabetically by name. - normalResults.sort(_orderResultsByScoreThenName); - nonMainIndexResults.sort(_orderResultsByScoreThenName); - - // Combine the result groups in (reverse) order. - // Non-main index entries are typically arbitrary cross-references, - // so display them after other results. - let results = [...nonMainIndexResults, ...normalResults]; - - // remove duplicate search results - // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept - let seen = new Set(); - results = results.reverse().reduce((acc, result) => { - let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); - if (!seen.has(resultStr)) { - acc.push(result); - seen.add(resultStr); - } - return acc; - }, []); - - return results.reverse(); - }, - - query: (query) => { - const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); - const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); - - // for debugging - //Search.lastresults = results.slice(); // a copy - // console.info("search results:", Search.lastresults); - - // print the results - _displayNextItem(results, results.length, searchTerms, highlightTerms); - }, - - /** - * search for object names - */ - performObjectSearch: (object, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const objects = Search._index.objects; - const objNames = Search._index.objnames; - const titles = Search._index.titles; - - const results = []; - - const objectSearchCallback = (prefix, match) => { - const name = match[4] - const fullname = (prefix ? prefix + "." : "") + name; - const fullnameLower = fullname.toLowerCase(); - if (fullnameLower.indexOf(object) < 0) return; - - let score = 0; - const parts = fullnameLower.split("."); - - // check for different match types: exact matches of full name or - // "last name" (i.e. last dotted part) - if (fullnameLower === object || parts.slice(-1)[0] === object) - score += Scorer.objNameMatch; - else if (parts.slice(-1)[0].indexOf(object) > -1) - score += Scorer.objPartialMatch; // matches in last name - - const objName = objNames[match[1]][2]; - const title = titles[match[0]]; - - // If more than one term searched for, we require other words to be - // found in the name/title/description - const otherTerms = new Set(objectTerms); - otherTerms.delete(object); - if (otherTerms.size > 0) { - const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); - if ( - [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) - ) - return; - } - - let anchor = match[3]; - if (anchor === "") anchor = fullname; - else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; - - const descr = objName + _(", in ") + title; - - // add custom score for some objects according to scorer - if (Scorer.objPrio.hasOwnProperty(match[2])) - score += Scorer.objPrio[match[2]]; - else score += Scorer.objPrioDefault; - - results.push([ - docNames[match[0]], - fullname, - "#" + anchor, - descr, - score, - filenames[match[0]], - SearchResultKind.object, - ]); - }; - Object.keys(objects).forEach((prefix) => - objects[prefix].forEach((array) => - objectSearchCallback(prefix, array) - ) - ); - return results; - }, - - /** - * search for full-text terms in the index - */ - performTermsSearch: (searchTerms, excludedTerms) => { - // prepare search - const terms = Search._index.terms; - const titleTerms = Search._index.titleterms; - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - - const scoreMap = new Map(); - const fileMap = new Map(); - - // perform the search on the required terms - searchTerms.forEach((word) => { - const files = []; - const arr = [ - { files: terms[word], score: Scorer.term }, - { files: titleTerms[word], score: Scorer.title }, - ]; - // add support for partial matches - if (word.length > 2) { - const escapedWord = _escapeRegExp(word); - if (!terms.hasOwnProperty(word)) { - Object.keys(terms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: terms[term], score: Scorer.partialTerm }); - }); - } - if (!titleTerms.hasOwnProperty(word)) { - Object.keys(titleTerms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); - }); - } - } - - // no match but word was a required one - if (arr.every((record) => record.files === undefined)) return; - - // found search word in contents - arr.forEach((record) => { - if (record.files === undefined) return; - - let recordFiles = record.files; - if (recordFiles.length === undefined) recordFiles = [recordFiles]; - files.push(...recordFiles); - - // set score for the word in each file - recordFiles.forEach((file) => { - if (!scoreMap.has(file)) scoreMap.set(file, {}); - scoreMap.get(file)[word] = record.score; - }); - }); - - // create the mapping - files.forEach((file) => { - if (!fileMap.has(file)) fileMap.set(file, [word]); - else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); - }); - }); - - // now check if the files don't contain excluded terms - const results = []; - for (const [file, wordList] of fileMap) { - // check if all requirements are matched - - // as search terms with length < 3 are discarded - const filteredTermCount = [...searchTerms].filter( - (term) => term.length > 2 - ).length; - if ( - wordList.length !== searchTerms.size && - wordList.length !== filteredTermCount - ) - continue; - - // ensure that none of the excluded terms is in the search result - if ( - [...excludedTerms].some( - (term) => - terms[term] === file || - titleTerms[term] === file || - (terms[term] || []).includes(file) || - (titleTerms[term] || []).includes(file) - ) - ) - break; - - // select one (max) score for the file. - const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); - // add result to the result list - results.push([ - docNames[file], - titles[file], - "", - null, - score, - filenames[file], - SearchResultKind.text, - ]); - } - return results; - }, - - /** - * helper function to return a node containing the - * search summary for a given text. keywords is a list - * of stemmed words. - */ - makeSearchSummary: (htmlText, keywords, anchor) => { - const text = Search.htmlToText(htmlText, anchor); - if (text === "") return null; - - const textLower = text.toLowerCase(); - const actualStartPosition = [...keywords] - .map((k) => textLower.indexOf(k.toLowerCase())) - .filter((i) => i > -1) - .slice(-1)[0]; - const startWithContext = Math.max(actualStartPosition - 120, 0); - - const top = startWithContext === 0 ? "" : "..."; - const tail = startWithContext + 240 < text.length ? "..." : ""; - - let summary = document.createElement("p"); - summary.classList.add("context"); - summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; - - return summary; - }, -}; - -_ready(Search.init); diff --git a/docs/0.3.3/_static/sphinx_highlight.js b/docs/0.3.3/_static/sphinx_highlight.js deleted file mode 100644 index 8a96c69a..00000000 --- a/docs/0.3.3/_static/sphinx_highlight.js +++ /dev/null @@ -1,154 +0,0 @@ -/* Highlighting utilities for Sphinx HTML documentation. */ -"use strict"; - -const SPHINX_HIGHLIGHT_ENABLED = true - -/** - * highlight a given string on a node by wrapping it in - * span elements with the given class name. - */ -const _highlight = (node, addItems, text, className) => { - if (node.nodeType === Node.TEXT_NODE) { - const val = node.nodeValue; - const parent = node.parentNode; - const pos = val.toLowerCase().indexOf(text); - if ( - pos >= 0 && - !parent.classList.contains(className) && - !parent.classList.contains("nohighlight") - ) { - let span; - - const closestNode = parent.closest("body, svg, foreignObject"); - const isInSVG = closestNode && closestNode.matches("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.classList.add(className); - } - - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - const rest = document.createTextNode(val.substr(pos + text.length)); - parent.insertBefore( - span, - parent.insertBefore( - rest, - node.nextSibling - ) - ); - node.nodeValue = val.substr(0, pos); - /* There may be more occurrences of search term in this node. So call this - * function recursively on the remaining fragment. - */ - _highlight(rest, addItems, text, className); - - if (isInSVG) { - const rect = document.createElementNS( - "http://www.w3.org/2000/svg", - "rect" - ); - const bbox = parent.getBBox(); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute("class", className); - addItems.push({ parent: parent, target: rect }); - } - } - } else if (node.matches && !node.matches("button, select, textarea")) { - node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); - } -}; -const _highlightText = (thisNode, text, className) => { - let addItems = []; - _highlight(thisNode, addItems, text, className); - addItems.forEach((obj) => - obj.parent.insertAdjacentElement("beforebegin", obj.target) - ); -}; - -/** - * Small JavaScript module for the documentation. - */ -const SphinxHighlight = { - - /** - * highlight the search words provided in localstorage in the text - */ - highlightSearchWords: () => { - if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight - - // get and clear terms from localstorage - const url = new URL(window.location); - const highlight = - localStorage.getItem("sphinx_highlight_terms") - || url.searchParams.get("highlight") - || ""; - localStorage.removeItem("sphinx_highlight_terms") - url.searchParams.delete("highlight"); - window.history.replaceState({}, "", url); - - // get individual terms from highlight string - const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); - if (terms.length === 0) return; // nothing to do - - // There should never be more than one element matching "div.body" - const divBody = document.querySelectorAll("div.body"); - const body = divBody.length ? divBody[0] : document.querySelector("body"); - window.setTimeout(() => { - terms.forEach((term) => _highlightText(body, term, "highlighted")); - }, 10); - - const searchBox = document.getElementById("searchbox"); - if (searchBox === null) return; - searchBox.appendChild( - document - .createRange() - .createContextualFragment( - '

' + - '' + - _("Hide Search Matches") + - "

" - ) - ); - }, - - /** - * helper function to hide the search marks again - */ - hideSearchWords: () => { - document - .querySelectorAll("#searchbox .highlight-link") - .forEach((el) => el.remove()); - document - .querySelectorAll("span.highlighted") - .forEach((el) => el.classList.remove("highlighted")); - localStorage.removeItem("sphinx_highlight_terms") - }, - - initEscapeListener: () => { - // only install a listener if it is really needed - if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; - - document.addEventListener("keydown", (event) => { - // bail for input elements - if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; - // bail with special keys - if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; - if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { - SphinxHighlight.hideSearchWords(); - event.preventDefault(); - } - }); - }, -}; - -_ready(() => { - /* Do not call highlightSearchWords() when we are on the search page. - * It will highlight words from the *previous* search query. - */ - if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); - SphinxHighlight.initEscapeListener(); -}); diff --git a/docs/0.3.3/autodoc/mmif.serialize.html b/docs/0.3.3/autodoc/mmif.serialize.html deleted file mode 100644 index 2ba326e7..00000000 --- a/docs/0.3.3/autodoc/mmif.serialize.html +++ /dev/null @@ -1,369 +0,0 @@ - - - - - - - - - mmif.serialize module — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.serialize module

-
-

mmif.serialize.model module

-
-
-

mmif.serialize.mmif module

-
-
-

mmif.serialize.view module

-
-
-

mmif.serialize.annotation module

-

The annotation module contains the classes used to represent a -MMIF annotation as a live Python object.

-

In MMIF, annotations are created by apps in a pipeline as a part -of a view. For documentation on how views are represented, see -mmif.serialize.view.

-
-
-class mmif.serialize.annotation.Annotation(anno_obj: bytes | str | dict | None = None)[source]
-

Bases: FreezableMmifObject

-

MmifObject that represents an annotation in a MMIF view.

-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]]) → None[source]
-

Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

-
- -
-
-property at_type: str | ThingTypesBase[source]
-
- -
-
-property id: str[source]
-
- -
-
-is_document()[source]
-
- -
-
-is_type(type: str | ThingTypesBase) → bool[source]
-

Check if the @type of this object matches.

-
- -
- -
-
-class mmif.serialize.annotation.AnnotationProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: FreezableMmifObject

-

AnnotationProperties object that represents the -properties object within a MMIF annotation.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
- -
-
-class mmif.serialize.annotation.Document(doc_obj: bytes | str | dict | None = None)[source]
-

Bases: Annotation

-

Document object that represents a single document in a MMIF file.

-

A document is identified by an ID, and contains certain attributes -and potentially contains the contents of the document itself, -metadata about how the document was created, and/or a list of -subdocuments grouped together logically.

-

If document_obj is not provided, an empty Document will be generated.

-
-
Parameters:
-

document_obj – the JSON data that defines the document

-
-
-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None]) → None[source]
-

Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

-
- -
-
-property location: str[source]
-
- -
-
-location_address() → str[source]
-
- -
-
-location_path() → str[source]
-
- -
-
-location_scheme() → str[source]
-
- -
-
-property parent: str[source]
-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.DocumentProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: AnnotationProperties

-

DocumentProperties object that represents the -properties object within a MMIF document.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
-
-property location: str[source]
-
- -
-
-location_address() → str[source]
-
- -
-
-location_path() → str[source]
-
- -
-
-location_scheme() → str[source]
-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.Text(text_obj: bytes | str | dict | None = None)[source]
-

Bases: FreezableMmifObject

-
-
-property lang: str[source]
-
- -
-
-property value: str[source]
-
- -
- -
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.3.3 - - -
-
- -
0.3.0
-
0.3.1
-
0.3.2
-
0.3.3
-
0.3.4
-
0.3.5
-
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-
0.4.1
-
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-
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-
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-
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-
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-
-
-
- - - \ No newline at end of file diff --git a/docs/0.3.3/autodoc/mmif.vocabulary.html b/docs/0.3.3/autodoc/mmif.vocabulary.html deleted file mode 100644 index e96b67d8..00000000 --- a/docs/0.3.3/autodoc/mmif.vocabulary.html +++ /dev/null @@ -1,306 +0,0 @@ - - - - - - - - - mmif.vocabulary module — mmif-python documentation - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.vocabulary module

-
-

mmif.vocabulary.annotation_types module

-
-
-class mmif.vocabulary.annotation_types.AnnotationTypes(value)[source]
-

Bases: AnnotationTypesBase

-

This enum contains the URIs for the MMIF annotation types defined in the spec version 0.3.1. -Use this to quickly get the correct URIs for those types, or use the objects themselves in your -code and they will serialize to the strings.

-
-
-Alignment = 'http://mmif.clams.ai/0.3.1/vocabulary/Alignment'[source]
-
- -
-
-Annotation = 'http://mmif.clams.ai/0.3.1/vocabulary/Annotation'[source]
-
- -
-
-BoundingBox = 'http://mmif.clams.ai/0.3.1/vocabulary/BoundingBox'[source]
-
- -
-
-Chapter = 'http://mmif.clams.ai/0.3.1/vocabulary/Chapter'[source]
-
- -
-
-Interval = 'http://mmif.clams.ai/0.3.1/vocabulary/Interval'[source]
-
- -
-
-Polygon = 'http://mmif.clams.ai/0.3.1/vocabulary/Polygon'[source]
-
- -
-
-Region = 'http://mmif.clams.ai/0.3.1/vocabulary/Region'[source]
-
- -
-
-Relation = 'http://mmif.clams.ai/0.3.1/vocabulary/Relation'[source]
-
- -
-
-Span = 'http://mmif.clams.ai/0.3.1/vocabulary/Span'[source]
-
- -
-
-TimeFrame = 'http://mmif.clams.ai/0.3.1/vocabulary/TimeFrame'[source]
-
- -
-
-TimePoint = 'http://mmif.clams.ai/0.3.1/vocabulary/TimePoint'[source]
-
- -
-
-VideoObject = 'http://mmif.clams.ai/0.3.1/vocabulary/VideoObject'[source]
-
- -
- -
-
-class mmif.vocabulary.annotation_types.AnnotationTypesBase(value)[source]
-

Bases: ThingTypesBase

-

Inherit from this class to build your own custom annotation -vocabularies. Each member’s name should be the name of the -type, and each member’s value should be the URI of that type.

-
- -
-
-

mmif.vocabulary.media_types module

-
-
-class mmif.vocabulary.document_types.DocumentTypes(value)[source]
-

Bases: DocumentTypesBase

-

This enum contains the URIs for the MMIF document types defined in the spec version 0.3.1. -Use this to quickly get the correct URIs for those types, or use the objects themselves in your -code and they will serialize to the strings.

-
-
-AudioDocument = 'http://mmif.clams.ai/0.3.1/vocabulary/AudioDocument'[source]
-
- -
-
-Document = 'http://mmif.clams.ai/0.3.1/vocabulary/Document'[source]
-
- -
-
-ImageDocument = 'http://mmif.clams.ai/0.3.1/vocabulary/ImageDocument'[source]
-
- -
-
-TextDocument = 'http://mmif.clams.ai/0.3.1/vocabulary/TextDocument'[source]
-
- -
-
-VideoDocument = 'http://mmif.clams.ai/0.3.1/vocabulary/VideoDocument'[source]
-
- -
- -
-
-class mmif.vocabulary.document_types.DocumentTypesBase(value)[source]
-

Bases: ThingTypesBase

-

Inherit from this class to build your own custom document -vocabularies. Each member’s name should be the name of the -type, and each member’s value should be the URI of that type.

-
- -
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.3.3 - - -
-
- -
0.3.0
-
0.3.1
-
0.3.2
-
0.3.3
-
0.3.4
-
0.3.5
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0.4.1
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0.4.2
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0.4.3
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0.4.5
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0.4.6
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0.4.7
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0.4.8
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0.5.2
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1.0.6
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1.0.7
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1.0.8
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1.0.9
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1.1.0
-
-
-
- - - \ No newline at end of file diff --git a/docs/0.3.3/consumer-tutorial.html b/docs/0.3.3/consumer-tutorial.html deleted file mode 100644 index 86a321b0..00000000 --- a/docs/0.3.3/consumer-tutorial.html +++ /dev/null @@ -1,175 +0,0 @@ - - - - - - - - - MMIF consumer — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • MMIF consumer
    • -
  • -
    • -
-
-
-
-
- -
-

MMIF consumer

-

A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the appliance documentation to learn more about the appliance.

-

MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance.

-
    -

  1. The code must be hosted on a public git repository (e.g. Github, Gitlab, …)

    2. -

  2. Must listen to 5000 port.

    3. -

  3. Must expose /display route .

    4. -

  4. /display router should response to GET requests.

    5. -

  5. In the GET request, a public URL of the input MMIF file is passed via file URL parameter.

    6. -

  6. On the codebase root, there must be a Dockerfile that can build a docker image that runs the web app.

    7. -
-

We provide an example consumer at https://github.com/clamsproject/mmif-visualizer.

-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.3.3 - - -
-
- -
0.3.0
-
0.3.1
-
0.3.2
-
0.3.3
-
0.3.4
-
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-
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-
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-
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- - - \ No newline at end of file diff --git a/docs/0.3.3/genindex.html b/docs/0.3.3/genindex.html deleted file mode 100644 index 56cf773c..00000000 --- a/docs/0.3.3/genindex.html +++ /dev/null @@ -1,407 +0,0 @@ - - - - - - - - Index — mmif-python documentation - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • Index
    • -
  • -
    • -
-
-
-
-
- - -

Index

- -
- A - | B - | C - | D - | I - | L - | M - | P - | R - | S - | T - | V - -
-

A

- - - -
- -

B

- - -
- -

C

- - -
- -

D

- - - -
- -

I

- - - -
- -

L

- - - -
- -

M

- - - -
    -
  • - mmif.serialize.annotation - -
    • -
  • - mmif.vocabulary.annotation_types - -
    • -
  • - mmif.vocabulary.document_types - -
    • -
- -

P

- - - -
- -

R

- - - -
- -

S

- - -
- -

T

- - - -
- -

V

- - - -
- - - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.3.3 - - -
-
- -
0.3.0
-
0.3.1
-
0.3.2
-
0.3.3
-
0.3.4
-
0.3.5
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0.4.0
-
0.4.1
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0.4.2
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0.4.3
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0.4.4
-
0.4.5
-
0.4.6
-
0.4.7
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0.4.8
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0.5.0
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0.5.1
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0.5.2
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1.0.0
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1.0.1
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1.0.10
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1.0.11
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1.0.12
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1.0.13
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1.0.14
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1.0.15
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1.0.16
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1.0.17
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1.0.18
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1.0.19
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1.0.2
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1.0.3
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1.0.4
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1.0.5
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1.0.6
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1.0.7
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1.0.8
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1.0.9
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1.1.0
-
-
-
- - - \ No newline at end of file diff --git a/docs/0.3.3/index.html b/docs/0.3.3/index.html deleted file mode 100644 index e092c9b9..00000000 --- a/docs/0.3.3/index.html +++ /dev/null @@ -1,201 +0,0 @@ - - - - - - - - - Welcome to mmif-python’s documentation! — mmif-python documentation - - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • Welcome to mmif-python’s documentation!
    • -
  • -
    • -
-
-
-
-
- -
-

Welcome to mmif-python’s documentation!

-
-
-

MMIF for python

-

NOTE that this project is in pre-alpha and being actively developed. Nothing is guaranteed to reliably work for the moment and developer need to be very careful when using APIs implemented here. Please use the issue track to report bugs and malfunctions.

-
-

MultiMedia Interchange Format

-

MMIF is a JSON(-LD)-based data format designed for transferring annotation data between computational analysis applications in CLAMS project.

-
-

Contents

- -
-
-

API documentation:

- -
-
-
-
-

Indices and tables

- -
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.3.3 - - -
-
- -
0.3.0
-
0.3.1
-
0.3.2
-
0.3.3
-
0.3.4
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0.3.5
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0.4.0
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0.4.1
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0.4.2
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0.4.3
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0.4.4
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0.4.5
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0.4.6
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0.4.7
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0.4.8
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0.5.0
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0.5.1
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0.5.2
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1.0.0
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1.0.1
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1.0.10
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1.0.11
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1.0.12
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1.0.13
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- - - \ No newline at end of file diff --git a/docs/0.3.3/introduction.html b/docs/0.3.3/introduction.html deleted file mode 100644 index b29d8667..00000000 --- a/docs/0.3.3/introduction.html +++ /dev/null @@ -1,231 +0,0 @@ - - - - - - - - - Getting Started — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • Getting Started
    • -
  • -
    • -
-
-
-
-
- -
-

Getting Started

-
-

Overview

-

MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF wbesite. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports de-/serialization of MMIF objects, as well as many navigation and manipulation helpers for MMIF objects.

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Prerequisites

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  • Python: mmif-python requires Python 3.6 or newer. We have no plan to support Python 2.7.

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Installation

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Package mmif-python is distributed via the official PyPI. Users are supposed to pip-install to get latest release.

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pip install mmif-python
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This will install a package mmif to local python. -The MMIF format and specification is evolving over time, and mmif-python package will be updated along with the changes in MMIF format. Note that MMIF format is not always backward-compatible. To find out more about relations between MMIF versions and mmif-python versions, and which supports which, please take time to read our decision on the subject here.

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MMIF Serialization

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mmif.serialize.mmif.Mmif represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of mmif.serialize.model.MmifObject, including the mmif.serialize.mmif.Mmif. To start with an existing MMIF str, simple initiate a new Mmif object with the file.

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import mmif
-from mmif import Mmif
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-mmif_str = """{
-"metadata": {
-  "mmif": "http://mmif.clams.ai/0.2.0"
-},
-"documents": [
-  {
-    "@type": "http://mmif.clams.ai/0.2.0/vocabulary/VideoDocument",
-    "properties": {
-      "id": "m1",
-      "mime": "video/mp4",
-      "location": "file:///var/archive/video-0012.mp4"
-    }
-  },
-  {
-    "@type": "http://mmif.clams.ai/0.2.0/vocabulary/TextDocument",
-    "properties": {
-      "id": "m2",
-      "mime": "text/plain",
-      "location": "file:///var/archive/video-0012-transcript.txt"
-    }
-  }
-],
-"views": []}"""
-mmif_obj = Mmif(mmif_str)
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Few notes;

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  1. MMIF does not carry the primary source files in it.

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  2. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version mmif-python implementation of the MMIF might not be able to load an unsupported version of MMIF string.

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When serializing back to str, call .serialize() (mmif.serialize.model.MmifObject.serialize()) on the object.

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To get subcomponents, you can use various getters implemented in subclasses. For more details, the API documentation (mmif package) will help.

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The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the `appliance documentation `_ to learn more about the appliance. - -MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance. - -#. The code must be hosted on a public git repository (e.g. Github, Gitlab, ...) -#. Must listen to ``5000`` port. -#. Must expose ``/display`` route . -#. ``/display`` router should response to ``GET`` requests. -#. In the ``GET`` request, a public URL of the input MMIF file is passed via ``file`` URL parameter. -#. On the codebase root, there must be a ``Dockerfile`` that can build a `docker `_ image that runs the web app. - -We provide an example consumer at https://github.com/clamsproject/mmif-visualizer. diff --git a/docs/0.3.4/_sources/index.rst.txt b/docs/0.3.4/_sources/index.rst.txt deleted file mode 100644 index 6146286d..00000000 --- a/docs/0.3.4/_sources/index.rst.txt +++ /dev/null @@ -1,25 +0,0 @@ -Welcome to mmif-python's documentation! -======================================= - -.. mdinclude:: ../README.md - -.. toctree:: - :maxdepth: 2 - :caption: Contents - - introduction - consumer-tutorial - -.. toctree:: - :maxdepth: 2 - :caption: API documentation: - - modules - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/docs/0.3.4/_sources/introduction.rst.txt b/docs/0.3.4/_sources/introduction.rst.txt deleted file mode 100644 index 6af8cd61..00000000 --- a/docs/0.3.4/_sources/introduction.rst.txt +++ /dev/null @@ -1,75 +0,0 @@ -.. _instroduction: - -Getting Started -=============== - - -Overview ---------- - -MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF wbesite `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports de-/serialization of MMIF objects, as well as many navigation and manipulation helpers for MMIF objects. - -Prerequisites -------------- - -* `Python `_: ``mmif-python`` requires Python 3.6 or newer. We have no plan to support `Python 2.7 `_. - -Installation ---------------- - -Package ``mmif-python`` is distributed via the official PyPI. Users are supposed to pip-install to get latest release. - -.. code-block:: bash - - pip install mmif-python - -This will install a package `mmif` to local python. -The MMIF format and specification is evolving over time, and ``mmif-python`` package will be updated along with the changes in MMIF format. Note that MMIF format is not always backward-compatible. To find out more about relations between MMIF versions and ``mmif-python`` versions, and which supports which, please take time to read our decision on the subject `here `_. - -MMIF Serialization ---------------------------- - -:class:`mmif.serialize.mmif.Mmif` represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of :class:`mmif.serialize.model.MmifObject`, including the :class:`mmif.serialize.mmif.Mmif`. To start with an existing MMIF :class:`str`, simple initiate a new ``Mmif`` object with the file. - -.. code-block:: python - - import mmif - from mmif import Mmif - - mmif_str = """{ - "metadata": { - "mmif": "http://mmif.clams.ai/0.2.0" - }, - "documents": [ - { - "@type": "http://mmif.clams.ai/0.2.0/vocabulary/VideoDocument", - "properties": { - "id": "m1", - "mime": "video/mp4", - "location": "file:///var/archive/video-0012.mp4" - } - }, - { - "@type": "http://mmif.clams.ai/0.2.0/vocabulary/TextDocument", - "properties": { - "id": "m2", - "mime": "text/plain", - "location": "file:///var/archive/video-0012-transcript.txt" - } - } - ], - "views": []}""" - mmif_obj = Mmif(mmif_str) - - -Few notes; - -#. MMIF does not carry the primary source files in it. -#. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version ``mmif-python`` implementation of the MMIF might not be able to load an unsupported version of MMIF string. - -When serializing back to :class:`str`, call ``.serialize()`` (:meth:`mmif.serialize.model.MmifObject.serialize`) on the object. - -To get subcomponents, you can use various getters implemented in subclasses. 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- -/** - * Simple result scoring code. - */ -if (typeof Scorer === "undefined") { - var Scorer = { - // Implement the following function to further tweak the score for each result - // The function takes a result array [docname, title, anchor, descr, score, filename] - // and returns the new score. - /* - score: result => { - const [docname, title, anchor, descr, score, filename, kind] = result - return score - }, - */ - - // query matches the full name of an object - objNameMatch: 11, - // or matches in the last dotted part of the object name - objPartialMatch: 6, - // Additive scores depending on the priority of the object - objPrio: { - 0: 15, // used to be importantResults - 1: 5, // used to be objectResults - 2: -5, // used to be unimportantResults - }, - // Used when the priority is not in the mapping. - objPrioDefault: 0, - - // query found in title - title: 15, - partialTitle: 7, - // query found in terms - term: 5, - partialTerm: 2, - }; -} - -// Global search result kind enum, used by themes to style search results. -class SearchResultKind { - static get index() { return "index"; } - static get object() { return "object"; } - static get text() { return "text"; } - static get title() { return "title"; } -} - -const _removeChildren = (element) => { - while (element && element.lastChild) element.removeChild(element.lastChild); -}; - -/** - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping - */ -const _escapeRegExp = (string) => - string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string - -const _displayItem = (item, searchTerms, highlightTerms) => { - const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; - const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; - const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; - const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; - const contentRoot = document.documentElement.dataset.content_root; - - const [docName, title, anchor, descr, score, _filename, kind] = item; - - let listItem = document.createElement("li"); - // Add a class representing the item's type: - // can be used by a theme's CSS selector for styling - // See SearchResultKind for the class names. - listItem.classList.add(`kind-${kind}`); - let requestUrl; - let linkUrl; - if (docBuilder === "dirhtml") { - // dirhtml builder - let dirname = docName + "/"; - if (dirname.match(/\/index\/$/)) - dirname = dirname.substring(0, dirname.length - 6); - else if (dirname === "index/") dirname = ""; - requestUrl = contentRoot + dirname; - linkUrl = requestUrl; - } else { - // normal html builders - requestUrl = contentRoot + docName + docFileSuffix; - linkUrl = docName + docLinkSuffix; - } - let linkEl = listItem.appendChild(document.createElement("a")); - linkEl.href = linkUrl + anchor; - linkEl.dataset.score = score; - linkEl.innerHTML = title; - if (descr) { - listItem.appendChild(document.createElement("span")).innerHTML = - " (" + descr + ")"; - // highlight search terms in the description - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - } - else if (showSearchSummary) - fetch(requestUrl) - .then((responseData) => responseData.text()) - .then((data) => { - if (data) - listItem.appendChild( - Search.makeSearchSummary(data, searchTerms, anchor) - ); - // highlight search terms in the summary - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - }); - Search.output.appendChild(listItem); -}; -const _finishSearch = (resultCount) => { - Search.stopPulse(); - Search.title.innerText = _("Search Results"); - if (!resultCount) - Search.status.innerText = Documentation.gettext( - "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." - ); - else - Search.status.innerText = Documentation.ngettext( - "Search finished, found one page matching the search query.", - "Search finished, found ${resultCount} pages matching the search query.", - resultCount, - ).replace('${resultCount}', resultCount); -}; -const _displayNextItem = ( - results, - resultCount, - searchTerms, - highlightTerms, -) => { - // results left, load the summary and display it - // this is intended to be dynamic (don't sub resultsCount) - if (results.length) { - _displayItem(results.pop(), searchTerms, highlightTerms); - setTimeout( - () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), - 5 - ); - } - // search finished, update title and status message - else _finishSearch(resultCount); -}; -// Helper function used by query() to order search results. -// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. -// Order the results by score (in opposite order of appearance, since the -// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. -const _orderResultsByScoreThenName = (a, b) => { - const leftScore = a[4]; - const rightScore = b[4]; - if (leftScore === rightScore) { - // same score: sort alphabetically - const leftTitle = a[1].toLowerCase(); - const rightTitle = b[1].toLowerCase(); - if (leftTitle === rightTitle) return 0; - return leftTitle > rightTitle ? -1 : 1; // inverted is intentional - } - return leftScore > rightScore ? 1 : -1; -}; - -/** - * Default splitQuery function. Can be overridden in ``sphinx.search`` with a - * custom function per language. - * - * The regular expression works by splitting the string on consecutive characters - * that are not Unicode letters, numbers, underscores, or emoji characters. - * This is the same as ``\W+`` in Python, preserving the surrogate pair area. - */ -if (typeof splitQuery === "undefined") { - var splitQuery = (query) => query - .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) - .filter(term => term) // remove remaining empty strings -} - -/** - * Search Module - */ -const Search = { - _index: null, - _queued_query: null, - _pulse_status: -1, - - htmlToText: (htmlString, anchor) => { - const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - for (const removalQuery of [".headerlink", "script", "style"]) { - htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); - } - if (anchor) { - const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); - if (anchorContent) return anchorContent.textContent; - - console.warn( - `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` - ); - } - - // if anchor not specified or not found, fall back to main content - const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent) return docContent.textContent; - - console.warn( - "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." - ); - return ""; - }, - - init: () => { - const query = new URLSearchParams(window.location.search).get("q"); - document - .querySelectorAll('input[name="q"]') - .forEach((el) => (el.value = query)); - if (query) Search.performSearch(query); - }, - - loadIndex: (url) => - (document.body.appendChild(document.createElement("script")).src = url), - - setIndex: (index) => { - Search._index = index; - if (Search._queued_query !== null) { - const query = Search._queued_query; - Search._queued_query = null; - Search.query(query); - } - }, - - hasIndex: () => Search._index !== null, - - deferQuery: (query) => (Search._queued_query = query), - - stopPulse: () => (Search._pulse_status = -1), - - startPulse: () => { - if (Search._pulse_status >= 0) return; - - const pulse = () => { - Search._pulse_status = (Search._pulse_status + 1) % 4; - Search.dots.innerText = ".".repeat(Search._pulse_status); - if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); - }; - pulse(); - }, - - /** - * perform a search for something (or wait until index is loaded) - */ - performSearch: (query) => { - // create the required interface elements - const searchText = document.createElement("h2"); - searchText.textContent = _("Searching"); - const searchSummary = document.createElement("p"); - searchSummary.classList.add("search-summary"); - searchSummary.innerText = ""; - const searchList = document.createElement("ul"); - searchList.setAttribute("role", "list"); - searchList.classList.add("search"); - - const out = document.getElementById("search-results"); - Search.title = out.appendChild(searchText); - Search.dots = Search.title.appendChild(document.createElement("span")); - Search.status = out.appendChild(searchSummary); - Search.output = out.appendChild(searchList); - - const searchProgress = document.getElementById("search-progress"); - // Some themes don't use the search progress node - if (searchProgress) { - searchProgress.innerText = _("Preparing search..."); - } - Search.startPulse(); - - // index already loaded, the browser was quick! - if (Search.hasIndex()) Search.query(query); - else Search.deferQuery(query); - }, - - _parseQuery: (query) => { - // stem the search terms and add them to the correct list - const stemmer = new Stemmer(); - const searchTerms = new Set(); - const excludedTerms = new Set(); - const highlightTerms = new Set(); - const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); - splitQuery(query.trim()).forEach((queryTerm) => { - const queryTermLower = queryTerm.toLowerCase(); - - // maybe skip this "word" - // stopwords array is from language_data.js - if ( - stopwords.indexOf(queryTermLower) !== -1 || - queryTerm.match(/^\d+$/) - ) - return; - - // stem the word - let word = stemmer.stemWord(queryTermLower); - // select the correct list - if (word[0] === "-") excludedTerms.add(word.substr(1)); - else { - searchTerms.add(word); - highlightTerms.add(queryTermLower); - } - }); - - if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js - localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) - } - - // console.debug("SEARCH: searching for:"); - // console.info("required: ", [...searchTerms]); - // console.info("excluded: ", [...excludedTerms]); - - return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; - }, - - /** - * execute search (requires search index to be loaded) - */ - _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - - // Collect multiple result groups to be sorted separately and then ordered. - // Each is an array of [docname, title, anchor, descr, score, filename, kind]. - const normalResults = []; - const nonMainIndexResults = []; - - _removeChildren(document.getElementById("search-progress")); - - const queryLower = query.toLowerCase().trim(); - for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { - for (const [file, id] of foundTitles) { - const score = Math.round(Scorer.title * queryLower.length / title.length); - const boost = titles[file] === title ? 1 : 0; // add a boost for document titles - normalResults.push([ - docNames[file], - titles[file] !== title ? `${titles[file]} > ${title}` : title, - id !== null ? "#" + id : "", - null, - score + boost, - filenames[file], - SearchResultKind.title, - ]); - } - } - } - - // search for explicit entries in index directives - for (const [entry, foundEntries] of Object.entries(indexEntries)) { - if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id, isMain] of foundEntries) { - const score = Math.round(100 * queryLower.length / entry.length); - const result = [ - docNames[file], - titles[file], - id ? "#" + id : "", - null, - score, - filenames[file], - SearchResultKind.index, - ]; - if (isMain) { - normalResults.push(result); - } else { - nonMainIndexResults.push(result); - } - } - } - } - - // lookup as object - objectTerms.forEach((term) => - normalResults.push(...Search.performObjectSearch(term, objectTerms)) - ); - - // lookup as search terms in fulltext - normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); - - // let the scorer override scores with a custom scoring function - if (Scorer.score) { - normalResults.forEach((item) => (item[4] = Scorer.score(item))); - nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); - } - - // Sort each group of results by score and then alphabetically by name. - normalResults.sort(_orderResultsByScoreThenName); - nonMainIndexResults.sort(_orderResultsByScoreThenName); - - // Combine the result groups in (reverse) order. - // Non-main index entries are typically arbitrary cross-references, - // so display them after other results. - let results = [...nonMainIndexResults, ...normalResults]; - - // remove duplicate search results - // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept - let seen = new Set(); - results = results.reverse().reduce((acc, result) => { - let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); - if (!seen.has(resultStr)) { - acc.push(result); - seen.add(resultStr); - } - return acc; - }, []); - - return results.reverse(); - }, - - query: (query) => { - const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); - const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); - - // for debugging - //Search.lastresults = results.slice(); // a copy - // console.info("search results:", Search.lastresults); - - // print the results - _displayNextItem(results, results.length, searchTerms, highlightTerms); - }, - - /** - * search for object names - */ - performObjectSearch: (object, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const objects = Search._index.objects; - const objNames = Search._index.objnames; - const titles = Search._index.titles; - - const results = []; - - const objectSearchCallback = (prefix, match) => { - const name = match[4] - const fullname = (prefix ? prefix + "." : "") + name; - const fullnameLower = fullname.toLowerCase(); - if (fullnameLower.indexOf(object) < 0) return; - - let score = 0; - const parts = fullnameLower.split("."); - - // check for different match types: exact matches of full name or - // "last name" (i.e. last dotted part) - if (fullnameLower === object || parts.slice(-1)[0] === object) - score += Scorer.objNameMatch; - else if (parts.slice(-1)[0].indexOf(object) > -1) - score += Scorer.objPartialMatch; // matches in last name - - const objName = objNames[match[1]][2]; - const title = titles[match[0]]; - - // If more than one term searched for, we require other words to be - // found in the name/title/description - const otherTerms = new Set(objectTerms); - otherTerms.delete(object); - if (otherTerms.size > 0) { - const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); - if ( - [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) - ) - return; - } - - let anchor = match[3]; - if (anchor === "") anchor = fullname; - else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; - - const descr = objName + _(", in ") + title; - - // add custom score for some objects according to scorer - if (Scorer.objPrio.hasOwnProperty(match[2])) - score += Scorer.objPrio[match[2]]; - else score += Scorer.objPrioDefault; - - results.push([ - docNames[match[0]], - fullname, - "#" + anchor, - descr, - score, - filenames[match[0]], - SearchResultKind.object, - ]); - }; - Object.keys(objects).forEach((prefix) => - objects[prefix].forEach((array) => - objectSearchCallback(prefix, array) - ) - ); - return results; - }, - - /** - * search for full-text terms in the index - */ - performTermsSearch: (searchTerms, excludedTerms) => { - // prepare search - const terms = Search._index.terms; - const titleTerms = Search._index.titleterms; - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - - const scoreMap = new Map(); - const fileMap = new Map(); - - // perform the search on the required terms - searchTerms.forEach((word) => { - const files = []; - const arr = [ - { files: terms[word], score: Scorer.term }, - { files: titleTerms[word], score: Scorer.title }, - ]; - // add support for partial matches - if (word.length > 2) { - const escapedWord = _escapeRegExp(word); - if (!terms.hasOwnProperty(word)) { - Object.keys(terms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: terms[term], score: Scorer.partialTerm }); - }); - } - if (!titleTerms.hasOwnProperty(word)) { - Object.keys(titleTerms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); - }); - } - } - - // no match but word was a required one - if (arr.every((record) => record.files === undefined)) return; - - // found search word in contents - arr.forEach((record) => { - if (record.files === undefined) return; - - let recordFiles = record.files; - if (recordFiles.length === undefined) recordFiles = [recordFiles]; - files.push(...recordFiles); - - // set score for the word in each file - recordFiles.forEach((file) => { - if (!scoreMap.has(file)) scoreMap.set(file, {}); - scoreMap.get(file)[word] = record.score; - }); - }); - - // create the mapping - files.forEach((file) => { - if (!fileMap.has(file)) fileMap.set(file, [word]); - else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); - }); - }); - - // now check if the files don't contain excluded terms - const results = []; - for (const [file, wordList] of fileMap) { - // check if all requirements are matched - - // as search terms with length < 3 are discarded - const filteredTermCount = [...searchTerms].filter( - (term) => term.length > 2 - ).length; - if ( - wordList.length !== searchTerms.size && - wordList.length !== filteredTermCount - ) - continue; - - // ensure that none of the excluded terms is in the search result - if ( - [...excludedTerms].some( - (term) => - terms[term] === file || - titleTerms[term] === file || - (terms[term] || []).includes(file) || - (titleTerms[term] || []).includes(file) - ) - ) - break; - - // select one (max) score for the file. - const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); - // add result to the result list - results.push([ - docNames[file], - titles[file], - "", - null, - score, - filenames[file], - SearchResultKind.text, - ]); - } - return results; - }, - - /** - * helper function to return a node containing the - * search summary for a given text. keywords is a list - * of stemmed words. - */ - makeSearchSummary: (htmlText, keywords, anchor) => { - const text = Search.htmlToText(htmlText, anchor); - if (text === "") return null; - - const textLower = text.toLowerCase(); - const actualStartPosition = [...keywords] - .map((k) => textLower.indexOf(k.toLowerCase())) - .filter((i) => i > -1) - .slice(-1)[0]; - const startWithContext = Math.max(actualStartPosition - 120, 0); - - const top = startWithContext === 0 ? "" : "..."; - const tail = startWithContext + 240 < text.length ? "..." : ""; - - let summary = document.createElement("p"); - summary.classList.add("context"); - summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; - - return summary; - }, -}; - -_ready(Search.init); diff --git a/docs/0.3.4/_static/sphinx_highlight.js b/docs/0.3.4/_static/sphinx_highlight.js deleted file mode 100644 index 8a96c69a..00000000 --- a/docs/0.3.4/_static/sphinx_highlight.js +++ /dev/null @@ -1,154 +0,0 @@ -/* Highlighting utilities for Sphinx HTML documentation. */ -"use strict"; - -const SPHINX_HIGHLIGHT_ENABLED = true - -/** - * highlight a given string on a node by wrapping it in - * span elements with the given class name. - */ -const _highlight = (node, addItems, text, className) => { - if (node.nodeType === Node.TEXT_NODE) { - const val = node.nodeValue; - const parent = node.parentNode; - const pos = val.toLowerCase().indexOf(text); - if ( - pos >= 0 && - !parent.classList.contains(className) && - !parent.classList.contains("nohighlight") - ) { - let span; - - const closestNode = parent.closest("body, svg, foreignObject"); - const isInSVG = closestNode && closestNode.matches("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.classList.add(className); - } - - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - const rest = document.createTextNode(val.substr(pos + text.length)); - parent.insertBefore( - span, - parent.insertBefore( - rest, - node.nextSibling - ) - ); - node.nodeValue = val.substr(0, pos); - /* There may be more occurrences of search term in this node. So call this - * function recursively on the remaining fragment. - */ - _highlight(rest, addItems, text, className); - - if (isInSVG) { - const rect = document.createElementNS( - "http://www.w3.org/2000/svg", - "rect" - ); - const bbox = parent.getBBox(); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute("class", className); - addItems.push({ parent: parent, target: rect }); - } - } - } else if (node.matches && !node.matches("button, select, textarea")) { - node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); - } -}; -const _highlightText = (thisNode, text, className) => { - let addItems = []; - _highlight(thisNode, addItems, text, className); - addItems.forEach((obj) => - obj.parent.insertAdjacentElement("beforebegin", obj.target) - ); -}; - -/** - * Small JavaScript module for the documentation. - */ -const SphinxHighlight = { - - /** - * highlight the search words provided in localstorage in the text - */ - highlightSearchWords: () => { - if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight - - // get and clear terms from localstorage - const url = new URL(window.location); - const highlight = - localStorage.getItem("sphinx_highlight_terms") - || url.searchParams.get("highlight") - || ""; - localStorage.removeItem("sphinx_highlight_terms") - url.searchParams.delete("highlight"); - window.history.replaceState({}, "", url); - - // get individual terms from highlight string - const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); - if (terms.length === 0) return; // nothing to do - - // There should never be more than one element matching "div.body" - const divBody = document.querySelectorAll("div.body"); - const body = divBody.length ? divBody[0] : document.querySelector("body"); - window.setTimeout(() => { - terms.forEach((term) => _highlightText(body, term, "highlighted")); - }, 10); - - const searchBox = document.getElementById("searchbox"); - if (searchBox === null) return; - searchBox.appendChild( - document - .createRange() - .createContextualFragment( - '

' + - '' + - _("Hide Search Matches") + - "

" - ) - ); - }, - - /** - * helper function to hide the search marks again - */ - hideSearchWords: () => { - document - .querySelectorAll("#searchbox .highlight-link") - .forEach((el) => el.remove()); - document - .querySelectorAll("span.highlighted") - .forEach((el) => el.classList.remove("highlighted")); - localStorage.removeItem("sphinx_highlight_terms") - }, - - initEscapeListener: () => { - // only install a listener if it is really needed - if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; - - document.addEventListener("keydown", (event) => { - // bail for input elements - if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; - // bail with special keys - if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; - if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { - SphinxHighlight.hideSearchWords(); - event.preventDefault(); - } - }); - }, -}; - -_ready(() => { - /* Do not call highlightSearchWords() when we are on the search page. - * It will highlight words from the *previous* search query. - */ - if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); - SphinxHighlight.initEscapeListener(); -}); diff --git a/docs/0.3.4/autodoc/mmif.serialize.html b/docs/0.3.4/autodoc/mmif.serialize.html deleted file mode 100644 index 48c539e0..00000000 --- a/docs/0.3.4/autodoc/mmif.serialize.html +++ /dev/null @@ -1,369 +0,0 @@ - - - - - - - - - mmif.serialize module — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.serialize module

-
-

mmif.serialize.model module

-
-
-

mmif.serialize.mmif module

-
-
-

mmif.serialize.view module

-
-
-

mmif.serialize.annotation module

-

The annotation module contains the classes used to represent a -MMIF annotation as a live Python object.

-

In MMIF, annotations are created by apps in a pipeline as a part -of a view. For documentation on how views are represented, see -mmif.serialize.view.

-
-
-class mmif.serialize.annotation.Annotation(anno_obj: bytes | str | dict | None = None)[source]
-

Bases: FreezableMmifObject

-

MmifObject that represents an annotation in a MMIF view.

-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]]) → None[source]
-

Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

-
- -
-
-property at_type: str | ThingTypesBase[source]
-
- -
-
-property id: str[source]
-
- -
-
-is_document()[source]
-
- -
-
-is_type(type: str | ThingTypesBase) → bool[source]
-

Check if the @type of this object matches.

-
- -
- -
-
-class mmif.serialize.annotation.AnnotationProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: FreezableMmifObject

-

AnnotationProperties object that represents the -properties object within a MMIF annotation.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
- -
-
-class mmif.serialize.annotation.Document(doc_obj: bytes | str | dict | None = None)[source]
-

Bases: Annotation

-

Document object that represents a single document in a MMIF file.

-

A document is identified by an ID, and contains certain attributes -and potentially contains the contents of the document itself, -metadata about how the document was created, and/or a list of -subdocuments grouped together logically.

-

If document_obj is not provided, an empty Document will be generated.

-
-
Parameters:
-

document_obj – the JSON data that defines the document

-
-
-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None]) → None[source]
-

Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

-
- -
-
-property location: str[source]
-
- -
-
-location_address() → str[source]
-
- -
-
-location_path() → str[source]
-
- -
-
-location_scheme() → str[source]
-
- -
-
-property parent: str[source]
-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.DocumentProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: AnnotationProperties

-

DocumentProperties object that represents the -properties object within a MMIF document.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
-
-property location: str[source]
-
- -
-
-location_address() → str[source]
-
- -
-
-location_path() → str[source]
-
- -
-
-location_scheme() → str[source]
-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.Text(text_obj: bytes | str | dict | None = None)[source]
-

Bases: FreezableMmifObject

-
-
-property lang: str[source]
-
- -
-
-property value: str[source]
-
- -
- -
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.3.4 - - -
-
- -
0.3.0
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0.3.1
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0.3.2
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0.3.3
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0.3.4
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0.3.5
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0.4.0
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0.4.1
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0.4.2
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- - - \ No newline at end of file diff --git a/docs/0.3.4/autodoc/mmif.vocabulary.html b/docs/0.3.4/autodoc/mmif.vocabulary.html deleted file mode 100644 index f6139f2e..00000000 --- a/docs/0.3.4/autodoc/mmif.vocabulary.html +++ /dev/null @@ -1,306 +0,0 @@ - - - - - - - - - mmif.vocabulary module — mmif-python documentation - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
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-
-
- -
-

mmif.vocabulary module

-
-

mmif.vocabulary.annotation_types module

-
-
-class mmif.vocabulary.annotation_types.AnnotationTypes(value)[source]
-

Bases: AnnotationTypesBase

-

This enum contains the URIs for the MMIF annotation types defined in the spec version 0.3.1. -Use this to quickly get the correct URIs for those types, or use the objects themselves in your -code and they will serialize to the strings.

-
-
-Alignment = 'http://mmif.clams.ai/0.3.1/vocabulary/Alignment'[source]
-
- -
-
-Annotation = 'http://mmif.clams.ai/0.3.1/vocabulary/Annotation'[source]
-
- -
-
-BoundingBox = 'http://mmif.clams.ai/0.3.1/vocabulary/BoundingBox'[source]
-
- -
-
-Chapter = 'http://mmif.clams.ai/0.3.1/vocabulary/Chapter'[source]
-
- -
-
-Interval = 'http://mmif.clams.ai/0.3.1/vocabulary/Interval'[source]
-
- -
-
-Polygon = 'http://mmif.clams.ai/0.3.1/vocabulary/Polygon'[source]
-
- -
-
-Region = 'http://mmif.clams.ai/0.3.1/vocabulary/Region'[source]
-
- -
-
-Relation = 'http://mmif.clams.ai/0.3.1/vocabulary/Relation'[source]
-
- -
-
-Span = 'http://mmif.clams.ai/0.3.1/vocabulary/Span'[source]
-
- -
-
-TimeFrame = 'http://mmif.clams.ai/0.3.1/vocabulary/TimeFrame'[source]
-
- -
-
-TimePoint = 'http://mmif.clams.ai/0.3.1/vocabulary/TimePoint'[source]
-
- -
-
-VideoObject = 'http://mmif.clams.ai/0.3.1/vocabulary/VideoObject'[source]
-
- -
- -
-
-class mmif.vocabulary.annotation_types.AnnotationTypesBase(value)[source]
-

Bases: ThingTypesBase

-

Inherit from this class to build your own custom annotation -vocabularies. Each member’s name should be the name of the -type, and each member’s value should be the URI of that type.

-
- -
-
-

mmif.vocabulary.media_types module

-
-
-class mmif.vocabulary.document_types.DocumentTypes(value)[source]
-

Bases: DocumentTypesBase

-

This enum contains the URIs for the MMIF document types defined in the spec version 0.3.1. -Use this to quickly get the correct URIs for those types, or use the objects themselves in your -code and they will serialize to the strings.

-
-
-AudioDocument = 'http://mmif.clams.ai/0.3.1/vocabulary/AudioDocument'[source]
-
- -
-
-Document = 'http://mmif.clams.ai/0.3.1/vocabulary/Document'[source]
-
- -
-
-ImageDocument = 'http://mmif.clams.ai/0.3.1/vocabulary/ImageDocument'[source]
-
- -
-
-TextDocument = 'http://mmif.clams.ai/0.3.1/vocabulary/TextDocument'[source]
-
- -
-
-VideoDocument = 'http://mmif.clams.ai/0.3.1/vocabulary/VideoDocument'[source]
-
- -
- -
-
-class mmif.vocabulary.document_types.DocumentTypesBase(value)[source]
-

Bases: ThingTypesBase

-

Inherit from this class to build your own custom document -vocabularies. Each member’s name should be the name of the -type, and each member’s value should be the URI of that type.

-
- -
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.3.4 - - -
-
- -
0.3.0
-
0.3.1
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0.3.2
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0.3.3
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0.3.4
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0.4.0
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- - - \ No newline at end of file diff --git a/docs/0.3.4/consumer-tutorial.html b/docs/0.3.4/consumer-tutorial.html deleted file mode 100644 index e8a5cb29..00000000 --- a/docs/0.3.4/consumer-tutorial.html +++ /dev/null @@ -1,175 +0,0 @@ - - - - - - - - - MMIF consumer — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • MMIF consumer
    • -
  • -
    • -
-
-
-
-
- -
-

MMIF consumer

-

A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the appliance documentation to learn more about the appliance.

-

MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance.

-
    -

  1. The code must be hosted on a public git repository (e.g. Github, Gitlab, …)

    2. -

  2. Must listen to 5000 port.

    3. -

  3. Must expose /display route .

    4. -

  4. /display router should response to GET requests.

    5. -

  5. In the GET request, a public URL of the input MMIF file is passed via file URL parameter.

    6. -

  6. On the codebase root, there must be a Dockerfile that can build a docker image that runs the web app.

    7. -
-

We provide an example consumer at https://github.com/clamsproject/mmif-visualizer.

-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.3.4 - - -
-
- -
0.3.0
-
0.3.1
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0.3.3
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0.4.1
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0.4.2
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- - - \ No newline at end of file diff --git a/docs/0.3.4/genindex.html b/docs/0.3.4/genindex.html deleted file mode 100644 index 4620dbd5..00000000 --- a/docs/0.3.4/genindex.html +++ /dev/null @@ -1,407 +0,0 @@ - - - - - - - - Index — mmif-python documentation - - - - - - - - - - - - - - - -
- - -
- -
-
-
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    -
    • -
  • Index
    • -
  • -
    • -
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- - -

Index

- -
- A - | B - | C - | D - | I - | L - | M - | P - | R - | S - | T - | V - -
-

A

- - - -
- -

B

- - -
- -

C

- - -
- -

D

- - - -
- -

I

- - - -
- -

L

- - - -
- -

M

- - - -
    -
  • - mmif.serialize.annotation - -
    • -
  • - mmif.vocabulary.annotation_types - -
    • -
  • - mmif.vocabulary.document_types - -
    • -
- -

P

- - - -
- -

R

- - - -
- -

S

- - -
- -

T

- - - -
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V

- - - -
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- - Other Versions - v: 0.3.4 - - -
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0.3.1
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0.3.2
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0.3.3
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0.3.4
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0.3.5
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0.4.0
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0.4.2
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- - - \ No newline at end of file diff --git a/docs/0.3.4/index.html b/docs/0.3.4/index.html deleted file mode 100644 index dbf8e7f2..00000000 --- a/docs/0.3.4/index.html +++ /dev/null @@ -1,201 +0,0 @@ - - - - - - - - - Welcome to mmif-python’s documentation! — mmif-python documentation - - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • Welcome to mmif-python’s documentation!
    • -
  • -
    • -
-
-
-
-
- -
-

Welcome to mmif-python’s documentation!

-
-
-

MMIF for python

-

NOTE that this project is in pre-alpha and being actively developed. Nothing is guaranteed to reliably work for the moment and developer need to be very careful when using APIs implemented here. Please use the issue track to report bugs and malfunctions.

-
-

MultiMedia Interchange Format

-

MMIF is a JSON(-LD)-based data format designed for transferring annotation data between computational analysis applications in CLAMS project.

-
-

Contents

- -
-
-

API documentation:

- -
-
-
-
-

Indices and tables

- -
- - -
-
- -
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- -
- - Other Versions - v: 0.3.4 - - -
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0.3.0
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0.3.1
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0.3.2
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0.3.3
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0.3.4
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- - - \ No newline at end of file diff --git a/docs/0.3.4/introduction.html b/docs/0.3.4/introduction.html deleted file mode 100644 index 1be92fa4..00000000 --- a/docs/0.3.4/introduction.html +++ /dev/null @@ -1,231 +0,0 @@ - - - - - - - - - Getting Started — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
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  • Getting Started
    • -
  • -
    • -
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- -
-

Getting Started

-
-

Overview

-

MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF wbesite. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports de-/serialization of MMIF objects, as well as many navigation and manipulation helpers for MMIF objects.

-
-
-

Prerequisites

-
    -

  • Python: mmif-python requires Python 3.6 or newer. We have no plan to support Python 2.7.

    • -
-
-
-

Installation

-

Package mmif-python is distributed via the official PyPI. Users are supposed to pip-install to get latest release.

-
pip install mmif-python
-
-
-

This will install a package mmif to local python. -The MMIF format and specification is evolving over time, and mmif-python package will be updated along with the changes in MMIF format. Note that MMIF format is not always backward-compatible. To find out more about relations between MMIF versions and mmif-python versions, and which supports which, please take time to read our decision on the subject here.

-
-
-

MMIF Serialization

-

mmif.serialize.mmif.Mmif represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of mmif.serialize.model.MmifObject, including the mmif.serialize.mmif.Mmif. To start with an existing MMIF str, simple initiate a new Mmif object with the file.

-
import mmif
-from mmif import Mmif
-
-mmif_str = """{
-"metadata": {
-  "mmif": "http://mmif.clams.ai/0.2.0"
-},
-"documents": [
-  {
-    "@type": "http://mmif.clams.ai/0.2.0/vocabulary/VideoDocument",
-    "properties": {
-      "id": "m1",
-      "mime": "video/mp4",
-      "location": "file:///var/archive/video-0012.mp4"
-    }
-  },
-  {
-    "@type": "http://mmif.clams.ai/0.2.0/vocabulary/TextDocument",
-    "properties": {
-      "id": "m2",
-      "mime": "text/plain",
-      "location": "file:///var/archive/video-0012-transcript.txt"
-    }
-  }
-],
-"views": []}"""
-mmif_obj = Mmif(mmif_str)
-
-
-

Few notes;

-
    -

  1. MMIF does not carry the primary source files in it.

    2. -

  2. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version mmif-python implementation of the MMIF might not be able to load an unsupported version of MMIF string.

    3. -
-

When serializing back to str, call .serialize() (mmif.serialize.model.MmifObject.serialize()) on the object.

-

To get subcomponents, you can use various getters implemented in subclasses. For more details, the API documentation (mmif package) will help.

-
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.3.4 - - -
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0.3.0
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0.3.1
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0.3.2
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0.3.3
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0.3.4
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- - - \ No newline at end of file diff --git a/docs/0.3.4/modules.html b/docs/0.3.4/modules.html deleted file mode 100644 index 90022f82..00000000 --- a/docs/0.3.4/modules.html +++ /dev/null @@ -1,249 +0,0 @@ - - - - - - - - - mmif package — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
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  • mmif package
    • -
  • -
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mmif package

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- -
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The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the `appliance documentation `_ to learn more about the appliance. - -MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance. - -#. The code must be hosted on a public git repository (e.g. Github, Gitlab, ...) -#. Must listen to ``5000`` port. -#. Must expose ``/display`` route . -#. ``/display`` router should response to ``GET`` requests. -#. In the ``GET`` request, a public URL of the input MMIF file is passed via ``file`` URL parameter. -#. On the codebase root, there must be a ``Dockerfile`` that can build a `docker `_ image that runs the web app. - -We provide an example consumer at https://github.com/clamsproject/mmif-visualizer. diff --git a/docs/0.3.5/_sources/index.rst.txt b/docs/0.3.5/_sources/index.rst.txt deleted file mode 100644 index 6146286d..00000000 --- a/docs/0.3.5/_sources/index.rst.txt +++ /dev/null @@ -1,25 +0,0 @@ -Welcome to mmif-python's documentation! -======================================= - -.. mdinclude:: ../README.md - -.. toctree:: - :maxdepth: 2 - :caption: Contents - - introduction - consumer-tutorial - -.. toctree:: - :maxdepth: 2 - :caption: API documentation: - - modules - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/docs/0.3.5/_sources/introduction.rst.txt b/docs/0.3.5/_sources/introduction.rst.txt deleted file mode 100644 index 6af8cd61..00000000 --- a/docs/0.3.5/_sources/introduction.rst.txt +++ /dev/null @@ -1,75 +0,0 @@ -.. _instroduction: - -Getting Started -=============== - - -Overview ---------- - -MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF wbesite `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports de-/serialization of MMIF objects, as well as many navigation and manipulation helpers for MMIF objects. - -Prerequisites -------------- - -* `Python `_: ``mmif-python`` requires Python 3.6 or newer. We have no plan to support `Python 2.7 `_. - -Installation ---------------- - -Package ``mmif-python`` is distributed via the official PyPI. Users are supposed to pip-install to get latest release. - -.. code-block:: bash - - pip install mmif-python - -This will install a package `mmif` to local python. -The MMIF format and specification is evolving over time, and ``mmif-python`` package will be updated along with the changes in MMIF format. Note that MMIF format is not always backward-compatible. To find out more about relations between MMIF versions and ``mmif-python`` versions, and which supports which, please take time to read our decision on the subject `here `_. - -MMIF Serialization ---------------------------- - -:class:`mmif.serialize.mmif.Mmif` represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of :class:`mmif.serialize.model.MmifObject`, including the :class:`mmif.serialize.mmif.Mmif`. To start with an existing MMIF :class:`str`, simple initiate a new ``Mmif`` object with the file. - -.. code-block:: python - - import mmif - from mmif import Mmif - - mmif_str = """{ - "metadata": { - "mmif": "http://mmif.clams.ai/0.2.0" - }, - "documents": [ - { - "@type": "http://mmif.clams.ai/0.2.0/vocabulary/VideoDocument", - "properties": { - "id": "m1", - "mime": "video/mp4", - "location": "file:///var/archive/video-0012.mp4" - } - }, - { - "@type": "http://mmif.clams.ai/0.2.0/vocabulary/TextDocument", - "properties": { - "id": "m2", - "mime": "text/plain", - "location": "file:///var/archive/video-0012-transcript.txt" - } - } - ], - "views": []}""" - mmif_obj = Mmif(mmif_str) - - -Few notes; - -#. MMIF does not carry the primary source files in it. -#. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version ``mmif-python`` implementation of the MMIF might not be able to load an unsupported version of MMIF string. - -When serializing back to :class:`str`, call ``.serialize()`` (:meth:`mmif.serialize.model.MmifObject.serialize`) on the object. - -To get subcomponents, you can use various getters implemented in subclasses. 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- -/** - * Simple result scoring code. - */ -if (typeof Scorer === "undefined") { - var Scorer = { - // Implement the following function to further tweak the score for each result - // The function takes a result array [docname, title, anchor, descr, score, filename] - // and returns the new score. - /* - score: result => { - const [docname, title, anchor, descr, score, filename, kind] = result - return score - }, - */ - - // query matches the full name of an object - objNameMatch: 11, - // or matches in the last dotted part of the object name - objPartialMatch: 6, - // Additive scores depending on the priority of the object - objPrio: { - 0: 15, // used to be importantResults - 1: 5, // used to be objectResults - 2: -5, // used to be unimportantResults - }, - // Used when the priority is not in the mapping. - objPrioDefault: 0, - - // query found in title - title: 15, - partialTitle: 7, - // query found in terms - term: 5, - partialTerm: 2, - }; -} - -// Global search result kind enum, used by themes to style search results. -class SearchResultKind { - static get index() { return "index"; } - static get object() { return "object"; } - static get text() { return "text"; } - static get title() { return "title"; } -} - -const _removeChildren = (element) => { - while (element && element.lastChild) element.removeChild(element.lastChild); -}; - -/** - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping - */ -const _escapeRegExp = (string) => - string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string - -const _displayItem = (item, searchTerms, highlightTerms) => { - const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; - const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; - const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; - const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; - const contentRoot = document.documentElement.dataset.content_root; - - const [docName, title, anchor, descr, score, _filename, kind] = item; - - let listItem = document.createElement("li"); - // Add a class representing the item's type: - // can be used by a theme's CSS selector for styling - // See SearchResultKind for the class names. - listItem.classList.add(`kind-${kind}`); - let requestUrl; - let linkUrl; - if (docBuilder === "dirhtml") { - // dirhtml builder - let dirname = docName + "/"; - if (dirname.match(/\/index\/$/)) - dirname = dirname.substring(0, dirname.length - 6); - else if (dirname === "index/") dirname = ""; - requestUrl = contentRoot + dirname; - linkUrl = requestUrl; - } else { - // normal html builders - requestUrl = contentRoot + docName + docFileSuffix; - linkUrl = docName + docLinkSuffix; - } - let linkEl = listItem.appendChild(document.createElement("a")); - linkEl.href = linkUrl + anchor; - linkEl.dataset.score = score; - linkEl.innerHTML = title; - if (descr) { - listItem.appendChild(document.createElement("span")).innerHTML = - " (" + descr + ")"; - // highlight search terms in the description - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - } - else if (showSearchSummary) - fetch(requestUrl) - .then((responseData) => responseData.text()) - .then((data) => { - if (data) - listItem.appendChild( - Search.makeSearchSummary(data, searchTerms, anchor) - ); - // highlight search terms in the summary - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - }); - Search.output.appendChild(listItem); -}; -const _finishSearch = (resultCount) => { - Search.stopPulse(); - Search.title.innerText = _("Search Results"); - if (!resultCount) - Search.status.innerText = Documentation.gettext( - "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." - ); - else - Search.status.innerText = Documentation.ngettext( - "Search finished, found one page matching the search query.", - "Search finished, found ${resultCount} pages matching the search query.", - resultCount, - ).replace('${resultCount}', resultCount); -}; -const _displayNextItem = ( - results, - resultCount, - searchTerms, - highlightTerms, -) => { - // results left, load the summary and display it - // this is intended to be dynamic (don't sub resultsCount) - if (results.length) { - _displayItem(results.pop(), searchTerms, highlightTerms); - setTimeout( - () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), - 5 - ); - } - // search finished, update title and status message - else _finishSearch(resultCount); -}; -// Helper function used by query() to order search results. -// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. -// Order the results by score (in opposite order of appearance, since the -// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. -const _orderResultsByScoreThenName = (a, b) => { - const leftScore = a[4]; - const rightScore = b[4]; - if (leftScore === rightScore) { - // same score: sort alphabetically - const leftTitle = a[1].toLowerCase(); - const rightTitle = b[1].toLowerCase(); - if (leftTitle === rightTitle) return 0; - return leftTitle > rightTitle ? -1 : 1; // inverted is intentional - } - return leftScore > rightScore ? 1 : -1; -}; - -/** - * Default splitQuery function. Can be overridden in ``sphinx.search`` with a - * custom function per language. - * - * The regular expression works by splitting the string on consecutive characters - * that are not Unicode letters, numbers, underscores, or emoji characters. - * This is the same as ``\W+`` in Python, preserving the surrogate pair area. - */ -if (typeof splitQuery === "undefined") { - var splitQuery = (query) => query - .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) - .filter(term => term) // remove remaining empty strings -} - -/** - * Search Module - */ -const Search = { - _index: null, - _queued_query: null, - _pulse_status: -1, - - htmlToText: (htmlString, anchor) => { - const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - for (const removalQuery of [".headerlink", "script", "style"]) { - htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); - } - if (anchor) { - const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); - if (anchorContent) return anchorContent.textContent; - - console.warn( - `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` - ); - } - - // if anchor not specified or not found, fall back to main content - const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent) return docContent.textContent; - - console.warn( - "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." - ); - return ""; - }, - - init: () => { - const query = new URLSearchParams(window.location.search).get("q"); - document - .querySelectorAll('input[name="q"]') - .forEach((el) => (el.value = query)); - if (query) Search.performSearch(query); - }, - - loadIndex: (url) => - (document.body.appendChild(document.createElement("script")).src = url), - - setIndex: (index) => { - Search._index = index; - if (Search._queued_query !== null) { - const query = Search._queued_query; - Search._queued_query = null; - Search.query(query); - } - }, - - hasIndex: () => Search._index !== null, - - deferQuery: (query) => (Search._queued_query = query), - - stopPulse: () => (Search._pulse_status = -1), - - startPulse: () => { - if (Search._pulse_status >= 0) return; - - const pulse = () => { - Search._pulse_status = (Search._pulse_status + 1) % 4; - Search.dots.innerText = ".".repeat(Search._pulse_status); - if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); - }; - pulse(); - }, - - /** - * perform a search for something (or wait until index is loaded) - */ - performSearch: (query) => { - // create the required interface elements - const searchText = document.createElement("h2"); - searchText.textContent = _("Searching"); - const searchSummary = document.createElement("p"); - searchSummary.classList.add("search-summary"); - searchSummary.innerText = ""; - const searchList = document.createElement("ul"); - searchList.setAttribute("role", "list"); - searchList.classList.add("search"); - - const out = document.getElementById("search-results"); - Search.title = out.appendChild(searchText); - Search.dots = Search.title.appendChild(document.createElement("span")); - Search.status = out.appendChild(searchSummary); - Search.output = out.appendChild(searchList); - - const searchProgress = document.getElementById("search-progress"); - // Some themes don't use the search progress node - if (searchProgress) { - searchProgress.innerText = _("Preparing search..."); - } - Search.startPulse(); - - // index already loaded, the browser was quick! - if (Search.hasIndex()) Search.query(query); - else Search.deferQuery(query); - }, - - _parseQuery: (query) => { - // stem the search terms and add them to the correct list - const stemmer = new Stemmer(); - const searchTerms = new Set(); - const excludedTerms = new Set(); - const highlightTerms = new Set(); - const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); - splitQuery(query.trim()).forEach((queryTerm) => { - const queryTermLower = queryTerm.toLowerCase(); - - // maybe skip this "word" - // stopwords array is from language_data.js - if ( - stopwords.indexOf(queryTermLower) !== -1 || - queryTerm.match(/^\d+$/) - ) - return; - - // stem the word - let word = stemmer.stemWord(queryTermLower); - // select the correct list - if (word[0] === "-") excludedTerms.add(word.substr(1)); - else { - searchTerms.add(word); - highlightTerms.add(queryTermLower); - } - }); - - if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js - localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) - } - - // console.debug("SEARCH: searching for:"); - // console.info("required: ", [...searchTerms]); - // console.info("excluded: ", [...excludedTerms]); - - return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; - }, - - /** - * execute search (requires search index to be loaded) - */ - _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - - // Collect multiple result groups to be sorted separately and then ordered. - // Each is an array of [docname, title, anchor, descr, score, filename, kind]. - const normalResults = []; - const nonMainIndexResults = []; - - _removeChildren(document.getElementById("search-progress")); - - const queryLower = query.toLowerCase().trim(); - for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { - for (const [file, id] of foundTitles) { - const score = Math.round(Scorer.title * queryLower.length / title.length); - const boost = titles[file] === title ? 1 : 0; // add a boost for document titles - normalResults.push([ - docNames[file], - titles[file] !== title ? `${titles[file]} > ${title}` : title, - id !== null ? "#" + id : "", - null, - score + boost, - filenames[file], - SearchResultKind.title, - ]); - } - } - } - - // search for explicit entries in index directives - for (const [entry, foundEntries] of Object.entries(indexEntries)) { - if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id, isMain] of foundEntries) { - const score = Math.round(100 * queryLower.length / entry.length); - const result = [ - docNames[file], - titles[file], - id ? "#" + id : "", - null, - score, - filenames[file], - SearchResultKind.index, - ]; - if (isMain) { - normalResults.push(result); - } else { - nonMainIndexResults.push(result); - } - } - } - } - - // lookup as object - objectTerms.forEach((term) => - normalResults.push(...Search.performObjectSearch(term, objectTerms)) - ); - - // lookup as search terms in fulltext - normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); - - // let the scorer override scores with a custom scoring function - if (Scorer.score) { - normalResults.forEach((item) => (item[4] = Scorer.score(item))); - nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); - } - - // Sort each group of results by score and then alphabetically by name. - normalResults.sort(_orderResultsByScoreThenName); - nonMainIndexResults.sort(_orderResultsByScoreThenName); - - // Combine the result groups in (reverse) order. - // Non-main index entries are typically arbitrary cross-references, - // so display them after other results. - let results = [...nonMainIndexResults, ...normalResults]; - - // remove duplicate search results - // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept - let seen = new Set(); - results = results.reverse().reduce((acc, result) => { - let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); - if (!seen.has(resultStr)) { - acc.push(result); - seen.add(resultStr); - } - return acc; - }, []); - - return results.reverse(); - }, - - query: (query) => { - const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); - const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); - - // for debugging - //Search.lastresults = results.slice(); // a copy - // console.info("search results:", Search.lastresults); - - // print the results - _displayNextItem(results, results.length, searchTerms, highlightTerms); - }, - - /** - * search for object names - */ - performObjectSearch: (object, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const objects = Search._index.objects; - const objNames = Search._index.objnames; - const titles = Search._index.titles; - - const results = []; - - const objectSearchCallback = (prefix, match) => { - const name = match[4] - const fullname = (prefix ? prefix + "." : "") + name; - const fullnameLower = fullname.toLowerCase(); - if (fullnameLower.indexOf(object) < 0) return; - - let score = 0; - const parts = fullnameLower.split("."); - - // check for different match types: exact matches of full name or - // "last name" (i.e. last dotted part) - if (fullnameLower === object || parts.slice(-1)[0] === object) - score += Scorer.objNameMatch; - else if (parts.slice(-1)[0].indexOf(object) > -1) - score += Scorer.objPartialMatch; // matches in last name - - const objName = objNames[match[1]][2]; - const title = titles[match[0]]; - - // If more than one term searched for, we require other words to be - // found in the name/title/description - const otherTerms = new Set(objectTerms); - otherTerms.delete(object); - if (otherTerms.size > 0) { - const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); - if ( - [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) - ) - return; - } - - let anchor = match[3]; - if (anchor === "") anchor = fullname; - else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; - - const descr = objName + _(", in ") + title; - - // add custom score for some objects according to scorer - if (Scorer.objPrio.hasOwnProperty(match[2])) - score += Scorer.objPrio[match[2]]; - else score += Scorer.objPrioDefault; - - results.push([ - docNames[match[0]], - fullname, - "#" + anchor, - descr, - score, - filenames[match[0]], - SearchResultKind.object, - ]); - }; - Object.keys(objects).forEach((prefix) => - objects[prefix].forEach((array) => - objectSearchCallback(prefix, array) - ) - ); - return results; - }, - - /** - * search for full-text terms in the index - */ - performTermsSearch: (searchTerms, excludedTerms) => { - // prepare search - const terms = Search._index.terms; - const titleTerms = Search._index.titleterms; - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - - const scoreMap = new Map(); - const fileMap = new Map(); - - // perform the search on the required terms - searchTerms.forEach((word) => { - const files = []; - const arr = [ - { files: terms[word], score: Scorer.term }, - { files: titleTerms[word], score: Scorer.title }, - ]; - // add support for partial matches - if (word.length > 2) { - const escapedWord = _escapeRegExp(word); - if (!terms.hasOwnProperty(word)) { - Object.keys(terms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: terms[term], score: Scorer.partialTerm }); - }); - } - if (!titleTerms.hasOwnProperty(word)) { - Object.keys(titleTerms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); - }); - } - } - - // no match but word was a required one - if (arr.every((record) => record.files === undefined)) return; - - // found search word in contents - arr.forEach((record) => { - if (record.files === undefined) return; - - let recordFiles = record.files; - if (recordFiles.length === undefined) recordFiles = [recordFiles]; - files.push(...recordFiles); - - // set score for the word in each file - recordFiles.forEach((file) => { - if (!scoreMap.has(file)) scoreMap.set(file, {}); - scoreMap.get(file)[word] = record.score; - }); - }); - - // create the mapping - files.forEach((file) => { - if (!fileMap.has(file)) fileMap.set(file, [word]); - else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); - }); - }); - - // now check if the files don't contain excluded terms - const results = []; - for (const [file, wordList] of fileMap) { - // check if all requirements are matched - - // as search terms with length < 3 are discarded - const filteredTermCount = [...searchTerms].filter( - (term) => term.length > 2 - ).length; - if ( - wordList.length !== searchTerms.size && - wordList.length !== filteredTermCount - ) - continue; - - // ensure that none of the excluded terms is in the search result - if ( - [...excludedTerms].some( - (term) => - terms[term] === file || - titleTerms[term] === file || - (terms[term] || []).includes(file) || - (titleTerms[term] || []).includes(file) - ) - ) - break; - - // select one (max) score for the file. - const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); - // add result to the result list - results.push([ - docNames[file], - titles[file], - "", - null, - score, - filenames[file], - SearchResultKind.text, - ]); - } - return results; - }, - - /** - * helper function to return a node containing the - * search summary for a given text. keywords is a list - * of stemmed words. - */ - makeSearchSummary: (htmlText, keywords, anchor) => { - const text = Search.htmlToText(htmlText, anchor); - if (text === "") return null; - - const textLower = text.toLowerCase(); - const actualStartPosition = [...keywords] - .map((k) => textLower.indexOf(k.toLowerCase())) - .filter((i) => i > -1) - .slice(-1)[0]; - const startWithContext = Math.max(actualStartPosition - 120, 0); - - const top = startWithContext === 0 ? "" : "..."; - const tail = startWithContext + 240 < text.length ? "..." : ""; - - let summary = document.createElement("p"); - summary.classList.add("context"); - summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; - - return summary; - }, -}; - -_ready(Search.init); diff --git a/docs/0.3.5/_static/sphinx_highlight.js b/docs/0.3.5/_static/sphinx_highlight.js deleted file mode 100644 index 8a96c69a..00000000 --- a/docs/0.3.5/_static/sphinx_highlight.js +++ /dev/null @@ -1,154 +0,0 @@ -/* Highlighting utilities for Sphinx HTML documentation. */ -"use strict"; - -const SPHINX_HIGHLIGHT_ENABLED = true - -/** - * highlight a given string on a node by wrapping it in - * span elements with the given class name. - */ -const _highlight = (node, addItems, text, className) => { - if (node.nodeType === Node.TEXT_NODE) { - const val = node.nodeValue; - const parent = node.parentNode; - const pos = val.toLowerCase().indexOf(text); - if ( - pos >= 0 && - !parent.classList.contains(className) && - !parent.classList.contains("nohighlight") - ) { - let span; - - const closestNode = parent.closest("body, svg, foreignObject"); - const isInSVG = closestNode && closestNode.matches("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.classList.add(className); - } - - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - const rest = document.createTextNode(val.substr(pos + text.length)); - parent.insertBefore( - span, - parent.insertBefore( - rest, - node.nextSibling - ) - ); - node.nodeValue = val.substr(0, pos); - /* There may be more occurrences of search term in this node. So call this - * function recursively on the remaining fragment. - */ - _highlight(rest, addItems, text, className); - - if (isInSVG) { - const rect = document.createElementNS( - "http://www.w3.org/2000/svg", - "rect" - ); - const bbox = parent.getBBox(); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute("class", className); - addItems.push({ parent: parent, target: rect }); - } - } - } else if (node.matches && !node.matches("button, select, textarea")) { - node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); - } -}; -const _highlightText = (thisNode, text, className) => { - let addItems = []; - _highlight(thisNode, addItems, text, className); - addItems.forEach((obj) => - obj.parent.insertAdjacentElement("beforebegin", obj.target) - ); -}; - -/** - * Small JavaScript module for the documentation. - */ -const SphinxHighlight = { - - /** - * highlight the search words provided in localstorage in the text - */ - highlightSearchWords: () => { - if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight - - // get and clear terms from localstorage - const url = new URL(window.location); - const highlight = - localStorage.getItem("sphinx_highlight_terms") - || url.searchParams.get("highlight") - || ""; - localStorage.removeItem("sphinx_highlight_terms") - url.searchParams.delete("highlight"); - window.history.replaceState({}, "", url); - - // get individual terms from highlight string - const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); - if (terms.length === 0) return; // nothing to do - - // There should never be more than one element matching "div.body" - const divBody = document.querySelectorAll("div.body"); - const body = divBody.length ? divBody[0] : document.querySelector("body"); - window.setTimeout(() => { - terms.forEach((term) => _highlightText(body, term, "highlighted")); - }, 10); - - const searchBox = document.getElementById("searchbox"); - if (searchBox === null) return; - searchBox.appendChild( - document - .createRange() - .createContextualFragment( - '

' + - '' + - _("Hide Search Matches") + - "

" - ) - ); - }, - - /** - * helper function to hide the search marks again - */ - hideSearchWords: () => { - document - .querySelectorAll("#searchbox .highlight-link") - .forEach((el) => el.remove()); - document - .querySelectorAll("span.highlighted") - .forEach((el) => el.classList.remove("highlighted")); - localStorage.removeItem("sphinx_highlight_terms") - }, - - initEscapeListener: () => { - // only install a listener if it is really needed - if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; - - document.addEventListener("keydown", (event) => { - // bail for input elements - if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; - // bail with special keys - if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; - if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { - SphinxHighlight.hideSearchWords(); - event.preventDefault(); - } - }); - }, -}; - -_ready(() => { - /* Do not call highlightSearchWords() when we are on the search page. - * It will highlight words from the *previous* search query. - */ - if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); - SphinxHighlight.initEscapeListener(); -}); diff --git a/docs/0.3.5/autodoc/mmif.serialize.html b/docs/0.3.5/autodoc/mmif.serialize.html deleted file mode 100644 index 8f250910..00000000 --- a/docs/0.3.5/autodoc/mmif.serialize.html +++ /dev/null @@ -1,369 +0,0 @@ - - - - - - - - - mmif.serialize module — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.serialize module

-
-

mmif.serialize.model module

-
-
-

mmif.serialize.mmif module

-
-
-

mmif.serialize.view module

-
-
-

mmif.serialize.annotation module

-

The annotation module contains the classes used to represent a -MMIF annotation as a live Python object.

-

In MMIF, annotations are created by apps in a pipeline as a part -of a view. For documentation on how views are represented, see -mmif.serialize.view.

-
-
-class mmif.serialize.annotation.Annotation(anno_obj: bytes | str | dict | None = None)[source]
-

Bases: FreezableMmifObject

-

MmifObject that represents an annotation in a MMIF view.

-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]]) → None[source]
-

Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

-
- -
-
-property at_type: TypesBase[source]
-
- -
-
-property id: str[source]
-
- -
-
-is_document()[source]
-
- -
-
-is_type(at_type: str | TypesBase) → bool[source]
-

Check if the @type of this object matches.

-
- -
- -
-
-class mmif.serialize.annotation.AnnotationProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: FreezableMmifObject

-

AnnotationProperties object that represents the -properties object within a MMIF annotation.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
- -
-
-class mmif.serialize.annotation.Document(doc_obj: bytes | str | dict | None = None)[source]
-

Bases: Annotation

-

Document object that represents a single document in a MMIF file.

-

A document is identified by an ID, and contains certain attributes -and potentially contains the contents of the document itself, -metadata about how the document was created, and/or a list of -subdocuments grouped together logically.

-

If document_obj is not provided, an empty Document will be generated.

-
-
Parameters:
-

document_obj – the JSON data that defines the document

-
-
-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None]) → None[source]
-

Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

-
- -
-
-property location: str[source]
-
- -
-
-location_address() → str[source]
-
- -
-
-location_path() → str[source]
-
- -
-
-location_scheme() → str[source]
-
- -
-
-property parent: str[source]
-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.DocumentProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: AnnotationProperties

-

DocumentProperties object that represents the -properties object within a MMIF document.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
-
-property location: str[source]
-
- -
-
-location_address() → str[source]
-
- -
-
-location_path() → str[source]
-
- -
-
-location_scheme() → str[source]
-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.Text(text_obj: bytes | str | dict | None = None)[source]
-

Bases: FreezableMmifObject

-
-
-property lang: str[source]
-
- -
-
-property value: str[source]
-
- -
- -
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.3.5 - - -
-
- -
0.3.0
-
0.3.1
-
0.3.2
-
0.3.3
-
0.3.4
-
0.3.5
-
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0.4.1
-
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-
0.4.3
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-
- - - \ No newline at end of file diff --git a/docs/0.3.5/autodoc/mmif.vocabulary.html b/docs/0.3.5/autodoc/mmif.vocabulary.html deleted file mode 100644 index 0f07deaf..00000000 --- a/docs/0.3.5/autodoc/mmif.vocabulary.html +++ /dev/null @@ -1,284 +0,0 @@ - - - - - - - - - mmif.vocabulary module — mmif-python documentation - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.vocabulary module

-
-

mmif.vocabulary.annotation_types module

-
-
-class mmif.vocabulary.annotation_types.AnnotationTypes(type_uri: str)[source]
-

Bases: AnnotationTypesBase

-

This class contains the CLAMS annotation types -defined in the spec version 0.3.1 as class variables.

-
-
-Alignment = http://mmif.clams.ai/0.3.1/vocabulary/Alignment[source]
-
- -
-
-Annotation = http://mmif.clams.ai/0.3.1/vocabulary/Annotation[source]
-
- -
-
-BoundingBox = http://mmif.clams.ai/0.3.1/vocabulary/BoundingBox[source]
-
- -
-
-Chapter = http://mmif.clams.ai/0.3.1/vocabulary/Chapter[source]
-
- -
-
-Interval = http://mmif.clams.ai/0.3.1/vocabulary/Interval[source]
-
- -
-
-Polygon = http://mmif.clams.ai/0.3.1/vocabulary/Polygon[source]
-
- -
-
-Region = http://mmif.clams.ai/0.3.1/vocabulary/Region[source]
-
- -
-
-Relation = http://mmif.clams.ai/0.3.1/vocabulary/Relation[source]
-
- -
-
-Span = http://mmif.clams.ai/0.3.1/vocabulary/Span[source]
-
- -
-
-TimeFrame = http://mmif.clams.ai/0.3.1/vocabulary/TimeFrame[source]
-
- -
-
-TimePoint = http://mmif.clams.ai/0.3.1/vocabulary/TimePoint[source]
-
- -
-
-VideoObject = http://mmif.clams.ai/0.3.1/vocabulary/VideoObject[source]
-
- -
- -
-
-

mmif.vocabulary.media_types module

-
-
-class mmif.vocabulary.document_types.DocumentTypes(type_uri: str)[source]
-

Bases: DocumentTypesBase

-

This class contains the CLAMS document types -defined in the spec version 0.3.1 as class variables.

-
-
-AudioDocument = http://mmif.clams.ai/0.3.1/vocabulary/AudioDocument[source]
-
- -
-
-Document = http://mmif.clams.ai/0.3.1/vocabulary/Document[source]
-
- -
-
-ImageDocument = http://mmif.clams.ai/0.3.1/vocabulary/ImageDocument[source]
-
- -
-
-TextDocument = http://mmif.clams.ai/0.3.1/vocabulary/TextDocument[source]
-
- -
-
-VideoDocument = http://mmif.clams.ai/0.3.1/vocabulary/VideoDocument[source]
-
- -
- -
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.3.5 - - -
-
- -
0.3.0
-
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0.3.2
-
0.3.3
-
0.3.4
-
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0.4.1
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0.4.2
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0.4.3
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0.4.5
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0.4.6
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0.4.7
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0.4.8
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0.5.1
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0.5.2
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1.0.0
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1.0.1
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- - - \ No newline at end of file diff --git a/docs/0.3.5/consumer-tutorial.html b/docs/0.3.5/consumer-tutorial.html deleted file mode 100644 index 5ccd62f3..00000000 --- a/docs/0.3.5/consumer-tutorial.html +++ /dev/null @@ -1,175 +0,0 @@ - - - - - - - - - MMIF consumer — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • MMIF consumer
    • -
  • -
    • -
-
-
-
-
- -
-

MMIF consumer

-

A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the appliance documentation to learn more about the appliance.

-

MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance.

-
    -

  1. The code must be hosted on a public git repository (e.g. Github, Gitlab, …)

    2. -

  2. Must listen to 5000 port.

    3. -

  3. Must expose /display route .

    4. -

  4. /display router should response to GET requests.

    5. -

  5. In the GET request, a public URL of the input MMIF file is passed via file URL parameter.

    6. -

  6. On the codebase root, there must be a Dockerfile that can build a docker image that runs the web app.

    7. -
-

We provide an example consumer at https://github.com/clamsproject/mmif-visualizer.

-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.3.5 - - -
-
- -
0.3.0
-
0.3.1
-
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-
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-
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- - - \ No newline at end of file diff --git a/docs/0.3.5/genindex.html b/docs/0.3.5/genindex.html deleted file mode 100644 index 9ce36073..00000000 --- a/docs/0.3.5/genindex.html +++ /dev/null @@ -1,403 +0,0 @@ - - - - - - - - Index — mmif-python documentation - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • Index
    • -
  • -
    • -
-
-
-
-
- - -

Index

- -
- A - | B - | C - | D - | I - | L - | M - | P - | R - | S - | T - | V - -
-

A

- - - -
- -

B

- - -
- -

C

- - -
- -

D

- - - -
- -

I

- - - -
- -

L

- - - -
- -

M

- - - -
    -
  • - mmif.serialize.annotation - -
    • -
  • - mmif.vocabulary.annotation_types - -
    • -
  • - mmif.vocabulary.document_types - -
    • -
- -

P

- - - -
- -

R

- - - -
- -

S

- - -
- -

T

- - - -
- -

V

- - - -
- - - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.3.5 - - -
-
- -
0.3.0
-
0.3.1
-
0.3.2
-
0.3.3
-
0.3.4
-
0.3.5
-
0.4.0
-
0.4.1
-
0.4.2
-
0.4.3
-
0.4.4
-
0.4.5
-
0.4.6
-
0.4.7
-
0.4.8
-
0.5.0
-
0.5.1
-
0.5.2
-
1.0.0
-
1.0.1
-
1.0.10
-
1.0.11
-
1.0.12
-
1.0.13
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1.0.14
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1.0.15
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1.0.16
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1.0.17
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1.0.18
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1.0.19
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1.0.3
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1.0.4
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1.0.6
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1.0.7
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-
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- - - \ No newline at end of file diff --git a/docs/0.3.5/index.html b/docs/0.3.5/index.html deleted file mode 100644 index 1a8d1302..00000000 --- a/docs/0.3.5/index.html +++ /dev/null @@ -1,201 +0,0 @@ - - - - - - - - - Welcome to mmif-python’s documentation! — mmif-python documentation - - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • Welcome to mmif-python’s documentation!
    • -
  • -
    • -
-
-
-
-
- -
-

Welcome to mmif-python’s documentation!

-
-
-

MMIF for python

-

NOTE that this project is in pre-alpha and being actively developed. Nothing is guaranteed to reliably work for the moment and developer need to be very careful when using APIs implemented here. Please use the issue track to report bugs and malfunctions.

-
-

MultiMedia Interchange Format

-

MMIF is a JSON(-LD)-based data format designed for transferring annotation data between computational analysis applications in CLAMS project.

-
-

Contents

- -
-
-

API documentation:

- -
-
-
-
-

Indices and tables

- -
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.3.5 - - -
-
- -
0.3.0
-
0.3.1
-
0.3.2
-
0.3.3
-
0.3.4
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0.3.5
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0.4.0
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0.4.1
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0.4.2
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0.4.3
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0.4.4
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0.4.5
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0.4.6
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0.4.7
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0.4.8
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0.5.0
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0.5.1
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0.5.2
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1.0.0
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1.0.1
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1.0.10
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1.0.11
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1.0.12
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1.0.13
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1.0.14
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1.0.15
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1.0.17
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- - - \ No newline at end of file diff --git a/docs/0.3.5/introduction.html b/docs/0.3.5/introduction.html deleted file mode 100644 index 0ae042c0..00000000 --- a/docs/0.3.5/introduction.html +++ /dev/null @@ -1,231 +0,0 @@ - - - - - - - - - Getting Started — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • Getting Started
    • -
  • -
    • -
-
-
-
-
- -
-

Getting Started

-
-

Overview

-

MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF wbesite. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports de-/serialization of MMIF objects, as well as many navigation and manipulation helpers for MMIF objects.

-
-
-

Prerequisites

-
    -

  • Python: mmif-python requires Python 3.6 or newer. We have no plan to support Python 2.7.

    • -
-
-
-

Installation

-

Package mmif-python is distributed via the official PyPI. Users are supposed to pip-install to get latest release.

-
pip install mmif-python
-
-
-

This will install a package mmif to local python. -The MMIF format and specification is evolving over time, and mmif-python package will be updated along with the changes in MMIF format. Note that MMIF format is not always backward-compatible. To find out more about relations between MMIF versions and mmif-python versions, and which supports which, please take time to read our decision on the subject here.

-
-
-

MMIF Serialization

-

mmif.serialize.mmif.Mmif represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of mmif.serialize.model.MmifObject, including the mmif.serialize.mmif.Mmif. To start with an existing MMIF str, simple initiate a new Mmif object with the file.

-
import mmif
-from mmif import Mmif
-
-mmif_str = """{
-"metadata": {
-  "mmif": "http://mmif.clams.ai/0.2.0"
-},
-"documents": [
-  {
-    "@type": "http://mmif.clams.ai/0.2.0/vocabulary/VideoDocument",
-    "properties": {
-      "id": "m1",
-      "mime": "video/mp4",
-      "location": "file:///var/archive/video-0012.mp4"
-    }
-  },
-  {
-    "@type": "http://mmif.clams.ai/0.2.0/vocabulary/TextDocument",
-    "properties": {
-      "id": "m2",
-      "mime": "text/plain",
-      "location": "file:///var/archive/video-0012-transcript.txt"
-    }
-  }
-],
-"views": []}"""
-mmif_obj = Mmif(mmif_str)
-
-
-

Few notes;

-
    -

  1. MMIF does not carry the primary source files in it.

    2. -

  2. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version mmif-python implementation of the MMIF might not be able to load an unsupported version of MMIF string.

    3. -
-

When serializing back to str, call .serialize() (mmif.serialize.model.MmifObject.serialize()) on the object.

-

To get subcomponents, you can use various getters implemented in subclasses. For more details, the API documentation (mmif package) will help.

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The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the `appliance documentation `_ to learn more about the appliance. - -MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance. - -#. The code must be hosted on a public git repository (e.g. Github, Gitlab, ...) -#. Must listen to ``5000`` port. -#. Must expose ``/display`` route . -#. ``/display`` router should response to ``GET`` requests. -#. In the ``GET`` request, a public URL of the input MMIF file is passed via ``file`` URL parameter. -#. On the codebase root, there must be a ``Dockerfile`` that can build a `docker `_ image that runs the web app. - -We provide an example consumer at https://github.com/clamsproject/mmif-visualizer. diff --git a/docs/0.4.0/_sources/index.rst.txt b/docs/0.4.0/_sources/index.rst.txt deleted file mode 100644 index 9b90b38e..00000000 --- a/docs/0.4.0/_sources/index.rst.txt +++ /dev/null @@ -1,26 +0,0 @@ -Welcome to mmif-python's documentation! -======================================= - -.. mdinclude:: ../README.md - -.. toctree:: - :maxdepth: 2 - :caption: Contents - - introduction - target-versions - consumer-tutorial - -.. toctree:: - :maxdepth: 2 - :caption: API documentation: - - modules - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/docs/0.4.0/_sources/introduction.rst.txt b/docs/0.4.0/_sources/introduction.rst.txt deleted file mode 100644 index 6fea3a3c..00000000 --- a/docs/0.4.0/_sources/introduction.rst.txt +++ /dev/null @@ -1,78 +0,0 @@ -.. _instroduction: - -Getting Started -=============== - - -Overview ---------- - -MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF wbesite `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports de-/serialization of MMIF objects, as well as many navigation and manipulation helpers for MMIF objects. - -Prerequisites -------------- - -* `Python `_: ``mmif-python`` requires Python 3.6 or newer. We have no plan to support `Python 2.7 `_. - -Installation ---------------- - -Package ``mmif-python`` is distributed via the official PyPI. Users are supposed to pip-install to get latest release. - -.. code-block:: bash - - pip install mmif-python - -This will install a package `mmif` to local python. - -The MMIF format and specification is evolving over time, and ``mmif-python`` package will be updated along with the changes in MMIF format. - -.. note:: MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and ``mmif-python`` versions, please take time to read our decision on the subject `here `_. If you need to know which python SDK supports which specification version, see :ref:`target-versions` page. - -MMIF Serialization ---------------------------- - -:class:`mmif.serialize.mmif.Mmif` represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of :class:`mmif.serialize.model.MmifObject`, including the :class:`mmif.serialize.mmif.Mmif`. To start with an existing MMIF :class:`str`, simple initiate a new ``Mmif`` object with the file. - -.. code-block:: python - - import mmif - from mmif import Mmif - - mmif_str = """{ - "metadata": { - "mmif": "http://mmif.clams.ai/0.2.0" - }, - "documents": [ - { - "@type": "http://mmif.clams.ai/0.2.0/vocabulary/VideoDocument", - "properties": { - "id": "m1", - "mime": "video/mp4", - "location": "file:///var/archive/video-0012.mp4" - } - }, - { - "@type": "http://mmif.clams.ai/0.2.0/vocabulary/TextDocument", - "properties": { - "id": "m2", - "mime": "text/plain", - "location": "file:///var/archive/video-0012-transcript.txt" - } - } - ], - "views": []}""" - mmif_obj = Mmif(mmif_str) - - -Few notes; - -#. MMIF does not carry the primary source files in it. -#. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version ``mmif-python`` implementation of the MMIF might not be able to load an unsupported version of MMIF string. - -When serializing back to :class:`str`, call ``.serialize()`` (:meth:`mmif.serialize.model.MmifObject.serialize`) on the object. - -To get subcomponents, you can use various getters implemented in subclasses. For more details, the API documentation (:ref:`apidoc`) will help. - diff --git a/docs/0.4.0/_sources/modules.rst.txt b/docs/0.4.0/_sources/modules.rst.txt deleted file mode 100644 index e4269c6d..00000000 --- a/docs/0.4.0/_sources/modules.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _apidoc: - -mmif package -============ - -.. toctree:: - :maxdepth: 4 - - autodoc/mmif.serialize - autodoc/mmif.vocabulary diff --git a/docs/0.4.0/_sources/target-versions.rst.txt b/docs/0.4.0/_sources/target-versions.rst.txt deleted file mode 100644 index 34216d3e..00000000 --- a/docs/0.4.0/_sources/target-versions.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _target-versions: - -Target MMIF Versions -==================== - -This article provides targeting MMIF specification versions of different versions of ``mmif-python`` SDK. - -.. csv-table:: Target Specification Versions - :file: target-versions.csv - :header-rows: 1 diff --git a/docs/0.4.0/_static/_sphinx_javascript_frameworks_compat.js b/docs/0.4.0/_static/_sphinx_javascript_frameworks_compat.js deleted file mode 100644 index 81415803..00000000 --- a/docs/0.4.0/_static/_sphinx_javascript_frameworks_compat.js +++ /dev/null @@ -1,123 +0,0 @@ -/* Compatability shim for jQuery and underscores.js. - * - * Copyright Sphinx contributors - * Released under the two clause BSD licence - */ - -/** - * small helper function to urldecode strings - * - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL - */ -jQuery.urldecode = function(x) { - if (!x) { - return x - } - return decodeURIComponent(x.replace(/\+/g, ' ')); -}; - -/** - * small helper function to urlencode strings - */ -jQuery.urlencode = encodeURIComponent; - -/** - * This function returns the parsed url parameters of the - * current request. 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- -/** - * Simple result scoring code. - */ -if (typeof Scorer === "undefined") { - var Scorer = { - // Implement the following function to further tweak the score for each result - // The function takes a result array [docname, title, anchor, descr, score, filename] - // and returns the new score. - /* - score: result => { - const [docname, title, anchor, descr, score, filename, kind] = result - return score - }, - */ - - // query matches the full name of an object - objNameMatch: 11, - // or matches in the last dotted part of the object name - objPartialMatch: 6, - // Additive scores depending on the priority of the object - objPrio: { - 0: 15, // used to be importantResults - 1: 5, // used to be objectResults - 2: -5, // used to be unimportantResults - }, - // Used when the priority is not in the mapping. - objPrioDefault: 0, - - // query found in title - title: 15, - partialTitle: 7, - // query found in terms - term: 5, - partialTerm: 2, - }; -} - -// Global search result kind enum, used by themes to style search results. -class SearchResultKind { - static get index() { return "index"; } - static get object() { return "object"; } - static get text() { return "text"; } - static get title() { return "title"; } -} - -const _removeChildren = (element) => { - while (element && element.lastChild) element.removeChild(element.lastChild); -}; - -/** - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping - */ -const _escapeRegExp = (string) => - string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string - -const _displayItem = (item, searchTerms, highlightTerms) => { - const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; - const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; - const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; - const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; - const contentRoot = document.documentElement.dataset.content_root; - - const [docName, title, anchor, descr, score, _filename, kind] = item; - - let listItem = document.createElement("li"); - // Add a class representing the item's type: - // can be used by a theme's CSS selector for styling - // See SearchResultKind for the class names. - listItem.classList.add(`kind-${kind}`); - let requestUrl; - let linkUrl; - if (docBuilder === "dirhtml") { - // dirhtml builder - let dirname = docName + "/"; - if (dirname.match(/\/index\/$/)) - dirname = dirname.substring(0, dirname.length - 6); - else if (dirname === "index/") dirname = ""; - requestUrl = contentRoot + dirname; - linkUrl = requestUrl; - } else { - // normal html builders - requestUrl = contentRoot + docName + docFileSuffix; - linkUrl = docName + docLinkSuffix; - } - let linkEl = listItem.appendChild(document.createElement("a")); - linkEl.href = linkUrl + anchor; - linkEl.dataset.score = score; - linkEl.innerHTML = title; - if (descr) { - listItem.appendChild(document.createElement("span")).innerHTML = - " (" + descr + ")"; - // highlight search terms in the description - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - } - else if (showSearchSummary) - fetch(requestUrl) - .then((responseData) => responseData.text()) - .then((data) => { - if (data) - listItem.appendChild( - Search.makeSearchSummary(data, searchTerms, anchor) - ); - // highlight search terms in the summary - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - }); - Search.output.appendChild(listItem); -}; -const _finishSearch = (resultCount) => { - Search.stopPulse(); - Search.title.innerText = _("Search Results"); - if (!resultCount) - Search.status.innerText = Documentation.gettext( - "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." - ); - else - Search.status.innerText = Documentation.ngettext( - "Search finished, found one page matching the search query.", - "Search finished, found ${resultCount} pages matching the search query.", - resultCount, - ).replace('${resultCount}', resultCount); -}; -const _displayNextItem = ( - results, - resultCount, - searchTerms, - highlightTerms, -) => { - // results left, load the summary and display it - // this is intended to be dynamic (don't sub resultsCount) - if (results.length) { - _displayItem(results.pop(), searchTerms, highlightTerms); - setTimeout( - () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), - 5 - ); - } - // search finished, update title and status message - else _finishSearch(resultCount); -}; -// Helper function used by query() to order search results. -// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. -// Order the results by score (in opposite order of appearance, since the -// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. -const _orderResultsByScoreThenName = (a, b) => { - const leftScore = a[4]; - const rightScore = b[4]; - if (leftScore === rightScore) { - // same score: sort alphabetically - const leftTitle = a[1].toLowerCase(); - const rightTitle = b[1].toLowerCase(); - if (leftTitle === rightTitle) return 0; - return leftTitle > rightTitle ? -1 : 1; // inverted is intentional - } - return leftScore > rightScore ? 1 : -1; -}; - -/** - * Default splitQuery function. Can be overridden in ``sphinx.search`` with a - * custom function per language. - * - * The regular expression works by splitting the string on consecutive characters - * that are not Unicode letters, numbers, underscores, or emoji characters. - * This is the same as ``\W+`` in Python, preserving the surrogate pair area. - */ -if (typeof splitQuery === "undefined") { - var splitQuery = (query) => query - .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) - .filter(term => term) // remove remaining empty strings -} - -/** - * Search Module - */ -const Search = { - _index: null, - _queued_query: null, - _pulse_status: -1, - - htmlToText: (htmlString, anchor) => { - const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - for (const removalQuery of [".headerlink", "script", "style"]) { - htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); - } - if (anchor) { - const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); - if (anchorContent) return anchorContent.textContent; - - console.warn( - `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` - ); - } - - // if anchor not specified or not found, fall back to main content - const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent) return docContent.textContent; - - console.warn( - "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." - ); - return ""; - }, - - init: () => { - const query = new URLSearchParams(window.location.search).get("q"); - document - .querySelectorAll('input[name="q"]') - .forEach((el) => (el.value = query)); - if (query) Search.performSearch(query); - }, - - loadIndex: (url) => - (document.body.appendChild(document.createElement("script")).src = url), - - setIndex: (index) => { - Search._index = index; - if (Search._queued_query !== null) { - const query = Search._queued_query; - Search._queued_query = null; - Search.query(query); - } - }, - - hasIndex: () => Search._index !== null, - - deferQuery: (query) => (Search._queued_query = query), - - stopPulse: () => (Search._pulse_status = -1), - - startPulse: () => { - if (Search._pulse_status >= 0) return; - - const pulse = () => { - Search._pulse_status = (Search._pulse_status + 1) % 4; - Search.dots.innerText = ".".repeat(Search._pulse_status); - if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); - }; - pulse(); - }, - - /** - * perform a search for something (or wait until index is loaded) - */ - performSearch: (query) => { - // create the required interface elements - const searchText = document.createElement("h2"); - searchText.textContent = _("Searching"); - const searchSummary = document.createElement("p"); - searchSummary.classList.add("search-summary"); - searchSummary.innerText = ""; - const searchList = document.createElement("ul"); - searchList.setAttribute("role", "list"); - searchList.classList.add("search"); - - const out = document.getElementById("search-results"); - Search.title = out.appendChild(searchText); - Search.dots = Search.title.appendChild(document.createElement("span")); - Search.status = out.appendChild(searchSummary); - Search.output = out.appendChild(searchList); - - const searchProgress = document.getElementById("search-progress"); - // Some themes don't use the search progress node - if (searchProgress) { - searchProgress.innerText = _("Preparing search..."); - } - Search.startPulse(); - - // index already loaded, the browser was quick! - if (Search.hasIndex()) Search.query(query); - else Search.deferQuery(query); - }, - - _parseQuery: (query) => { - // stem the search terms and add them to the correct list - const stemmer = new Stemmer(); - const searchTerms = new Set(); - const excludedTerms = new Set(); - const highlightTerms = new Set(); - const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); - splitQuery(query.trim()).forEach((queryTerm) => { - const queryTermLower = queryTerm.toLowerCase(); - - // maybe skip this "word" - // stopwords array is from language_data.js - if ( - stopwords.indexOf(queryTermLower) !== -1 || - queryTerm.match(/^\d+$/) - ) - return; - - // stem the word - let word = stemmer.stemWord(queryTermLower); - // select the correct list - if (word[0] === "-") excludedTerms.add(word.substr(1)); - else { - searchTerms.add(word); - highlightTerms.add(queryTermLower); - } - }); - - if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js - localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) - } - - // console.debug("SEARCH: searching for:"); - // console.info("required: ", [...searchTerms]); - // console.info("excluded: ", [...excludedTerms]); - - return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; - }, - - /** - * execute search (requires search index to be loaded) - */ - _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - - // Collect multiple result groups to be sorted separately and then ordered. - // Each is an array of [docname, title, anchor, descr, score, filename, kind]. - const normalResults = []; - const nonMainIndexResults = []; - - _removeChildren(document.getElementById("search-progress")); - - const queryLower = query.toLowerCase().trim(); - for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { - for (const [file, id] of foundTitles) { - const score = Math.round(Scorer.title * queryLower.length / title.length); - const boost = titles[file] === title ? 1 : 0; // add a boost for document titles - normalResults.push([ - docNames[file], - titles[file] !== title ? `${titles[file]} > ${title}` : title, - id !== null ? "#" + id : "", - null, - score + boost, - filenames[file], - SearchResultKind.title, - ]); - } - } - } - - // search for explicit entries in index directives - for (const [entry, foundEntries] of Object.entries(indexEntries)) { - if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id, isMain] of foundEntries) { - const score = Math.round(100 * queryLower.length / entry.length); - const result = [ - docNames[file], - titles[file], - id ? "#" + id : "", - null, - score, - filenames[file], - SearchResultKind.index, - ]; - if (isMain) { - normalResults.push(result); - } else { - nonMainIndexResults.push(result); - } - } - } - } - - // lookup as object - objectTerms.forEach((term) => - normalResults.push(...Search.performObjectSearch(term, objectTerms)) - ); - - // lookup as search terms in fulltext - normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); - - // let the scorer override scores with a custom scoring function - if (Scorer.score) { - normalResults.forEach((item) => (item[4] = Scorer.score(item))); - nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); - } - - // Sort each group of results by score and then alphabetically by name. - normalResults.sort(_orderResultsByScoreThenName); - nonMainIndexResults.sort(_orderResultsByScoreThenName); - - // Combine the result groups in (reverse) order. - // Non-main index entries are typically arbitrary cross-references, - // so display them after other results. - let results = [...nonMainIndexResults, ...normalResults]; - - // remove duplicate search results - // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept - let seen = new Set(); - results = results.reverse().reduce((acc, result) => { - let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); - if (!seen.has(resultStr)) { - acc.push(result); - seen.add(resultStr); - } - return acc; - }, []); - - return results.reverse(); - }, - - query: (query) => { - const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); - const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); - - // for debugging - //Search.lastresults = results.slice(); // a copy - // console.info("search results:", Search.lastresults); - - // print the results - _displayNextItem(results, results.length, searchTerms, highlightTerms); - }, - - /** - * search for object names - */ - performObjectSearch: (object, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const objects = Search._index.objects; - const objNames = Search._index.objnames; - const titles = Search._index.titles; - - const results = []; - - const objectSearchCallback = (prefix, match) => { - const name = match[4] - const fullname = (prefix ? prefix + "." : "") + name; - const fullnameLower = fullname.toLowerCase(); - if (fullnameLower.indexOf(object) < 0) return; - - let score = 0; - const parts = fullnameLower.split("."); - - // check for different match types: exact matches of full name or - // "last name" (i.e. last dotted part) - if (fullnameLower === object || parts.slice(-1)[0] === object) - score += Scorer.objNameMatch; - else if (parts.slice(-1)[0].indexOf(object) > -1) - score += Scorer.objPartialMatch; // matches in last name - - const objName = objNames[match[1]][2]; - const title = titles[match[0]]; - - // If more than one term searched for, we require other words to be - // found in the name/title/description - const otherTerms = new Set(objectTerms); - otherTerms.delete(object); - if (otherTerms.size > 0) { - const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); - if ( - [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) - ) - return; - } - - let anchor = match[3]; - if (anchor === "") anchor = fullname; - else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; - - const descr = objName + _(", in ") + title; - - // add custom score for some objects according to scorer - if (Scorer.objPrio.hasOwnProperty(match[2])) - score += Scorer.objPrio[match[2]]; - else score += Scorer.objPrioDefault; - - results.push([ - docNames[match[0]], - fullname, - "#" + anchor, - descr, - score, - filenames[match[0]], - SearchResultKind.object, - ]); - }; - Object.keys(objects).forEach((prefix) => - objects[prefix].forEach((array) => - objectSearchCallback(prefix, array) - ) - ); - return results; - }, - - /** - * search for full-text terms in the index - */ - performTermsSearch: (searchTerms, excludedTerms) => { - // prepare search - const terms = Search._index.terms; - const titleTerms = Search._index.titleterms; - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - - const scoreMap = new Map(); - const fileMap = new Map(); - - // perform the search on the required terms - searchTerms.forEach((word) => { - const files = []; - const arr = [ - { files: terms[word], score: Scorer.term }, - { files: titleTerms[word], score: Scorer.title }, - ]; - // add support for partial matches - if (word.length > 2) { - const escapedWord = _escapeRegExp(word); - if (!terms.hasOwnProperty(word)) { - Object.keys(terms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: terms[term], score: Scorer.partialTerm }); - }); - } - if (!titleTerms.hasOwnProperty(word)) { - Object.keys(titleTerms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); - }); - } - } - - // no match but word was a required one - if (arr.every((record) => record.files === undefined)) return; - - // found search word in contents - arr.forEach((record) => { - if (record.files === undefined) return; - - let recordFiles = record.files; - if (recordFiles.length === undefined) recordFiles = [recordFiles]; - files.push(...recordFiles); - - // set score for the word in each file - recordFiles.forEach((file) => { - if (!scoreMap.has(file)) scoreMap.set(file, {}); - scoreMap.get(file)[word] = record.score; - }); - }); - - // create the mapping - files.forEach((file) => { - if (!fileMap.has(file)) fileMap.set(file, [word]); - else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); - }); - }); - - // now check if the files don't contain excluded terms - const results = []; - for (const [file, wordList] of fileMap) { - // check if all requirements are matched - - // as search terms with length < 3 are discarded - const filteredTermCount = [...searchTerms].filter( - (term) => term.length > 2 - ).length; - if ( - wordList.length !== searchTerms.size && - wordList.length !== filteredTermCount - ) - continue; - - // ensure that none of the excluded terms is in the search result - if ( - [...excludedTerms].some( - (term) => - terms[term] === file || - titleTerms[term] === file || - (terms[term] || []).includes(file) || - (titleTerms[term] || []).includes(file) - ) - ) - break; - - // select one (max) score for the file. - const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); - // add result to the result list - results.push([ - docNames[file], - titles[file], - "", - null, - score, - filenames[file], - SearchResultKind.text, - ]); - } - return results; - }, - - /** - * helper function to return a node containing the - * search summary for a given text. keywords is a list - * of stemmed words. - */ - makeSearchSummary: (htmlText, keywords, anchor) => { - const text = Search.htmlToText(htmlText, anchor); - if (text === "") return null; - - const textLower = text.toLowerCase(); - const actualStartPosition = [...keywords] - .map((k) => textLower.indexOf(k.toLowerCase())) - .filter((i) => i > -1) - .slice(-1)[0]; - const startWithContext = Math.max(actualStartPosition - 120, 0); - - const top = startWithContext === 0 ? "" : "..."; - const tail = startWithContext + 240 < text.length ? "..." : ""; - - let summary = document.createElement("p"); - summary.classList.add("context"); - summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; - - return summary; - }, -}; - -_ready(Search.init); diff --git a/docs/0.4.0/_static/sphinx_highlight.js b/docs/0.4.0/_static/sphinx_highlight.js deleted file mode 100644 index 8a96c69a..00000000 --- a/docs/0.4.0/_static/sphinx_highlight.js +++ /dev/null @@ -1,154 +0,0 @@ -/* Highlighting utilities for Sphinx HTML documentation. */ -"use strict"; - -const SPHINX_HIGHLIGHT_ENABLED = true - -/** - * highlight a given string on a node by wrapping it in - * span elements with the given class name. - */ -const _highlight = (node, addItems, text, className) => { - if (node.nodeType === Node.TEXT_NODE) { - const val = node.nodeValue; - const parent = node.parentNode; - const pos = val.toLowerCase().indexOf(text); - if ( - pos >= 0 && - !parent.classList.contains(className) && - !parent.classList.contains("nohighlight") - ) { - let span; - - const closestNode = parent.closest("body, svg, foreignObject"); - const isInSVG = closestNode && closestNode.matches("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.classList.add(className); - } - - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - const rest = document.createTextNode(val.substr(pos + text.length)); - parent.insertBefore( - span, - parent.insertBefore( - rest, - node.nextSibling - ) - ); - node.nodeValue = val.substr(0, pos); - /* There may be more occurrences of search term in this node. So call this - * function recursively on the remaining fragment. - */ - _highlight(rest, addItems, text, className); - - if (isInSVG) { - const rect = document.createElementNS( - "http://www.w3.org/2000/svg", - "rect" - ); - const bbox = parent.getBBox(); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute("class", className); - addItems.push({ parent: parent, target: rect }); - } - } - } else if (node.matches && !node.matches("button, select, textarea")) { - node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); - } -}; -const _highlightText = (thisNode, text, className) => { - let addItems = []; - _highlight(thisNode, addItems, text, className); - addItems.forEach((obj) => - obj.parent.insertAdjacentElement("beforebegin", obj.target) - ); -}; - -/** - * Small JavaScript module for the documentation. - */ -const SphinxHighlight = { - - /** - * highlight the search words provided in localstorage in the text - */ - highlightSearchWords: () => { - if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight - - // get and clear terms from localstorage - const url = new URL(window.location); - const highlight = - localStorage.getItem("sphinx_highlight_terms") - || url.searchParams.get("highlight") - || ""; - localStorage.removeItem("sphinx_highlight_terms") - url.searchParams.delete("highlight"); - window.history.replaceState({}, "", url); - - // get individual terms from highlight string - const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); - if (terms.length === 0) return; // nothing to do - - // There should never be more than one element matching "div.body" - const divBody = document.querySelectorAll("div.body"); - const body = divBody.length ? divBody[0] : document.querySelector("body"); - window.setTimeout(() => { - terms.forEach((term) => _highlightText(body, term, "highlighted")); - }, 10); - - const searchBox = document.getElementById("searchbox"); - if (searchBox === null) return; - searchBox.appendChild( - document - .createRange() - .createContextualFragment( - '

' + - '' + - _("Hide Search Matches") + - "

" - ) - ); - }, - - /** - * helper function to hide the search marks again - */ - hideSearchWords: () => { - document - .querySelectorAll("#searchbox .highlight-link") - .forEach((el) => el.remove()); - document - .querySelectorAll("span.highlighted") - .forEach((el) => el.classList.remove("highlighted")); - localStorage.removeItem("sphinx_highlight_terms") - }, - - initEscapeListener: () => { - // only install a listener if it is really needed - if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; - - document.addEventListener("keydown", (event) => { - // bail for input elements - if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; - // bail with special keys - if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; - if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { - SphinxHighlight.hideSearchWords(); - event.preventDefault(); - } - }); - }, -}; - -_ready(() => { - /* Do not call highlightSearchWords() when we are on the search page. - * It will highlight words from the *previous* search query. - */ - if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); - SphinxHighlight.initEscapeListener(); -}); diff --git a/docs/0.4.0/autodoc/mmif.serialize.html b/docs/0.4.0/autodoc/mmif.serialize.html deleted file mode 100644 index 77650bca..00000000 --- a/docs/0.4.0/autodoc/mmif.serialize.html +++ /dev/null @@ -1,370 +0,0 @@ - - - - - - - - - mmif.serialize module — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.serialize module

-
-

mmif.serialize.model module

-
-
-

mmif.serialize.mmif module

-
-
-

mmif.serialize.view module

-
-
-

mmif.serialize.annotation module

-

The annotation module contains the classes used to represent a -MMIF annotation as a live Python object.

-

In MMIF, annotations are created by apps in a pipeline as a part -of a view. For documentation on how views are represented, see -mmif.serialize.view.

-
-
-class mmif.serialize.annotation.Annotation(anno_obj: bytes | str | dict | None = None)[source]
-

Bases: FreezableMmifObject

-

MmifObject that represents an annotation in a MMIF view.

-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]]) → None[source]
-

Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

-
- -
-
-property at_type: TypesBase[source]
-
- -
-
-property id: str[source]
-
- -
-
-is_document()[source]
-
- -
-
-is_type(at_type: str | TypesBase) → bool[source]
-

Check if the @type of this object matches.

-
- -
- -
-
-class mmif.serialize.annotation.AnnotationProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: FreezableMmifObject

-

AnnotationProperties object that represents the -properties object within a MMIF annotation.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
- -
-
-class mmif.serialize.annotation.Document(doc_obj: bytes | str | dict | None = None)[source]
-

Bases: Annotation

-

Document object that represents a single document in a MMIF file.

-

A document is identified by an ID, and contains certain attributes -and potentially contains the contents of the document itself, -metadata about how the document was created, and/or a list of -subdocuments grouped together logically.

-

If document_obj is not provided, an empty Document will be generated.

-
-
Parameters:
-

document_obj – the JSON data that defines the document

-
-
-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None]) → None[source]
-

Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

-
- -
-
-property location: str[source]
-
- -
-
-location_address() → str[source]
-
- -
-
-location_path() → str[source]
-
- -
-
-location_scheme() → str[source]
-
- -
-
-property parent: str[source]
-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.DocumentProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: AnnotationProperties

-

DocumentProperties object that represents the -properties object within a MMIF document.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
-
-property location: str[source]
-
- -
-
-location_address() → str[source]
-
- -
-
-location_path() → str[source]
-
- -
-
-location_scheme() → str[source]
-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.Text(text_obj: bytes | str | dict | None = None)[source]
-

Bases: FreezableMmifObject

-
-
-property lang: str[source]
-
- -
-
-property value: str[source]
-
- -
- -
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.4.0 - - -
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0.3.0
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0.3.1
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0.3.2
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0.3.3
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0.3.4
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- - - \ No newline at end of file diff --git a/docs/0.4.0/autodoc/mmif.vocabulary.html b/docs/0.4.0/autodoc/mmif.vocabulary.html deleted file mode 100644 index 825dd95c..00000000 --- a/docs/0.4.0/autodoc/mmif.vocabulary.html +++ /dev/null @@ -1,285 +0,0 @@ - - - - - - - - - mmif.vocabulary module — mmif-python documentation - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.vocabulary module

-
-

mmif.vocabulary.annotation_types module

-
-
-class mmif.vocabulary.annotation_types.AnnotationTypes(type_uri: str)[source]
-

Bases: AnnotationTypesBase

-

This class contains the CLAMS annotation types -defined in the spec version 0.4.2 as class variables.

-
-
-Alignment = http://mmif.clams.ai/0.4.2/vocabulary/Alignment[source]
-
- -
-
-Annotation = http://mmif.clams.ai/0.4.2/vocabulary/Annotation[source]
-
- -
-
-BoundingBox = http://mmif.clams.ai/0.4.2/vocabulary/BoundingBox[source]
-
- -
-
-Chapter = http://mmif.clams.ai/0.4.2/vocabulary/Chapter[source]
-
- -
-
-Interval = http://mmif.clams.ai/0.4.2/vocabulary/Interval[source]
-
- -
-
-Polygon = http://mmif.clams.ai/0.4.2/vocabulary/Polygon[source]
-
- -
-
-Region = http://mmif.clams.ai/0.4.2/vocabulary/Region[source]
-
- -
-
-Relation = http://mmif.clams.ai/0.4.2/vocabulary/Relation[source]
-
- -
-
-Span = http://mmif.clams.ai/0.4.2/vocabulary/Span[source]
-
- -
-
-TimeFrame = http://mmif.clams.ai/0.4.2/vocabulary/TimeFrame[source]
-
- -
-
-TimePoint = http://mmif.clams.ai/0.4.2/vocabulary/TimePoint[source]
-
- -
-
-VideoObject = http://mmif.clams.ai/0.4.2/vocabulary/VideoObject[source]
-
- -
- -
-
-

mmif.vocabulary.document_types module

-
-
-class mmif.vocabulary.document_types.DocumentTypes(type_uri: str)[source]
-

Bases: DocumentTypesBase

-

This class contains the CLAMS document types -defined in the spec version 0.4.2 as class variables.

-
-
-AudioDocument = http://mmif.clams.ai/0.4.2/vocabulary/AudioDocument[source]
-
- -
-
-Document = http://mmif.clams.ai/0.4.2/vocabulary/Document[source]
-
- -
-
-ImageDocument = http://mmif.clams.ai/0.4.2/vocabulary/ImageDocument[source]
-
- -
-
-TextDocument = http://mmif.clams.ai/0.4.2/vocabulary/TextDocument[source]
-
- -
-
-VideoDocument = http://mmif.clams.ai/0.4.2/vocabulary/VideoDocument[source]
-
- -
- -
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.4.0 - - -
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0.3.1
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- - - \ No newline at end of file diff --git a/docs/0.4.0/consumer-tutorial.html b/docs/0.4.0/consumer-tutorial.html deleted file mode 100644 index f94ef66d..00000000 --- a/docs/0.4.0/consumer-tutorial.html +++ /dev/null @@ -1,176 +0,0 @@ - - - - - - - - - MMIF consumer — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • MMIF consumer
    • -
  • -
    • -
-
-
-
-
- -
-

MMIF consumer

-

A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the appliance documentation to learn more about the appliance.

-

MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance.

-
    -

  1. The code must be hosted on a public git repository (e.g. Github, Gitlab, …)

    2. -

  2. Must listen to 5000 port.

    3. -

  3. Must expose /display route .

    4. -

  4. /display router should response to GET requests.

    5. -

  5. In the GET request, a public URL of the input MMIF file is passed via file URL parameter.

    6. -

  6. On the codebase root, there must be a Dockerfile that can build a docker image that runs the web app.

    7. -
-

We provide an example consumer at https://github.com/clamsproject/mmif-visualizer.

-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.4.0 - - -
-
- -
0.3.0
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0.3.1
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0.3.3
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0.3.4
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- - -
- -
-
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    -
    • -
  • Index
    • -
  • -
    • -
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- - -

Index

- -
- A - | B - | C - | D - | I - | L - | M - | P - | R - | S - | T - | V - -
-

A

- - - -
- -

B

- - -
- -

C

- - -
- -

D

- - - -
- -

I

- - - -
- -

L

- - - -
- -

M

- - - -
    -
  • - mmif.serialize.annotation - -
    • -
  • - mmif.vocabulary.annotation_types - -
    • -
  • - mmif.vocabulary.document_types - -
    • -
- -

P

- - - -
- -

R

- - - -
- -

S

- - -
- -

T

- - - -
- -

V

- - - -
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- - Other Versions - v: 0.4.0 - - -
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0.3.2
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0.3.3
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0.3.4
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0.4.1
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- - -
- -
-
-
-
    -
    • -
  • Welcome to mmif-python’s documentation!
    • -
  • -
    • -
-
-
-
-
- -
-

Welcome to mmif-python’s documentation!

-
-
-

MMIF for python

-

NOTE that this project is in pre-alpha and being actively developed. Nothing is guaranteed to reliably work for the moment and developer need to be very careful when using APIs implemented here. Please use the issue track to report bugs and malfunctions.

-
-

MultiMedia Interchange Format

-

MMIF is a JSON(-LD)-based data format designed for transferring annotation data between computational analysis applications in CLAMS project.

-
-

Contents

- -
-
-

API documentation:

- -
-
-
-
-

Indices and tables

- -
- - -
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- -
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- - Other Versions - v: 0.4.0 - - -
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- - - \ No newline at end of file diff --git a/docs/0.4.0/introduction.html b/docs/0.4.0/introduction.html deleted file mode 100644 index 2f56e8eb..00000000 --- a/docs/0.4.0/introduction.html +++ /dev/null @@ -1,236 +0,0 @@ - - - - - - - - - Getting Started — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
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  • Getting Started
    • -
  • -
    • -
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Getting Started

-
-

Overview

-

MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF wbesite. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports de-/serialization of MMIF objects, as well as many navigation and manipulation helpers for MMIF objects.

-
-
-

Prerequisites

-
    -

  • Python: mmif-python requires Python 3.6 or newer. We have no plan to support Python 2.7.

    • -
-
-
-

Installation

-

Package mmif-python is distributed via the official PyPI. Users are supposed to pip-install to get latest release.

-
pip install mmif-python
-
-
-

This will install a package mmif to local python.

-

The MMIF format and specification is evolving over time, and mmif-python package will be updated along with the changes in MMIF format.

-
-

Note

-

MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and mmif-python versions, please take time to read our decision on the subject here. If you need to know which python SDK supports which specification version, see Target MMIF Versions page.

-
-
-
-

MMIF Serialization

-

mmif.serialize.mmif.Mmif represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of mmif.serialize.model.MmifObject, including the mmif.serialize.mmif.Mmif. To start with an existing MMIF str, simple initiate a new Mmif object with the file.

-
import mmif
-from mmif import Mmif
-
-mmif_str = """{
-"metadata": {
-  "mmif": "http://mmif.clams.ai/0.2.0"
-},
-"documents": [
-  {
-    "@type": "http://mmif.clams.ai/0.2.0/vocabulary/VideoDocument",
-    "properties": {
-      "id": "m1",
-      "mime": "video/mp4",
-      "location": "file:///var/archive/video-0012.mp4"
-    }
-  },
-  {
-    "@type": "http://mmif.clams.ai/0.2.0/vocabulary/TextDocument",
-    "properties": {
-      "id": "m2",
-      "mime": "text/plain",
-      "location": "file:///var/archive/video-0012-transcript.txt"
-    }
-  }
-],
-"views": []}"""
-mmif_obj = Mmif(mmif_str)
-
-
-

Few notes;

-
    -

  1. MMIF does not carry the primary source files in it.

    2. -

  2. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version mmif-python implementation of the MMIF might not be able to load an unsupported version of MMIF string.

    3. -
-

When serializing back to str, call .serialize() (mmif.serialize.model.MmifObject.serialize()) on the object.

-

To get subcomponents, you can use various getters implemented in subclasses. For more details, the API documentation (mmif package) will help.

-
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.4.0 - - -
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0.3.0
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0.3.2
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0.3.3
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0.3.4
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- - - \ No newline at end of file diff --git a/docs/0.4.0/modules.html b/docs/0.4.0/modules.html deleted file mode 100644 index e90e11c9..00000000 --- a/docs/0.4.0/modules.html +++ /dev/null @@ -1,248 +0,0 @@ - - - - - - - - - mmif package — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
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  • mmif package
    • -
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mmif package

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- - - \ No newline at end of file diff --git a/docs/0.4.0/objects.inv b/docs/0.4.0/objects.inv deleted file mode 100644 index b1b1b9b5..00000000 --- a/docs/0.4.0/objects.inv +++ /dev/null @@ -1,9 +0,0 @@ -# Sphinx inventory version 2 -# Project: mmif-python -# Version: 0.4.0 -# The remainder of this file is compressed using zlib. -xڽ0y -WڽmV95F}>I I 1l9Ԡ'TnsBK#*? FܘSEB$Qd -hL&aU@ EYⅪ#(su)xc@ǧA|Xgs߇O#S}U3opgk|AUk=G8bĩHK'=קg OS`9/@ȯuBnM3H7IaWO`_r9 iv:8wlW;RQ}Gjtu/K0ˣ-026W R_zۂ.c9<(j#Rɖ"X;įncd~ʄöLQY~T}/Xj)Z0'[NIpCu7%o.M~ .m$ -y:X -m4ɵxC;C40SRL$p'wo~\ k - - - - - Python Module Index — mmif-python documentation - - - - - - - - - - - - - - - - - - -
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Python Module Index

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    - mmif.serialize.annotation -
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- - - \ No newline at end of file diff --git a/docs/0.4.0/search.html b/docs/0.4.0/search.html deleted file mode 100644 index 865a3ddf..00000000 --- a/docs/0.4.0/search.html +++ /dev/null @@ -1,177 +0,0 @@ - - - - - - - - Search — mmif-python documentation - - - - - - - - - - - - - - - - - - -
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- - - - - - - - \ No newline at end of file diff --git a/docs/0.4.0/searchindex.js b/docs/0.4.0/searchindex.js deleted file mode 100644 index 40529d6a..00000000 --- a/docs/0.4.0/searchindex.js +++ /dev/null @@ -1 +0,0 @@ -Search.setIndex({"alltitles": {"API documentation:": [[3, null]], "Contents": [[3, null]], "Getting Started": [[4, null]], "Indices and tables": [[3, "indices-and-tables"]], "Installation": [[4, "installation"]], "MMIF Serialization": [[4, "mmif-serialization"]], "MMIF consumer": [[2, null]], "MMIF for python": [[3, "mmif-for-python"]], "MultiMedia Interchange Format": [[3, "multimedia-interchange-format"]], "Overview": [[4, "overview"]], "Prerequisites": [[4, "prerequisites"]], "Target MMIF Versions": [[6, null]], "Target Specification Versions": [[6, "id1"]], "Welcome to mmif-python\u2019s documentation!": [[3, null]], "mmif package": [[5, null]], "mmif.serialize module": [[0, null]], "mmif.serialize.annotation module": [[0, "module-mmif.serialize.annotation"]], 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"modul": [0, 1], "multimedia": 3, "overview": 4, "packag": 5, "prerequisit": 4, "python": 3, "serial": [0, 4], "specif": 6, "start": 4, "tabl": 3, "target": 6, "version": 6, "view": 0, "vocabulari": 1, "welcom": 3}}) \ No newline at end of file diff --git a/docs/0.4.0/target-versions.html b/docs/0.4.0/target-versions.html deleted file mode 100644 index 0685ebcb..00000000 --- a/docs/0.4.0/target-versions.html +++ /dev/null @@ -1,206 +0,0 @@ - - - - - - - - - Target MMIF Versions — mmif-python documentation - - - - - - - - - - - - - - - - - -
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Target MMIF Versions

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This article provides targeting MMIF specification versions of different versions of mmif-python SDK.

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Target Specification Versions

mmif-python version

Target MMIF Specification

0.4.0

0.4.0

0.3.5

0.3.1

0.3.4

0.3.1

0.3.3

0.3.1

0.3.2

0.3.1

0.3.1

0.3.0

0.3.0

0.3.0

0.2.2

0.2.1

0.2.1

0.2.1

0.2.0

0.2.1

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The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the `appliance documentation `_ to learn more about the appliance. - -MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance. - -#. The code must be hosted on a public git repository (e.g. Github, Gitlab, ...) -#. Must listen to ``5000`` port. -#. Must expose ``/display`` route . -#. ``/display`` router should response to ``GET`` requests. -#. In the ``GET`` request, a public URL of the input MMIF file is passed via ``file`` URL parameter. -#. On the codebase root, there must be a ``Dockerfile`` that can build a `docker `_ image that runs the web app. - -We provide an example consumer at https://github.com/clamsproject/mmif-visualizer. diff --git a/docs/0.4.1/_sources/index.rst.txt b/docs/0.4.1/_sources/index.rst.txt deleted file mode 100644 index 9b90b38e..00000000 --- a/docs/0.4.1/_sources/index.rst.txt +++ /dev/null @@ -1,26 +0,0 @@ -Welcome to mmif-python's documentation! -======================================= - -.. mdinclude:: ../README.md - -.. toctree:: - :maxdepth: 2 - :caption: Contents - - introduction - target-versions - consumer-tutorial - -.. toctree:: - :maxdepth: 2 - :caption: API documentation: - - modules - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/docs/0.4.1/_sources/introduction.rst.txt b/docs/0.4.1/_sources/introduction.rst.txt deleted file mode 100644 index 6fea3a3c..00000000 --- a/docs/0.4.1/_sources/introduction.rst.txt +++ /dev/null @@ -1,78 +0,0 @@ -.. _instroduction: - -Getting Started -=============== - - -Overview ---------- - -MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF wbesite `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports de-/serialization of MMIF objects, as well as many navigation and manipulation helpers for MMIF objects. - -Prerequisites -------------- - -* `Python `_: ``mmif-python`` requires Python 3.6 or newer. We have no plan to support `Python 2.7 `_. - -Installation ---------------- - -Package ``mmif-python`` is distributed via the official PyPI. Users are supposed to pip-install to get latest release. - -.. code-block:: bash - - pip install mmif-python - -This will install a package `mmif` to local python. - -The MMIF format and specification is evolving over time, and ``mmif-python`` package will be updated along with the changes in MMIF format. - -.. note:: MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and ``mmif-python`` versions, please take time to read our decision on the subject `here `_. If you need to know which python SDK supports which specification version, see :ref:`target-versions` page. - -MMIF Serialization ---------------------------- - -:class:`mmif.serialize.mmif.Mmif` represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of :class:`mmif.serialize.model.MmifObject`, including the :class:`mmif.serialize.mmif.Mmif`. To start with an existing MMIF :class:`str`, simple initiate a new ``Mmif`` object with the file. - -.. code-block:: python - - import mmif - from mmif import Mmif - - mmif_str = """{ - "metadata": { - "mmif": "http://mmif.clams.ai/0.2.0" - }, - "documents": [ - { - "@type": "http://mmif.clams.ai/0.2.0/vocabulary/VideoDocument", - "properties": { - "id": "m1", - "mime": "video/mp4", - "location": "file:///var/archive/video-0012.mp4" - } - }, - { - "@type": "http://mmif.clams.ai/0.2.0/vocabulary/TextDocument", - "properties": { - "id": "m2", - "mime": "text/plain", - "location": "file:///var/archive/video-0012-transcript.txt" - } - } - ], - "views": []}""" - mmif_obj = Mmif(mmif_str) - - -Few notes; - -#. MMIF does not carry the primary source files in it. -#. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version ``mmif-python`` implementation of the MMIF might not be able to load an unsupported version of MMIF string. - -When serializing back to :class:`str`, call ``.serialize()`` (:meth:`mmif.serialize.model.MmifObject.serialize`) on the object. - -To get subcomponents, you can use various getters implemented in subclasses. For more details, the API documentation (:ref:`apidoc`) will help. - diff --git a/docs/0.4.1/_sources/modules.rst.txt b/docs/0.4.1/_sources/modules.rst.txt deleted file mode 100644 index e4269c6d..00000000 --- a/docs/0.4.1/_sources/modules.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _apidoc: - -mmif package -============ - -.. toctree:: - :maxdepth: 4 - - autodoc/mmif.serialize - autodoc/mmif.vocabulary diff --git a/docs/0.4.1/_sources/target-versions.rst.txt b/docs/0.4.1/_sources/target-versions.rst.txt deleted file mode 100644 index 34216d3e..00000000 --- a/docs/0.4.1/_sources/target-versions.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _target-versions: - -Target MMIF Versions -==================== - -This article provides targeting MMIF specification versions of different versions of ``mmif-python`` SDK. - -.. csv-table:: Target Specification Versions - :file: target-versions.csv - :header-rows: 1 diff --git a/docs/0.4.1/_static/_sphinx_javascript_frameworks_compat.js b/docs/0.4.1/_static/_sphinx_javascript_frameworks_compat.js deleted file mode 100644 index 81415803..00000000 --- a/docs/0.4.1/_static/_sphinx_javascript_frameworks_compat.js +++ /dev/null @@ -1,123 +0,0 @@ -/* Compatability shim for jQuery and underscores.js. - * - * Copyright Sphinx contributors - * Released under the two clause BSD licence - */ - -/** - * small helper function to urldecode strings - * - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL - */ -jQuery.urldecode = function(x) { - if (!x) { - return x - } - return decodeURIComponent(x.replace(/\+/g, ' ')); -}; - -/** - * small helper function to urlencode strings - */ -jQuery.urlencode = encodeURIComponent; - -/** - * This function returns the parsed url parameters of the - * current request. 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- -/** - * Simple result scoring code. - */ -if (typeof Scorer === "undefined") { - var Scorer = { - // Implement the following function to further tweak the score for each result - // The function takes a result array [docname, title, anchor, descr, score, filename] - // and returns the new score. - /* - score: result => { - const [docname, title, anchor, descr, score, filename, kind] = result - return score - }, - */ - - // query matches the full name of an object - objNameMatch: 11, - // or matches in the last dotted part of the object name - objPartialMatch: 6, - // Additive scores depending on the priority of the object - objPrio: { - 0: 15, // used to be importantResults - 1: 5, // used to be objectResults - 2: -5, // used to be unimportantResults - }, - // Used when the priority is not in the mapping. - objPrioDefault: 0, - - // query found in title - title: 15, - partialTitle: 7, - // query found in terms - term: 5, - partialTerm: 2, - }; -} - -// Global search result kind enum, used by themes to style search results. -class SearchResultKind { - static get index() { return "index"; } - static get object() { return "object"; } - static get text() { return "text"; } - static get title() { return "title"; } -} - -const _removeChildren = (element) => { - while (element && element.lastChild) element.removeChild(element.lastChild); -}; - -/** - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping - */ -const _escapeRegExp = (string) => - string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string - -const _displayItem = (item, searchTerms, highlightTerms) => { - const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; - const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; - const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; - const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; - const contentRoot = document.documentElement.dataset.content_root; - - const [docName, title, anchor, descr, score, _filename, kind] = item; - - let listItem = document.createElement("li"); - // Add a class representing the item's type: - // can be used by a theme's CSS selector for styling - // See SearchResultKind for the class names. - listItem.classList.add(`kind-${kind}`); - let requestUrl; - let linkUrl; - if (docBuilder === "dirhtml") { - // dirhtml builder - let dirname = docName + "/"; - if (dirname.match(/\/index\/$/)) - dirname = dirname.substring(0, dirname.length - 6); - else if (dirname === "index/") dirname = ""; - requestUrl = contentRoot + dirname; - linkUrl = requestUrl; - } else { - // normal html builders - requestUrl = contentRoot + docName + docFileSuffix; - linkUrl = docName + docLinkSuffix; - } - let linkEl = listItem.appendChild(document.createElement("a")); - linkEl.href = linkUrl + anchor; - linkEl.dataset.score = score; - linkEl.innerHTML = title; - if (descr) { - listItem.appendChild(document.createElement("span")).innerHTML = - " (" + descr + ")"; - // highlight search terms in the description - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - } - else if (showSearchSummary) - fetch(requestUrl) - .then((responseData) => responseData.text()) - .then((data) => { - if (data) - listItem.appendChild( - Search.makeSearchSummary(data, searchTerms, anchor) - ); - // highlight search terms in the summary - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - }); - Search.output.appendChild(listItem); -}; -const _finishSearch = (resultCount) => { - Search.stopPulse(); - Search.title.innerText = _("Search Results"); - if (!resultCount) - Search.status.innerText = Documentation.gettext( - "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." - ); - else - Search.status.innerText = Documentation.ngettext( - "Search finished, found one page matching the search query.", - "Search finished, found ${resultCount} pages matching the search query.", - resultCount, - ).replace('${resultCount}', resultCount); -}; -const _displayNextItem = ( - results, - resultCount, - searchTerms, - highlightTerms, -) => { - // results left, load the summary and display it - // this is intended to be dynamic (don't sub resultsCount) - if (results.length) { - _displayItem(results.pop(), searchTerms, highlightTerms); - setTimeout( - () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), - 5 - ); - } - // search finished, update title and status message - else _finishSearch(resultCount); -}; -// Helper function used by query() to order search results. -// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. -// Order the results by score (in opposite order of appearance, since the -// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. -const _orderResultsByScoreThenName = (a, b) => { - const leftScore = a[4]; - const rightScore = b[4]; - if (leftScore === rightScore) { - // same score: sort alphabetically - const leftTitle = a[1].toLowerCase(); - const rightTitle = b[1].toLowerCase(); - if (leftTitle === rightTitle) return 0; - return leftTitle > rightTitle ? -1 : 1; // inverted is intentional - } - return leftScore > rightScore ? 1 : -1; -}; - -/** - * Default splitQuery function. Can be overridden in ``sphinx.search`` with a - * custom function per language. - * - * The regular expression works by splitting the string on consecutive characters - * that are not Unicode letters, numbers, underscores, or emoji characters. - * This is the same as ``\W+`` in Python, preserving the surrogate pair area. - */ -if (typeof splitQuery === "undefined") { - var splitQuery = (query) => query - .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) - .filter(term => term) // remove remaining empty strings -} - -/** - * Search Module - */ -const Search = { - _index: null, - _queued_query: null, - _pulse_status: -1, - - htmlToText: (htmlString, anchor) => { - const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - for (const removalQuery of [".headerlink", "script", "style"]) { - htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); - } - if (anchor) { - const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); - if (anchorContent) return anchorContent.textContent; - - console.warn( - `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` - ); - } - - // if anchor not specified or not found, fall back to main content - const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent) return docContent.textContent; - - console.warn( - "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." - ); - return ""; - }, - - init: () => { - const query = new URLSearchParams(window.location.search).get("q"); - document - .querySelectorAll('input[name="q"]') - .forEach((el) => (el.value = query)); - if (query) Search.performSearch(query); - }, - - loadIndex: (url) => - (document.body.appendChild(document.createElement("script")).src = url), - - setIndex: (index) => { - Search._index = index; - if (Search._queued_query !== null) { - const query = Search._queued_query; - Search._queued_query = null; - Search.query(query); - } - }, - - hasIndex: () => Search._index !== null, - - deferQuery: (query) => (Search._queued_query = query), - - stopPulse: () => (Search._pulse_status = -1), - - startPulse: () => { - if (Search._pulse_status >= 0) return; - - const pulse = () => { - Search._pulse_status = (Search._pulse_status + 1) % 4; - Search.dots.innerText = ".".repeat(Search._pulse_status); - if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); - }; - pulse(); - }, - - /** - * perform a search for something (or wait until index is loaded) - */ - performSearch: (query) => { - // create the required interface elements - const searchText = document.createElement("h2"); - searchText.textContent = _("Searching"); - const searchSummary = document.createElement("p"); - searchSummary.classList.add("search-summary"); - searchSummary.innerText = ""; - const searchList = document.createElement("ul"); - searchList.setAttribute("role", "list"); - searchList.classList.add("search"); - - const out = document.getElementById("search-results"); - Search.title = out.appendChild(searchText); - Search.dots = Search.title.appendChild(document.createElement("span")); - Search.status = out.appendChild(searchSummary); - Search.output = out.appendChild(searchList); - - const searchProgress = document.getElementById("search-progress"); - // Some themes don't use the search progress node - if (searchProgress) { - searchProgress.innerText = _("Preparing search..."); - } - Search.startPulse(); - - // index already loaded, the browser was quick! - if (Search.hasIndex()) Search.query(query); - else Search.deferQuery(query); - }, - - _parseQuery: (query) => { - // stem the search terms and add them to the correct list - const stemmer = new Stemmer(); - const searchTerms = new Set(); - const excludedTerms = new Set(); - const highlightTerms = new Set(); - const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); - splitQuery(query.trim()).forEach((queryTerm) => { - const queryTermLower = queryTerm.toLowerCase(); - - // maybe skip this "word" - // stopwords array is from language_data.js - if ( - stopwords.indexOf(queryTermLower) !== -1 || - queryTerm.match(/^\d+$/) - ) - return; - - // stem the word - let word = stemmer.stemWord(queryTermLower); - // select the correct list - if (word[0] === "-") excludedTerms.add(word.substr(1)); - else { - searchTerms.add(word); - highlightTerms.add(queryTermLower); - } - }); - - if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js - localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) - } - - // console.debug("SEARCH: searching for:"); - // console.info("required: ", [...searchTerms]); - // console.info("excluded: ", [...excludedTerms]); - - return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; - }, - - /** - * execute search (requires search index to be loaded) - */ - _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - - // Collect multiple result groups to be sorted separately and then ordered. - // Each is an array of [docname, title, anchor, descr, score, filename, kind]. - const normalResults = []; - const nonMainIndexResults = []; - - _removeChildren(document.getElementById("search-progress")); - - const queryLower = query.toLowerCase().trim(); - for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { - for (const [file, id] of foundTitles) { - const score = Math.round(Scorer.title * queryLower.length / title.length); - const boost = titles[file] === title ? 1 : 0; // add a boost for document titles - normalResults.push([ - docNames[file], - titles[file] !== title ? `${titles[file]} > ${title}` : title, - id !== null ? "#" + id : "", - null, - score + boost, - filenames[file], - SearchResultKind.title, - ]); - } - } - } - - // search for explicit entries in index directives - for (const [entry, foundEntries] of Object.entries(indexEntries)) { - if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id, isMain] of foundEntries) { - const score = Math.round(100 * queryLower.length / entry.length); - const result = [ - docNames[file], - titles[file], - id ? "#" + id : "", - null, - score, - filenames[file], - SearchResultKind.index, - ]; - if (isMain) { - normalResults.push(result); - } else { - nonMainIndexResults.push(result); - } - } - } - } - - // lookup as object - objectTerms.forEach((term) => - normalResults.push(...Search.performObjectSearch(term, objectTerms)) - ); - - // lookup as search terms in fulltext - normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); - - // let the scorer override scores with a custom scoring function - if (Scorer.score) { - normalResults.forEach((item) => (item[4] = Scorer.score(item))); - nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); - } - - // Sort each group of results by score and then alphabetically by name. - normalResults.sort(_orderResultsByScoreThenName); - nonMainIndexResults.sort(_orderResultsByScoreThenName); - - // Combine the result groups in (reverse) order. - // Non-main index entries are typically arbitrary cross-references, - // so display them after other results. - let results = [...nonMainIndexResults, ...normalResults]; - - // remove duplicate search results - // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept - let seen = new Set(); - results = results.reverse().reduce((acc, result) => { - let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); - if (!seen.has(resultStr)) { - acc.push(result); - seen.add(resultStr); - } - return acc; - }, []); - - return results.reverse(); - }, - - query: (query) => { - const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); - const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); - - // for debugging - //Search.lastresults = results.slice(); // a copy - // console.info("search results:", Search.lastresults); - - // print the results - _displayNextItem(results, results.length, searchTerms, highlightTerms); - }, - - /** - * search for object names - */ - performObjectSearch: (object, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const objects = Search._index.objects; - const objNames = Search._index.objnames; - const titles = Search._index.titles; - - const results = []; - - const objectSearchCallback = (prefix, match) => { - const name = match[4] - const fullname = (prefix ? prefix + "." : "") + name; - const fullnameLower = fullname.toLowerCase(); - if (fullnameLower.indexOf(object) < 0) return; - - let score = 0; - const parts = fullnameLower.split("."); - - // check for different match types: exact matches of full name or - // "last name" (i.e. last dotted part) - if (fullnameLower === object || parts.slice(-1)[0] === object) - score += Scorer.objNameMatch; - else if (parts.slice(-1)[0].indexOf(object) > -1) - score += Scorer.objPartialMatch; // matches in last name - - const objName = objNames[match[1]][2]; - const title = titles[match[0]]; - - // If more than one term searched for, we require other words to be - // found in the name/title/description - const otherTerms = new Set(objectTerms); - otherTerms.delete(object); - if (otherTerms.size > 0) { - const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); - if ( - [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) - ) - return; - } - - let anchor = match[3]; - if (anchor === "") anchor = fullname; - else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; - - const descr = objName + _(", in ") + title; - - // add custom score for some objects according to scorer - if (Scorer.objPrio.hasOwnProperty(match[2])) - score += Scorer.objPrio[match[2]]; - else score += Scorer.objPrioDefault; - - results.push([ - docNames[match[0]], - fullname, - "#" + anchor, - descr, - score, - filenames[match[0]], - SearchResultKind.object, - ]); - }; - Object.keys(objects).forEach((prefix) => - objects[prefix].forEach((array) => - objectSearchCallback(prefix, array) - ) - ); - return results; - }, - - /** - * search for full-text terms in the index - */ - performTermsSearch: (searchTerms, excludedTerms) => { - // prepare search - const terms = Search._index.terms; - const titleTerms = Search._index.titleterms; - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - - const scoreMap = new Map(); - const fileMap = new Map(); - - // perform the search on the required terms - searchTerms.forEach((word) => { - const files = []; - const arr = [ - { files: terms[word], score: Scorer.term }, - { files: titleTerms[word], score: Scorer.title }, - ]; - // add support for partial matches - if (word.length > 2) { - const escapedWord = _escapeRegExp(word); - if (!terms.hasOwnProperty(word)) { - Object.keys(terms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: terms[term], score: Scorer.partialTerm }); - }); - } - if (!titleTerms.hasOwnProperty(word)) { - Object.keys(titleTerms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); - }); - } - } - - // no match but word was a required one - if (arr.every((record) => record.files === undefined)) return; - - // found search word in contents - arr.forEach((record) => { - if (record.files === undefined) return; - - let recordFiles = record.files; - if (recordFiles.length === undefined) recordFiles = [recordFiles]; - files.push(...recordFiles); - - // set score for the word in each file - recordFiles.forEach((file) => { - if (!scoreMap.has(file)) scoreMap.set(file, {}); - scoreMap.get(file)[word] = record.score; - }); - }); - - // create the mapping - files.forEach((file) => { - if (!fileMap.has(file)) fileMap.set(file, [word]); - else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); - }); - }); - - // now check if the files don't contain excluded terms - const results = []; - for (const [file, wordList] of fileMap) { - // check if all requirements are matched - - // as search terms with length < 3 are discarded - const filteredTermCount = [...searchTerms].filter( - (term) => term.length > 2 - ).length; - if ( - wordList.length !== searchTerms.size && - wordList.length !== filteredTermCount - ) - continue; - - // ensure that none of the excluded terms is in the search result - if ( - [...excludedTerms].some( - (term) => - terms[term] === file || - titleTerms[term] === file || - (terms[term] || []).includes(file) || - (titleTerms[term] || []).includes(file) - ) - ) - break; - - // select one (max) score for the file. - const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); - // add result to the result list - results.push([ - docNames[file], - titles[file], - "", - null, - score, - filenames[file], - SearchResultKind.text, - ]); - } - return results; - }, - - /** - * helper function to return a node containing the - * search summary for a given text. keywords is a list - * of stemmed words. - */ - makeSearchSummary: (htmlText, keywords, anchor) => { - const text = Search.htmlToText(htmlText, anchor); - if (text === "") return null; - - const textLower = text.toLowerCase(); - const actualStartPosition = [...keywords] - .map((k) => textLower.indexOf(k.toLowerCase())) - .filter((i) => i > -1) - .slice(-1)[0]; - const startWithContext = Math.max(actualStartPosition - 120, 0); - - const top = startWithContext === 0 ? "" : "..."; - const tail = startWithContext + 240 < text.length ? "..." : ""; - - let summary = document.createElement("p"); - summary.classList.add("context"); - summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; - - return summary; - }, -}; - -_ready(Search.init); diff --git a/docs/0.4.1/_static/sphinx_highlight.js b/docs/0.4.1/_static/sphinx_highlight.js deleted file mode 100644 index 8a96c69a..00000000 --- a/docs/0.4.1/_static/sphinx_highlight.js +++ /dev/null @@ -1,154 +0,0 @@ -/* Highlighting utilities for Sphinx HTML documentation. */ -"use strict"; - -const SPHINX_HIGHLIGHT_ENABLED = true - -/** - * highlight a given string on a node by wrapping it in - * span elements with the given class name. - */ -const _highlight = (node, addItems, text, className) => { - if (node.nodeType === Node.TEXT_NODE) { - const val = node.nodeValue; - const parent = node.parentNode; - const pos = val.toLowerCase().indexOf(text); - if ( - pos >= 0 && - !parent.classList.contains(className) && - !parent.classList.contains("nohighlight") - ) { - let span; - - const closestNode = parent.closest("body, svg, foreignObject"); - const isInSVG = closestNode && closestNode.matches("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.classList.add(className); - } - - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - const rest = document.createTextNode(val.substr(pos + text.length)); - parent.insertBefore( - span, - parent.insertBefore( - rest, - node.nextSibling - ) - ); - node.nodeValue = val.substr(0, pos); - /* There may be more occurrences of search term in this node. So call this - * function recursively on the remaining fragment. - */ - _highlight(rest, addItems, text, className); - - if (isInSVG) { - const rect = document.createElementNS( - "http://www.w3.org/2000/svg", - "rect" - ); - const bbox = parent.getBBox(); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute("class", className); - addItems.push({ parent: parent, target: rect }); - } - } - } else if (node.matches && !node.matches("button, select, textarea")) { - node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); - } -}; -const _highlightText = (thisNode, text, className) => { - let addItems = []; - _highlight(thisNode, addItems, text, className); - addItems.forEach((obj) => - obj.parent.insertAdjacentElement("beforebegin", obj.target) - ); -}; - -/** - * Small JavaScript module for the documentation. - */ -const SphinxHighlight = { - - /** - * highlight the search words provided in localstorage in the text - */ - highlightSearchWords: () => { - if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight - - // get and clear terms from localstorage - const url = new URL(window.location); - const highlight = - localStorage.getItem("sphinx_highlight_terms") - || url.searchParams.get("highlight") - || ""; - localStorage.removeItem("sphinx_highlight_terms") - url.searchParams.delete("highlight"); - window.history.replaceState({}, "", url); - - // get individual terms from highlight string - const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); - if (terms.length === 0) return; // nothing to do - - // There should never be more than one element matching "div.body" - const divBody = document.querySelectorAll("div.body"); - const body = divBody.length ? divBody[0] : document.querySelector("body"); - window.setTimeout(() => { - terms.forEach((term) => _highlightText(body, term, "highlighted")); - }, 10); - - const searchBox = document.getElementById("searchbox"); - if (searchBox === null) return; - searchBox.appendChild( - document - .createRange() - .createContextualFragment( - '

' + - '' + - _("Hide Search Matches") + - "

" - ) - ); - }, - - /** - * helper function to hide the search marks again - */ - hideSearchWords: () => { - document - .querySelectorAll("#searchbox .highlight-link") - .forEach((el) => el.remove()); - document - .querySelectorAll("span.highlighted") - .forEach((el) => el.classList.remove("highlighted")); - localStorage.removeItem("sphinx_highlight_terms") - }, - - initEscapeListener: () => { - // only install a listener if it is really needed - if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; - - document.addEventListener("keydown", (event) => { - // bail for input elements - if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; - // bail with special keys - if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; - if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { - SphinxHighlight.hideSearchWords(); - event.preventDefault(); - } - }); - }, -}; - -_ready(() => { - /* Do not call highlightSearchWords() when we are on the search page. - * It will highlight words from the *previous* search query. - */ - if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); - SphinxHighlight.initEscapeListener(); -}); diff --git a/docs/0.4.1/autodoc/mmif.serialize.html b/docs/0.4.1/autodoc/mmif.serialize.html deleted file mode 100644 index 4223b2f1..00000000 --- a/docs/0.4.1/autodoc/mmif.serialize.html +++ /dev/null @@ -1,370 +0,0 @@ - - - - - - - - - mmif.serialize module — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.serialize module

-
-

mmif.serialize.model module

-
-
-

mmif.serialize.mmif module

-
-
-

mmif.serialize.view module

-
-
-

mmif.serialize.annotation module

-

The annotation module contains the classes used to represent a -MMIF annotation as a live Python object.

-

In MMIF, annotations are created by apps in a pipeline as a part -of a view. For documentation on how views are represented, see -mmif.serialize.view.

-
-
-class mmif.serialize.annotation.Annotation(anno_obj: bytes | str | dict | None = None)[source]
-

Bases: FreezableMmifObject

-

MmifObject that represents an annotation in a MMIF view.

-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]]) → None[source]
-

Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

-
- -
-
-property at_type: TypesBase[source]
-
- -
-
-property id: str[source]
-
- -
-
-is_document()[source]
-
- -
-
-is_type(at_type: str | TypesBase) → bool[source]
-

Check if the @type of this object matches.

-
- -
- -
-
-class mmif.serialize.annotation.AnnotationProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: FreezableMmifObject

-

AnnotationProperties object that represents the -properties object within a MMIF annotation.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
- -
-
-class mmif.serialize.annotation.Document(doc_obj: bytes | str | dict | None = None)[source]
-

Bases: Annotation

-

Document object that represents a single document in a MMIF file.

-

A document is identified by an ID, and contains certain attributes -and potentially contains the contents of the document itself, -metadata about how the document was created, and/or a list of -subdocuments grouped together logically.

-

If document_obj is not provided, an empty Document will be generated.

-
-
Parameters:
-

document_obj – the JSON data that defines the document

-
-
-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None]) → None[source]
-

Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

-
- -
-
-property location: str[source]
-
- -
-
-location_address() → str[source]
-
- -
-
-location_path() → str[source]
-
- -
-
-location_scheme() → str[source]
-
- -
-
-property parent: str[source]
-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.DocumentProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: AnnotationProperties

-

DocumentProperties object that represents the -properties object within a MMIF document.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
-
-property location: str[source]
-
- -
-
-location_address() → str[source]
-
- -
-
-location_path() → str[source]
-
- -
-
-location_scheme() → str[source]
-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.Text(text_obj: bytes | str | dict | None = None)[source]
-

Bases: FreezableMmifObject

-
-
-property lang: str[source]
-
- -
-
-property value: str[source]
-
- -
- -
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.4.1 - - -
-
- -
0.3.0
-
0.3.1
-
0.3.2
-
0.3.3
-
0.3.4
-
0.3.5
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-
- - - \ No newline at end of file diff --git a/docs/0.4.1/autodoc/mmif.vocabulary.html b/docs/0.4.1/autodoc/mmif.vocabulary.html deleted file mode 100644 index cfa8638f..00000000 --- a/docs/0.4.1/autodoc/mmif.vocabulary.html +++ /dev/null @@ -1,285 +0,0 @@ - - - - - - - - - mmif.vocabulary module — mmif-python documentation - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.vocabulary module

-
-

mmif.vocabulary.annotation_types module

-
-
-class mmif.vocabulary.annotation_types.AnnotationTypes(type_uri: str)[source]
-

Bases: AnnotationTypesBase

-

This class contains the CLAMS annotation types -defined in the spec version 0.4.2 as class variables.

-
-
-Alignment = http://mmif.clams.ai/0.4.2/vocabulary/Alignment[source]
-
- -
-
-Annotation = http://mmif.clams.ai/0.4.2/vocabulary/Annotation[source]
-
- -
-
-BoundingBox = http://mmif.clams.ai/0.4.2/vocabulary/BoundingBox[source]
-
- -
-
-Chapter = http://mmif.clams.ai/0.4.2/vocabulary/Chapter[source]
-
- -
-
-Interval = http://mmif.clams.ai/0.4.2/vocabulary/Interval[source]
-
- -
-
-Polygon = http://mmif.clams.ai/0.4.2/vocabulary/Polygon[source]
-
- -
-
-Region = http://mmif.clams.ai/0.4.2/vocabulary/Region[source]
-
- -
-
-Relation = http://mmif.clams.ai/0.4.2/vocabulary/Relation[source]
-
- -
-
-Span = http://mmif.clams.ai/0.4.2/vocabulary/Span[source]
-
- -
-
-TimeFrame = http://mmif.clams.ai/0.4.2/vocabulary/TimeFrame[source]
-
- -
-
-TimePoint = http://mmif.clams.ai/0.4.2/vocabulary/TimePoint[source]
-
- -
-
-VideoObject = http://mmif.clams.ai/0.4.2/vocabulary/VideoObject[source]
-
- -
- -
-
-

mmif.vocabulary.document_types module

-
-
-class mmif.vocabulary.document_types.DocumentTypes(type_uri: str)[source]
-

Bases: DocumentTypesBase

-

This class contains the CLAMS document types -defined in the spec version 0.4.2 as class variables.

-
-
-AudioDocument = http://mmif.clams.ai/0.4.2/vocabulary/AudioDocument[source]
-
- -
-
-Document = http://mmif.clams.ai/0.4.2/vocabulary/Document[source]
-
- -
-
-ImageDocument = http://mmif.clams.ai/0.4.2/vocabulary/ImageDocument[source]
-
- -
-
-TextDocument = http://mmif.clams.ai/0.4.2/vocabulary/TextDocument[source]
-
- -
-
-VideoDocument = http://mmif.clams.ai/0.4.2/vocabulary/VideoDocument[source]
-
- -
- -
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.4.1 - - -
-
- -
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0.4.5
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0.4.8
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- - - \ No newline at end of file diff --git a/docs/0.4.1/consumer-tutorial.html b/docs/0.4.1/consumer-tutorial.html deleted file mode 100644 index ba3b49a5..00000000 --- a/docs/0.4.1/consumer-tutorial.html +++ /dev/null @@ -1,176 +0,0 @@ - - - - - - - - - MMIF consumer — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • MMIF consumer
    • -
  • -
    • -
-
-
-
-
- -
-

MMIF consumer

-

A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the appliance documentation to learn more about the appliance.

-

MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance.

-
    -

  1. The code must be hosted on a public git repository (e.g. Github, Gitlab, …)

    2. -

  2. Must listen to 5000 port.

    3. -

  3. Must expose /display route .

    4. -

  4. /display router should response to GET requests.

    5. -

  5. In the GET request, a public URL of the input MMIF file is passed via file URL parameter.

    6. -

  6. On the codebase root, there must be a Dockerfile that can build a docker image that runs the web app.

    7. -
-

We provide an example consumer at https://github.com/clamsproject/mmif-visualizer.

-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.4.1 - - -
-
- -
0.3.0
-
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-
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-
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-
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- - - \ No newline at end of file diff --git a/docs/0.4.1/genindex.html b/docs/0.4.1/genindex.html deleted file mode 100644 index 49f76d50..00000000 --- a/docs/0.4.1/genindex.html +++ /dev/null @@ -1,404 +0,0 @@ - - - - - - - - Index — mmif-python documentation - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • Index
    • -
  • -
    • -
-
-
-
-
- - -

Index

- -
- A - | B - | C - | D - | I - | L - | M - | P - | R - | S - | T - | V - -
-

A

- - - -
- -

B

- - -
- -

C

- - -
- -

D

- - - -
- -

I

- - - -
- -

L

- - - -
- -

M

- - - -
    -
  • - mmif.serialize.annotation - -
    • -
  • - mmif.vocabulary.annotation_types - -
    • -
  • - mmif.vocabulary.document_types - -
    • -
- -

P

- - - -
- -

R

- - - -
- -

S

- - -
- -

T

- - - -
- -

V

- - - -
- - - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.4.1 - - -
-
- -
0.3.0
-
0.3.1
-
0.3.2
-
0.3.3
-
0.3.4
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0.3.5
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0.4.0
-
0.4.1
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0.4.2
-
0.4.3
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0.4.4
-
0.4.5
-
0.4.6
-
0.4.7
-
0.4.8
-
0.5.0
-
0.5.1
-
0.5.2
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1.0.0
-
1.0.1
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1.0.10
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1.0.11
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1.0.12
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1.0.13
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1.0.14
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1.0.15
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1.0.16
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- - - \ No newline at end of file diff --git a/docs/0.4.1/index.html b/docs/0.4.1/index.html deleted file mode 100644 index e20f67e5..00000000 --- a/docs/0.4.1/index.html +++ /dev/null @@ -1,203 +0,0 @@ - - - - - - - - - Welcome to mmif-python’s documentation! — mmif-python documentation - - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • Welcome to mmif-python’s documentation!
    • -
  • -
    • -
-
-
-
-
- -
-

Welcome to mmif-python’s documentation!

-
-
-

MMIF for python

-

NOTE that this project is in pre-alpha and being actively developed. Nothing is guaranteed to reliably work for the moment and developer need to be very careful when using APIs implemented here. Please use the issue track to report bugs and malfunctions.

-
-

MultiMedia Interchange Format

-

MMIF is a JSON(-LD)-based data format designed for transferring annotation data between computational analysis applications in CLAMS project.

-
-

Contents

- -
-
-

API documentation:

- -
-
-
-
-

Indices and tables

- -
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.4.1 - - -
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- -
0.3.0
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0.3.1
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0.3.2
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0.3.3
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0.3.4
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0.3.5
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0.4.0
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0.4.1
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0.4.2
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0.4.3
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0.4.4
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0.4.5
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0.4.6
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0.4.7
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0.4.8
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0.5.0
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0.5.1
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0.5.2
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1.0.0
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1.0.1
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1.0.10
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1.0.11
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1.0.12
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- - - \ No newline at end of file diff --git a/docs/0.4.1/introduction.html b/docs/0.4.1/introduction.html deleted file mode 100644 index 6abb060d..00000000 --- a/docs/0.4.1/introduction.html +++ /dev/null @@ -1,236 +0,0 @@ - - - - - - - - - Getting Started — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • Getting Started
    • -
  • -
    • -
-
-
-
-
- -
-

Getting Started

-
-

Overview

-

MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF wbesite. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports de-/serialization of MMIF objects, as well as many navigation and manipulation helpers for MMIF objects.

-
-
-

Prerequisites

-
    -

  • Python: mmif-python requires Python 3.6 or newer. We have no plan to support Python 2.7.

    • -
-
-
-

Installation

-

Package mmif-python is distributed via the official PyPI. Users are supposed to pip-install to get latest release.

-
pip install mmif-python
-
-
-

This will install a package mmif to local python.

-

The MMIF format and specification is evolving over time, and mmif-python package will be updated along with the changes in MMIF format.

-
-

Note

-

MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and mmif-python versions, please take time to read our decision on the subject here. If you need to know which python SDK supports which specification version, see Target MMIF Versions page.

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MMIF Serialization

-

mmif.serialize.mmif.Mmif represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of mmif.serialize.model.MmifObject, including the mmif.serialize.mmif.Mmif. To start with an existing MMIF str, simple initiate a new Mmif object with the file.

-
import mmif
-from mmif import Mmif
-
-mmif_str = """{
-"metadata": {
-  "mmif": "http://mmif.clams.ai/0.2.0"
-},
-"documents": [
-  {
-    "@type": "http://mmif.clams.ai/0.2.0/vocabulary/VideoDocument",
-    "properties": {
-      "id": "m1",
-      "mime": "video/mp4",
-      "location": "file:///var/archive/video-0012.mp4"
-    }
-  },
-  {
-    "@type": "http://mmif.clams.ai/0.2.0/vocabulary/TextDocument",
-    "properties": {
-      "id": "m2",
-      "mime": "text/plain",
-      "location": "file:///var/archive/video-0012-transcript.txt"
-    }
-  }
-],
-"views": []}"""
-mmif_obj = Mmif(mmif_str)
-
-
-

Few notes;

-
    -

  1. MMIF does not carry the primary source files in it.

    2. -

  2. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version mmif-python implementation of the MMIF might not be able to load an unsupported version of MMIF string.

    3. -
-

When serializing back to str, call .serialize() (mmif.serialize.model.MmifObject.serialize()) on the object.

-

To get subcomponents, you can use various getters implemented in subclasses. For more details, the API documentation (mmif package) will help.

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"modul": [0, 1], "multimedia": 3, "overview": 4, "packag": 5, "prerequisit": 4, "python": 3, "serial": [0, 4], "specif": 6, "start": 4, "tabl": 3, "target": 6, "version": 6, "view": 0, "vocabulari": 1, "welcom": 3}}) \ No newline at end of file diff --git a/docs/0.4.1/target-versions.html b/docs/0.4.1/target-versions.html deleted file mode 100644 index 28db5981..00000000 --- a/docs/0.4.1/target-versions.html +++ /dev/null @@ -1,209 +0,0 @@ - - - - - - - - - Target MMIF Versions — mmif-python documentation - - - - - - - - - - - - - - - - - -
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This article provides targeting MMIF specification versions of different versions of mmif-python SDK.

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0.3.3

0.3.1

0.3.2

0.3.1

0.3.1

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The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the `appliance documentation `_ to learn more about the appliance. - -MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance. - -#. The code must be hosted on a public git repository (e.g. Github, Gitlab, ...) -#. Must listen to ``5000`` port. -#. Must expose ``/display`` route . -#. ``/display`` router should response to ``GET`` requests. -#. In the ``GET`` request, a public URL of the input MMIF file is passed via ``file`` URL parameter. -#. On the codebase root, there must be a ``Dockerfile`` that can build a `docker `_ image that runs the web app. - -We provide an example consumer at https://github.com/clamsproject/mmif-visualizer. diff --git a/docs/0.4.2/_sources/index.rst.txt b/docs/0.4.2/_sources/index.rst.txt deleted file mode 100644 index 9b90b38e..00000000 --- a/docs/0.4.2/_sources/index.rst.txt +++ /dev/null @@ -1,26 +0,0 @@ -Welcome to mmif-python's documentation! -======================================= - -.. mdinclude:: ../README.md - -.. toctree:: - :maxdepth: 2 - :caption: Contents - - introduction - target-versions - consumer-tutorial - -.. toctree:: - :maxdepth: 2 - :caption: API documentation: - - modules - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/docs/0.4.2/_sources/introduction.rst.txt b/docs/0.4.2/_sources/introduction.rst.txt deleted file mode 100644 index 6fea3a3c..00000000 --- a/docs/0.4.2/_sources/introduction.rst.txt +++ /dev/null @@ -1,78 +0,0 @@ -.. _instroduction: - -Getting Started -=============== - - -Overview ---------- - -MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF wbesite `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports de-/serialization of MMIF objects, as well as many navigation and manipulation helpers for MMIF objects. - -Prerequisites -------------- - -* `Python `_: ``mmif-python`` requires Python 3.6 or newer. We have no plan to support `Python 2.7 `_. - -Installation ---------------- - -Package ``mmif-python`` is distributed via the official PyPI. Users are supposed to pip-install to get latest release. - -.. code-block:: bash - - pip install mmif-python - -This will install a package `mmif` to local python. - -The MMIF format and specification is evolving over time, and ``mmif-python`` package will be updated along with the changes in MMIF format. - -.. note:: MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and ``mmif-python`` versions, please take time to read our decision on the subject `here `_. If you need to know which python SDK supports which specification version, see :ref:`target-versions` page. - -MMIF Serialization ---------------------------- - -:class:`mmif.serialize.mmif.Mmif` represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of :class:`mmif.serialize.model.MmifObject`, including the :class:`mmif.serialize.mmif.Mmif`. To start with an existing MMIF :class:`str`, simple initiate a new ``Mmif`` object with the file. - -.. code-block:: python - - import mmif - from mmif import Mmif - - mmif_str = """{ - "metadata": { - "mmif": "http://mmif.clams.ai/0.2.0" - }, - "documents": [ - { - "@type": "http://mmif.clams.ai/0.2.0/vocabulary/VideoDocument", - "properties": { - "id": "m1", - "mime": "video/mp4", - "location": "file:///var/archive/video-0012.mp4" - } - }, - { - "@type": "http://mmif.clams.ai/0.2.0/vocabulary/TextDocument", - "properties": { - "id": "m2", - "mime": "text/plain", - "location": "file:///var/archive/video-0012-transcript.txt" - } - } - ], - "views": []}""" - mmif_obj = Mmif(mmif_str) - - -Few notes; - -#. MMIF does not carry the primary source files in it. -#. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version ``mmif-python`` implementation of the MMIF might not be able to load an unsupported version of MMIF string. - -When serializing back to :class:`str`, call ``.serialize()`` (:meth:`mmif.serialize.model.MmifObject.serialize`) on the object. - -To get subcomponents, you can use various getters implemented in subclasses. For more details, the API documentation (:ref:`apidoc`) will help. - diff --git a/docs/0.4.2/_sources/modules.rst.txt b/docs/0.4.2/_sources/modules.rst.txt deleted file mode 100644 index e4269c6d..00000000 --- a/docs/0.4.2/_sources/modules.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _apidoc: - -mmif package -============ - -.. toctree:: - :maxdepth: 4 - - autodoc/mmif.serialize - autodoc/mmif.vocabulary diff --git a/docs/0.4.2/_sources/target-versions.rst.txt b/docs/0.4.2/_sources/target-versions.rst.txt deleted file mode 100644 index 34216d3e..00000000 --- a/docs/0.4.2/_sources/target-versions.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _target-versions: - -Target MMIF Versions -==================== - -This article provides targeting MMIF specification versions of different versions of ``mmif-python`` SDK. - -.. csv-table:: Target Specification Versions - :file: target-versions.csv - :header-rows: 1 diff --git a/docs/0.4.2/_static/_sphinx_javascript_frameworks_compat.js b/docs/0.4.2/_static/_sphinx_javascript_frameworks_compat.js deleted file mode 100644 index 81415803..00000000 --- a/docs/0.4.2/_static/_sphinx_javascript_frameworks_compat.js +++ /dev/null @@ -1,123 +0,0 @@ -/* Compatability shim for jQuery and underscores.js. - * - * Copyright Sphinx contributors - * Released under the two clause BSD licence - */ - -/** - * small helper function to urldecode strings - * - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL - */ -jQuery.urldecode = function(x) { - if (!x) { - return x - } - return decodeURIComponent(x.replace(/\+/g, ' ')); -}; - -/** - * small helper function to urlencode strings - */ -jQuery.urlencode = encodeURIComponent; - -/** - * This function returns the parsed url parameters of the - * current request. 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- -/** - * Simple result scoring code. - */ -if (typeof Scorer === "undefined") { - var Scorer = { - // Implement the following function to further tweak the score for each result - // The function takes a result array [docname, title, anchor, descr, score, filename] - // and returns the new score. - /* - score: result => { - const [docname, title, anchor, descr, score, filename, kind] = result - return score - }, - */ - - // query matches the full name of an object - objNameMatch: 11, - // or matches in the last dotted part of the object name - objPartialMatch: 6, - // Additive scores depending on the priority of the object - objPrio: { - 0: 15, // used to be importantResults - 1: 5, // used to be objectResults - 2: -5, // used to be unimportantResults - }, - // Used when the priority is not in the mapping. - objPrioDefault: 0, - - // query found in title - title: 15, - partialTitle: 7, - // query found in terms - term: 5, - partialTerm: 2, - }; -} - -// Global search result kind enum, used by themes to style search results. -class SearchResultKind { - static get index() { return "index"; } - static get object() { return "object"; } - static get text() { return "text"; } - static get title() { return "title"; } -} - -const _removeChildren = (element) => { - while (element && element.lastChild) element.removeChild(element.lastChild); -}; - -/** - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping - */ -const _escapeRegExp = (string) => - string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string - -const _displayItem = (item, searchTerms, highlightTerms) => { - const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; - const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; - const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; - const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; - const contentRoot = document.documentElement.dataset.content_root; - - const [docName, title, anchor, descr, score, _filename, kind] = item; - - let listItem = document.createElement("li"); - // Add a class representing the item's type: - // can be used by a theme's CSS selector for styling - // See SearchResultKind for the class names. - listItem.classList.add(`kind-${kind}`); - let requestUrl; - let linkUrl; - if (docBuilder === "dirhtml") { - // dirhtml builder - let dirname = docName + "/"; - if (dirname.match(/\/index\/$/)) - dirname = dirname.substring(0, dirname.length - 6); - else if (dirname === "index/") dirname = ""; - requestUrl = contentRoot + dirname; - linkUrl = requestUrl; - } else { - // normal html builders - requestUrl = contentRoot + docName + docFileSuffix; - linkUrl = docName + docLinkSuffix; - } - let linkEl = listItem.appendChild(document.createElement("a")); - linkEl.href = linkUrl + anchor; - linkEl.dataset.score = score; - linkEl.innerHTML = title; - if (descr) { - listItem.appendChild(document.createElement("span")).innerHTML = - " (" + descr + ")"; - // highlight search terms in the description - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - } - else if (showSearchSummary) - fetch(requestUrl) - .then((responseData) => responseData.text()) - .then((data) => { - if (data) - listItem.appendChild( - Search.makeSearchSummary(data, searchTerms, anchor) - ); - // highlight search terms in the summary - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - }); - Search.output.appendChild(listItem); -}; -const _finishSearch = (resultCount) => { - Search.stopPulse(); - Search.title.innerText = _("Search Results"); - if (!resultCount) - Search.status.innerText = Documentation.gettext( - "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." - ); - else - Search.status.innerText = Documentation.ngettext( - "Search finished, found one page matching the search query.", - "Search finished, found ${resultCount} pages matching the search query.", - resultCount, - ).replace('${resultCount}', resultCount); -}; -const _displayNextItem = ( - results, - resultCount, - searchTerms, - highlightTerms, -) => { - // results left, load the summary and display it - // this is intended to be dynamic (don't sub resultsCount) - if (results.length) { - _displayItem(results.pop(), searchTerms, highlightTerms); - setTimeout( - () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), - 5 - ); - } - // search finished, update title and status message - else _finishSearch(resultCount); -}; -// Helper function used by query() to order search results. -// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. -// Order the results by score (in opposite order of appearance, since the -// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. -const _orderResultsByScoreThenName = (a, b) => { - const leftScore = a[4]; - const rightScore = b[4]; - if (leftScore === rightScore) { - // same score: sort alphabetically - const leftTitle = a[1].toLowerCase(); - const rightTitle = b[1].toLowerCase(); - if (leftTitle === rightTitle) return 0; - return leftTitle > rightTitle ? -1 : 1; // inverted is intentional - } - return leftScore > rightScore ? 1 : -1; -}; - -/** - * Default splitQuery function. Can be overridden in ``sphinx.search`` with a - * custom function per language. - * - * The regular expression works by splitting the string on consecutive characters - * that are not Unicode letters, numbers, underscores, or emoji characters. - * This is the same as ``\W+`` in Python, preserving the surrogate pair area. - */ -if (typeof splitQuery === "undefined") { - var splitQuery = (query) => query - .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) - .filter(term => term) // remove remaining empty strings -} - -/** - * Search Module - */ -const Search = { - _index: null, - _queued_query: null, - _pulse_status: -1, - - htmlToText: (htmlString, anchor) => { - const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - for (const removalQuery of [".headerlink", "script", "style"]) { - htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); - } - if (anchor) { - const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); - if (anchorContent) return anchorContent.textContent; - - console.warn( - `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` - ); - } - - // if anchor not specified or not found, fall back to main content - const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent) return docContent.textContent; - - console.warn( - "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." - ); - return ""; - }, - - init: () => { - const query = new URLSearchParams(window.location.search).get("q"); - document - .querySelectorAll('input[name="q"]') - .forEach((el) => (el.value = query)); - if (query) Search.performSearch(query); - }, - - loadIndex: (url) => - (document.body.appendChild(document.createElement("script")).src = url), - - setIndex: (index) => { - Search._index = index; - if (Search._queued_query !== null) { - const query = Search._queued_query; - Search._queued_query = null; - Search.query(query); - } - }, - - hasIndex: () => Search._index !== null, - - deferQuery: (query) => (Search._queued_query = query), - - stopPulse: () => (Search._pulse_status = -1), - - startPulse: () => { - if (Search._pulse_status >= 0) return; - - const pulse = () => { - Search._pulse_status = (Search._pulse_status + 1) % 4; - Search.dots.innerText = ".".repeat(Search._pulse_status); - if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); - }; - pulse(); - }, - - /** - * perform a search for something (or wait until index is loaded) - */ - performSearch: (query) => { - // create the required interface elements - const searchText = document.createElement("h2"); - searchText.textContent = _("Searching"); - const searchSummary = document.createElement("p"); - searchSummary.classList.add("search-summary"); - searchSummary.innerText = ""; - const searchList = document.createElement("ul"); - searchList.setAttribute("role", "list"); - searchList.classList.add("search"); - - const out = document.getElementById("search-results"); - Search.title = out.appendChild(searchText); - Search.dots = Search.title.appendChild(document.createElement("span")); - Search.status = out.appendChild(searchSummary); - Search.output = out.appendChild(searchList); - - const searchProgress = document.getElementById("search-progress"); - // Some themes don't use the search progress node - if (searchProgress) { - searchProgress.innerText = _("Preparing search..."); - } - Search.startPulse(); - - // index already loaded, the browser was quick! - if (Search.hasIndex()) Search.query(query); - else Search.deferQuery(query); - }, - - _parseQuery: (query) => { - // stem the search terms and add them to the correct list - const stemmer = new Stemmer(); - const searchTerms = new Set(); - const excludedTerms = new Set(); - const highlightTerms = new Set(); - const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); - splitQuery(query.trim()).forEach((queryTerm) => { - const queryTermLower = queryTerm.toLowerCase(); - - // maybe skip this "word" - // stopwords array is from language_data.js - if ( - stopwords.indexOf(queryTermLower) !== -1 || - queryTerm.match(/^\d+$/) - ) - return; - - // stem the word - let word = stemmer.stemWord(queryTermLower); - // select the correct list - if (word[0] === "-") excludedTerms.add(word.substr(1)); - else { - searchTerms.add(word); - highlightTerms.add(queryTermLower); - } - }); - - if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js - localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) - } - - // console.debug("SEARCH: searching for:"); - // console.info("required: ", [...searchTerms]); - // console.info("excluded: ", [...excludedTerms]); - - return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; - }, - - /** - * execute search (requires search index to be loaded) - */ - _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - - // Collect multiple result groups to be sorted separately and then ordered. - // Each is an array of [docname, title, anchor, descr, score, filename, kind]. - const normalResults = []; - const nonMainIndexResults = []; - - _removeChildren(document.getElementById("search-progress")); - - const queryLower = query.toLowerCase().trim(); - for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { - for (const [file, id] of foundTitles) { - const score = Math.round(Scorer.title * queryLower.length / title.length); - const boost = titles[file] === title ? 1 : 0; // add a boost for document titles - normalResults.push([ - docNames[file], - titles[file] !== title ? `${titles[file]} > ${title}` : title, - id !== null ? "#" + id : "", - null, - score + boost, - filenames[file], - SearchResultKind.title, - ]); - } - } - } - - // search for explicit entries in index directives - for (const [entry, foundEntries] of Object.entries(indexEntries)) { - if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id, isMain] of foundEntries) { - const score = Math.round(100 * queryLower.length / entry.length); - const result = [ - docNames[file], - titles[file], - id ? "#" + id : "", - null, - score, - filenames[file], - SearchResultKind.index, - ]; - if (isMain) { - normalResults.push(result); - } else { - nonMainIndexResults.push(result); - } - } - } - } - - // lookup as object - objectTerms.forEach((term) => - normalResults.push(...Search.performObjectSearch(term, objectTerms)) - ); - - // lookup as search terms in fulltext - normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); - - // let the scorer override scores with a custom scoring function - if (Scorer.score) { - normalResults.forEach((item) => (item[4] = Scorer.score(item))); - nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); - } - - // Sort each group of results by score and then alphabetically by name. - normalResults.sort(_orderResultsByScoreThenName); - nonMainIndexResults.sort(_orderResultsByScoreThenName); - - // Combine the result groups in (reverse) order. - // Non-main index entries are typically arbitrary cross-references, - // so display them after other results. - let results = [...nonMainIndexResults, ...normalResults]; - - // remove duplicate search results - // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept - let seen = new Set(); - results = results.reverse().reduce((acc, result) => { - let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); - if (!seen.has(resultStr)) { - acc.push(result); - seen.add(resultStr); - } - return acc; - }, []); - - return results.reverse(); - }, - - query: (query) => { - const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); - const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); - - // for debugging - //Search.lastresults = results.slice(); // a copy - // console.info("search results:", Search.lastresults); - - // print the results - _displayNextItem(results, results.length, searchTerms, highlightTerms); - }, - - /** - * search for object names - */ - performObjectSearch: (object, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const objects = Search._index.objects; - const objNames = Search._index.objnames; - const titles = Search._index.titles; - - const results = []; - - const objectSearchCallback = (prefix, match) => { - const name = match[4] - const fullname = (prefix ? prefix + "." : "") + name; - const fullnameLower = fullname.toLowerCase(); - if (fullnameLower.indexOf(object) < 0) return; - - let score = 0; - const parts = fullnameLower.split("."); - - // check for different match types: exact matches of full name or - // "last name" (i.e. last dotted part) - if (fullnameLower === object || parts.slice(-1)[0] === object) - score += Scorer.objNameMatch; - else if (parts.slice(-1)[0].indexOf(object) > -1) - score += Scorer.objPartialMatch; // matches in last name - - const objName = objNames[match[1]][2]; - const title = titles[match[0]]; - - // If more than one term searched for, we require other words to be - // found in the name/title/description - const otherTerms = new Set(objectTerms); - otherTerms.delete(object); - if (otherTerms.size > 0) { - const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); - if ( - [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) - ) - return; - } - - let anchor = match[3]; - if (anchor === "") anchor = fullname; - else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; - - const descr = objName + _(", in ") + title; - - // add custom score for some objects according to scorer - if (Scorer.objPrio.hasOwnProperty(match[2])) - score += Scorer.objPrio[match[2]]; - else score += Scorer.objPrioDefault; - - results.push([ - docNames[match[0]], - fullname, - "#" + anchor, - descr, - score, - filenames[match[0]], - SearchResultKind.object, - ]); - }; - Object.keys(objects).forEach((prefix) => - objects[prefix].forEach((array) => - objectSearchCallback(prefix, array) - ) - ); - return results; - }, - - /** - * search for full-text terms in the index - */ - performTermsSearch: (searchTerms, excludedTerms) => { - // prepare search - const terms = Search._index.terms; - const titleTerms = Search._index.titleterms; - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - - const scoreMap = new Map(); - const fileMap = new Map(); - - // perform the search on the required terms - searchTerms.forEach((word) => { - const files = []; - const arr = [ - { files: terms[word], score: Scorer.term }, - { files: titleTerms[word], score: Scorer.title }, - ]; - // add support for partial matches - if (word.length > 2) { - const escapedWord = _escapeRegExp(word); - if (!terms.hasOwnProperty(word)) { - Object.keys(terms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: terms[term], score: Scorer.partialTerm }); - }); - } - if (!titleTerms.hasOwnProperty(word)) { - Object.keys(titleTerms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); - }); - } - } - - // no match but word was a required one - if (arr.every((record) => record.files === undefined)) return; - - // found search word in contents - arr.forEach((record) => { - if (record.files === undefined) return; - - let recordFiles = record.files; - if (recordFiles.length === undefined) recordFiles = [recordFiles]; - files.push(...recordFiles); - - // set score for the word in each file - recordFiles.forEach((file) => { - if (!scoreMap.has(file)) scoreMap.set(file, {}); - scoreMap.get(file)[word] = record.score; - }); - }); - - // create the mapping - files.forEach((file) => { - if (!fileMap.has(file)) fileMap.set(file, [word]); - else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); - }); - }); - - // now check if the files don't contain excluded terms - const results = []; - for (const [file, wordList] of fileMap) { - // check if all requirements are matched - - // as search terms with length < 3 are discarded - const filteredTermCount = [...searchTerms].filter( - (term) => term.length > 2 - ).length; - if ( - wordList.length !== searchTerms.size && - wordList.length !== filteredTermCount - ) - continue; - - // ensure that none of the excluded terms is in the search result - if ( - [...excludedTerms].some( - (term) => - terms[term] === file || - titleTerms[term] === file || - (terms[term] || []).includes(file) || - (titleTerms[term] || []).includes(file) - ) - ) - break; - - // select one (max) score for the file. - const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); - // add result to the result list - results.push([ - docNames[file], - titles[file], - "", - null, - score, - filenames[file], - SearchResultKind.text, - ]); - } - return results; - }, - - /** - * helper function to return a node containing the - * search summary for a given text. keywords is a list - * of stemmed words. - */ - makeSearchSummary: (htmlText, keywords, anchor) => { - const text = Search.htmlToText(htmlText, anchor); - if (text === "") return null; - - const textLower = text.toLowerCase(); - const actualStartPosition = [...keywords] - .map((k) => textLower.indexOf(k.toLowerCase())) - .filter((i) => i > -1) - .slice(-1)[0]; - const startWithContext = Math.max(actualStartPosition - 120, 0); - - const top = startWithContext === 0 ? "" : "..."; - const tail = startWithContext + 240 < text.length ? "..." : ""; - - let summary = document.createElement("p"); - summary.classList.add("context"); - summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; - - return summary; - }, -}; - -_ready(Search.init); diff --git a/docs/0.4.2/_static/sphinx_highlight.js b/docs/0.4.2/_static/sphinx_highlight.js deleted file mode 100644 index 8a96c69a..00000000 --- a/docs/0.4.2/_static/sphinx_highlight.js +++ /dev/null @@ -1,154 +0,0 @@ -/* Highlighting utilities for Sphinx HTML documentation. */ -"use strict"; - -const SPHINX_HIGHLIGHT_ENABLED = true - -/** - * highlight a given string on a node by wrapping it in - * span elements with the given class name. - */ -const _highlight = (node, addItems, text, className) => { - if (node.nodeType === Node.TEXT_NODE) { - const val = node.nodeValue; - const parent = node.parentNode; - const pos = val.toLowerCase().indexOf(text); - if ( - pos >= 0 && - !parent.classList.contains(className) && - !parent.classList.contains("nohighlight") - ) { - let span; - - const closestNode = parent.closest("body, svg, foreignObject"); - const isInSVG = closestNode && closestNode.matches("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.classList.add(className); - } - - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - const rest = document.createTextNode(val.substr(pos + text.length)); - parent.insertBefore( - span, - parent.insertBefore( - rest, - node.nextSibling - ) - ); - node.nodeValue = val.substr(0, pos); - /* There may be more occurrences of search term in this node. So call this - * function recursively on the remaining fragment. - */ - _highlight(rest, addItems, text, className); - - if (isInSVG) { - const rect = document.createElementNS( - "http://www.w3.org/2000/svg", - "rect" - ); - const bbox = parent.getBBox(); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute("class", className); - addItems.push({ parent: parent, target: rect }); - } - } - } else if (node.matches && !node.matches("button, select, textarea")) { - node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); - } -}; -const _highlightText = (thisNode, text, className) => { - let addItems = []; - _highlight(thisNode, addItems, text, className); - addItems.forEach((obj) => - obj.parent.insertAdjacentElement("beforebegin", obj.target) - ); -}; - -/** - * Small JavaScript module for the documentation. - */ -const SphinxHighlight = { - - /** - * highlight the search words provided in localstorage in the text - */ - highlightSearchWords: () => { - if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight - - // get and clear terms from localstorage - const url = new URL(window.location); - const highlight = - localStorage.getItem("sphinx_highlight_terms") - || url.searchParams.get("highlight") - || ""; - localStorage.removeItem("sphinx_highlight_terms") - url.searchParams.delete("highlight"); - window.history.replaceState({}, "", url); - - // get individual terms from highlight string - const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); - if (terms.length === 0) return; // nothing to do - - // There should never be more than one element matching "div.body" - const divBody = document.querySelectorAll("div.body"); - const body = divBody.length ? divBody[0] : document.querySelector("body"); - window.setTimeout(() => { - terms.forEach((term) => _highlightText(body, term, "highlighted")); - }, 10); - - const searchBox = document.getElementById("searchbox"); - if (searchBox === null) return; - searchBox.appendChild( - document - .createRange() - .createContextualFragment( - '

' + - '' + - _("Hide Search Matches") + - "

" - ) - ); - }, - - /** - * helper function to hide the search marks again - */ - hideSearchWords: () => { - document - .querySelectorAll("#searchbox .highlight-link") - .forEach((el) => el.remove()); - document - .querySelectorAll("span.highlighted") - .forEach((el) => el.classList.remove("highlighted")); - localStorage.removeItem("sphinx_highlight_terms") - }, - - initEscapeListener: () => { - // only install a listener if it is really needed - if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; - - document.addEventListener("keydown", (event) => { - // bail for input elements - if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; - // bail with special keys - if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; - if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { - SphinxHighlight.hideSearchWords(); - event.preventDefault(); - } - }); - }, -}; - -_ready(() => { - /* Do not call highlightSearchWords() when we are on the search page. - * It will highlight words from the *previous* search query. - */ - if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); - SphinxHighlight.initEscapeListener(); -}); diff --git a/docs/0.4.2/autodoc/mmif.serialize.html b/docs/0.4.2/autodoc/mmif.serialize.html deleted file mode 100644 index c04cbb13..00000000 --- a/docs/0.4.2/autodoc/mmif.serialize.html +++ /dev/null @@ -1,370 +0,0 @@ - - - - - - - - - mmif.serialize module — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.serialize module

-
-

mmif.serialize.model module

-
-
-

mmif.serialize.mmif module

-
-
-

mmif.serialize.view module

-
-
-

mmif.serialize.annotation module

-

The annotation module contains the classes used to represent a -MMIF annotation as a live Python object.

-

In MMIF, annotations are created by apps in a pipeline as a part -of a view. For documentation on how views are represented, see -mmif.serialize.view.

-
-
-class mmif.serialize.annotation.Annotation(anno_obj: bytes | str | dict | None = None)[source]
-

Bases: FreezableMmifObject

-

MmifObject that represents an annotation in a MMIF view.

-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]]) → None[source]
-

Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

-
- -
-
-property at_type: TypesBase[source]
-
- -
-
-property id: str[source]
-
- -
-
-is_document()[source]
-
- -
-
-is_type(at_type: str | TypesBase) → bool[source]
-

Check if the @type of this object matches.

-
- -
- -
-
-class mmif.serialize.annotation.AnnotationProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: FreezableMmifObject

-

AnnotationProperties object that represents the -properties object within a MMIF annotation.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
- -
-
-class mmif.serialize.annotation.Document(doc_obj: bytes | str | dict | None = None)[source]
-

Bases: Annotation

-

Document object that represents a single document in a MMIF file.

-

A document is identified by an ID, and contains certain attributes -and potentially contains the contents of the document itself, -metadata about how the document was created, and/or a list of -subdocuments grouped together logically.

-

If document_obj is not provided, an empty Document will be generated.

-
-
Parameters:
-

document_obj – the JSON data that defines the document

-
-
-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None]) → None[source]
-

Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

-
- -
-
-property location: str[source]
-
- -
-
-location_address() → str[source]
-
- -
-
-location_path() → str[source]
-
- -
-
-location_scheme() → str[source]
-
- -
-
-property parent: str[source]
-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.DocumentProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: AnnotationProperties

-

DocumentProperties object that represents the -properties object within a MMIF document.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
-
-property location: str[source]
-
- -
-
-location_address() → str[source]
-
- -
-
-location_path() → str[source]
-
- -
-
-location_scheme() → str[source]
-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.Text(text_obj: bytes | str | dict | None = None)[source]
-

Bases: FreezableMmifObject

-
-
-property lang: str[source]
-
- -
-
-property value: str[source]
-
- -
- -
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.4.2 - - -
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0.3.0
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0.3.1
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0.3.2
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0.3.3
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0.3.4
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0.4.1
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- - - \ No newline at end of file diff --git a/docs/0.4.2/autodoc/mmif.vocabulary.html b/docs/0.4.2/autodoc/mmif.vocabulary.html deleted file mode 100644 index 5473ded9..00000000 --- a/docs/0.4.2/autodoc/mmif.vocabulary.html +++ /dev/null @@ -1,285 +0,0 @@ - - - - - - - - - mmif.vocabulary module — mmif-python documentation - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.vocabulary module

-
-

mmif.vocabulary.annotation_types module

-
-
-class mmif.vocabulary.annotation_types.AnnotationTypes(type_uri: str)[source]
-

Bases: AnnotationTypesBase

-

This class contains the CLAMS annotation types -defined in the spec version 0.4.2 as class variables.

-
-
-Alignment = http://mmif.clams.ai/0.4.2/vocabulary/Alignment[source]
-
- -
-
-Annotation = http://mmif.clams.ai/0.4.2/vocabulary/Annotation[source]
-
- -
-
-BoundingBox = http://mmif.clams.ai/0.4.2/vocabulary/BoundingBox[source]
-
- -
-
-Chapter = http://mmif.clams.ai/0.4.2/vocabulary/Chapter[source]
-
- -
-
-Interval = http://mmif.clams.ai/0.4.2/vocabulary/Interval[source]
-
- -
-
-Polygon = http://mmif.clams.ai/0.4.2/vocabulary/Polygon[source]
-
- -
-
-Region = http://mmif.clams.ai/0.4.2/vocabulary/Region[source]
-
- -
-
-Relation = http://mmif.clams.ai/0.4.2/vocabulary/Relation[source]
-
- -
-
-Span = http://mmif.clams.ai/0.4.2/vocabulary/Span[source]
-
- -
-
-TimeFrame = http://mmif.clams.ai/0.4.2/vocabulary/TimeFrame[source]
-
- -
-
-TimePoint = http://mmif.clams.ai/0.4.2/vocabulary/TimePoint[source]
-
- -
-
-VideoObject = http://mmif.clams.ai/0.4.2/vocabulary/VideoObject[source]
-
- -
- -
-
-

mmif.vocabulary.document_types module

-
-
-class mmif.vocabulary.document_types.DocumentTypes(type_uri: str)[source]
-

Bases: DocumentTypesBase

-

This class contains the CLAMS document types -defined in the spec version 0.4.2 as class variables.

-
-
-AudioDocument = http://mmif.clams.ai/0.4.2/vocabulary/AudioDocument[source]
-
- -
-
-Document = http://mmif.clams.ai/0.4.2/vocabulary/Document[source]
-
- -
-
-ImageDocument = http://mmif.clams.ai/0.4.2/vocabulary/ImageDocument[source]
-
- -
-
-TextDocument = http://mmif.clams.ai/0.4.2/vocabulary/TextDocument[source]
-
- -
-
-VideoDocument = http://mmif.clams.ai/0.4.2/vocabulary/VideoDocument[source]
-
- -
- -
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.4.2 - - -
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- -
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0.3.1
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0.3.3
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- - - \ No newline at end of file diff --git a/docs/0.4.2/consumer-tutorial.html b/docs/0.4.2/consumer-tutorial.html deleted file mode 100644 index 0764e244..00000000 --- a/docs/0.4.2/consumer-tutorial.html +++ /dev/null @@ -1,176 +0,0 @@ - - - - - - - - - MMIF consumer — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • MMIF consumer
    • -
  • -
    • -
-
-
-
-
- -
-

MMIF consumer

-

A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the appliance documentation to learn more about the appliance.

-

MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance.

-
    -

  1. The code must be hosted on a public git repository (e.g. Github, Gitlab, …)

    2. -

  2. Must listen to 5000 port.

    3. -

  3. Must expose /display route .

    4. -

  4. /display router should response to GET requests.

    5. -

  5. In the GET request, a public URL of the input MMIF file is passed via file URL parameter.

    6. -

  6. On the codebase root, there must be a Dockerfile that can build a docker image that runs the web app.

    7. -
-

We provide an example consumer at https://github.com/clamsproject/mmif-visualizer.

-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.4.2 - - -
-
- -
0.3.0
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0.3.1
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0.3.3
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- - -
- -
-
-
-
    -
    • -
  • Index
    • -
  • -
    • -
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- - -

Index

- -
- A - | B - | C - | D - | I - | L - | M - | P - | R - | S - | T - | V - -
-

A

- - - -
- -

B

- - -
- -

C

- - -
- -

D

- - - -
- -

I

- - - -
- -

L

- - - -
- -

M

- - - -
    -
  • - mmif.serialize.annotation - -
    • -
  • - mmif.vocabulary.annotation_types - -
    • -
  • - mmif.vocabulary.document_types - -
    • -
- -

P

- - - -
- -

R

- - - -
- -

S

- - -
- -

T

- - - -
- -

V

- - - -
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- - Other Versions - v: 0.4.2 - - -
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0.3.1
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0.3.2
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0.3.3
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0.3.4
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0.4.1
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0.4.2
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- - -
- -
-
-
-
    -
    • -
  • Welcome to mmif-python’s documentation!
    • -
  • -
    • -
-
-
-
-
- -
-

Welcome to mmif-python’s documentation!

-
-
-

MMIF for python

-

NOTE that this project is in pre-alpha and being actively developed. Nothing is guaranteed to reliably work for the moment and developer need to be very careful when using APIs implemented here. Please use the issue track to report bugs and malfunctions.

-
-

MultiMedia Interchange Format

-

MMIF is a JSON(-LD)-based data format designed for transferring annotation data between computational analysis applications in CLAMS project.

-
-

Contents

- -
-
-

API documentation:

- -
-
-
-
-

Indices and tables

- -
- - -
-
- -
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- -
- - Other Versions - v: 0.4.2 - - -
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0.3.2
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- - - \ No newline at end of file diff --git a/docs/0.4.2/introduction.html b/docs/0.4.2/introduction.html deleted file mode 100644 index 97e20016..00000000 --- a/docs/0.4.2/introduction.html +++ /dev/null @@ -1,236 +0,0 @@ - - - - - - - - - Getting Started — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
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  • Getting Started
    • -
  • -
    • -
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Getting Started

-
-

Overview

-

MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF wbesite. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports de-/serialization of MMIF objects, as well as many navigation and manipulation helpers for MMIF objects.

-
-
-

Prerequisites

-
    -

  • Python: mmif-python requires Python 3.6 or newer. We have no plan to support Python 2.7.

    • -
-
-
-

Installation

-

Package mmif-python is distributed via the official PyPI. Users are supposed to pip-install to get latest release.

-
pip install mmif-python
-
-
-

This will install a package mmif to local python.

-

The MMIF format and specification is evolving over time, and mmif-python package will be updated along with the changes in MMIF format.

-
-

Note

-

MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and mmif-python versions, please take time to read our decision on the subject here. If you need to know which python SDK supports which specification version, see Target MMIF Versions page.

-
-
-
-

MMIF Serialization

-

mmif.serialize.mmif.Mmif represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of mmif.serialize.model.MmifObject, including the mmif.serialize.mmif.Mmif. To start with an existing MMIF str, simple initiate a new Mmif object with the file.

-
import mmif
-from mmif import Mmif
-
-mmif_str = """{
-"metadata": {
-  "mmif": "http://mmif.clams.ai/0.2.0"
-},
-"documents": [
-  {
-    "@type": "http://mmif.clams.ai/0.2.0/vocabulary/VideoDocument",
-    "properties": {
-      "id": "m1",
-      "mime": "video/mp4",
-      "location": "file:///var/archive/video-0012.mp4"
-    }
-  },
-  {
-    "@type": "http://mmif.clams.ai/0.2.0/vocabulary/TextDocument",
-    "properties": {
-      "id": "m2",
-      "mime": "text/plain",
-      "location": "file:///var/archive/video-0012-transcript.txt"
-    }
-  }
-],
-"views": []}"""
-mmif_obj = Mmif(mmif_str)
-
-
-

Few notes;

-
    -

  1. MMIF does not carry the primary source files in it.

    2. -

  2. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version mmif-python implementation of the MMIF might not be able to load an unsupported version of MMIF string.

    3. -
-

When serializing back to str, call .serialize() (mmif.serialize.model.MmifObject.serialize()) on the object.

-

To get subcomponents, you can use various getters implemented in subclasses. For more details, the API documentation (mmif package) will help.

-
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.4.2 - - -
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0.3.0
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0.3.3
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0.3.4
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- - - \ No newline at end of file diff --git a/docs/0.4.2/modules.html b/docs/0.4.2/modules.html deleted file mode 100644 index a47684fb..00000000 --- a/docs/0.4.2/modules.html +++ /dev/null @@ -1,248 +0,0 @@ - - - - - - - - - mmif package — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
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  • mmif package
    • -
  • -
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mmif package

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- - - \ No newline at end of file diff --git a/docs/0.4.2/objects.inv b/docs/0.4.2/objects.inv deleted file mode 100644 index 1e4d2297..00000000 --- a/docs/0.4.2/objects.inv +++ /dev/null @@ -1,9 +0,0 @@ -# Sphinx inventory version 2 -# Project: mmif-python -# Version: 0.4.2 -# The remainder of this file is compressed using zlib. -xڽ0y -WڽmV95F}>I I 1l9Ԡ'TnsBK#*? FܘSEB$Qd -hL&aU@ EYⅪ#(su)xc@ǧA|Xgs߇O#S}U3opgk|AUk=G8bĩHK'=קg OS`9/@ȯuBnM3H7IaWO`_r9 iv:8wlW;RQ}Gjtu/K0ˣ-026W R_zۂ.c9<(j#Rɖ"X;įncd~ʄöLQY~T}/Xj)Z0'[NIpCu7%o.M~ .m$ -y:X -m4ɵxC;C40SRL$p'wo~\ k - - - - - Python Module Index — mmif-python documentation - - - - - - - - - - - - - - - - - - -
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Python Module Index

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    - mmif.serialize.annotation -
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- - - \ No newline at end of file diff --git a/docs/0.4.2/search.html b/docs/0.4.2/search.html deleted file mode 100644 index 4b09068c..00000000 --- a/docs/0.4.2/search.html +++ /dev/null @@ -1,177 +0,0 @@ - - - - - - - - Search — mmif-python documentation - - - - - - - - - - - - - - - - - - -
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- - - - - - - - \ No newline at end of file diff --git a/docs/0.4.2/searchindex.js b/docs/0.4.2/searchindex.js deleted file mode 100644 index 40529d6a..00000000 --- a/docs/0.4.2/searchindex.js +++ /dev/null @@ -1 +0,0 @@ -Search.setIndex({"alltitles": {"API documentation:": [[3, null]], "Contents": [[3, null]], "Getting Started": [[4, null]], "Indices and tables": [[3, "indices-and-tables"]], "Installation": [[4, "installation"]], "MMIF Serialization": [[4, "mmif-serialization"]], "MMIF consumer": [[2, null]], "MMIF for python": [[3, "mmif-for-python"]], "MultiMedia Interchange Format": [[3, "multimedia-interchange-format"]], "Overview": [[4, "overview"]], "Prerequisites": [[4, "prerequisites"]], "Target MMIF Versions": [[6, null]], "Target Specification Versions": [[6, "id1"]], "Welcome to mmif-python\u2019s documentation!": [[3, null]], "mmif package": [[5, null]], "mmif.serialize module": [[0, null]], "mmif.serialize.annotation module": [[0, "module-mmif.serialize.annotation"]], 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"modul": [0, 1], "multimedia": 3, "overview": 4, "packag": 5, "prerequisit": 4, "python": 3, "serial": [0, 4], "specif": 6, "start": 4, "tabl": 3, "target": 6, "version": 6, "view": 0, "vocabulari": 1, "welcom": 3}}) \ No newline at end of file diff --git a/docs/0.4.2/target-versions.html b/docs/0.4.2/target-versions.html deleted file mode 100644 index d701fbb7..00000000 --- a/docs/0.4.2/target-versions.html +++ /dev/null @@ -1,212 +0,0 @@ - - - - - - - - - Target MMIF Versions — mmif-python documentation - - - - - - - - - - - - - - - - - -
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Target MMIF Versions

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This article provides targeting MMIF specification versions of different versions of mmif-python SDK.

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Target Specification Versions

mmif-python version

Target MMIF Specification

0.4.2

0.4.2

0.4.1

0.4.0

0.4.0

0.4.0

0.3.5

0.3.1

0.3.4

0.3.1

0.3.3

0.3.1

0.3.2

0.3.1

0.3.1

0.3.0

0.3.0

0.3.0

0.2.2

0.2.1

0.2.1

0.2.1

0.2.0

0.2.1

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The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the `appliance documentation `_ to learn more about the appliance. - -MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance. - -#. The code must be hosted on a public git repository (e.g. Github, Gitlab, ...) -#. Must listen to ``5000`` port. -#. Must expose ``/display`` route . -#. ``/display`` router should response to ``GET`` requests. -#. In the ``GET`` request, a public URL of the input MMIF file is passed via ``file`` URL parameter. -#. On the codebase root, there must be a ``Dockerfile`` that can build a `docker `_ image that runs the web app. - -We provide an example consumer at https://github.com/clamsproject/mmif-visualizer. diff --git a/docs/0.4.3/_sources/index.rst.txt b/docs/0.4.3/_sources/index.rst.txt deleted file mode 100644 index 9b90b38e..00000000 --- a/docs/0.4.3/_sources/index.rst.txt +++ /dev/null @@ -1,26 +0,0 @@ -Welcome to mmif-python's documentation! -======================================= - -.. mdinclude:: ../README.md - -.. toctree:: - :maxdepth: 2 - :caption: Contents - - introduction - target-versions - consumer-tutorial - -.. toctree:: - :maxdepth: 2 - :caption: API documentation: - - modules - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/docs/0.4.3/_sources/introduction.rst.txt b/docs/0.4.3/_sources/introduction.rst.txt deleted file mode 100644 index 6fea3a3c..00000000 --- a/docs/0.4.3/_sources/introduction.rst.txt +++ /dev/null @@ -1,78 +0,0 @@ -.. _instroduction: - -Getting Started -=============== - - -Overview ---------- - -MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF wbesite `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports de-/serialization of MMIF objects, as well as many navigation and manipulation helpers for MMIF objects. - -Prerequisites -------------- - -* `Python `_: ``mmif-python`` requires Python 3.6 or newer. We have no plan to support `Python 2.7 `_. - -Installation ---------------- - -Package ``mmif-python`` is distributed via the official PyPI. Users are supposed to pip-install to get latest release. - -.. code-block:: bash - - pip install mmif-python - -This will install a package `mmif` to local python. - -The MMIF format and specification is evolving over time, and ``mmif-python`` package will be updated along with the changes in MMIF format. - -.. note:: MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and ``mmif-python`` versions, please take time to read our decision on the subject `here `_. If you need to know which python SDK supports which specification version, see :ref:`target-versions` page. - -MMIF Serialization ---------------------------- - -:class:`mmif.serialize.mmif.Mmif` represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of :class:`mmif.serialize.model.MmifObject`, including the :class:`mmif.serialize.mmif.Mmif`. To start with an existing MMIF :class:`str`, simple initiate a new ``Mmif`` object with the file. - -.. code-block:: python - - import mmif - from mmif import Mmif - - mmif_str = """{ - "metadata": { - "mmif": "http://mmif.clams.ai/0.2.0" - }, - "documents": [ - { - "@type": "http://mmif.clams.ai/0.2.0/vocabulary/VideoDocument", - "properties": { - "id": "m1", - "mime": "video/mp4", - "location": "file:///var/archive/video-0012.mp4" - } - }, - { - "@type": "http://mmif.clams.ai/0.2.0/vocabulary/TextDocument", - "properties": { - "id": "m2", - "mime": "text/plain", - "location": "file:///var/archive/video-0012-transcript.txt" - } - } - ], - "views": []}""" - mmif_obj = Mmif(mmif_str) - - -Few notes; - -#. MMIF does not carry the primary source files in it. -#. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version ``mmif-python`` implementation of the MMIF might not be able to load an unsupported version of MMIF string. - -When serializing back to :class:`str`, call ``.serialize()`` (:meth:`mmif.serialize.model.MmifObject.serialize`) on the object. - -To get subcomponents, you can use various getters implemented in subclasses. For more details, the API documentation (:ref:`apidoc`) will help. - diff --git a/docs/0.4.3/_sources/modules.rst.txt b/docs/0.4.3/_sources/modules.rst.txt deleted file mode 100644 index e4269c6d..00000000 --- a/docs/0.4.3/_sources/modules.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _apidoc: - -mmif package -============ - -.. toctree:: - :maxdepth: 4 - - autodoc/mmif.serialize - autodoc/mmif.vocabulary diff --git a/docs/0.4.3/_sources/target-versions.rst.txt b/docs/0.4.3/_sources/target-versions.rst.txt deleted file mode 100644 index 34216d3e..00000000 --- a/docs/0.4.3/_sources/target-versions.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _target-versions: - -Target MMIF Versions -==================== - -This article provides targeting MMIF specification versions of different versions of ``mmif-python`` SDK. - -.. csv-table:: Target Specification Versions - :file: target-versions.csv - :header-rows: 1 diff --git a/docs/0.4.3/_static/_sphinx_javascript_frameworks_compat.js b/docs/0.4.3/_static/_sphinx_javascript_frameworks_compat.js deleted file mode 100644 index 81415803..00000000 --- a/docs/0.4.3/_static/_sphinx_javascript_frameworks_compat.js +++ /dev/null @@ -1,123 +0,0 @@ -/* Compatability shim for jQuery and underscores.js. - * - * Copyright Sphinx contributors - * Released under the two clause BSD licence - */ - -/** - * small helper function to urldecode strings - * - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL - */ -jQuery.urldecode = function(x) { - if (!x) { - return x - } - return decodeURIComponent(x.replace(/\+/g, ' ')); -}; - -/** - * small helper function to urlencode strings - */ -jQuery.urlencode = encodeURIComponent; - -/** - * This function returns the parsed url parameters of the - * current request. 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- -/** - * Simple result scoring code. - */ -if (typeof Scorer === "undefined") { - var Scorer = { - // Implement the following function to further tweak the score for each result - // The function takes a result array [docname, title, anchor, descr, score, filename] - // and returns the new score. - /* - score: result => { - const [docname, title, anchor, descr, score, filename, kind] = result - return score - }, - */ - - // query matches the full name of an object - objNameMatch: 11, - // or matches in the last dotted part of the object name - objPartialMatch: 6, - // Additive scores depending on the priority of the object - objPrio: { - 0: 15, // used to be importantResults - 1: 5, // used to be objectResults - 2: -5, // used to be unimportantResults - }, - // Used when the priority is not in the mapping. - objPrioDefault: 0, - - // query found in title - title: 15, - partialTitle: 7, - // query found in terms - term: 5, - partialTerm: 2, - }; -} - -// Global search result kind enum, used by themes to style search results. -class SearchResultKind { - static get index() { return "index"; } - static get object() { return "object"; } - static get text() { return "text"; } - static get title() { return "title"; } -} - -const _removeChildren = (element) => { - while (element && element.lastChild) element.removeChild(element.lastChild); -}; - -/** - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping - */ -const _escapeRegExp = (string) => - string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string - -const _displayItem = (item, searchTerms, highlightTerms) => { - const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; - const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; - const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; - const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; - const contentRoot = document.documentElement.dataset.content_root; - - const [docName, title, anchor, descr, score, _filename, kind] = item; - - let listItem = document.createElement("li"); - // Add a class representing the item's type: - // can be used by a theme's CSS selector for styling - // See SearchResultKind for the class names. - listItem.classList.add(`kind-${kind}`); - let requestUrl; - let linkUrl; - if (docBuilder === "dirhtml") { - // dirhtml builder - let dirname = docName + "/"; - if (dirname.match(/\/index\/$/)) - dirname = dirname.substring(0, dirname.length - 6); - else if (dirname === "index/") dirname = ""; - requestUrl = contentRoot + dirname; - linkUrl = requestUrl; - } else { - // normal html builders - requestUrl = contentRoot + docName + docFileSuffix; - linkUrl = docName + docLinkSuffix; - } - let linkEl = listItem.appendChild(document.createElement("a")); - linkEl.href = linkUrl + anchor; - linkEl.dataset.score = score; - linkEl.innerHTML = title; - if (descr) { - listItem.appendChild(document.createElement("span")).innerHTML = - " (" + descr + ")"; - // highlight search terms in the description - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - } - else if (showSearchSummary) - fetch(requestUrl) - .then((responseData) => responseData.text()) - .then((data) => { - if (data) - listItem.appendChild( - Search.makeSearchSummary(data, searchTerms, anchor) - ); - // highlight search terms in the summary - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - }); - Search.output.appendChild(listItem); -}; -const _finishSearch = (resultCount) => { - Search.stopPulse(); - Search.title.innerText = _("Search Results"); - if (!resultCount) - Search.status.innerText = Documentation.gettext( - "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." - ); - else - Search.status.innerText = Documentation.ngettext( - "Search finished, found one page matching the search query.", - "Search finished, found ${resultCount} pages matching the search query.", - resultCount, - ).replace('${resultCount}', resultCount); -}; -const _displayNextItem = ( - results, - resultCount, - searchTerms, - highlightTerms, -) => { - // results left, load the summary and display it - // this is intended to be dynamic (don't sub resultsCount) - if (results.length) { - _displayItem(results.pop(), searchTerms, highlightTerms); - setTimeout( - () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), - 5 - ); - } - // search finished, update title and status message - else _finishSearch(resultCount); -}; -// Helper function used by query() to order search results. -// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. -// Order the results by score (in opposite order of appearance, since the -// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. -const _orderResultsByScoreThenName = (a, b) => { - const leftScore = a[4]; - const rightScore = b[4]; - if (leftScore === rightScore) { - // same score: sort alphabetically - const leftTitle = a[1].toLowerCase(); - const rightTitle = b[1].toLowerCase(); - if (leftTitle === rightTitle) return 0; - return leftTitle > rightTitle ? -1 : 1; // inverted is intentional - } - return leftScore > rightScore ? 1 : -1; -}; - -/** - * Default splitQuery function. Can be overridden in ``sphinx.search`` with a - * custom function per language. - * - * The regular expression works by splitting the string on consecutive characters - * that are not Unicode letters, numbers, underscores, or emoji characters. - * This is the same as ``\W+`` in Python, preserving the surrogate pair area. - */ -if (typeof splitQuery === "undefined") { - var splitQuery = (query) => query - .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) - .filter(term => term) // remove remaining empty strings -} - -/** - * Search Module - */ -const Search = { - _index: null, - _queued_query: null, - _pulse_status: -1, - - htmlToText: (htmlString, anchor) => { - const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - for (const removalQuery of [".headerlink", "script", "style"]) { - htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); - } - if (anchor) { - const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); - if (anchorContent) return anchorContent.textContent; - - console.warn( - `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` - ); - } - - // if anchor not specified or not found, fall back to main content - const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent) return docContent.textContent; - - console.warn( - "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." - ); - return ""; - }, - - init: () => { - const query = new URLSearchParams(window.location.search).get("q"); - document - .querySelectorAll('input[name="q"]') - .forEach((el) => (el.value = query)); - if (query) Search.performSearch(query); - }, - - loadIndex: (url) => - (document.body.appendChild(document.createElement("script")).src = url), - - setIndex: (index) => { - Search._index = index; - if (Search._queued_query !== null) { - const query = Search._queued_query; - Search._queued_query = null; - Search.query(query); - } - }, - - hasIndex: () => Search._index !== null, - - deferQuery: (query) => (Search._queued_query = query), - - stopPulse: () => (Search._pulse_status = -1), - - startPulse: () => { - if (Search._pulse_status >= 0) return; - - const pulse = () => { - Search._pulse_status = (Search._pulse_status + 1) % 4; - Search.dots.innerText = ".".repeat(Search._pulse_status); - if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); - }; - pulse(); - }, - - /** - * perform a search for something (or wait until index is loaded) - */ - performSearch: (query) => { - // create the required interface elements - const searchText = document.createElement("h2"); - searchText.textContent = _("Searching"); - const searchSummary = document.createElement("p"); - searchSummary.classList.add("search-summary"); - searchSummary.innerText = ""; - const searchList = document.createElement("ul"); - searchList.setAttribute("role", "list"); - searchList.classList.add("search"); - - const out = document.getElementById("search-results"); - Search.title = out.appendChild(searchText); - Search.dots = Search.title.appendChild(document.createElement("span")); - Search.status = out.appendChild(searchSummary); - Search.output = out.appendChild(searchList); - - const searchProgress = document.getElementById("search-progress"); - // Some themes don't use the search progress node - if (searchProgress) { - searchProgress.innerText = _("Preparing search..."); - } - Search.startPulse(); - - // index already loaded, the browser was quick! - if (Search.hasIndex()) Search.query(query); - else Search.deferQuery(query); - }, - - _parseQuery: (query) => { - // stem the search terms and add them to the correct list - const stemmer = new Stemmer(); - const searchTerms = new Set(); - const excludedTerms = new Set(); - const highlightTerms = new Set(); - const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); - splitQuery(query.trim()).forEach((queryTerm) => { - const queryTermLower = queryTerm.toLowerCase(); - - // maybe skip this "word" - // stopwords array is from language_data.js - if ( - stopwords.indexOf(queryTermLower) !== -1 || - queryTerm.match(/^\d+$/) - ) - return; - - // stem the word - let word = stemmer.stemWord(queryTermLower); - // select the correct list - if (word[0] === "-") excludedTerms.add(word.substr(1)); - else { - searchTerms.add(word); - highlightTerms.add(queryTermLower); - } - }); - - if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js - localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) - } - - // console.debug("SEARCH: searching for:"); - // console.info("required: ", [...searchTerms]); - // console.info("excluded: ", [...excludedTerms]); - - return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; - }, - - /** - * execute search (requires search index to be loaded) - */ - _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - - // Collect multiple result groups to be sorted separately and then ordered. - // Each is an array of [docname, title, anchor, descr, score, filename, kind]. - const normalResults = []; - const nonMainIndexResults = []; - - _removeChildren(document.getElementById("search-progress")); - - const queryLower = query.toLowerCase().trim(); - for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { - for (const [file, id] of foundTitles) { - const score = Math.round(Scorer.title * queryLower.length / title.length); - const boost = titles[file] === title ? 1 : 0; // add a boost for document titles - normalResults.push([ - docNames[file], - titles[file] !== title ? `${titles[file]} > ${title}` : title, - id !== null ? "#" + id : "", - null, - score + boost, - filenames[file], - SearchResultKind.title, - ]); - } - } - } - - // search for explicit entries in index directives - for (const [entry, foundEntries] of Object.entries(indexEntries)) { - if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id, isMain] of foundEntries) { - const score = Math.round(100 * queryLower.length / entry.length); - const result = [ - docNames[file], - titles[file], - id ? "#" + id : "", - null, - score, - filenames[file], - SearchResultKind.index, - ]; - if (isMain) { - normalResults.push(result); - } else { - nonMainIndexResults.push(result); - } - } - } - } - - // lookup as object - objectTerms.forEach((term) => - normalResults.push(...Search.performObjectSearch(term, objectTerms)) - ); - - // lookup as search terms in fulltext - normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); - - // let the scorer override scores with a custom scoring function - if (Scorer.score) { - normalResults.forEach((item) => (item[4] = Scorer.score(item))); - nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); - } - - // Sort each group of results by score and then alphabetically by name. - normalResults.sort(_orderResultsByScoreThenName); - nonMainIndexResults.sort(_orderResultsByScoreThenName); - - // Combine the result groups in (reverse) order. - // Non-main index entries are typically arbitrary cross-references, - // so display them after other results. - let results = [...nonMainIndexResults, ...normalResults]; - - // remove duplicate search results - // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept - let seen = new Set(); - results = results.reverse().reduce((acc, result) => { - let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); - if (!seen.has(resultStr)) { - acc.push(result); - seen.add(resultStr); - } - return acc; - }, []); - - return results.reverse(); - }, - - query: (query) => { - const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); - const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); - - // for debugging - //Search.lastresults = results.slice(); // a copy - // console.info("search results:", Search.lastresults); - - // print the results - _displayNextItem(results, results.length, searchTerms, highlightTerms); - }, - - /** - * search for object names - */ - performObjectSearch: (object, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const objects = Search._index.objects; - const objNames = Search._index.objnames; - const titles = Search._index.titles; - - const results = []; - - const objectSearchCallback = (prefix, match) => { - const name = match[4] - const fullname = (prefix ? prefix + "." : "") + name; - const fullnameLower = fullname.toLowerCase(); - if (fullnameLower.indexOf(object) < 0) return; - - let score = 0; - const parts = fullnameLower.split("."); - - // check for different match types: exact matches of full name or - // "last name" (i.e. last dotted part) - if (fullnameLower === object || parts.slice(-1)[0] === object) - score += Scorer.objNameMatch; - else if (parts.slice(-1)[0].indexOf(object) > -1) - score += Scorer.objPartialMatch; // matches in last name - - const objName = objNames[match[1]][2]; - const title = titles[match[0]]; - - // If more than one term searched for, we require other words to be - // found in the name/title/description - const otherTerms = new Set(objectTerms); - otherTerms.delete(object); - if (otherTerms.size > 0) { - const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); - if ( - [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) - ) - return; - } - - let anchor = match[3]; - if (anchor === "") anchor = fullname; - else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; - - const descr = objName + _(", in ") + title; - - // add custom score for some objects according to scorer - if (Scorer.objPrio.hasOwnProperty(match[2])) - score += Scorer.objPrio[match[2]]; - else score += Scorer.objPrioDefault; - - results.push([ - docNames[match[0]], - fullname, - "#" + anchor, - descr, - score, - filenames[match[0]], - SearchResultKind.object, - ]); - }; - Object.keys(objects).forEach((prefix) => - objects[prefix].forEach((array) => - objectSearchCallback(prefix, array) - ) - ); - return results; - }, - - /** - * search for full-text terms in the index - */ - performTermsSearch: (searchTerms, excludedTerms) => { - // prepare search - const terms = Search._index.terms; - const titleTerms = Search._index.titleterms; - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - - const scoreMap = new Map(); - const fileMap = new Map(); - - // perform the search on the required terms - searchTerms.forEach((word) => { - const files = []; - const arr = [ - { files: terms[word], score: Scorer.term }, - { files: titleTerms[word], score: Scorer.title }, - ]; - // add support for partial matches - if (word.length > 2) { - const escapedWord = _escapeRegExp(word); - if (!terms.hasOwnProperty(word)) { - Object.keys(terms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: terms[term], score: Scorer.partialTerm }); - }); - } - if (!titleTerms.hasOwnProperty(word)) { - Object.keys(titleTerms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); - }); - } - } - - // no match but word was a required one - if (arr.every((record) => record.files === undefined)) return; - - // found search word in contents - arr.forEach((record) => { - if (record.files === undefined) return; - - let recordFiles = record.files; - if (recordFiles.length === undefined) recordFiles = [recordFiles]; - files.push(...recordFiles); - - // set score for the word in each file - recordFiles.forEach((file) => { - if (!scoreMap.has(file)) scoreMap.set(file, {}); - scoreMap.get(file)[word] = record.score; - }); - }); - - // create the mapping - files.forEach((file) => { - if (!fileMap.has(file)) fileMap.set(file, [word]); - else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); - }); - }); - - // now check if the files don't contain excluded terms - const results = []; - for (const [file, wordList] of fileMap) { - // check if all requirements are matched - - // as search terms with length < 3 are discarded - const filteredTermCount = [...searchTerms].filter( - (term) => term.length > 2 - ).length; - if ( - wordList.length !== searchTerms.size && - wordList.length !== filteredTermCount - ) - continue; - - // ensure that none of the excluded terms is in the search result - if ( - [...excludedTerms].some( - (term) => - terms[term] === file || - titleTerms[term] === file || - (terms[term] || []).includes(file) || - (titleTerms[term] || []).includes(file) - ) - ) - break; - - // select one (max) score for the file. - const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); - // add result to the result list - results.push([ - docNames[file], - titles[file], - "", - null, - score, - filenames[file], - SearchResultKind.text, - ]); - } - return results; - }, - - /** - * helper function to return a node containing the - * search summary for a given text. keywords is a list - * of stemmed words. - */ - makeSearchSummary: (htmlText, keywords, anchor) => { - const text = Search.htmlToText(htmlText, anchor); - if (text === "") return null; - - const textLower = text.toLowerCase(); - const actualStartPosition = [...keywords] - .map((k) => textLower.indexOf(k.toLowerCase())) - .filter((i) => i > -1) - .slice(-1)[0]; - const startWithContext = Math.max(actualStartPosition - 120, 0); - - const top = startWithContext === 0 ? "" : "..."; - const tail = startWithContext + 240 < text.length ? "..." : ""; - - let summary = document.createElement("p"); - summary.classList.add("context"); - summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; - - return summary; - }, -}; - -_ready(Search.init); diff --git a/docs/0.4.3/_static/sphinx_highlight.js b/docs/0.4.3/_static/sphinx_highlight.js deleted file mode 100644 index 8a96c69a..00000000 --- a/docs/0.4.3/_static/sphinx_highlight.js +++ /dev/null @@ -1,154 +0,0 @@ -/* Highlighting utilities for Sphinx HTML documentation. */ -"use strict"; - -const SPHINX_HIGHLIGHT_ENABLED = true - -/** - * highlight a given string on a node by wrapping it in - * span elements with the given class name. - */ -const _highlight = (node, addItems, text, className) => { - if (node.nodeType === Node.TEXT_NODE) { - const val = node.nodeValue; - const parent = node.parentNode; - const pos = val.toLowerCase().indexOf(text); - if ( - pos >= 0 && - !parent.classList.contains(className) && - !parent.classList.contains("nohighlight") - ) { - let span; - - const closestNode = parent.closest("body, svg, foreignObject"); - const isInSVG = closestNode && closestNode.matches("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.classList.add(className); - } - - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - const rest = document.createTextNode(val.substr(pos + text.length)); - parent.insertBefore( - span, - parent.insertBefore( - rest, - node.nextSibling - ) - ); - node.nodeValue = val.substr(0, pos); - /* There may be more occurrences of search term in this node. So call this - * function recursively on the remaining fragment. - */ - _highlight(rest, addItems, text, className); - - if (isInSVG) { - const rect = document.createElementNS( - "http://www.w3.org/2000/svg", - "rect" - ); - const bbox = parent.getBBox(); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute("class", className); - addItems.push({ parent: parent, target: rect }); - } - } - } else if (node.matches && !node.matches("button, select, textarea")) { - node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); - } -}; -const _highlightText = (thisNode, text, className) => { - let addItems = []; - _highlight(thisNode, addItems, text, className); - addItems.forEach((obj) => - obj.parent.insertAdjacentElement("beforebegin", obj.target) - ); -}; - -/** - * Small JavaScript module for the documentation. - */ -const SphinxHighlight = { - - /** - * highlight the search words provided in localstorage in the text - */ - highlightSearchWords: () => { - if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight - - // get and clear terms from localstorage - const url = new URL(window.location); - const highlight = - localStorage.getItem("sphinx_highlight_terms") - || url.searchParams.get("highlight") - || ""; - localStorage.removeItem("sphinx_highlight_terms") - url.searchParams.delete("highlight"); - window.history.replaceState({}, "", url); - - // get individual terms from highlight string - const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); - if (terms.length === 0) return; // nothing to do - - // There should never be more than one element matching "div.body" - const divBody = document.querySelectorAll("div.body"); - const body = divBody.length ? divBody[0] : document.querySelector("body"); - window.setTimeout(() => { - terms.forEach((term) => _highlightText(body, term, "highlighted")); - }, 10); - - const searchBox = document.getElementById("searchbox"); - if (searchBox === null) return; - searchBox.appendChild( - document - .createRange() - .createContextualFragment( - '

' + - '' + - _("Hide Search Matches") + - "

" - ) - ); - }, - - /** - * helper function to hide the search marks again - */ - hideSearchWords: () => { - document - .querySelectorAll("#searchbox .highlight-link") - .forEach((el) => el.remove()); - document - .querySelectorAll("span.highlighted") - .forEach((el) => el.classList.remove("highlighted")); - localStorage.removeItem("sphinx_highlight_terms") - }, - - initEscapeListener: () => { - // only install a listener if it is really needed - if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; - - document.addEventListener("keydown", (event) => { - // bail for input elements - if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; - // bail with special keys - if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; - if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { - SphinxHighlight.hideSearchWords(); - event.preventDefault(); - } - }); - }, -}; - -_ready(() => { - /* Do not call highlightSearchWords() when we are on the search page. - * It will highlight words from the *previous* search query. - */ - if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); - SphinxHighlight.initEscapeListener(); -}); diff --git a/docs/0.4.3/autodoc/mmif.serialize.html b/docs/0.4.3/autodoc/mmif.serialize.html deleted file mode 100644 index ae784b48..00000000 --- a/docs/0.4.3/autodoc/mmif.serialize.html +++ /dev/null @@ -1,370 +0,0 @@ - - - - - - - - - mmif.serialize module — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.serialize module

-
-

mmif.serialize.model module

-
-
-

mmif.serialize.mmif module

-
-
-

mmif.serialize.view module

-
-
-

mmif.serialize.annotation module

-

The annotation module contains the classes used to represent a -MMIF annotation as a live Python object.

-

In MMIF, annotations are created by apps in a pipeline as a part -of a view. For documentation on how views are represented, see -mmif.serialize.view.

-
-
-class mmif.serialize.annotation.Annotation(anno_obj: bytes | str | dict | None = None)[source]
-

Bases: FreezableMmifObject

-

MmifObject that represents an annotation in a MMIF view.

-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]]) → None[source]
-

Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

-
- -
-
-property at_type: TypesBase[source]
-
- -
-
-property id: str[source]
-
- -
-
-is_document()[source]
-
- -
-
-is_type(at_type: str | TypesBase) → bool[source]
-

Check if the @type of this object matches.

-
- -
- -
-
-class mmif.serialize.annotation.AnnotationProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: FreezableMmifObject

-

AnnotationProperties object that represents the -properties object within a MMIF annotation.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
- -
-
-class mmif.serialize.annotation.Document(doc_obj: bytes | str | dict | None = None)[source]
-

Bases: Annotation

-

Document object that represents a single document in a MMIF file.

-

A document is identified by an ID, and contains certain attributes -and potentially contains the contents of the document itself, -metadata about how the document was created, and/or a list of -subdocuments grouped together logically.

-

If document_obj is not provided, an empty Document will be generated.

-
-
Parameters:
-

document_obj – the JSON data that defines the document

-
-
-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None]) → None[source]
-

Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

-
- -
-
-property location: str[source]
-
- -
-
-location_address() → str[source]
-
- -
-
-location_path() → str[source]
-
- -
-
-location_scheme() → str[source]
-
- -
-
-property parent: str[source]
-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.DocumentProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: AnnotationProperties

-

DocumentProperties object that represents the -properties object within a MMIF document.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
-
-property location: str[source]
-
- -
-
-location_address() → str[source]
-
- -
-
-location_path() → str[source]
-
- -
-
-location_scheme() → str[source]
-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.Text(text_obj: bytes | str | dict | None = None)[source]
-

Bases: FreezableMmifObject

-
-
-property lang: str[source]
-
- -
-
-property value: str[source]
-
- -
- -
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.4.3 - - -
-
- -
0.3.0
-
0.3.1
-
0.3.2
-
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-
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- - - \ No newline at end of file diff --git a/docs/0.4.3/autodoc/mmif.vocabulary.html b/docs/0.4.3/autodoc/mmif.vocabulary.html deleted file mode 100644 index d9c3daaf..00000000 --- a/docs/0.4.3/autodoc/mmif.vocabulary.html +++ /dev/null @@ -1,285 +0,0 @@ - - - - - - - - - mmif.vocabulary module — mmif-python documentation - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.vocabulary module

-
-

mmif.vocabulary.annotation_types module

-
-
-class mmif.vocabulary.annotation_types.AnnotationTypes(type_uri: str)[source]
-

Bases: AnnotationTypesBase

-

This class contains the CLAMS annotation types -defined in the spec version 0.4.2 as class variables.

-
-
-Alignment = http://mmif.clams.ai/0.4.2/vocabulary/Alignment[source]
-
- -
-
-Annotation = http://mmif.clams.ai/0.4.2/vocabulary/Annotation[source]
-
- -
-
-BoundingBox = http://mmif.clams.ai/0.4.2/vocabulary/BoundingBox[source]
-
- -
-
-Chapter = http://mmif.clams.ai/0.4.2/vocabulary/Chapter[source]
-
- -
-
-Interval = http://mmif.clams.ai/0.4.2/vocabulary/Interval[source]
-
- -
-
-Polygon = http://mmif.clams.ai/0.4.2/vocabulary/Polygon[source]
-
- -
-
-Region = http://mmif.clams.ai/0.4.2/vocabulary/Region[source]
-
- -
-
-Relation = http://mmif.clams.ai/0.4.2/vocabulary/Relation[source]
-
- -
-
-Span = http://mmif.clams.ai/0.4.2/vocabulary/Span[source]
-
- -
-
-TimeFrame = http://mmif.clams.ai/0.4.2/vocabulary/TimeFrame[source]
-
- -
-
-TimePoint = http://mmif.clams.ai/0.4.2/vocabulary/TimePoint[source]
-
- -
-
-VideoObject = http://mmif.clams.ai/0.4.2/vocabulary/VideoObject[source]
-
- -
- -
-
-

mmif.vocabulary.document_types module

-
-
-class mmif.vocabulary.document_types.DocumentTypes(type_uri: str)[source]
-

Bases: DocumentTypesBase

-

This class contains the CLAMS document types -defined in the spec version 0.4.2 as class variables.

-
-
-AudioDocument = http://mmif.clams.ai/0.4.2/vocabulary/AudioDocument[source]
-
- -
-
-Document = http://mmif.clams.ai/0.4.2/vocabulary/Document[source]
-
- -
-
-ImageDocument = http://mmif.clams.ai/0.4.2/vocabulary/ImageDocument[source]
-
- -
-
-TextDocument = http://mmif.clams.ai/0.4.2/vocabulary/TextDocument[source]
-
- -
-
-VideoDocument = http://mmif.clams.ai/0.4.2/vocabulary/VideoDocument[source]
-
- -
- -
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.4.3 - - -
-
- -
0.3.0
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- - - \ No newline at end of file diff --git a/docs/0.4.3/consumer-tutorial.html b/docs/0.4.3/consumer-tutorial.html deleted file mode 100644 index 9e10d7a2..00000000 --- a/docs/0.4.3/consumer-tutorial.html +++ /dev/null @@ -1,176 +0,0 @@ - - - - - - - - - MMIF consumer — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • MMIF consumer
    • -
  • -
    • -
-
-
-
-
- -
-

MMIF consumer

-

A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the appliance documentation to learn more about the appliance.

-

MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance.

-
    -

  1. The code must be hosted on a public git repository (e.g. Github, Gitlab, …)

    2. -

  2. Must listen to 5000 port.

    3. -

  3. Must expose /display route .

    4. -

  4. /display router should response to GET requests.

    5. -

  5. In the GET request, a public URL of the input MMIF file is passed via file URL parameter.

    6. -

  6. On the codebase root, there must be a Dockerfile that can build a docker image that runs the web app.

    7. -
-

We provide an example consumer at https://github.com/clamsproject/mmif-visualizer.

-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.4.3 - - -
-
- -
0.3.0
-
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-
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-
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- - - \ No newline at end of file diff --git a/docs/0.4.3/genindex.html b/docs/0.4.3/genindex.html deleted file mode 100644 index 4acb4ba6..00000000 --- a/docs/0.4.3/genindex.html +++ /dev/null @@ -1,404 +0,0 @@ - - - - - - - - Index — mmif-python documentation - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • Index
    • -
  • -
    • -
-
-
-
-
- - -

Index

- -
- A - | B - | C - | D - | I - | L - | M - | P - | R - | S - | T - | V - -
-

A

- - - -
- -

B

- - -
- -

C

- - -
- -

D

- - - -
- -

I

- - - -
- -

L

- - - -
- -

M

- - - -
    -
  • - mmif.serialize.annotation - -
    • -
  • - mmif.vocabulary.annotation_types - -
    • -
  • - mmif.vocabulary.document_types - -
    • -
- -

P

- - - -
- -

R

- - - -
- -

S

- - -
- -

T

- - - -
- -

V

- - - -
- - - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.4.3 - - -
-
- -
0.3.0
-
0.3.1
-
0.3.2
-
0.3.3
-
0.3.4
-
0.3.5
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0.4.0
-
0.4.1
-
0.4.2
-
0.4.3
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0.4.4
-
0.4.5
-
0.4.6
-
0.4.7
-
0.4.8
-
0.5.0
-
0.5.1
-
0.5.2
-
1.0.0
-
1.0.1
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1.0.10
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1.0.11
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1.0.12
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1.0.13
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1.0.14
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1.0.15
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1.0.16
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1.0.6
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- - - \ No newline at end of file diff --git a/docs/0.4.3/index.html b/docs/0.4.3/index.html deleted file mode 100644 index c0ed634b..00000000 --- a/docs/0.4.3/index.html +++ /dev/null @@ -1,203 +0,0 @@ - - - - - - - - - Welcome to mmif-python’s documentation! — mmif-python documentation - - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • Welcome to mmif-python’s documentation!
    • -
  • -
    • -
-
-
-
-
- -
-

Welcome to mmif-python’s documentation!

-
-
-

MMIF for python

-

NOTE that this project is in pre-alpha and being actively developed. Nothing is guaranteed to reliably work for the moment and developer need to be very careful when using APIs implemented here. Please use the issue track to report bugs and malfunctions.

-
-

MultiMedia Interchange Format

-

MMIF is a JSON(-LD)-based data format designed for transferring annotation data between computational analysis applications in CLAMS project.

-
-

Contents

- -
-
-

API documentation:

- -
-
-
-
-

Indices and tables

- -
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.4.3 - - -
-
- -
0.3.0
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0.3.1
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0.3.2
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0.3.3
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0.3.4
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0.3.5
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0.4.0
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0.4.1
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0.4.2
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0.4.3
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0.4.4
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0.4.5
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0.4.6
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0.4.7
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0.4.8
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0.5.0
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0.5.1
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0.5.2
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1.0.0
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1.0.1
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1.0.10
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1.0.11
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- - - \ No newline at end of file diff --git a/docs/0.4.3/introduction.html b/docs/0.4.3/introduction.html deleted file mode 100644 index 5012afbe..00000000 --- a/docs/0.4.3/introduction.html +++ /dev/null @@ -1,236 +0,0 @@ - - - - - - - - - Getting Started — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • Getting Started
    • -
  • -
    • -
-
-
-
-
- -
-

Getting Started

-
-

Overview

-

MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF wbesite. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports de-/serialization of MMIF objects, as well as many navigation and manipulation helpers for MMIF objects.

-
-
-

Prerequisites

-
    -

  • Python: mmif-python requires Python 3.6 or newer. We have no plan to support Python 2.7.

    • -
-
-
-

Installation

-

Package mmif-python is distributed via the official PyPI. Users are supposed to pip-install to get latest release.

-
pip install mmif-python
-
-
-

This will install a package mmif to local python.

-

The MMIF format and specification is evolving over time, and mmif-python package will be updated along with the changes in MMIF format.

-
-

Note

-

MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and mmif-python versions, please take time to read our decision on the subject here. If you need to know which python SDK supports which specification version, see Target MMIF Versions page.

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MMIF Serialization

-

mmif.serialize.mmif.Mmif represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of mmif.serialize.model.MmifObject, including the mmif.serialize.mmif.Mmif. To start with an existing MMIF str, simple initiate a new Mmif object with the file.

-
import mmif
-from mmif import Mmif
-
-mmif_str = """{
-"metadata": {
-  "mmif": "http://mmif.clams.ai/0.2.0"
-},
-"documents": [
-  {
-    "@type": "http://mmif.clams.ai/0.2.0/vocabulary/VideoDocument",
-    "properties": {
-      "id": "m1",
-      "mime": "video/mp4",
-      "location": "file:///var/archive/video-0012.mp4"
-    }
-  },
-  {
-    "@type": "http://mmif.clams.ai/0.2.0/vocabulary/TextDocument",
-    "properties": {
-      "id": "m2",
-      "mime": "text/plain",
-      "location": "file:///var/archive/video-0012-transcript.txt"
-    }
-  }
-],
-"views": []}"""
-mmif_obj = Mmif(mmif_str)
-
-
-

Few notes;

-
    -

  1. MMIF does not carry the primary source files in it.

    2. -

  2. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version mmif-python implementation of the MMIF might not be able to load an unsupported version of MMIF string.

    3. -
-

When serializing back to str, call .serialize() (mmif.serialize.model.MmifObject.serialize()) on the object.

-

To get subcomponents, you can use various getters implemented in subclasses. For more details, the API documentation (mmif package) will help.

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"modul": [0, 1], "multimedia": 3, "overview": 4, "packag": 5, "prerequisit": 4, "python": 3, "serial": [0, 4], "specif": 6, "start": 4, "tabl": 3, "target": 6, "version": 6, "view": 0, "vocabulari": 1, "welcom": 3}}) \ No newline at end of file diff --git a/docs/0.4.3/target-versions.html b/docs/0.4.3/target-versions.html deleted file mode 100644 index fc7d1ef1..00000000 --- a/docs/0.4.3/target-versions.html +++ /dev/null @@ -1,215 +0,0 @@ - - - - - - - - - Target MMIF Versions — mmif-python documentation - - - - - - - - - - - - - - - - - -
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This article provides targeting MMIF specification versions of different versions of mmif-python SDK.

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The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the `appliance documentation `_ to learn more about the appliance. - -MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance. - -#. The code must be hosted on a public git repository (e.g. Github, Gitlab, ...) -#. Must listen to ``5000`` port. -#. Must expose ``/display`` route . -#. ``/display`` router should response to ``GET`` requests. -#. In the ``GET`` request, a public URL of the input MMIF file is passed via ``file`` URL parameter. -#. On the codebase root, there must be a ``Dockerfile`` that can build a `docker `_ image that runs the web app. - -We provide an example consumer at https://github.com/clamsproject/mmif-visualizer. diff --git a/docs/0.4.4/_sources/index.rst.txt b/docs/0.4.4/_sources/index.rst.txt deleted file mode 100644 index 9b90b38e..00000000 --- a/docs/0.4.4/_sources/index.rst.txt +++ /dev/null @@ -1,26 +0,0 @@ -Welcome to mmif-python's documentation! -======================================= - -.. mdinclude:: ../README.md - -.. toctree:: - :maxdepth: 2 - :caption: Contents - - introduction - target-versions - consumer-tutorial - -.. toctree:: - :maxdepth: 2 - :caption: API documentation: - - modules - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/docs/0.4.4/_sources/introduction.rst.txt b/docs/0.4.4/_sources/introduction.rst.txt deleted file mode 100644 index 6fea3a3c..00000000 --- a/docs/0.4.4/_sources/introduction.rst.txt +++ /dev/null @@ -1,78 +0,0 @@ -.. _instroduction: - -Getting Started -=============== - - -Overview ---------- - -MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF wbesite `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports de-/serialization of MMIF objects, as well as many navigation and manipulation helpers for MMIF objects. - -Prerequisites -------------- - -* `Python `_: ``mmif-python`` requires Python 3.6 or newer. We have no plan to support `Python 2.7 `_. - -Installation ---------------- - -Package ``mmif-python`` is distributed via the official PyPI. Users are supposed to pip-install to get latest release. - -.. code-block:: bash - - pip install mmif-python - -This will install a package `mmif` to local python. - -The MMIF format and specification is evolving over time, and ``mmif-python`` package will be updated along with the changes in MMIF format. - -.. note:: MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and ``mmif-python`` versions, please take time to read our decision on the subject `here `_. If you need to know which python SDK supports which specification version, see :ref:`target-versions` page. - -MMIF Serialization ---------------------------- - -:class:`mmif.serialize.mmif.Mmif` represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of :class:`mmif.serialize.model.MmifObject`, including the :class:`mmif.serialize.mmif.Mmif`. To start with an existing MMIF :class:`str`, simple initiate a new ``Mmif`` object with the file. - -.. code-block:: python - - import mmif - from mmif import Mmif - - mmif_str = """{ - "metadata": { - "mmif": "http://mmif.clams.ai/0.2.0" - }, - "documents": [ - { - "@type": "http://mmif.clams.ai/0.2.0/vocabulary/VideoDocument", - "properties": { - "id": "m1", - "mime": "video/mp4", - "location": "file:///var/archive/video-0012.mp4" - } - }, - { - "@type": "http://mmif.clams.ai/0.2.0/vocabulary/TextDocument", - "properties": { - "id": "m2", - "mime": "text/plain", - "location": "file:///var/archive/video-0012-transcript.txt" - } - } - ], - "views": []}""" - mmif_obj = Mmif(mmif_str) - - -Few notes; - -#. MMIF does not carry the primary source files in it. -#. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version ``mmif-python`` implementation of the MMIF might not be able to load an unsupported version of MMIF string. - -When serializing back to :class:`str`, call ``.serialize()`` (:meth:`mmif.serialize.model.MmifObject.serialize`) on the object. - -To get subcomponents, you can use various getters implemented in subclasses. For more details, the API documentation (:ref:`apidoc`) will help. - diff --git a/docs/0.4.4/_sources/modules.rst.txt b/docs/0.4.4/_sources/modules.rst.txt deleted file mode 100644 index e4269c6d..00000000 --- a/docs/0.4.4/_sources/modules.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _apidoc: - -mmif package -============ - -.. toctree:: - :maxdepth: 4 - - autodoc/mmif.serialize - autodoc/mmif.vocabulary diff --git a/docs/0.4.4/_sources/target-versions.rst.txt b/docs/0.4.4/_sources/target-versions.rst.txt deleted file mode 100644 index 34216d3e..00000000 --- a/docs/0.4.4/_sources/target-versions.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _target-versions: - -Target MMIF Versions -==================== - -This article provides targeting MMIF specification versions of different versions of ``mmif-python`` SDK. - -.. csv-table:: Target Specification Versions - :file: target-versions.csv - :header-rows: 1 diff --git a/docs/0.4.4/_static/_sphinx_javascript_frameworks_compat.js b/docs/0.4.4/_static/_sphinx_javascript_frameworks_compat.js deleted file mode 100644 index 81415803..00000000 --- a/docs/0.4.4/_static/_sphinx_javascript_frameworks_compat.js +++ /dev/null @@ -1,123 +0,0 @@ -/* Compatability shim for jQuery and underscores.js. - * - * Copyright Sphinx contributors - * Released under the two clause BSD licence - */ - -/** - * small helper function to urldecode strings - * - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL - */ -jQuery.urldecode = function(x) { - if (!x) { - return x - } - return decodeURIComponent(x.replace(/\+/g, ' ')); -}; - -/** - * small helper function to urlencode strings - */ -jQuery.urlencode = encodeURIComponent; - -/** - * This function returns the parsed url parameters of the - * current request. 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- -/** - * Simple result scoring code. - */ -if (typeof Scorer === "undefined") { - var Scorer = { - // Implement the following function to further tweak the score for each result - // The function takes a result array [docname, title, anchor, descr, score, filename] - // and returns the new score. - /* - score: result => { - const [docname, title, anchor, descr, score, filename, kind] = result - return score - }, - */ - - // query matches the full name of an object - objNameMatch: 11, - // or matches in the last dotted part of the object name - objPartialMatch: 6, - // Additive scores depending on the priority of the object - objPrio: { - 0: 15, // used to be importantResults - 1: 5, // used to be objectResults - 2: -5, // used to be unimportantResults - }, - // Used when the priority is not in the mapping. - objPrioDefault: 0, - - // query found in title - title: 15, - partialTitle: 7, - // query found in terms - term: 5, - partialTerm: 2, - }; -} - -// Global search result kind enum, used by themes to style search results. -class SearchResultKind { - static get index() { return "index"; } - static get object() { return "object"; } - static get text() { return "text"; } - static get title() { return "title"; } -} - -const _removeChildren = (element) => { - while (element && element.lastChild) element.removeChild(element.lastChild); -}; - -/** - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping - */ -const _escapeRegExp = (string) => - string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string - -const _displayItem = (item, searchTerms, highlightTerms) => { - const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; - const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; - const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; - const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; - const contentRoot = document.documentElement.dataset.content_root; - - const [docName, title, anchor, descr, score, _filename, kind] = item; - - let listItem = document.createElement("li"); - // Add a class representing the item's type: - // can be used by a theme's CSS selector for styling - // See SearchResultKind for the class names. - listItem.classList.add(`kind-${kind}`); - let requestUrl; - let linkUrl; - if (docBuilder === "dirhtml") { - // dirhtml builder - let dirname = docName + "/"; - if (dirname.match(/\/index\/$/)) - dirname = dirname.substring(0, dirname.length - 6); - else if (dirname === "index/") dirname = ""; - requestUrl = contentRoot + dirname; - linkUrl = requestUrl; - } else { - // normal html builders - requestUrl = contentRoot + docName + docFileSuffix; - linkUrl = docName + docLinkSuffix; - } - let linkEl = listItem.appendChild(document.createElement("a")); - linkEl.href = linkUrl + anchor; - linkEl.dataset.score = score; - linkEl.innerHTML = title; - if (descr) { - listItem.appendChild(document.createElement("span")).innerHTML = - " (" + descr + ")"; - // highlight search terms in the description - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - } - else if (showSearchSummary) - fetch(requestUrl) - .then((responseData) => responseData.text()) - .then((data) => { - if (data) - listItem.appendChild( - Search.makeSearchSummary(data, searchTerms, anchor) - ); - // highlight search terms in the summary - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - }); - Search.output.appendChild(listItem); -}; -const _finishSearch = (resultCount) => { - Search.stopPulse(); - Search.title.innerText = _("Search Results"); - if (!resultCount) - Search.status.innerText = Documentation.gettext( - "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." - ); - else - Search.status.innerText = Documentation.ngettext( - "Search finished, found one page matching the search query.", - "Search finished, found ${resultCount} pages matching the search query.", - resultCount, - ).replace('${resultCount}', resultCount); -}; -const _displayNextItem = ( - results, - resultCount, - searchTerms, - highlightTerms, -) => { - // results left, load the summary and display it - // this is intended to be dynamic (don't sub resultsCount) - if (results.length) { - _displayItem(results.pop(), searchTerms, highlightTerms); - setTimeout( - () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), - 5 - ); - } - // search finished, update title and status message - else _finishSearch(resultCount); -}; -// Helper function used by query() to order search results. -// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. -// Order the results by score (in opposite order of appearance, since the -// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. -const _orderResultsByScoreThenName = (a, b) => { - const leftScore = a[4]; - const rightScore = b[4]; - if (leftScore === rightScore) { - // same score: sort alphabetically - const leftTitle = a[1].toLowerCase(); - const rightTitle = b[1].toLowerCase(); - if (leftTitle === rightTitle) return 0; - return leftTitle > rightTitle ? -1 : 1; // inverted is intentional - } - return leftScore > rightScore ? 1 : -1; -}; - -/** - * Default splitQuery function. Can be overridden in ``sphinx.search`` with a - * custom function per language. - * - * The regular expression works by splitting the string on consecutive characters - * that are not Unicode letters, numbers, underscores, or emoji characters. - * This is the same as ``\W+`` in Python, preserving the surrogate pair area. - */ -if (typeof splitQuery === "undefined") { - var splitQuery = (query) => query - .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) - .filter(term => term) // remove remaining empty strings -} - -/** - * Search Module - */ -const Search = { - _index: null, - _queued_query: null, - _pulse_status: -1, - - htmlToText: (htmlString, anchor) => { - const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - for (const removalQuery of [".headerlink", "script", "style"]) { - htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); - } - if (anchor) { - const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); - if (anchorContent) return anchorContent.textContent; - - console.warn( - `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` - ); - } - - // if anchor not specified or not found, fall back to main content - const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent) return docContent.textContent; - - console.warn( - "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." - ); - return ""; - }, - - init: () => { - const query = new URLSearchParams(window.location.search).get("q"); - document - .querySelectorAll('input[name="q"]') - .forEach((el) => (el.value = query)); - if (query) Search.performSearch(query); - }, - - loadIndex: (url) => - (document.body.appendChild(document.createElement("script")).src = url), - - setIndex: (index) => { - Search._index = index; - if (Search._queued_query !== null) { - const query = Search._queued_query; - Search._queued_query = null; - Search.query(query); - } - }, - - hasIndex: () => Search._index !== null, - - deferQuery: (query) => (Search._queued_query = query), - - stopPulse: () => (Search._pulse_status = -1), - - startPulse: () => { - if (Search._pulse_status >= 0) return; - - const pulse = () => { - Search._pulse_status = (Search._pulse_status + 1) % 4; - Search.dots.innerText = ".".repeat(Search._pulse_status); - if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); - }; - pulse(); - }, - - /** - * perform a search for something (or wait until index is loaded) - */ - performSearch: (query) => { - // create the required interface elements - const searchText = document.createElement("h2"); - searchText.textContent = _("Searching"); - const searchSummary = document.createElement("p"); - searchSummary.classList.add("search-summary"); - searchSummary.innerText = ""; - const searchList = document.createElement("ul"); - searchList.setAttribute("role", "list"); - searchList.classList.add("search"); - - const out = document.getElementById("search-results"); - Search.title = out.appendChild(searchText); - Search.dots = Search.title.appendChild(document.createElement("span")); - Search.status = out.appendChild(searchSummary); - Search.output = out.appendChild(searchList); - - const searchProgress = document.getElementById("search-progress"); - // Some themes don't use the search progress node - if (searchProgress) { - searchProgress.innerText = _("Preparing search..."); - } - Search.startPulse(); - - // index already loaded, the browser was quick! - if (Search.hasIndex()) Search.query(query); - else Search.deferQuery(query); - }, - - _parseQuery: (query) => { - // stem the search terms and add them to the correct list - const stemmer = new Stemmer(); - const searchTerms = new Set(); - const excludedTerms = new Set(); - const highlightTerms = new Set(); - const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); - splitQuery(query.trim()).forEach((queryTerm) => { - const queryTermLower = queryTerm.toLowerCase(); - - // maybe skip this "word" - // stopwords array is from language_data.js - if ( - stopwords.indexOf(queryTermLower) !== -1 || - queryTerm.match(/^\d+$/) - ) - return; - - // stem the word - let word = stemmer.stemWord(queryTermLower); - // select the correct list - if (word[0] === "-") excludedTerms.add(word.substr(1)); - else { - searchTerms.add(word); - highlightTerms.add(queryTermLower); - } - }); - - if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js - localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) - } - - // console.debug("SEARCH: searching for:"); - // console.info("required: ", [...searchTerms]); - // console.info("excluded: ", [...excludedTerms]); - - return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; - }, - - /** - * execute search (requires search index to be loaded) - */ - _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - - // Collect multiple result groups to be sorted separately and then ordered. - // Each is an array of [docname, title, anchor, descr, score, filename, kind]. - const normalResults = []; - const nonMainIndexResults = []; - - _removeChildren(document.getElementById("search-progress")); - - const queryLower = query.toLowerCase().trim(); - for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { - for (const [file, id] of foundTitles) { - const score = Math.round(Scorer.title * queryLower.length / title.length); - const boost = titles[file] === title ? 1 : 0; // add a boost for document titles - normalResults.push([ - docNames[file], - titles[file] !== title ? `${titles[file]} > ${title}` : title, - id !== null ? "#" + id : "", - null, - score + boost, - filenames[file], - SearchResultKind.title, - ]); - } - } - } - - // search for explicit entries in index directives - for (const [entry, foundEntries] of Object.entries(indexEntries)) { - if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id, isMain] of foundEntries) { - const score = Math.round(100 * queryLower.length / entry.length); - const result = [ - docNames[file], - titles[file], - id ? "#" + id : "", - null, - score, - filenames[file], - SearchResultKind.index, - ]; - if (isMain) { - normalResults.push(result); - } else { - nonMainIndexResults.push(result); - } - } - } - } - - // lookup as object - objectTerms.forEach((term) => - normalResults.push(...Search.performObjectSearch(term, objectTerms)) - ); - - // lookup as search terms in fulltext - normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); - - // let the scorer override scores with a custom scoring function - if (Scorer.score) { - normalResults.forEach((item) => (item[4] = Scorer.score(item))); - nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); - } - - // Sort each group of results by score and then alphabetically by name. - normalResults.sort(_orderResultsByScoreThenName); - nonMainIndexResults.sort(_orderResultsByScoreThenName); - - // Combine the result groups in (reverse) order. - // Non-main index entries are typically arbitrary cross-references, - // so display them after other results. - let results = [...nonMainIndexResults, ...normalResults]; - - // remove duplicate search results - // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept - let seen = new Set(); - results = results.reverse().reduce((acc, result) => { - let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); - if (!seen.has(resultStr)) { - acc.push(result); - seen.add(resultStr); - } - return acc; - }, []); - - return results.reverse(); - }, - - query: (query) => { - const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); - const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); - - // for debugging - //Search.lastresults = results.slice(); // a copy - // console.info("search results:", Search.lastresults); - - // print the results - _displayNextItem(results, results.length, searchTerms, highlightTerms); - }, - - /** - * search for object names - */ - performObjectSearch: (object, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const objects = Search._index.objects; - const objNames = Search._index.objnames; - const titles = Search._index.titles; - - const results = []; - - const objectSearchCallback = (prefix, match) => { - const name = match[4] - const fullname = (prefix ? prefix + "." : "") + name; - const fullnameLower = fullname.toLowerCase(); - if (fullnameLower.indexOf(object) < 0) return; - - let score = 0; - const parts = fullnameLower.split("."); - - // check for different match types: exact matches of full name or - // "last name" (i.e. last dotted part) - if (fullnameLower === object || parts.slice(-1)[0] === object) - score += Scorer.objNameMatch; - else if (parts.slice(-1)[0].indexOf(object) > -1) - score += Scorer.objPartialMatch; // matches in last name - - const objName = objNames[match[1]][2]; - const title = titles[match[0]]; - - // If more than one term searched for, we require other words to be - // found in the name/title/description - const otherTerms = new Set(objectTerms); - otherTerms.delete(object); - if (otherTerms.size > 0) { - const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); - if ( - [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) - ) - return; - } - - let anchor = match[3]; - if (anchor === "") anchor = fullname; - else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; - - const descr = objName + _(", in ") + title; - - // add custom score for some objects according to scorer - if (Scorer.objPrio.hasOwnProperty(match[2])) - score += Scorer.objPrio[match[2]]; - else score += Scorer.objPrioDefault; - - results.push([ - docNames[match[0]], - fullname, - "#" + anchor, - descr, - score, - filenames[match[0]], - SearchResultKind.object, - ]); - }; - Object.keys(objects).forEach((prefix) => - objects[prefix].forEach((array) => - objectSearchCallback(prefix, array) - ) - ); - return results; - }, - - /** - * search for full-text terms in the index - */ - performTermsSearch: (searchTerms, excludedTerms) => { - // prepare search - const terms = Search._index.terms; - const titleTerms = Search._index.titleterms; - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - - const scoreMap = new Map(); - const fileMap = new Map(); - - // perform the search on the required terms - searchTerms.forEach((word) => { - const files = []; - const arr = [ - { files: terms[word], score: Scorer.term }, - { files: titleTerms[word], score: Scorer.title }, - ]; - // add support for partial matches - if (word.length > 2) { - const escapedWord = _escapeRegExp(word); - if (!terms.hasOwnProperty(word)) { - Object.keys(terms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: terms[term], score: Scorer.partialTerm }); - }); - } - if (!titleTerms.hasOwnProperty(word)) { - Object.keys(titleTerms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); - }); - } - } - - // no match but word was a required one - if (arr.every((record) => record.files === undefined)) return; - - // found search word in contents - arr.forEach((record) => { - if (record.files === undefined) return; - - let recordFiles = record.files; - if (recordFiles.length === undefined) recordFiles = [recordFiles]; - files.push(...recordFiles); - - // set score for the word in each file - recordFiles.forEach((file) => { - if (!scoreMap.has(file)) scoreMap.set(file, {}); - scoreMap.get(file)[word] = record.score; - }); - }); - - // create the mapping - files.forEach((file) => { - if (!fileMap.has(file)) fileMap.set(file, [word]); - else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); - }); - }); - - // now check if the files don't contain excluded terms - const results = []; - for (const [file, wordList] of fileMap) { - // check if all requirements are matched - - // as search terms with length < 3 are discarded - const filteredTermCount = [...searchTerms].filter( - (term) => term.length > 2 - ).length; - if ( - wordList.length !== searchTerms.size && - wordList.length !== filteredTermCount - ) - continue; - - // ensure that none of the excluded terms is in the search result - if ( - [...excludedTerms].some( - (term) => - terms[term] === file || - titleTerms[term] === file || - (terms[term] || []).includes(file) || - (titleTerms[term] || []).includes(file) - ) - ) - break; - - // select one (max) score for the file. - const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); - // add result to the result list - results.push([ - docNames[file], - titles[file], - "", - null, - score, - filenames[file], - SearchResultKind.text, - ]); - } - return results; - }, - - /** - * helper function to return a node containing the - * search summary for a given text. keywords is a list - * of stemmed words. - */ - makeSearchSummary: (htmlText, keywords, anchor) => { - const text = Search.htmlToText(htmlText, anchor); - if (text === "") return null; - - const textLower = text.toLowerCase(); - const actualStartPosition = [...keywords] - .map((k) => textLower.indexOf(k.toLowerCase())) - .filter((i) => i > -1) - .slice(-1)[0]; - const startWithContext = Math.max(actualStartPosition - 120, 0); - - const top = startWithContext === 0 ? "" : "..."; - const tail = startWithContext + 240 < text.length ? "..." : ""; - - let summary = document.createElement("p"); - summary.classList.add("context"); - summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; - - return summary; - }, -}; - -_ready(Search.init); diff --git a/docs/0.4.4/_static/sphinx_highlight.js b/docs/0.4.4/_static/sphinx_highlight.js deleted file mode 100644 index 8a96c69a..00000000 --- a/docs/0.4.4/_static/sphinx_highlight.js +++ /dev/null @@ -1,154 +0,0 @@ -/* Highlighting utilities for Sphinx HTML documentation. */ -"use strict"; - -const SPHINX_HIGHLIGHT_ENABLED = true - -/** - * highlight a given string on a node by wrapping it in - * span elements with the given class name. - */ -const _highlight = (node, addItems, text, className) => { - if (node.nodeType === Node.TEXT_NODE) { - const val = node.nodeValue; - const parent = node.parentNode; - const pos = val.toLowerCase().indexOf(text); - if ( - pos >= 0 && - !parent.classList.contains(className) && - !parent.classList.contains("nohighlight") - ) { - let span; - - const closestNode = parent.closest("body, svg, foreignObject"); - const isInSVG = closestNode && closestNode.matches("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.classList.add(className); - } - - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - const rest = document.createTextNode(val.substr(pos + text.length)); - parent.insertBefore( - span, - parent.insertBefore( - rest, - node.nextSibling - ) - ); - node.nodeValue = val.substr(0, pos); - /* There may be more occurrences of search term in this node. So call this - * function recursively on the remaining fragment. - */ - _highlight(rest, addItems, text, className); - - if (isInSVG) { - const rect = document.createElementNS( - "http://www.w3.org/2000/svg", - "rect" - ); - const bbox = parent.getBBox(); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute("class", className); - addItems.push({ parent: parent, target: rect }); - } - } - } else if (node.matches && !node.matches("button, select, textarea")) { - node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); - } -}; -const _highlightText = (thisNode, text, className) => { - let addItems = []; - _highlight(thisNode, addItems, text, className); - addItems.forEach((obj) => - obj.parent.insertAdjacentElement("beforebegin", obj.target) - ); -}; - -/** - * Small JavaScript module for the documentation. - */ -const SphinxHighlight = { - - /** - * highlight the search words provided in localstorage in the text - */ - highlightSearchWords: () => { - if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight - - // get and clear terms from localstorage - const url = new URL(window.location); - const highlight = - localStorage.getItem("sphinx_highlight_terms") - || url.searchParams.get("highlight") - || ""; - localStorage.removeItem("sphinx_highlight_terms") - url.searchParams.delete("highlight"); - window.history.replaceState({}, "", url); - - // get individual terms from highlight string - const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); - if (terms.length === 0) return; // nothing to do - - // There should never be more than one element matching "div.body" - const divBody = document.querySelectorAll("div.body"); - const body = divBody.length ? divBody[0] : document.querySelector("body"); - window.setTimeout(() => { - terms.forEach((term) => _highlightText(body, term, "highlighted")); - }, 10); - - const searchBox = document.getElementById("searchbox"); - if (searchBox === null) return; - searchBox.appendChild( - document - .createRange() - .createContextualFragment( - '

' + - '' + - _("Hide Search Matches") + - "

" - ) - ); - }, - - /** - * helper function to hide the search marks again - */ - hideSearchWords: () => { - document - .querySelectorAll("#searchbox .highlight-link") - .forEach((el) => el.remove()); - document - .querySelectorAll("span.highlighted") - .forEach((el) => el.classList.remove("highlighted")); - localStorage.removeItem("sphinx_highlight_terms") - }, - - initEscapeListener: () => { - // only install a listener if it is really needed - if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; - - document.addEventListener("keydown", (event) => { - // bail for input elements - if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; - // bail with special keys - if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; - if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { - SphinxHighlight.hideSearchWords(); - event.preventDefault(); - } - }); - }, -}; - -_ready(() => { - /* Do not call highlightSearchWords() when we are on the search page. - * It will highlight words from the *previous* search query. - */ - if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); - SphinxHighlight.initEscapeListener(); -}); diff --git a/docs/0.4.4/autodoc/mmif.serialize.html b/docs/0.4.4/autodoc/mmif.serialize.html deleted file mode 100644 index ee741535..00000000 --- a/docs/0.4.4/autodoc/mmif.serialize.html +++ /dev/null @@ -1,370 +0,0 @@ - - - - - - - - - mmif.serialize module — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.serialize module

-
-

mmif.serialize.model module

-
-
-

mmif.serialize.mmif module

-
-
-

mmif.serialize.view module

-
-
-

mmif.serialize.annotation module

-

The annotation module contains the classes used to represent a -MMIF annotation as a live Python object.

-

In MMIF, annotations are created by apps in a pipeline as a part -of a view. For documentation on how views are represented, see -mmif.serialize.view.

-
-
-class mmif.serialize.annotation.Annotation(anno_obj: bytes | str | dict | None = None)[source]
-

Bases: FreezableMmifObject

-

MmifObject that represents an annotation in a MMIF view.

-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]]) → None[source]
-

Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

-
- -
-
-property at_type: TypesBase[source]
-
- -
-
-property id: str[source]
-
- -
-
-is_document()[source]
-
- -
-
-is_type(at_type: str | TypesBase) → bool[source]
-

Check if the @type of this object matches.

-
- -
- -
-
-class mmif.serialize.annotation.AnnotationProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: FreezableMmifObject

-

AnnotationProperties object that represents the -properties object within a MMIF annotation.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
- -
-
-class mmif.serialize.annotation.Document(doc_obj: bytes | str | dict | None = None)[source]
-

Bases: Annotation

-

Document object that represents a single document in a MMIF file.

-

A document is identified by an ID, and contains certain attributes -and potentially contains the contents of the document itself, -metadata about how the document was created, and/or a list of -subdocuments grouped together logically.

-

If document_obj is not provided, an empty Document will be generated.

-
-
Parameters:
-

document_obj – the JSON data that defines the document

-
-
-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None]) → None[source]
-

Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

-
- -
-
-property location: str[source]
-
- -
-
-location_address() → str[source]
-
- -
-
-location_path() → str[source]
-
- -
-
-location_scheme() → str[source]
-
- -
-
-property parent: str[source]
-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.DocumentProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: AnnotationProperties

-

DocumentProperties object that represents the -properties object within a MMIF document.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
-
-property location: str[source]
-
- -
-
-location_address() → str[source]
-
- -
-
-location_path() → str[source]
-
- -
-
-location_scheme() → str[source]
-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.Text(text_obj: bytes | str | dict | None = None)[source]
-

Bases: FreezableMmifObject

-
-
-property lang: str[source]
-
- -
-
-property value: str[source]
-
- -
- -
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.4.4 - - -
-
- -
0.3.0
-
0.3.1
-
0.3.2
-
0.3.3
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0.3.4
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0.3.5
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0.4.1
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0.4.3
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- - - \ No newline at end of file diff --git a/docs/0.4.4/autodoc/mmif.vocabulary.html b/docs/0.4.4/autodoc/mmif.vocabulary.html deleted file mode 100644 index 6e08426b..00000000 --- a/docs/0.4.4/autodoc/mmif.vocabulary.html +++ /dev/null @@ -1,285 +0,0 @@ - - - - - - - - - mmif.vocabulary module — mmif-python documentation - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.vocabulary module

-
-

mmif.vocabulary.annotation_types module

-
-
-class mmif.vocabulary.annotation_types.AnnotationTypes(type_uri: str)[source]
-

Bases: AnnotationTypesBase

-

This class contains the CLAMS annotation types -defined in the spec version 0.4.2 as class variables.

-
-
-Alignment = http://mmif.clams.ai/0.4.2/vocabulary/Alignment[source]
-
- -
-
-Annotation = http://mmif.clams.ai/0.4.2/vocabulary/Annotation[source]
-
- -
-
-BoundingBox = http://mmif.clams.ai/0.4.2/vocabulary/BoundingBox[source]
-
- -
-
-Chapter = http://mmif.clams.ai/0.4.2/vocabulary/Chapter[source]
-
- -
-
-Interval = http://mmif.clams.ai/0.4.2/vocabulary/Interval[source]
-
- -
-
-Polygon = http://mmif.clams.ai/0.4.2/vocabulary/Polygon[source]
-
- -
-
-Region = http://mmif.clams.ai/0.4.2/vocabulary/Region[source]
-
- -
-
-Relation = http://mmif.clams.ai/0.4.2/vocabulary/Relation[source]
-
- -
-
-Span = http://mmif.clams.ai/0.4.2/vocabulary/Span[source]
-
- -
-
-TimeFrame = http://mmif.clams.ai/0.4.2/vocabulary/TimeFrame[source]
-
- -
-
-TimePoint = http://mmif.clams.ai/0.4.2/vocabulary/TimePoint[source]
-
- -
-
-VideoObject = http://mmif.clams.ai/0.4.2/vocabulary/VideoObject[source]
-
- -
- -
-
-

mmif.vocabulary.document_types module

-
-
-class mmif.vocabulary.document_types.DocumentTypes(type_uri: str)[source]
-

Bases: DocumentTypesBase

-

This class contains the CLAMS document types -defined in the spec version 0.4.2 as class variables.

-
-
-AudioDocument = http://mmif.clams.ai/0.4.2/vocabulary/AudioDocument[source]
-
- -
-
-Document = http://mmif.clams.ai/0.4.2/vocabulary/Document[source]
-
- -
-
-ImageDocument = http://mmif.clams.ai/0.4.2/vocabulary/ImageDocument[source]
-
- -
-
-TextDocument = http://mmif.clams.ai/0.4.2/vocabulary/TextDocument[source]
-
- -
-
-VideoDocument = http://mmif.clams.ai/0.4.2/vocabulary/VideoDocument[source]
-
- -
- -
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.4.4 - - -
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- -
0.3.0
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0.3.1
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0.3.2
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0.3.3
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0.3.4
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- - - \ No newline at end of file diff --git a/docs/0.4.4/consumer-tutorial.html b/docs/0.4.4/consumer-tutorial.html deleted file mode 100644 index b4fb7386..00000000 --- a/docs/0.4.4/consumer-tutorial.html +++ /dev/null @@ -1,176 +0,0 @@ - - - - - - - - - MMIF consumer — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • MMIF consumer
    • -
  • -
    • -
-
-
-
-
- -
-

MMIF consumer

-

A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the appliance documentation to learn more about the appliance.

-

MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance.

-
    -

  1. The code must be hosted on a public git repository (e.g. Github, Gitlab, …)

    2. -

  2. Must listen to 5000 port.

    3. -

  3. Must expose /display route .

    4. -

  4. /display router should response to GET requests.

    5. -

  5. In the GET request, a public URL of the input MMIF file is passed via file URL parameter.

    6. -

  6. On the codebase root, there must be a Dockerfile that can build a docker image that runs the web app.

    7. -
-

We provide an example consumer at https://github.com/clamsproject/mmif-visualizer.

-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.4.4 - - -
-
- -
0.3.0
-
0.3.1
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0.3.2
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0.3.3
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0.3.4
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0.4.1
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- - -
- -
-
-
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    -
    • -
  • Index
    • -
  • -
    • -
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- - -

Index

- -
- A - | B - | C - | D - | I - | L - | M - | P - | R - | S - | T - | V - -
-

A

- - - -
- -

B

- - -
- -

C

- - -
- -

D

- - - -
- -

I

- - - -
- -

L

- - - -
- -

M

- - - -
    -
  • - mmif.serialize.annotation - -
    • -
  • - mmif.vocabulary.annotation_types - -
    • -
  • - mmif.vocabulary.document_types - -
    • -
- -

P

- - - -
- -

R

- - - -
- -

S

- - -
- -

T

- - - -
- -

V

- - - -
- - - -
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- -
-
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- -
- - Other Versions - v: 0.4.4 - - -
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0.3.2
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0.3.3
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0.3.4
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0.4.1
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0.4.2
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- - -
- -
-
-
-
    -
    • -
  • Welcome to mmif-python’s documentation!
    • -
  • -
    • -
-
-
-
-
- -
-

Welcome to mmif-python’s documentation!

-
-
-

MMIF for python

-

NOTE that this project is in pre-alpha and being actively developed. Nothing is guaranteed to reliably work for the moment and developer need to be very careful when using APIs implemented here. Please use the issue track to report bugs and malfunctions.

-
-

MultiMedia Interchange Format

-

MMIF is a JSON(-LD)-based data format designed for transferring annotation data between computational analysis applications in CLAMS project.

-
-

Contents

- -
-
-

API documentation:

- -
-
-
-
-

Indices and tables

- -
- - -
-
- -
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-
- -
- - Other Versions - v: 0.4.4 - - -
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0.3.0
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0.3.1
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0.3.2
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- - - \ No newline at end of file diff --git a/docs/0.4.4/introduction.html b/docs/0.4.4/introduction.html deleted file mode 100644 index e1e89cc0..00000000 --- a/docs/0.4.4/introduction.html +++ /dev/null @@ -1,236 +0,0 @@ - - - - - - - - - Getting Started — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
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  • Getting Started
    • -
  • -
    • -
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Getting Started

-
-

Overview

-

MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF wbesite. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports de-/serialization of MMIF objects, as well as many navigation and manipulation helpers for MMIF objects.

-
-
-

Prerequisites

-
    -

  • Python: mmif-python requires Python 3.6 or newer. We have no plan to support Python 2.7.

    • -
-
-
-

Installation

-

Package mmif-python is distributed via the official PyPI. Users are supposed to pip-install to get latest release.

-
pip install mmif-python
-
-
-

This will install a package mmif to local python.

-

The MMIF format and specification is evolving over time, and mmif-python package will be updated along with the changes in MMIF format.

-
-

Note

-

MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and mmif-python versions, please take time to read our decision on the subject here. If you need to know which python SDK supports which specification version, see Target MMIF Versions page.

-
-
-
-

MMIF Serialization

-

mmif.serialize.mmif.Mmif represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of mmif.serialize.model.MmifObject, including the mmif.serialize.mmif.Mmif. To start with an existing MMIF str, simple initiate a new Mmif object with the file.

-
import mmif
-from mmif import Mmif
-
-mmif_str = """{
-"metadata": {
-  "mmif": "http://mmif.clams.ai/0.2.0"
-},
-"documents": [
-  {
-    "@type": "http://mmif.clams.ai/0.2.0/vocabulary/VideoDocument",
-    "properties": {
-      "id": "m1",
-      "mime": "video/mp4",
-      "location": "file:///var/archive/video-0012.mp4"
-    }
-  },
-  {
-    "@type": "http://mmif.clams.ai/0.2.0/vocabulary/TextDocument",
-    "properties": {
-      "id": "m2",
-      "mime": "text/plain",
-      "location": "file:///var/archive/video-0012-transcript.txt"
-    }
-  }
-],
-"views": []}"""
-mmif_obj = Mmif(mmif_str)
-
-
-

Few notes;

-
    -

  1. MMIF does not carry the primary source files in it.

    2. -

  2. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version mmif-python implementation of the MMIF might not be able to load an unsupported version of MMIF string.

    3. -
-

When serializing back to str, call .serialize() (mmif.serialize.model.MmifObject.serialize()) on the object.

-

To get subcomponents, you can use various getters implemented in subclasses. For more details, the API documentation (mmif package) will help.

-
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.4.4 - - -
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0.3.0
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0.3.1
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0.3.2
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0.3.3
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0.3.4
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- - - \ No newline at end of file diff --git a/docs/0.4.4/modules.html b/docs/0.4.4/modules.html deleted file mode 100644 index 02ffb6c4..00000000 --- a/docs/0.4.4/modules.html +++ /dev/null @@ -1,248 +0,0 @@ - - - - - - - - - mmif package — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
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  • mmif package
    • -
  • -
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mmif package

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- - - \ No newline at end of file diff --git a/docs/0.4.4/objects.inv b/docs/0.4.4/objects.inv deleted file mode 100644 index 5f363fb6..00000000 --- a/docs/0.4.4/objects.inv +++ /dev/null @@ -1,9 +0,0 @@ -# Sphinx inventory version 2 -# Project: mmif-python -# Version: 0.4.4 -# The remainder of this file is compressed using zlib. -xڽ0y -WڽmV95F}>I I 1l9Ԡ'TnsBK#*? FܘSEB$Qd -hL&aU@ EYⅪ#(su)xc@ǧA|Xgs߇O#S}U3opgk|AUk=G8bĩHK'=קg OS`9/@ȯuBnM3H7IaWO`_r9 iv:8wlW;RQ}Gjtu/K0ˣ-026W R_zۂ.c9<(j#Rɖ"X;įncd~ʄöLQY~T}/Xj)Z0'[NIpCu7%o.M~ .m$ -y:X -m4ɵxC;C40SRL$p'wo~\ k - - - - - Python Module Index — mmif-python documentation - - - - - - - - - - - - - - - - - - -
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Python Module Index

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    - mmif.serialize.annotation -
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- - - \ No newline at end of file diff --git a/docs/0.4.4/search.html b/docs/0.4.4/search.html deleted file mode 100644 index 651660f3..00000000 --- a/docs/0.4.4/search.html +++ /dev/null @@ -1,177 +0,0 @@ - - - - - - - - Search — mmif-python documentation - - - - - - - - - - - - - - - - - - -
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- - - - - - - - \ No newline at end of file diff --git a/docs/0.4.4/searchindex.js b/docs/0.4.4/searchindex.js deleted file mode 100644 index 40529d6a..00000000 --- a/docs/0.4.4/searchindex.js +++ /dev/null @@ -1 +0,0 @@ -Search.setIndex({"alltitles": {"API documentation:": [[3, null]], "Contents": [[3, null]], "Getting Started": [[4, null]], "Indices and tables": [[3, "indices-and-tables"]], "Installation": [[4, "installation"]], "MMIF Serialization": [[4, "mmif-serialization"]], "MMIF consumer": [[2, null]], "MMIF for python": [[3, "mmif-for-python"]], "MultiMedia Interchange Format": [[3, "multimedia-interchange-format"]], "Overview": [[4, "overview"]], "Prerequisites": [[4, "prerequisites"]], "Target MMIF Versions": [[6, null]], "Target Specification Versions": [[6, "id1"]], "Welcome to mmif-python\u2019s documentation!": [[3, null]], "mmif package": [[5, null]], "mmif.serialize module": [[0, null]], "mmif.serialize.annotation module": [[0, "module-mmif.serialize.annotation"]], 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"modul": [0, 1], "multimedia": 3, "overview": 4, "packag": 5, "prerequisit": 4, "python": 3, "serial": [0, 4], "specif": 6, "start": 4, "tabl": 3, "target": 6, "version": 6, "view": 0, "vocabulari": 1, "welcom": 3}}) \ No newline at end of file diff --git a/docs/0.4.4/target-versions.html b/docs/0.4.4/target-versions.html deleted file mode 100644 index 01c26f1c..00000000 --- a/docs/0.4.4/target-versions.html +++ /dev/null @@ -1,218 +0,0 @@ - - - - - - - - - Target MMIF Versions — mmif-python documentation - - - - - - - - - - - - - - - - - -
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Target MMIF Versions

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This article provides targeting MMIF specification versions of different versions of mmif-python SDK.

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Target Specification Versions

mmif-python version

Target MMIF Specification

0.4.4

0.4.2

0.4.3

0.4.0

0.4.2

0.4.0

0.4.1

0.4.0

0.4.0

0.4.0

0.3.5

0.3.1

0.3.4

0.3.1

0.3.3

0.3.1

0.3.2

0.3.1

0.3.1

0.3.0

0.3.0

0.3.0

0.2.2

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0.2.1

0.2.1

0.2.0

0.2.1

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The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the `appliance documentation `_ to learn more about the appliance. - -MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance. - -#. The code must be hosted on a public git repository (e.g. Github, Gitlab, ...) -#. Must listen to ``5000`` port. -#. Must expose ``/display`` route . -#. ``/display`` router should response to ``GET`` requests. -#. In the ``GET`` request, a public URL of the input MMIF file is passed via ``file`` URL parameter. -#. On the codebase root, there must be a ``Dockerfile`` that can build a `docker `_ image that runs the web app. - -We provide an example consumer at https://github.com/clamsproject/mmif-visualizer. diff --git a/docs/0.4.5/_sources/index.rst.txt b/docs/0.4.5/_sources/index.rst.txt deleted file mode 100644 index 9b90b38e..00000000 --- a/docs/0.4.5/_sources/index.rst.txt +++ /dev/null @@ -1,26 +0,0 @@ -Welcome to mmif-python's documentation! -======================================= - -.. mdinclude:: ../README.md - -.. toctree:: - :maxdepth: 2 - :caption: Contents - - introduction - target-versions - consumer-tutorial - -.. toctree:: - :maxdepth: 2 - :caption: API documentation: - - modules - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/docs/0.4.5/_sources/introduction.rst.txt b/docs/0.4.5/_sources/introduction.rst.txt deleted file mode 100644 index 6fea3a3c..00000000 --- a/docs/0.4.5/_sources/introduction.rst.txt +++ /dev/null @@ -1,78 +0,0 @@ -.. _instroduction: - -Getting Started -=============== - - -Overview ---------- - -MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF wbesite `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports de-/serialization of MMIF objects, as well as many navigation and manipulation helpers for MMIF objects. - -Prerequisites -------------- - -* `Python `_: ``mmif-python`` requires Python 3.6 or newer. We have no plan to support `Python 2.7 `_. - -Installation ---------------- - -Package ``mmif-python`` is distributed via the official PyPI. Users are supposed to pip-install to get latest release. - -.. code-block:: bash - - pip install mmif-python - -This will install a package `mmif` to local python. - -The MMIF format and specification is evolving over time, and ``mmif-python`` package will be updated along with the changes in MMIF format. - -.. note:: MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and ``mmif-python`` versions, please take time to read our decision on the subject `here `_. If you need to know which python SDK supports which specification version, see :ref:`target-versions` page. - -MMIF Serialization ---------------------------- - -:class:`mmif.serialize.mmif.Mmif` represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of :class:`mmif.serialize.model.MmifObject`, including the :class:`mmif.serialize.mmif.Mmif`. To start with an existing MMIF :class:`str`, simple initiate a new ``Mmif`` object with the file. - -.. code-block:: python - - import mmif - from mmif import Mmif - - mmif_str = """{ - "metadata": { - "mmif": "http://mmif.clams.ai/0.2.0" - }, - "documents": [ - { - "@type": "http://mmif.clams.ai/0.2.0/vocabulary/VideoDocument", - "properties": { - "id": "m1", - "mime": "video/mp4", - "location": "file:///var/archive/video-0012.mp4" - } - }, - { - "@type": "http://mmif.clams.ai/0.2.0/vocabulary/TextDocument", - "properties": { - "id": "m2", - "mime": "text/plain", - "location": "file:///var/archive/video-0012-transcript.txt" - } - } - ], - "views": []}""" - mmif_obj = Mmif(mmif_str) - - -Few notes; - -#. MMIF does not carry the primary source files in it. -#. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version ``mmif-python`` implementation of the MMIF might not be able to load an unsupported version of MMIF string. - -When serializing back to :class:`str`, call ``.serialize()`` (:meth:`mmif.serialize.model.MmifObject.serialize`) on the object. - -To get subcomponents, you can use various getters implemented in subclasses. For more details, the API documentation (:ref:`apidoc`) will help. - diff --git a/docs/0.4.5/_sources/modules.rst.txt b/docs/0.4.5/_sources/modules.rst.txt deleted file mode 100644 index e4269c6d..00000000 --- a/docs/0.4.5/_sources/modules.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _apidoc: - -mmif package -============ - -.. toctree:: - :maxdepth: 4 - - autodoc/mmif.serialize - autodoc/mmif.vocabulary diff --git a/docs/0.4.5/_sources/target-versions.rst.txt b/docs/0.4.5/_sources/target-versions.rst.txt deleted file mode 100644 index 34216d3e..00000000 --- a/docs/0.4.5/_sources/target-versions.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _target-versions: - -Target MMIF Versions -==================== - -This article provides targeting MMIF specification versions of different versions of ``mmif-python`` SDK. - -.. csv-table:: Target Specification Versions - :file: target-versions.csv - :header-rows: 1 diff --git a/docs/0.4.5/_static/_sphinx_javascript_frameworks_compat.js b/docs/0.4.5/_static/_sphinx_javascript_frameworks_compat.js deleted file mode 100644 index 81415803..00000000 --- a/docs/0.4.5/_static/_sphinx_javascript_frameworks_compat.js +++ /dev/null @@ -1,123 +0,0 @@ -/* Compatability shim for jQuery and underscores.js. - * - * Copyright Sphinx contributors - * Released under the two clause BSD licence - */ - -/** - * small helper function to urldecode strings - * - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL - */ -jQuery.urldecode = function(x) { - if (!x) { - return x - } - return decodeURIComponent(x.replace(/\+/g, ' ')); -}; - -/** - * small helper function to urlencode strings - */ -jQuery.urlencode = encodeURIComponent; - -/** - * This function returns the parsed url parameters of the - * current request. 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- -/** - * Simple result scoring code. - */ -if (typeof Scorer === "undefined") { - var Scorer = { - // Implement the following function to further tweak the score for each result - // The function takes a result array [docname, title, anchor, descr, score, filename] - // and returns the new score. - /* - score: result => { - const [docname, title, anchor, descr, score, filename, kind] = result - return score - }, - */ - - // query matches the full name of an object - objNameMatch: 11, - // or matches in the last dotted part of the object name - objPartialMatch: 6, - // Additive scores depending on the priority of the object - objPrio: { - 0: 15, // used to be importantResults - 1: 5, // used to be objectResults - 2: -5, // used to be unimportantResults - }, - // Used when the priority is not in the mapping. - objPrioDefault: 0, - - // query found in title - title: 15, - partialTitle: 7, - // query found in terms - term: 5, - partialTerm: 2, - }; -} - -// Global search result kind enum, used by themes to style search results. -class SearchResultKind { - static get index() { return "index"; } - static get object() { return "object"; } - static get text() { return "text"; } - static get title() { return "title"; } -} - -const _removeChildren = (element) => { - while (element && element.lastChild) element.removeChild(element.lastChild); -}; - -/** - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping - */ -const _escapeRegExp = (string) => - string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string - -const _displayItem = (item, searchTerms, highlightTerms) => { - const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; - const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; - const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; - const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; - const contentRoot = document.documentElement.dataset.content_root; - - const [docName, title, anchor, descr, score, _filename, kind] = item; - - let listItem = document.createElement("li"); - // Add a class representing the item's type: - // can be used by a theme's CSS selector for styling - // See SearchResultKind for the class names. - listItem.classList.add(`kind-${kind}`); - let requestUrl; - let linkUrl; - if (docBuilder === "dirhtml") { - // dirhtml builder - let dirname = docName + "/"; - if (dirname.match(/\/index\/$/)) - dirname = dirname.substring(0, dirname.length - 6); - else if (dirname === "index/") dirname = ""; - requestUrl = contentRoot + dirname; - linkUrl = requestUrl; - } else { - // normal html builders - requestUrl = contentRoot + docName + docFileSuffix; - linkUrl = docName + docLinkSuffix; - } - let linkEl = listItem.appendChild(document.createElement("a")); - linkEl.href = linkUrl + anchor; - linkEl.dataset.score = score; - linkEl.innerHTML = title; - if (descr) { - listItem.appendChild(document.createElement("span")).innerHTML = - " (" + descr + ")"; - // highlight search terms in the description - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - } - else if (showSearchSummary) - fetch(requestUrl) - .then((responseData) => responseData.text()) - .then((data) => { - if (data) - listItem.appendChild( - Search.makeSearchSummary(data, searchTerms, anchor) - ); - // highlight search terms in the summary - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - }); - Search.output.appendChild(listItem); -}; -const _finishSearch = (resultCount) => { - Search.stopPulse(); - Search.title.innerText = _("Search Results"); - if (!resultCount) - Search.status.innerText = Documentation.gettext( - "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." - ); - else - Search.status.innerText = Documentation.ngettext( - "Search finished, found one page matching the search query.", - "Search finished, found ${resultCount} pages matching the search query.", - resultCount, - ).replace('${resultCount}', resultCount); -}; -const _displayNextItem = ( - results, - resultCount, - searchTerms, - highlightTerms, -) => { - // results left, load the summary and display it - // this is intended to be dynamic (don't sub resultsCount) - if (results.length) { - _displayItem(results.pop(), searchTerms, highlightTerms); - setTimeout( - () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), - 5 - ); - } - // search finished, update title and status message - else _finishSearch(resultCount); -}; -// Helper function used by query() to order search results. -// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. -// Order the results by score (in opposite order of appearance, since the -// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. -const _orderResultsByScoreThenName = (a, b) => { - const leftScore = a[4]; - const rightScore = b[4]; - if (leftScore === rightScore) { - // same score: sort alphabetically - const leftTitle = a[1].toLowerCase(); - const rightTitle = b[1].toLowerCase(); - if (leftTitle === rightTitle) return 0; - return leftTitle > rightTitle ? -1 : 1; // inverted is intentional - } - return leftScore > rightScore ? 1 : -1; -}; - -/** - * Default splitQuery function. Can be overridden in ``sphinx.search`` with a - * custom function per language. - * - * The regular expression works by splitting the string on consecutive characters - * that are not Unicode letters, numbers, underscores, or emoji characters. - * This is the same as ``\W+`` in Python, preserving the surrogate pair area. - */ -if (typeof splitQuery === "undefined") { - var splitQuery = (query) => query - .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) - .filter(term => term) // remove remaining empty strings -} - -/** - * Search Module - */ -const Search = { - _index: null, - _queued_query: null, - _pulse_status: -1, - - htmlToText: (htmlString, anchor) => { - const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - for (const removalQuery of [".headerlink", "script", "style"]) { - htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); - } - if (anchor) { - const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); - if (anchorContent) return anchorContent.textContent; - - console.warn( - `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` - ); - } - - // if anchor not specified or not found, fall back to main content - const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent) return docContent.textContent; - - console.warn( - "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." - ); - return ""; - }, - - init: () => { - const query = new URLSearchParams(window.location.search).get("q"); - document - .querySelectorAll('input[name="q"]') - .forEach((el) => (el.value = query)); - if (query) Search.performSearch(query); - }, - - loadIndex: (url) => - (document.body.appendChild(document.createElement("script")).src = url), - - setIndex: (index) => { - Search._index = index; - if (Search._queued_query !== null) { - const query = Search._queued_query; - Search._queued_query = null; - Search.query(query); - } - }, - - hasIndex: () => Search._index !== null, - - deferQuery: (query) => (Search._queued_query = query), - - stopPulse: () => (Search._pulse_status = -1), - - startPulse: () => { - if (Search._pulse_status >= 0) return; - - const pulse = () => { - Search._pulse_status = (Search._pulse_status + 1) % 4; - Search.dots.innerText = ".".repeat(Search._pulse_status); - if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); - }; - pulse(); - }, - - /** - * perform a search for something (or wait until index is loaded) - */ - performSearch: (query) => { - // create the required interface elements - const searchText = document.createElement("h2"); - searchText.textContent = _("Searching"); - const searchSummary = document.createElement("p"); - searchSummary.classList.add("search-summary"); - searchSummary.innerText = ""; - const searchList = document.createElement("ul"); - searchList.setAttribute("role", "list"); - searchList.classList.add("search"); - - const out = document.getElementById("search-results"); - Search.title = out.appendChild(searchText); - Search.dots = Search.title.appendChild(document.createElement("span")); - Search.status = out.appendChild(searchSummary); - Search.output = out.appendChild(searchList); - - const searchProgress = document.getElementById("search-progress"); - // Some themes don't use the search progress node - if (searchProgress) { - searchProgress.innerText = _("Preparing search..."); - } - Search.startPulse(); - - // index already loaded, the browser was quick! - if (Search.hasIndex()) Search.query(query); - else Search.deferQuery(query); - }, - - _parseQuery: (query) => { - // stem the search terms and add them to the correct list - const stemmer = new Stemmer(); - const searchTerms = new Set(); - const excludedTerms = new Set(); - const highlightTerms = new Set(); - const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); - splitQuery(query.trim()).forEach((queryTerm) => { - const queryTermLower = queryTerm.toLowerCase(); - - // maybe skip this "word" - // stopwords array is from language_data.js - if ( - stopwords.indexOf(queryTermLower) !== -1 || - queryTerm.match(/^\d+$/) - ) - return; - - // stem the word - let word = stemmer.stemWord(queryTermLower); - // select the correct list - if (word[0] === "-") excludedTerms.add(word.substr(1)); - else { - searchTerms.add(word); - highlightTerms.add(queryTermLower); - } - }); - - if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js - localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) - } - - // console.debug("SEARCH: searching for:"); - // console.info("required: ", [...searchTerms]); - // console.info("excluded: ", [...excludedTerms]); - - return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; - }, - - /** - * execute search (requires search index to be loaded) - */ - _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - - // Collect multiple result groups to be sorted separately and then ordered. - // Each is an array of [docname, title, anchor, descr, score, filename, kind]. - const normalResults = []; - const nonMainIndexResults = []; - - _removeChildren(document.getElementById("search-progress")); - - const queryLower = query.toLowerCase().trim(); - for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { - for (const [file, id] of foundTitles) { - const score = Math.round(Scorer.title * queryLower.length / title.length); - const boost = titles[file] === title ? 1 : 0; // add a boost for document titles - normalResults.push([ - docNames[file], - titles[file] !== title ? `${titles[file]} > ${title}` : title, - id !== null ? "#" + id : "", - null, - score + boost, - filenames[file], - SearchResultKind.title, - ]); - } - } - } - - // search for explicit entries in index directives - for (const [entry, foundEntries] of Object.entries(indexEntries)) { - if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id, isMain] of foundEntries) { - const score = Math.round(100 * queryLower.length / entry.length); - const result = [ - docNames[file], - titles[file], - id ? "#" + id : "", - null, - score, - filenames[file], - SearchResultKind.index, - ]; - if (isMain) { - normalResults.push(result); - } else { - nonMainIndexResults.push(result); - } - } - } - } - - // lookup as object - objectTerms.forEach((term) => - normalResults.push(...Search.performObjectSearch(term, objectTerms)) - ); - - // lookup as search terms in fulltext - normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); - - // let the scorer override scores with a custom scoring function - if (Scorer.score) { - normalResults.forEach((item) => (item[4] = Scorer.score(item))); - nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); - } - - // Sort each group of results by score and then alphabetically by name. - normalResults.sort(_orderResultsByScoreThenName); - nonMainIndexResults.sort(_orderResultsByScoreThenName); - - // Combine the result groups in (reverse) order. - // Non-main index entries are typically arbitrary cross-references, - // so display them after other results. - let results = [...nonMainIndexResults, ...normalResults]; - - // remove duplicate search results - // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept - let seen = new Set(); - results = results.reverse().reduce((acc, result) => { - let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); - if (!seen.has(resultStr)) { - acc.push(result); - seen.add(resultStr); - } - return acc; - }, []); - - return results.reverse(); - }, - - query: (query) => { - const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); - const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); - - // for debugging - //Search.lastresults = results.slice(); // a copy - // console.info("search results:", Search.lastresults); - - // print the results - _displayNextItem(results, results.length, searchTerms, highlightTerms); - }, - - /** - * search for object names - */ - performObjectSearch: (object, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const objects = Search._index.objects; - const objNames = Search._index.objnames; - const titles = Search._index.titles; - - const results = []; - - const objectSearchCallback = (prefix, match) => { - const name = match[4] - const fullname = (prefix ? prefix + "." : "") + name; - const fullnameLower = fullname.toLowerCase(); - if (fullnameLower.indexOf(object) < 0) return; - - let score = 0; - const parts = fullnameLower.split("."); - - // check for different match types: exact matches of full name or - // "last name" (i.e. last dotted part) - if (fullnameLower === object || parts.slice(-1)[0] === object) - score += Scorer.objNameMatch; - else if (parts.slice(-1)[0].indexOf(object) > -1) - score += Scorer.objPartialMatch; // matches in last name - - const objName = objNames[match[1]][2]; - const title = titles[match[0]]; - - // If more than one term searched for, we require other words to be - // found in the name/title/description - const otherTerms = new Set(objectTerms); - otherTerms.delete(object); - if (otherTerms.size > 0) { - const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); - if ( - [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) - ) - return; - } - - let anchor = match[3]; - if (anchor === "") anchor = fullname; - else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; - - const descr = objName + _(", in ") + title; - - // add custom score for some objects according to scorer - if (Scorer.objPrio.hasOwnProperty(match[2])) - score += Scorer.objPrio[match[2]]; - else score += Scorer.objPrioDefault; - - results.push([ - docNames[match[0]], - fullname, - "#" + anchor, - descr, - score, - filenames[match[0]], - SearchResultKind.object, - ]); - }; - Object.keys(objects).forEach((prefix) => - objects[prefix].forEach((array) => - objectSearchCallback(prefix, array) - ) - ); - return results; - }, - - /** - * search for full-text terms in the index - */ - performTermsSearch: (searchTerms, excludedTerms) => { - // prepare search - const terms = Search._index.terms; - const titleTerms = Search._index.titleterms; - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - - const scoreMap = new Map(); - const fileMap = new Map(); - - // perform the search on the required terms - searchTerms.forEach((word) => { - const files = []; - const arr = [ - { files: terms[word], score: Scorer.term }, - { files: titleTerms[word], score: Scorer.title }, - ]; - // add support for partial matches - if (word.length > 2) { - const escapedWord = _escapeRegExp(word); - if (!terms.hasOwnProperty(word)) { - Object.keys(terms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: terms[term], score: Scorer.partialTerm }); - }); - } - if (!titleTerms.hasOwnProperty(word)) { - Object.keys(titleTerms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); - }); - } - } - - // no match but word was a required one - if (arr.every((record) => record.files === undefined)) return; - - // found search word in contents - arr.forEach((record) => { - if (record.files === undefined) return; - - let recordFiles = record.files; - if (recordFiles.length === undefined) recordFiles = [recordFiles]; - files.push(...recordFiles); - - // set score for the word in each file - recordFiles.forEach((file) => { - if (!scoreMap.has(file)) scoreMap.set(file, {}); - scoreMap.get(file)[word] = record.score; - }); - }); - - // create the mapping - files.forEach((file) => { - if (!fileMap.has(file)) fileMap.set(file, [word]); - else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); - }); - }); - - // now check if the files don't contain excluded terms - const results = []; - for (const [file, wordList] of fileMap) { - // check if all requirements are matched - - // as search terms with length < 3 are discarded - const filteredTermCount = [...searchTerms].filter( - (term) => term.length > 2 - ).length; - if ( - wordList.length !== searchTerms.size && - wordList.length !== filteredTermCount - ) - continue; - - // ensure that none of the excluded terms is in the search result - if ( - [...excludedTerms].some( - (term) => - terms[term] === file || - titleTerms[term] === file || - (terms[term] || []).includes(file) || - (titleTerms[term] || []).includes(file) - ) - ) - break; - - // select one (max) score for the file. - const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); - // add result to the result list - results.push([ - docNames[file], - titles[file], - "", - null, - score, - filenames[file], - SearchResultKind.text, - ]); - } - return results; - }, - - /** - * helper function to return a node containing the - * search summary for a given text. keywords is a list - * of stemmed words. - */ - makeSearchSummary: (htmlText, keywords, anchor) => { - const text = Search.htmlToText(htmlText, anchor); - if (text === "") return null; - - const textLower = text.toLowerCase(); - const actualStartPosition = [...keywords] - .map((k) => textLower.indexOf(k.toLowerCase())) - .filter((i) => i > -1) - .slice(-1)[0]; - const startWithContext = Math.max(actualStartPosition - 120, 0); - - const top = startWithContext === 0 ? "" : "..."; - const tail = startWithContext + 240 < text.length ? "..." : ""; - - let summary = document.createElement("p"); - summary.classList.add("context"); - summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; - - return summary; - }, -}; - -_ready(Search.init); diff --git a/docs/0.4.5/_static/sphinx_highlight.js b/docs/0.4.5/_static/sphinx_highlight.js deleted file mode 100644 index 8a96c69a..00000000 --- a/docs/0.4.5/_static/sphinx_highlight.js +++ /dev/null @@ -1,154 +0,0 @@ -/* Highlighting utilities for Sphinx HTML documentation. */ -"use strict"; - -const SPHINX_HIGHLIGHT_ENABLED = true - -/** - * highlight a given string on a node by wrapping it in - * span elements with the given class name. - */ -const _highlight = (node, addItems, text, className) => { - if (node.nodeType === Node.TEXT_NODE) { - const val = node.nodeValue; - const parent = node.parentNode; - const pos = val.toLowerCase().indexOf(text); - if ( - pos >= 0 && - !parent.classList.contains(className) && - !parent.classList.contains("nohighlight") - ) { - let span; - - const closestNode = parent.closest("body, svg, foreignObject"); - const isInSVG = closestNode && closestNode.matches("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.classList.add(className); - } - - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - const rest = document.createTextNode(val.substr(pos + text.length)); - parent.insertBefore( - span, - parent.insertBefore( - rest, - node.nextSibling - ) - ); - node.nodeValue = val.substr(0, pos); - /* There may be more occurrences of search term in this node. So call this - * function recursively on the remaining fragment. - */ - _highlight(rest, addItems, text, className); - - if (isInSVG) { - const rect = document.createElementNS( - "http://www.w3.org/2000/svg", - "rect" - ); - const bbox = parent.getBBox(); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute("class", className); - addItems.push({ parent: parent, target: rect }); - } - } - } else if (node.matches && !node.matches("button, select, textarea")) { - node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); - } -}; -const _highlightText = (thisNode, text, className) => { - let addItems = []; - _highlight(thisNode, addItems, text, className); - addItems.forEach((obj) => - obj.parent.insertAdjacentElement("beforebegin", obj.target) - ); -}; - -/** - * Small JavaScript module for the documentation. - */ -const SphinxHighlight = { - - /** - * highlight the search words provided in localstorage in the text - */ - highlightSearchWords: () => { - if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight - - // get and clear terms from localstorage - const url = new URL(window.location); - const highlight = - localStorage.getItem("sphinx_highlight_terms") - || url.searchParams.get("highlight") - || ""; - localStorage.removeItem("sphinx_highlight_terms") - url.searchParams.delete("highlight"); - window.history.replaceState({}, "", url); - - // get individual terms from highlight string - const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); - if (terms.length === 0) return; // nothing to do - - // There should never be more than one element matching "div.body" - const divBody = document.querySelectorAll("div.body"); - const body = divBody.length ? divBody[0] : document.querySelector("body"); - window.setTimeout(() => { - terms.forEach((term) => _highlightText(body, term, "highlighted")); - }, 10); - - const searchBox = document.getElementById("searchbox"); - if (searchBox === null) return; - searchBox.appendChild( - document - .createRange() - .createContextualFragment( - '

' + - '' + - _("Hide Search Matches") + - "

" - ) - ); - }, - - /** - * helper function to hide the search marks again - */ - hideSearchWords: () => { - document - .querySelectorAll("#searchbox .highlight-link") - .forEach((el) => el.remove()); - document - .querySelectorAll("span.highlighted") - .forEach((el) => el.classList.remove("highlighted")); - localStorage.removeItem("sphinx_highlight_terms") - }, - - initEscapeListener: () => { - // only install a listener if it is really needed - if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; - - document.addEventListener("keydown", (event) => { - // bail for input elements - if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; - // bail with special keys - if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; - if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { - SphinxHighlight.hideSearchWords(); - event.preventDefault(); - } - }); - }, -}; - -_ready(() => { - /* Do not call highlightSearchWords() when we are on the search page. - * It will highlight words from the *previous* search query. - */ - if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); - SphinxHighlight.initEscapeListener(); -}); diff --git a/docs/0.4.5/autodoc/mmif.serialize.html b/docs/0.4.5/autodoc/mmif.serialize.html deleted file mode 100644 index e5ad5422..00000000 --- a/docs/0.4.5/autodoc/mmif.serialize.html +++ /dev/null @@ -1,370 +0,0 @@ - - - - - - - - - mmif.serialize module — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.serialize module

-
-

mmif.serialize.model module

-
-
-

mmif.serialize.mmif module

-
-
-

mmif.serialize.view module

-
-
-

mmif.serialize.annotation module

-

The annotation module contains the classes used to represent a -MMIF annotation as a live Python object.

-

In MMIF, annotations are created by apps in a pipeline as a part -of a view. For documentation on how views are represented, see -mmif.serialize.view.

-
-
-class mmif.serialize.annotation.Annotation(anno_obj: bytes | str | dict | None = None)[source]
-

Bases: FreezableMmifObject

-

MmifObject that represents an annotation in a MMIF view.

-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]]) → None[source]
-

Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

-
- -
-
-property at_type: TypesBase[source]
-
- -
-
-property id: str[source]
-
- -
-
-is_document()[source]
-
- -
-
-is_type(at_type: str | TypesBase) → bool[source]
-

Check if the @type of this object matches.

-
- -
- -
-
-class mmif.serialize.annotation.AnnotationProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: FreezableMmifObject

-

AnnotationProperties object that represents the -properties object within a MMIF annotation.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
- -
-
-class mmif.serialize.annotation.Document(doc_obj: bytes | str | dict | None = None)[source]
-

Bases: Annotation

-

Document object that represents a single document in a MMIF file.

-

A document is identified by an ID, and contains certain attributes -and potentially contains the contents of the document itself, -metadata about how the document was created, and/or a list of -subdocuments grouped together logically.

-

If document_obj is not provided, an empty Document will be generated.

-
-
Parameters:
-

document_obj – the JSON data that defines the document

-
-
-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None]) → None[source]
-

Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

-
- -
-
-property location: str[source]
-
- -
-
-location_address() → str[source]
-
- -
-
-location_path() → str[source]
-
- -
-
-location_scheme() → str[source]
-
- -
-
-property parent: str[source]
-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.DocumentProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: AnnotationProperties

-

DocumentProperties object that represents the -properties object within a MMIF document.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
-
-property location: str[source]
-
- -
-
-location_address() → str[source]
-
- -
-
-location_path() → str[source]
-
- -
-
-location_scheme() → str[source]
-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.Text(text_obj: bytes | str | dict | None = None)[source]
-

Bases: FreezableMmifObject

-
-
-property lang: str[source]
-
- -
-
-property value: str[source]
-
- -
- -
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.4.5 - - -
-
- -
0.3.0
-
0.3.1
-
0.3.2
-
0.3.3
-
0.3.4
-
0.3.5
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0.4.2
-
0.4.3
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-
- - - \ No newline at end of file diff --git a/docs/0.4.5/autodoc/mmif.vocabulary.html b/docs/0.4.5/autodoc/mmif.vocabulary.html deleted file mode 100644 index a6e9ca9e..00000000 --- a/docs/0.4.5/autodoc/mmif.vocabulary.html +++ /dev/null @@ -1,285 +0,0 @@ - - - - - - - - - mmif.vocabulary module — mmif-python documentation - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.vocabulary module

-
-

mmif.vocabulary.annotation_types module

-
-
-class mmif.vocabulary.annotation_types.AnnotationTypes(type_uri: str)[source]
-

Bases: AnnotationTypesBase

-

This class contains the CLAMS annotation types -defined in the spec version 0.4.2 as class variables.

-
-
-Alignment = http://mmif.clams.ai/0.4.2/vocabulary/Alignment[source]
-
- -
-
-Annotation = http://mmif.clams.ai/0.4.2/vocabulary/Annotation[source]
-
- -
-
-BoundingBox = http://mmif.clams.ai/0.4.2/vocabulary/BoundingBox[source]
-
- -
-
-Chapter = http://mmif.clams.ai/0.4.2/vocabulary/Chapter[source]
-
- -
-
-Interval = http://mmif.clams.ai/0.4.2/vocabulary/Interval[source]
-
- -
-
-Polygon = http://mmif.clams.ai/0.4.2/vocabulary/Polygon[source]
-
- -
-
-Region = http://mmif.clams.ai/0.4.2/vocabulary/Region[source]
-
- -
-
-Relation = http://mmif.clams.ai/0.4.2/vocabulary/Relation[source]
-
- -
-
-Span = http://mmif.clams.ai/0.4.2/vocabulary/Span[source]
-
- -
-
-TimeFrame = http://mmif.clams.ai/0.4.2/vocabulary/TimeFrame[source]
-
- -
-
-TimePoint = http://mmif.clams.ai/0.4.2/vocabulary/TimePoint[source]
-
- -
-
-VideoObject = http://mmif.clams.ai/0.4.2/vocabulary/VideoObject[source]
-
- -
- -
-
-

mmif.vocabulary.document_types module

-
-
-class mmif.vocabulary.document_types.DocumentTypes(type_uri: str)[source]
-

Bases: DocumentTypesBase

-

This class contains the CLAMS document types -defined in the spec version 0.4.2 as class variables.

-
-
-AudioDocument = http://mmif.clams.ai/0.4.2/vocabulary/AudioDocument[source]
-
- -
-
-Document = http://mmif.clams.ai/0.4.2/vocabulary/Document[source]
-
- -
-
-ImageDocument = http://mmif.clams.ai/0.4.2/vocabulary/ImageDocument[source]
-
- -
-
-TextDocument = http://mmif.clams.ai/0.4.2/vocabulary/TextDocument[source]
-
- -
-
-VideoDocument = http://mmif.clams.ai/0.4.2/vocabulary/VideoDocument[source]
-
- -
- -
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.4.5 - - -
-
- -
0.3.0
-
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0.4.1
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0.4.3
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0.4.5
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0.4.6
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0.4.7
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0.4.8
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0.5.2
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-
- - - \ No newline at end of file diff --git a/docs/0.4.5/consumer-tutorial.html b/docs/0.4.5/consumer-tutorial.html deleted file mode 100644 index f86667f9..00000000 --- a/docs/0.4.5/consumer-tutorial.html +++ /dev/null @@ -1,176 +0,0 @@ - - - - - - - - - MMIF consumer — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • MMIF consumer
    • -
  • -
    • -
-
-
-
-
- -
-

MMIF consumer

-

A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the appliance documentation to learn more about the appliance.

-

MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance.

-
    -

  1. The code must be hosted on a public git repository (e.g. Github, Gitlab, …)

    2. -

  2. Must listen to 5000 port.

    3. -

  3. Must expose /display route .

    4. -

  4. /display router should response to GET requests.

    5. -

  5. In the GET request, a public URL of the input MMIF file is passed via file URL parameter.

    6. -

  6. On the codebase root, there must be a Dockerfile that can build a docker image that runs the web app.

    7. -
-

We provide an example consumer at https://github.com/clamsproject/mmif-visualizer.

-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.4.5 - - -
-
- -
0.3.0
-
0.3.1
-
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-
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-
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- - - \ No newline at end of file diff --git a/docs/0.4.5/genindex.html b/docs/0.4.5/genindex.html deleted file mode 100644 index 7d0a1546..00000000 --- a/docs/0.4.5/genindex.html +++ /dev/null @@ -1,404 +0,0 @@ - - - - - - - - Index — mmif-python documentation - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • Index
    • -
  • -
    • -
-
-
-
-
- - -

Index

- -
- A - | B - | C - | D - | I - | L - | M - | P - | R - | S - | T - | V - -
-

A

- - - -
- -

B

- - -
- -

C

- - -
- -

D

- - - -
- -

I

- - - -
- -

L

- - - -
- -

M

- - - -
    -
  • - mmif.serialize.annotation - -
    • -
  • - mmif.vocabulary.annotation_types - -
    • -
  • - mmif.vocabulary.document_types - -
    • -
- -

P

- - - -
- -

R

- - - -
- -

S

- - -
- -

T

- - - -
- -

V

- - - -
- - - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.4.5 - - -
-
- -
0.3.0
-
0.3.1
-
0.3.2
-
0.3.3
-
0.3.4
-
0.3.5
-
0.4.0
-
0.4.1
-
0.4.2
-
0.4.3
-
0.4.4
-
0.4.5
-
0.4.6
-
0.4.7
-
0.4.8
-
0.5.0
-
0.5.1
-
0.5.2
-
1.0.0
-
1.0.1
-
1.0.10
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1.0.11
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1.0.12
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1.0.13
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1.0.14
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1.0.15
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1.0.16
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1.0.18
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- - - \ No newline at end of file diff --git a/docs/0.4.5/index.html b/docs/0.4.5/index.html deleted file mode 100644 index bb906a69..00000000 --- a/docs/0.4.5/index.html +++ /dev/null @@ -1,203 +0,0 @@ - - - - - - - - - Welcome to mmif-python’s documentation! — mmif-python documentation - - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • Welcome to mmif-python’s documentation!
    • -
  • -
    • -
-
-
-
-
- -
-

Welcome to mmif-python’s documentation!

-
-
-

MMIF for python

-

NOTE that this project is in pre-alpha and being actively developed. Nothing is guaranteed to reliably work for the moment and developer need to be very careful when using APIs implemented here. Please use the issue track to report bugs and malfunctions.

-
-

MultiMedia Interchange Format

-

MMIF is a JSON(-LD)-based data format designed for transferring annotation data between computational analysis applications in CLAMS project.

-
-

Contents

- -
-
-

API documentation:

- -
-
-
-
-

Indices and tables

- -
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.4.5 - - -
-
- -
0.3.0
-
0.3.1
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0.3.2
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0.3.3
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0.3.4
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0.3.5
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0.4.0
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0.4.1
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0.4.2
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0.4.3
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0.4.4
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0.4.5
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0.4.6
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0.4.7
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0.4.8
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0.5.0
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0.5.1
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0.5.2
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1.0.0
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1.0.1
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1.0.10
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1.0.11
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1.0.12
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1.0.13
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1.0.15
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- - - \ No newline at end of file diff --git a/docs/0.4.5/introduction.html b/docs/0.4.5/introduction.html deleted file mode 100644 index ae692045..00000000 --- a/docs/0.4.5/introduction.html +++ /dev/null @@ -1,236 +0,0 @@ - - - - - - - - - Getting Started — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • Getting Started
    • -
  • -
    • -
-
-
-
-
- -
-

Getting Started

-
-

Overview

-

MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF wbesite. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports de-/serialization of MMIF objects, as well as many navigation and manipulation helpers for MMIF objects.

-
-
-

Prerequisites

-
    -

  • Python: mmif-python requires Python 3.6 or newer. We have no plan to support Python 2.7.

    • -
-
-
-

Installation

-

Package mmif-python is distributed via the official PyPI. Users are supposed to pip-install to get latest release.

-
pip install mmif-python
-
-
-

This will install a package mmif to local python.

-

The MMIF format and specification is evolving over time, and mmif-python package will be updated along with the changes in MMIF format.

-
-

Note

-

MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and mmif-python versions, please take time to read our decision on the subject here. If you need to know which python SDK supports which specification version, see Target MMIF Versions page.

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MMIF Serialization

-

mmif.serialize.mmif.Mmif represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of mmif.serialize.model.MmifObject, including the mmif.serialize.mmif.Mmif. To start with an existing MMIF str, simple initiate a new Mmif object with the file.

-
import mmif
-from mmif import Mmif
-
-mmif_str = """{
-"metadata": {
-  "mmif": "http://mmif.clams.ai/0.2.0"
-},
-"documents": [
-  {
-    "@type": "http://mmif.clams.ai/0.2.0/vocabulary/VideoDocument",
-    "properties": {
-      "id": "m1",
-      "mime": "video/mp4",
-      "location": "file:///var/archive/video-0012.mp4"
-    }
-  },
-  {
-    "@type": "http://mmif.clams.ai/0.2.0/vocabulary/TextDocument",
-    "properties": {
-      "id": "m2",
-      "mime": "text/plain",
-      "location": "file:///var/archive/video-0012-transcript.txt"
-    }
-  }
-],
-"views": []}"""
-mmif_obj = Mmif(mmif_str)
-
-
-

Few notes;

-
    -

  1. MMIF does not carry the primary source files in it.

    2. -

  2. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version mmif-python implementation of the MMIF might not be able to load an unsupported version of MMIF string.

    3. -
-

When serializing back to str, call .serialize() (mmif.serialize.model.MmifObject.serialize()) on the object.

-

To get subcomponents, you can use various getters implemented in subclasses. For more details, the API documentation (mmif package) will help.

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"modul": [0, 1], "multimedia": 3, "overview": 4, "packag": 5, "prerequisit": 4, "python": 3, "serial": [0, 4], "specif": 6, "start": 4, "tabl": 3, "target": 6, "version": 6, "view": 0, "vocabulari": 1, "welcom": 3}}) \ No newline at end of file diff --git a/docs/0.4.5/target-versions.html b/docs/0.4.5/target-versions.html deleted file mode 100644 index 87f72001..00000000 --- a/docs/0.4.5/target-versions.html +++ /dev/null @@ -1,221 +0,0 @@ - - - - - - - - - Target MMIF Versions — mmif-python documentation - - - - - - - - - - - - - - - - - -
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The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the `appliance documentation `_ to learn more about the appliance. - -MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance. - -#. The code must be hosted on a public git repository (e.g. Github, Gitlab, ...) -#. Must listen to ``5000`` port. -#. Must expose ``/display`` route . -#. ``/display`` router should response to ``GET`` requests. -#. In the ``GET`` request, a public URL of the input MMIF file is passed via ``file`` URL parameter. -#. On the codebase root, there must be a ``Dockerfile`` that can build a `docker `_ image that runs the web app. - -We provide an example consumer at https://github.com/clamsproject/mmif-visualizer. diff --git a/docs/0.4.6/_sources/index.rst.txt b/docs/0.4.6/_sources/index.rst.txt deleted file mode 100644 index 9b90b38e..00000000 --- a/docs/0.4.6/_sources/index.rst.txt +++ /dev/null @@ -1,26 +0,0 @@ -Welcome to mmif-python's documentation! -======================================= - -.. mdinclude:: ../README.md - -.. toctree:: - :maxdepth: 2 - :caption: Contents - - introduction - target-versions - consumer-tutorial - -.. toctree:: - :maxdepth: 2 - :caption: API documentation: - - modules - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/docs/0.4.6/_sources/introduction.rst.txt b/docs/0.4.6/_sources/introduction.rst.txt deleted file mode 100644 index 6fea3a3c..00000000 --- a/docs/0.4.6/_sources/introduction.rst.txt +++ /dev/null @@ -1,78 +0,0 @@ -.. _instroduction: - -Getting Started -=============== - - -Overview ---------- - -MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF wbesite `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports de-/serialization of MMIF objects, as well as many navigation and manipulation helpers for MMIF objects. - -Prerequisites -------------- - -* `Python `_: ``mmif-python`` requires Python 3.6 or newer. We have no plan to support `Python 2.7 `_. - -Installation ---------------- - -Package ``mmif-python`` is distributed via the official PyPI. Users are supposed to pip-install to get latest release. - -.. code-block:: bash - - pip install mmif-python - -This will install a package `mmif` to local python. - -The MMIF format and specification is evolving over time, and ``mmif-python`` package will be updated along with the changes in MMIF format. - -.. note:: MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and ``mmif-python`` versions, please take time to read our decision on the subject `here `_. If you need to know which python SDK supports which specification version, see :ref:`target-versions` page. - -MMIF Serialization ---------------------------- - -:class:`mmif.serialize.mmif.Mmif` represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of :class:`mmif.serialize.model.MmifObject`, including the :class:`mmif.serialize.mmif.Mmif`. To start with an existing MMIF :class:`str`, simple initiate a new ``Mmif`` object with the file. - -.. code-block:: python - - import mmif - from mmif import Mmif - - mmif_str = """{ - "metadata": { - "mmif": "http://mmif.clams.ai/0.2.0" - }, - "documents": [ - { - "@type": "http://mmif.clams.ai/0.2.0/vocabulary/VideoDocument", - "properties": { - "id": "m1", - "mime": "video/mp4", - "location": "file:///var/archive/video-0012.mp4" - } - }, - { - "@type": "http://mmif.clams.ai/0.2.0/vocabulary/TextDocument", - "properties": { - "id": "m2", - "mime": "text/plain", - "location": "file:///var/archive/video-0012-transcript.txt" - } - } - ], - "views": []}""" - mmif_obj = Mmif(mmif_str) - - -Few notes; - -#. MMIF does not carry the primary source files in it. -#. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version ``mmif-python`` implementation of the MMIF might not be able to load an unsupported version of MMIF string. - -When serializing back to :class:`str`, call ``.serialize()`` (:meth:`mmif.serialize.model.MmifObject.serialize`) on the object. - -To get subcomponents, you can use various getters implemented in subclasses. For more details, the API documentation (:ref:`apidoc`) will help. - diff --git a/docs/0.4.6/_sources/modules.rst.txt b/docs/0.4.6/_sources/modules.rst.txt deleted file mode 100644 index e4269c6d..00000000 --- a/docs/0.4.6/_sources/modules.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _apidoc: - -mmif package -============ - -.. toctree:: - :maxdepth: 4 - - autodoc/mmif.serialize - autodoc/mmif.vocabulary diff --git a/docs/0.4.6/_sources/target-versions.rst.txt b/docs/0.4.6/_sources/target-versions.rst.txt deleted file mode 100644 index 34216d3e..00000000 --- a/docs/0.4.6/_sources/target-versions.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _target-versions: - -Target MMIF Versions -==================== - -This article provides targeting MMIF specification versions of different versions of ``mmif-python`` SDK. - -.. csv-table:: Target Specification Versions - :file: target-versions.csv - :header-rows: 1 diff --git a/docs/0.4.6/_static/_sphinx_javascript_frameworks_compat.js b/docs/0.4.6/_static/_sphinx_javascript_frameworks_compat.js deleted file mode 100644 index 81415803..00000000 --- a/docs/0.4.6/_static/_sphinx_javascript_frameworks_compat.js +++ /dev/null @@ -1,123 +0,0 @@ -/* Compatability shim for jQuery and underscores.js. - * - * Copyright Sphinx contributors - * Released under the two clause BSD licence - */ - -/** - * small helper function to urldecode strings - * - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL - */ -jQuery.urldecode = function(x) { - if (!x) { - return x - } - return decodeURIComponent(x.replace(/\+/g, ' ')); -}; - -/** - * small helper function to urlencode strings - */ -jQuery.urlencode = encodeURIComponent; - -/** - * This function returns the parsed url parameters of the - * current request. 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- -/** - * Simple result scoring code. - */ -if (typeof Scorer === "undefined") { - var Scorer = { - // Implement the following function to further tweak the score for each result - // The function takes a result array [docname, title, anchor, descr, score, filename] - // and returns the new score. - /* - score: result => { - const [docname, title, anchor, descr, score, filename, kind] = result - return score - }, - */ - - // query matches the full name of an object - objNameMatch: 11, - // or matches in the last dotted part of the object name - objPartialMatch: 6, - // Additive scores depending on the priority of the object - objPrio: { - 0: 15, // used to be importantResults - 1: 5, // used to be objectResults - 2: -5, // used to be unimportantResults - }, - // Used when the priority is not in the mapping. - objPrioDefault: 0, - - // query found in title - title: 15, - partialTitle: 7, - // query found in terms - term: 5, - partialTerm: 2, - }; -} - -// Global search result kind enum, used by themes to style search results. -class SearchResultKind { - static get index() { return "index"; } - static get object() { return "object"; } - static get text() { return "text"; } - static get title() { return "title"; } -} - -const _removeChildren = (element) => { - while (element && element.lastChild) element.removeChild(element.lastChild); -}; - -/** - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping - */ -const _escapeRegExp = (string) => - string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string - -const _displayItem = (item, searchTerms, highlightTerms) => { - const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; - const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; - const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; - const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; - const contentRoot = document.documentElement.dataset.content_root; - - const [docName, title, anchor, descr, score, _filename, kind] = item; - - let listItem = document.createElement("li"); - // Add a class representing the item's type: - // can be used by a theme's CSS selector for styling - // See SearchResultKind for the class names. - listItem.classList.add(`kind-${kind}`); - let requestUrl; - let linkUrl; - if (docBuilder === "dirhtml") { - // dirhtml builder - let dirname = docName + "/"; - if (dirname.match(/\/index\/$/)) - dirname = dirname.substring(0, dirname.length - 6); - else if (dirname === "index/") dirname = ""; - requestUrl = contentRoot + dirname; - linkUrl = requestUrl; - } else { - // normal html builders - requestUrl = contentRoot + docName + docFileSuffix; - linkUrl = docName + docLinkSuffix; - } - let linkEl = listItem.appendChild(document.createElement("a")); - linkEl.href = linkUrl + anchor; - linkEl.dataset.score = score; - linkEl.innerHTML = title; - if (descr) { - listItem.appendChild(document.createElement("span")).innerHTML = - " (" + descr + ")"; - // highlight search terms in the description - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - } - else if (showSearchSummary) - fetch(requestUrl) - .then((responseData) => responseData.text()) - .then((data) => { - if (data) - listItem.appendChild( - Search.makeSearchSummary(data, searchTerms, anchor) - ); - // highlight search terms in the summary - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - }); - Search.output.appendChild(listItem); -}; -const _finishSearch = (resultCount) => { - Search.stopPulse(); - Search.title.innerText = _("Search Results"); - if (!resultCount) - Search.status.innerText = Documentation.gettext( - "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." - ); - else - Search.status.innerText = Documentation.ngettext( - "Search finished, found one page matching the search query.", - "Search finished, found ${resultCount} pages matching the search query.", - resultCount, - ).replace('${resultCount}', resultCount); -}; -const _displayNextItem = ( - results, - resultCount, - searchTerms, - highlightTerms, -) => { - // results left, load the summary and display it - // this is intended to be dynamic (don't sub resultsCount) - if (results.length) { - _displayItem(results.pop(), searchTerms, highlightTerms); - setTimeout( - () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), - 5 - ); - } - // search finished, update title and status message - else _finishSearch(resultCount); -}; -// Helper function used by query() to order search results. -// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. -// Order the results by score (in opposite order of appearance, since the -// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. -const _orderResultsByScoreThenName = (a, b) => { - const leftScore = a[4]; - const rightScore = b[4]; - if (leftScore === rightScore) { - // same score: sort alphabetically - const leftTitle = a[1].toLowerCase(); - const rightTitle = b[1].toLowerCase(); - if (leftTitle === rightTitle) return 0; - return leftTitle > rightTitle ? -1 : 1; // inverted is intentional - } - return leftScore > rightScore ? 1 : -1; -}; - -/** - * Default splitQuery function. Can be overridden in ``sphinx.search`` with a - * custom function per language. - * - * The regular expression works by splitting the string on consecutive characters - * that are not Unicode letters, numbers, underscores, or emoji characters. - * This is the same as ``\W+`` in Python, preserving the surrogate pair area. - */ -if (typeof splitQuery === "undefined") { - var splitQuery = (query) => query - .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) - .filter(term => term) // remove remaining empty strings -} - -/** - * Search Module - */ -const Search = { - _index: null, - _queued_query: null, - _pulse_status: -1, - - htmlToText: (htmlString, anchor) => { - const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - for (const removalQuery of [".headerlink", "script", "style"]) { - htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); - } - if (anchor) { - const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); - if (anchorContent) return anchorContent.textContent; - - console.warn( - `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` - ); - } - - // if anchor not specified or not found, fall back to main content - const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent) return docContent.textContent; - - console.warn( - "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." - ); - return ""; - }, - - init: () => { - const query = new URLSearchParams(window.location.search).get("q"); - document - .querySelectorAll('input[name="q"]') - .forEach((el) => (el.value = query)); - if (query) Search.performSearch(query); - }, - - loadIndex: (url) => - (document.body.appendChild(document.createElement("script")).src = url), - - setIndex: (index) => { - Search._index = index; - if (Search._queued_query !== null) { - const query = Search._queued_query; - Search._queued_query = null; - Search.query(query); - } - }, - - hasIndex: () => Search._index !== null, - - deferQuery: (query) => (Search._queued_query = query), - - stopPulse: () => (Search._pulse_status = -1), - - startPulse: () => { - if (Search._pulse_status >= 0) return; - - const pulse = () => { - Search._pulse_status = (Search._pulse_status + 1) % 4; - Search.dots.innerText = ".".repeat(Search._pulse_status); - if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); - }; - pulse(); - }, - - /** - * perform a search for something (or wait until index is loaded) - */ - performSearch: (query) => { - // create the required interface elements - const searchText = document.createElement("h2"); - searchText.textContent = _("Searching"); - const searchSummary = document.createElement("p"); - searchSummary.classList.add("search-summary"); - searchSummary.innerText = ""; - const searchList = document.createElement("ul"); - searchList.setAttribute("role", "list"); - searchList.classList.add("search"); - - const out = document.getElementById("search-results"); - Search.title = out.appendChild(searchText); - Search.dots = Search.title.appendChild(document.createElement("span")); - Search.status = out.appendChild(searchSummary); - Search.output = out.appendChild(searchList); - - const searchProgress = document.getElementById("search-progress"); - // Some themes don't use the search progress node - if (searchProgress) { - searchProgress.innerText = _("Preparing search..."); - } - Search.startPulse(); - - // index already loaded, the browser was quick! - if (Search.hasIndex()) Search.query(query); - else Search.deferQuery(query); - }, - - _parseQuery: (query) => { - // stem the search terms and add them to the correct list - const stemmer = new Stemmer(); - const searchTerms = new Set(); - const excludedTerms = new Set(); - const highlightTerms = new Set(); - const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); - splitQuery(query.trim()).forEach((queryTerm) => { - const queryTermLower = queryTerm.toLowerCase(); - - // maybe skip this "word" - // stopwords array is from language_data.js - if ( - stopwords.indexOf(queryTermLower) !== -1 || - queryTerm.match(/^\d+$/) - ) - return; - - // stem the word - let word = stemmer.stemWord(queryTermLower); - // select the correct list - if (word[0] === "-") excludedTerms.add(word.substr(1)); - else { - searchTerms.add(word); - highlightTerms.add(queryTermLower); - } - }); - - if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js - localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) - } - - // console.debug("SEARCH: searching for:"); - // console.info("required: ", [...searchTerms]); - // console.info("excluded: ", [...excludedTerms]); - - return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; - }, - - /** - * execute search (requires search index to be loaded) - */ - _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - - // Collect multiple result groups to be sorted separately and then ordered. - // Each is an array of [docname, title, anchor, descr, score, filename, kind]. - const normalResults = []; - const nonMainIndexResults = []; - - _removeChildren(document.getElementById("search-progress")); - - const queryLower = query.toLowerCase().trim(); - for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { - for (const [file, id] of foundTitles) { - const score = Math.round(Scorer.title * queryLower.length / title.length); - const boost = titles[file] === title ? 1 : 0; // add a boost for document titles - normalResults.push([ - docNames[file], - titles[file] !== title ? `${titles[file]} > ${title}` : title, - id !== null ? "#" + id : "", - null, - score + boost, - filenames[file], - SearchResultKind.title, - ]); - } - } - } - - // search for explicit entries in index directives - for (const [entry, foundEntries] of Object.entries(indexEntries)) { - if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id, isMain] of foundEntries) { - const score = Math.round(100 * queryLower.length / entry.length); - const result = [ - docNames[file], - titles[file], - id ? "#" + id : "", - null, - score, - filenames[file], - SearchResultKind.index, - ]; - if (isMain) { - normalResults.push(result); - } else { - nonMainIndexResults.push(result); - } - } - } - } - - // lookup as object - objectTerms.forEach((term) => - normalResults.push(...Search.performObjectSearch(term, objectTerms)) - ); - - // lookup as search terms in fulltext - normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); - - // let the scorer override scores with a custom scoring function - if (Scorer.score) { - normalResults.forEach((item) => (item[4] = Scorer.score(item))); - nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); - } - - // Sort each group of results by score and then alphabetically by name. - normalResults.sort(_orderResultsByScoreThenName); - nonMainIndexResults.sort(_orderResultsByScoreThenName); - - // Combine the result groups in (reverse) order. - // Non-main index entries are typically arbitrary cross-references, - // so display them after other results. - let results = [...nonMainIndexResults, ...normalResults]; - - // remove duplicate search results - // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept - let seen = new Set(); - results = results.reverse().reduce((acc, result) => { - let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); - if (!seen.has(resultStr)) { - acc.push(result); - seen.add(resultStr); - } - return acc; - }, []); - - return results.reverse(); - }, - - query: (query) => { - const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); - const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); - - // for debugging - //Search.lastresults = results.slice(); // a copy - // console.info("search results:", Search.lastresults); - - // print the results - _displayNextItem(results, results.length, searchTerms, highlightTerms); - }, - - /** - * search for object names - */ - performObjectSearch: (object, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const objects = Search._index.objects; - const objNames = Search._index.objnames; - const titles = Search._index.titles; - - const results = []; - - const objectSearchCallback = (prefix, match) => { - const name = match[4] - const fullname = (prefix ? prefix + "." : "") + name; - const fullnameLower = fullname.toLowerCase(); - if (fullnameLower.indexOf(object) < 0) return; - - let score = 0; - const parts = fullnameLower.split("."); - - // check for different match types: exact matches of full name or - // "last name" (i.e. last dotted part) - if (fullnameLower === object || parts.slice(-1)[0] === object) - score += Scorer.objNameMatch; - else if (parts.slice(-1)[0].indexOf(object) > -1) - score += Scorer.objPartialMatch; // matches in last name - - const objName = objNames[match[1]][2]; - const title = titles[match[0]]; - - // If more than one term searched for, we require other words to be - // found in the name/title/description - const otherTerms = new Set(objectTerms); - otherTerms.delete(object); - if (otherTerms.size > 0) { - const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); - if ( - [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) - ) - return; - } - - let anchor = match[3]; - if (anchor === "") anchor = fullname; - else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; - - const descr = objName + _(", in ") + title; - - // add custom score for some objects according to scorer - if (Scorer.objPrio.hasOwnProperty(match[2])) - score += Scorer.objPrio[match[2]]; - else score += Scorer.objPrioDefault; - - results.push([ - docNames[match[0]], - fullname, - "#" + anchor, - descr, - score, - filenames[match[0]], - SearchResultKind.object, - ]); - }; - Object.keys(objects).forEach((prefix) => - objects[prefix].forEach((array) => - objectSearchCallback(prefix, array) - ) - ); - return results; - }, - - /** - * search for full-text terms in the index - */ - performTermsSearch: (searchTerms, excludedTerms) => { - // prepare search - const terms = Search._index.terms; - const titleTerms = Search._index.titleterms; - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - - const scoreMap = new Map(); - const fileMap = new Map(); - - // perform the search on the required terms - searchTerms.forEach((word) => { - const files = []; - const arr = [ - { files: terms[word], score: Scorer.term }, - { files: titleTerms[word], score: Scorer.title }, - ]; - // add support for partial matches - if (word.length > 2) { - const escapedWord = _escapeRegExp(word); - if (!terms.hasOwnProperty(word)) { - Object.keys(terms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: terms[term], score: Scorer.partialTerm }); - }); - } - if (!titleTerms.hasOwnProperty(word)) { - Object.keys(titleTerms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); - }); - } - } - - // no match but word was a required one - if (arr.every((record) => record.files === undefined)) return; - - // found search word in contents - arr.forEach((record) => { - if (record.files === undefined) return; - - let recordFiles = record.files; - if (recordFiles.length === undefined) recordFiles = [recordFiles]; - files.push(...recordFiles); - - // set score for the word in each file - recordFiles.forEach((file) => { - if (!scoreMap.has(file)) scoreMap.set(file, {}); - scoreMap.get(file)[word] = record.score; - }); - }); - - // create the mapping - files.forEach((file) => { - if (!fileMap.has(file)) fileMap.set(file, [word]); - else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); - }); - }); - - // now check if the files don't contain excluded terms - const results = []; - for (const [file, wordList] of fileMap) { - // check if all requirements are matched - - // as search terms with length < 3 are discarded - const filteredTermCount = [...searchTerms].filter( - (term) => term.length > 2 - ).length; - if ( - wordList.length !== searchTerms.size && - wordList.length !== filteredTermCount - ) - continue; - - // ensure that none of the excluded terms is in the search result - if ( - [...excludedTerms].some( - (term) => - terms[term] === file || - titleTerms[term] === file || - (terms[term] || []).includes(file) || - (titleTerms[term] || []).includes(file) - ) - ) - break; - - // select one (max) score for the file. - const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); - // add result to the result list - results.push([ - docNames[file], - titles[file], - "", - null, - score, - filenames[file], - SearchResultKind.text, - ]); - } - return results; - }, - - /** - * helper function to return a node containing the - * search summary for a given text. keywords is a list - * of stemmed words. - */ - makeSearchSummary: (htmlText, keywords, anchor) => { - const text = Search.htmlToText(htmlText, anchor); - if (text === "") return null; - - const textLower = text.toLowerCase(); - const actualStartPosition = [...keywords] - .map((k) => textLower.indexOf(k.toLowerCase())) - .filter((i) => i > -1) - .slice(-1)[0]; - const startWithContext = Math.max(actualStartPosition - 120, 0); - - const top = startWithContext === 0 ? "" : "..."; - const tail = startWithContext + 240 < text.length ? "..." : ""; - - let summary = document.createElement("p"); - summary.classList.add("context"); - summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; - - return summary; - }, -}; - -_ready(Search.init); diff --git a/docs/0.4.6/_static/sphinx_highlight.js b/docs/0.4.6/_static/sphinx_highlight.js deleted file mode 100644 index 8a96c69a..00000000 --- a/docs/0.4.6/_static/sphinx_highlight.js +++ /dev/null @@ -1,154 +0,0 @@ -/* Highlighting utilities for Sphinx HTML documentation. */ -"use strict"; - -const SPHINX_HIGHLIGHT_ENABLED = true - -/** - * highlight a given string on a node by wrapping it in - * span elements with the given class name. - */ -const _highlight = (node, addItems, text, className) => { - if (node.nodeType === Node.TEXT_NODE) { - const val = node.nodeValue; - const parent = node.parentNode; - const pos = val.toLowerCase().indexOf(text); - if ( - pos >= 0 && - !parent.classList.contains(className) && - !parent.classList.contains("nohighlight") - ) { - let span; - - const closestNode = parent.closest("body, svg, foreignObject"); - const isInSVG = closestNode && closestNode.matches("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.classList.add(className); - } - - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - const rest = document.createTextNode(val.substr(pos + text.length)); - parent.insertBefore( - span, - parent.insertBefore( - rest, - node.nextSibling - ) - ); - node.nodeValue = val.substr(0, pos); - /* There may be more occurrences of search term in this node. So call this - * function recursively on the remaining fragment. - */ - _highlight(rest, addItems, text, className); - - if (isInSVG) { - const rect = document.createElementNS( - "http://www.w3.org/2000/svg", - "rect" - ); - const bbox = parent.getBBox(); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute("class", className); - addItems.push({ parent: parent, target: rect }); - } - } - } else if (node.matches && !node.matches("button, select, textarea")) { - node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); - } -}; -const _highlightText = (thisNode, text, className) => { - let addItems = []; - _highlight(thisNode, addItems, text, className); - addItems.forEach((obj) => - obj.parent.insertAdjacentElement("beforebegin", obj.target) - ); -}; - -/** - * Small JavaScript module for the documentation. - */ -const SphinxHighlight = { - - /** - * highlight the search words provided in localstorage in the text - */ - highlightSearchWords: () => { - if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight - - // get and clear terms from localstorage - const url = new URL(window.location); - const highlight = - localStorage.getItem("sphinx_highlight_terms") - || url.searchParams.get("highlight") - || ""; - localStorage.removeItem("sphinx_highlight_terms") - url.searchParams.delete("highlight"); - window.history.replaceState({}, "", url); - - // get individual terms from highlight string - const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); - if (terms.length === 0) return; // nothing to do - - // There should never be more than one element matching "div.body" - const divBody = document.querySelectorAll("div.body"); - const body = divBody.length ? divBody[0] : document.querySelector("body"); - window.setTimeout(() => { - terms.forEach((term) => _highlightText(body, term, "highlighted")); - }, 10); - - const searchBox = document.getElementById("searchbox"); - if (searchBox === null) return; - searchBox.appendChild( - document - .createRange() - .createContextualFragment( - '

' + - '' + - _("Hide Search Matches") + - "

" - ) - ); - }, - - /** - * helper function to hide the search marks again - */ - hideSearchWords: () => { - document - .querySelectorAll("#searchbox .highlight-link") - .forEach((el) => el.remove()); - document - .querySelectorAll("span.highlighted") - .forEach((el) => el.classList.remove("highlighted")); - localStorage.removeItem("sphinx_highlight_terms") - }, - - initEscapeListener: () => { - // only install a listener if it is really needed - if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; - - document.addEventListener("keydown", (event) => { - // bail for input elements - if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; - // bail with special keys - if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; - if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { - SphinxHighlight.hideSearchWords(); - event.preventDefault(); - } - }); - }, -}; - -_ready(() => { - /* Do not call highlightSearchWords() when we are on the search page. - * It will highlight words from the *previous* search query. - */ - if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); - SphinxHighlight.initEscapeListener(); -}); diff --git a/docs/0.4.6/autodoc/mmif.serialize.html b/docs/0.4.6/autodoc/mmif.serialize.html deleted file mode 100644 index f5e845aa..00000000 --- a/docs/0.4.6/autodoc/mmif.serialize.html +++ /dev/null @@ -1,390 +0,0 @@ - - - - - - - - - mmif.serialize module — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.serialize module

-
-

mmif.serialize.model module

-
-
-

mmif.serialize.mmif module

-
-
-

mmif.serialize.view module

-
-
-

mmif.serialize.annotation module

-

The annotation module contains the classes used to represent a -MMIF annotation as a live Python object.

-

In MMIF, annotations are created by apps in a pipeline as a part -of a view. For documentation on how views are represented, see -mmif.serialize.view.

-
-
-class mmif.serialize.annotation.Annotation(anno_obj: bytes | str | dict | None = None)[source]
-

Bases: FreezableMmifObject

-

MmifObject that represents an annotation in a MMIF view.

-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]]) → None[source]
-

Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

-
- -
-
-property at_type: TypesBase[source]
-
- -
-
-property id: str[source]
-
- -
-
-is_document()[source]
-
- -
-
-is_type(at_type: str | TypesBase) → bool[source]
-

Check if the @type of this object matches.

-
- -
- -
-
-class mmif.serialize.annotation.AnnotationProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: FreezableMmifObject

-

AnnotationProperties object that represents the -properties object within a MMIF annotation.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
- -
-
-class mmif.serialize.annotation.Document(doc_obj: bytes | str | dict | None = None)[source]
-

Bases: Annotation

-

Document object that represents a single document in a MMIF file.

-

A document is identified by an ID, and contains certain attributes -and potentially contains the contents of the document itself, -metadata about how the document was created, and/or a list of -subdocuments grouped together logically.

-

If document_obj is not provided, an empty Document will be generated.

-
-
Parameters:
-

document_obj – the JSON data that defines the document

-
-
-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None]) → None[source]
-

Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

-
- -
-
-property location: str | None[source]
-

location property must be a legitimate URI. That is, should the document be a local file -then the file:// scheme must be used. -Returns None when no location is set.

-
- -
-
-location_address() → str | None[source]
-

Retrieves the full address from the document location URI. -Returns None when no location is set.

-
- -
-
-location_path() → str | None[source]
-

Retrieves only path name of the document location (hostname is ignored). -Useful to get a path of a local file. -Returns None when no location is set.

-
- -
-
-location_scheme() → str | None[source]
-

Retrieves URI scheme of the document location. -Returns None when no location is set.

-
- -
-
-property parent: str[source]
-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.DocumentProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: AnnotationProperties

-

DocumentProperties object that represents the -properties object within a MMIF document.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
-
-property location: str | None[source]
-

location property must be a legitimate URI. That is, should the document be a local file -then the file:// scheme must be used. -Returns None when no location is set.

-
- -
-
-location_address() → str | None[source]
-

Retrieves the full address from the document location URI. -Returns None when no location is set.

-
- -
-
-location_path() → str | None[source]
-

Retrieves only path name of the document location (hostname is ignored). -Useful to get a path of a local file. -Returns None when no location is set.

-
- -
-
-location_scheme() → str | None[source]
-

Retrieves URI scheme of the document location. -Returns None when no location is set.

-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.Text(text_obj: bytes | str | dict | None = None)[source]
-

Bases: FreezableMmifObject

-
-
-property lang: str[source]
-
- -
-
-property value: str[source]
-
- -
- -
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.4.6 - - -
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0.3.0
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0.3.1
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0.3.2
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0.3.3
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0.3.4
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0.4.1
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- - - \ No newline at end of file diff --git a/docs/0.4.6/autodoc/mmif.vocabulary.html b/docs/0.4.6/autodoc/mmif.vocabulary.html deleted file mode 100644 index 305eb6aa..00000000 --- a/docs/0.4.6/autodoc/mmif.vocabulary.html +++ /dev/null @@ -1,285 +0,0 @@ - - - - - - - - - mmif.vocabulary module — mmif-python documentation - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.vocabulary module

-
-

mmif.vocabulary.annotation_types module

-
-
-class mmif.vocabulary.annotation_types.AnnotationTypes(type_uri: str)[source]
-

Bases: AnnotationTypesBase

-

This class contains the CLAMS annotation types -defined in the spec version 0.4.2 as class variables.

-
-
-Alignment = http://mmif.clams.ai/0.4.2/vocabulary/Alignment[source]
-
- -
-
-Annotation = http://mmif.clams.ai/0.4.2/vocabulary/Annotation[source]
-
- -
-
-BoundingBox = http://mmif.clams.ai/0.4.2/vocabulary/BoundingBox[source]
-
- -
-
-Chapter = http://mmif.clams.ai/0.4.2/vocabulary/Chapter[source]
-
- -
-
-Interval = http://mmif.clams.ai/0.4.2/vocabulary/Interval[source]
-
- -
-
-Polygon = http://mmif.clams.ai/0.4.2/vocabulary/Polygon[source]
-
- -
-
-Region = http://mmif.clams.ai/0.4.2/vocabulary/Region[source]
-
- -
-
-Relation = http://mmif.clams.ai/0.4.2/vocabulary/Relation[source]
-
- -
-
-Span = http://mmif.clams.ai/0.4.2/vocabulary/Span[source]
-
- -
-
-TimeFrame = http://mmif.clams.ai/0.4.2/vocabulary/TimeFrame[source]
-
- -
-
-TimePoint = http://mmif.clams.ai/0.4.2/vocabulary/TimePoint[source]
-
- -
-
-VideoObject = http://mmif.clams.ai/0.4.2/vocabulary/VideoObject[source]
-
- -
- -
-
-

mmif.vocabulary.document_types module

-
-
-class mmif.vocabulary.document_types.DocumentTypes(type_uri: str)[source]
-

Bases: DocumentTypesBase

-

This class contains the CLAMS document types -defined in the spec version 0.4.2 as class variables.

-
-
-AudioDocument = http://mmif.clams.ai/0.4.2/vocabulary/AudioDocument[source]
-
- -
-
-Document = http://mmif.clams.ai/0.4.2/vocabulary/Document[source]
-
- -
-
-ImageDocument = http://mmif.clams.ai/0.4.2/vocabulary/ImageDocument[source]
-
- -
-
-TextDocument = http://mmif.clams.ai/0.4.2/vocabulary/TextDocument[source]
-
- -
-
-VideoDocument = http://mmif.clams.ai/0.4.2/vocabulary/VideoDocument[source]
-
- -
- -
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.4.6 - - -
-
- -
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0.4.7
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0.4.8
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0.5.2
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- - - \ No newline at end of file diff --git a/docs/0.4.6/consumer-tutorial.html b/docs/0.4.6/consumer-tutorial.html deleted file mode 100644 index 43494e11..00000000 --- a/docs/0.4.6/consumer-tutorial.html +++ /dev/null @@ -1,176 +0,0 @@ - - - - - - - - - MMIF consumer — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • MMIF consumer
    • -
  • -
    • -
-
-
-
-
- -
-

MMIF consumer

-

A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the appliance documentation to learn more about the appliance.

-

MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance.

-
    -

  1. The code must be hosted on a public git repository (e.g. Github, Gitlab, …)

    2. -

  2. Must listen to 5000 port.

    3. -

  3. Must expose /display route .

    4. -

  4. /display router should response to GET requests.

    5. -

  5. In the GET request, a public URL of the input MMIF file is passed via file URL parameter.

    6. -

  6. On the codebase root, there must be a Dockerfile that can build a docker image that runs the web app.

    7. -
-

We provide an example consumer at https://github.com/clamsproject/mmif-visualizer.

-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.4.6 - - -
-
- -
0.3.0
-
0.3.1
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0.3.2
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0.3.3
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0.4.1
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0.4.2
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- - -
- -
-
-
-
    -
    • -
  • Index
    • -
  • -
    • -
-
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-
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- - -

Index

- -
- A - | B - | C - | D - | I - | L - | M - | P - | R - | S - | T - | V - -
-

A

- - - -
- -

B

- - -
- -

C

- - -
- -

D

- - - -
- -

I

- - - -
- -

L

- - - -
- -

M

- - - -
    -
  • - mmif.serialize.annotation - -
    • -
  • - mmif.vocabulary.annotation_types - -
    • -
  • - mmif.vocabulary.document_types - -
    • -
- -

P

- - - -
- -

R

- - - -
- -

S

- - -
- -

T

- - - -
- -

V

- - - -
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-
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- - Other Versions - v: 0.4.6 - - -
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0.3.0
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0.3.1
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0.3.2
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0.3.3
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0.3.4
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0.4.1
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0.4.2
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0.4.3
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0.4.6
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0.4.7
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0.5.2
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1.0.1
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1.0.10
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- - -
- -
-
-
-
    -
    • -
  • Welcome to mmif-python’s documentation!
    • -
  • -
    • -
-
-
-
-
- -
-

Welcome to mmif-python’s documentation!

-
-
-

MMIF for python

-

NOTE that this project is in pre-alpha and being actively developed. Nothing is guaranteed to reliably work for the moment and developer need to be very careful when using APIs implemented here. Please use the issue track to report bugs and malfunctions.

-
-

MultiMedia Interchange Format

-

MMIF is a JSON(-LD)-based data format designed for transferring annotation data between computational analysis applications in CLAMS project.

-
-

Contents

- -
-
-

API documentation:

- -
-
-
-
-

Indices and tables

- -
- - -
-
- -
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- -
- - Other Versions - v: 0.4.6 - - -
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0.3.0
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0.3.1
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0.3.2
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0.3.4
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- - - \ No newline at end of file diff --git a/docs/0.4.6/introduction.html b/docs/0.4.6/introduction.html deleted file mode 100644 index 6c062c72..00000000 --- a/docs/0.4.6/introduction.html +++ /dev/null @@ -1,236 +0,0 @@ - - - - - - - - - Getting Started — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
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  • Getting Started
    • -
  • -
    • -
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Getting Started

-
-

Overview

-

MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF wbesite. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports de-/serialization of MMIF objects, as well as many navigation and manipulation helpers for MMIF objects.

-
-
-

Prerequisites

-
    -

  • Python: mmif-python requires Python 3.6 or newer. We have no plan to support Python 2.7.

    • -
-
-
-

Installation

-

Package mmif-python is distributed via the official PyPI. Users are supposed to pip-install to get latest release.

-
pip install mmif-python
-
-
-

This will install a package mmif to local python.

-

The MMIF format and specification is evolving over time, and mmif-python package will be updated along with the changes in MMIF format.

-
-

Note

-

MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and mmif-python versions, please take time to read our decision on the subject here. If you need to know which python SDK supports which specification version, see Target MMIF Versions page.

-
-
-
-

MMIF Serialization

-

mmif.serialize.mmif.Mmif represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of mmif.serialize.model.MmifObject, including the mmif.serialize.mmif.Mmif. To start with an existing MMIF str, simple initiate a new Mmif object with the file.

-
import mmif
-from mmif import Mmif
-
-mmif_str = """{
-"metadata": {
-  "mmif": "http://mmif.clams.ai/0.2.0"
-},
-"documents": [
-  {
-    "@type": "http://mmif.clams.ai/0.2.0/vocabulary/VideoDocument",
-    "properties": {
-      "id": "m1",
-      "mime": "video/mp4",
-      "location": "file:///var/archive/video-0012.mp4"
-    }
-  },
-  {
-    "@type": "http://mmif.clams.ai/0.2.0/vocabulary/TextDocument",
-    "properties": {
-      "id": "m2",
-      "mime": "text/plain",
-      "location": "file:///var/archive/video-0012-transcript.txt"
-    }
-  }
-],
-"views": []}"""
-mmif_obj = Mmif(mmif_str)
-
-
-

Few notes;

-
    -

  1. MMIF does not carry the primary source files in it.

    2. -

  2. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version mmif-python implementation of the MMIF might not be able to load an unsupported version of MMIF string.

    3. -
-

When serializing back to str, call .serialize() (mmif.serialize.model.MmifObject.serialize()) on the object.

-

To get subcomponents, you can use various getters implemented in subclasses. For more details, the API documentation (mmif package) will help.

-
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.4.6 - - -
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0.3.0
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0.3.1
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0.3.3
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0.3.4
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0.3.5
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0.4.0
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0.4.1
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- - - \ No newline at end of file diff --git a/docs/0.4.6/modules.html b/docs/0.4.6/modules.html deleted file mode 100644 index f7ab5895..00000000 --- a/docs/0.4.6/modules.html +++ /dev/null @@ -1,248 +0,0 @@ - - - - - - - - - mmif package — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
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  • mmif package
    • -
  • -
    • -
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mmif package

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- - - \ No newline at end of file diff --git a/docs/0.4.6/objects.inv b/docs/0.4.6/objects.inv deleted file mode 100644 index 64f252eb..00000000 --- a/docs/0.4.6/objects.inv +++ /dev/null @@ -1,9 +0,0 @@ -# Sphinx inventory version 2 -# Project: mmif-python -# Version: 0.4.6 -# The remainder of this file is compressed using zlib. -xڽ0y -WڽmV95F}>I I 1l9Ԡ'TnsBK#*? FܘSEB$Qd -hL&aU@ EYⅪ#(su)xc@ǧA|Xgs߇O#S}U3opgk|AUk=G8bĩHK'=קg OS`9/@ȯuBnM3H7IaWO`_r9 iv:8wlW;RQ}Gjtu/K0ˣ-026W R_zۂ.c9<(j#Rɖ"X;įncd~ʄöLQY~T}/Xj)Z0'[NIpCu7%o.M~ .m$ -y:X -m4ɵxC;C40SRL$p'wo~\ k - - - - - Python Module Index — mmif-python documentation - - - - - - - - - - - - - - - - - - -
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- - - - - - - - \ No newline at end of file diff --git a/docs/0.4.6/searchindex.js b/docs/0.4.6/searchindex.js deleted file mode 100644 index 90a35360..00000000 --- a/docs/0.4.6/searchindex.js +++ /dev/null @@ -1 +0,0 @@ -Search.setIndex({"alltitles": {"API documentation:": [[3, null]], "Contents": [[3, null]], "Getting Started": [[4, null]], "Indices and tables": [[3, "indices-and-tables"]], "Installation": [[4, "installation"]], "MMIF Serialization": [[4, "mmif-serialization"]], "MMIF consumer": [[2, null]], "MMIF for python": [[3, "mmif-for-python"]], "MultiMedia Interchange Format": [[3, "multimedia-interchange-format"]], "Overview": [[4, "overview"]], "Prerequisites": [[4, "prerequisites"]], "Target MMIF Versions": [[6, null]], "Target Specification Versions": [[6, "id1"]], "Welcome to mmif-python\u2019s documentation!": [[3, null]], "mmif package": [[5, null]], "mmif.serialize module": [[0, null]], "mmif.serialize.annotation module": [[0, "module-mmif.serialize.annotation"]], 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"annotation_typ": 1, "api": 3, "consum": 2, "content": 3, "document": 3, "document_typ": 1, "format": 3, "get": 4, "indic": 3, "instal": 4, "interchang": 3, "mmif": [0, 1, 2, 3, 4, 5, 6], "model": 0, "modul": [0, 1], "multimedia": 3, "overview": 4, "packag": 5, "prerequisit": 4, "python": 3, "serial": [0, 4], "specif": 6, "start": 4, "tabl": 3, "target": 6, "version": 6, "view": 0, "vocabulari": 1, "welcom": 3}}) \ No newline at end of file diff --git a/docs/0.4.6/target-versions.html b/docs/0.4.6/target-versions.html deleted file mode 100644 index 8f9bcb72..00000000 --- a/docs/0.4.6/target-versions.html +++ /dev/null @@ -1,224 +0,0 @@ - - - - - - - - - Target MMIF Versions — mmif-python documentation - - - - - - - - - - - - - - - - - -
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Target MMIF Versions

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This article provides targeting MMIF specification versions of different versions of mmif-python SDK.

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Target Specification Versions

mmif-python version

Target MMIF Specification

0.4.6

0.4.2

0.4.5

0.4.0

0.4.4

0.4.0

0.4.3

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- - - \ No newline at end of file diff --git a/docs/0.4.7/.buildinfo b/docs/0.4.7/.buildinfo deleted file mode 100644 index 96b95514..00000000 --- a/docs/0.4.7/.buildinfo +++ /dev/null @@ -1,4 +0,0 @@ -# Sphinx build info version 1 -# This file records the configuration used when building these files. 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The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the `appliance documentation `_ to learn more about the appliance. - -MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance. - -#. The code must be hosted on a public git repository (e.g. Github, Gitlab, ...) -#. Must listen to ``5000`` port. -#. Must expose ``/display`` route . -#. ``/display`` router should response to ``GET`` requests. -#. In the ``GET`` request, a public URL of the input MMIF file is passed via ``file`` URL parameter. -#. On the codebase root, there must be a ``Dockerfile`` that can build a `docker `_ image that runs the web app. - -We provide an example consumer at https://github.com/clamsproject/mmif-visualizer. diff --git a/docs/0.4.7/_sources/index.rst.txt b/docs/0.4.7/_sources/index.rst.txt deleted file mode 100644 index 9b90b38e..00000000 --- a/docs/0.4.7/_sources/index.rst.txt +++ /dev/null @@ -1,26 +0,0 @@ -Welcome to mmif-python's documentation! -======================================= - -.. mdinclude:: ../README.md - -.. toctree:: - :maxdepth: 2 - :caption: Contents - - introduction - target-versions - consumer-tutorial - -.. toctree:: - :maxdepth: 2 - :caption: API documentation: - - modules - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/docs/0.4.7/_sources/introduction.rst.txt b/docs/0.4.7/_sources/introduction.rst.txt deleted file mode 100644 index 6fea3a3c..00000000 --- a/docs/0.4.7/_sources/introduction.rst.txt +++ /dev/null @@ -1,78 +0,0 @@ -.. _instroduction: - -Getting Started -=============== - - -Overview ---------- - -MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF wbesite `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports de-/serialization of MMIF objects, as well as many navigation and manipulation helpers for MMIF objects. - -Prerequisites -------------- - -* `Python `_: ``mmif-python`` requires Python 3.6 or newer. We have no plan to support `Python 2.7 `_. - -Installation ---------------- - -Package ``mmif-python`` is distributed via the official PyPI. Users are supposed to pip-install to get latest release. - -.. code-block:: bash - - pip install mmif-python - -This will install a package `mmif` to local python. - -The MMIF format and specification is evolving over time, and ``mmif-python`` package will be updated along with the changes in MMIF format. - -.. note:: MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and ``mmif-python`` versions, please take time to read our decision on the subject `here `_. If you need to know which python SDK supports which specification version, see :ref:`target-versions` page. - -MMIF Serialization ---------------------------- - -:class:`mmif.serialize.mmif.Mmif` represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of :class:`mmif.serialize.model.MmifObject`, including the :class:`mmif.serialize.mmif.Mmif`. To start with an existing MMIF :class:`str`, simple initiate a new ``Mmif`` object with the file. - -.. code-block:: python - - import mmif - from mmif import Mmif - - mmif_str = """{ - "metadata": { - "mmif": "http://mmif.clams.ai/0.2.0" - }, - "documents": [ - { - "@type": "http://mmif.clams.ai/0.2.0/vocabulary/VideoDocument", - "properties": { - "id": "m1", - "mime": "video/mp4", - "location": "file:///var/archive/video-0012.mp4" - } - }, - { - "@type": "http://mmif.clams.ai/0.2.0/vocabulary/TextDocument", - "properties": { - "id": "m2", - "mime": "text/plain", - "location": "file:///var/archive/video-0012-transcript.txt" - } - } - ], - "views": []}""" - mmif_obj = Mmif(mmif_str) - - -Few notes; - -#. MMIF does not carry the primary source files in it. -#. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version ``mmif-python`` implementation of the MMIF might not be able to load an unsupported version of MMIF string. - -When serializing back to :class:`str`, call ``.serialize()`` (:meth:`mmif.serialize.model.MmifObject.serialize`) on the object. - -To get subcomponents, you can use various getters implemented in subclasses. For more details, the API documentation (:ref:`apidoc`) will help. - diff --git a/docs/0.4.7/_sources/modules.rst.txt b/docs/0.4.7/_sources/modules.rst.txt deleted file mode 100644 index e4269c6d..00000000 --- a/docs/0.4.7/_sources/modules.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _apidoc: - -mmif package -============ - -.. toctree:: - :maxdepth: 4 - - autodoc/mmif.serialize - autodoc/mmif.vocabulary diff --git a/docs/0.4.7/_sources/target-versions.rst.txt b/docs/0.4.7/_sources/target-versions.rst.txt deleted file mode 100644 index 34216d3e..00000000 --- a/docs/0.4.7/_sources/target-versions.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _target-versions: - -Target MMIF Versions -==================== - -This article provides targeting MMIF specification versions of different versions of ``mmif-python`` SDK. - -.. csv-table:: Target Specification Versions - :file: target-versions.csv - :header-rows: 1 diff --git a/docs/0.4.7/_static/_sphinx_javascript_frameworks_compat.js b/docs/0.4.7/_static/_sphinx_javascript_frameworks_compat.js deleted file mode 100644 index 81415803..00000000 --- a/docs/0.4.7/_static/_sphinx_javascript_frameworks_compat.js +++ /dev/null @@ -1,123 +0,0 @@ -/* Compatability shim for jQuery and underscores.js. - * - * Copyright Sphinx contributors - * Released under the two clause BSD licence - */ - -/** - * small helper function to urldecode strings - * - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL - */ -jQuery.urldecode = function(x) { - if (!x) { - return x - } - return decodeURIComponent(x.replace(/\+/g, ' ')); -}; - -/** - * small helper function to urlencode strings - */ -jQuery.urlencode = encodeURIComponent; - -/** - * This function returns the parsed url parameters of the - * current request. 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- -/** - * Simple result scoring code. - */ -if (typeof Scorer === "undefined") { - var Scorer = { - // Implement the following function to further tweak the score for each result - // The function takes a result array [docname, title, anchor, descr, score, filename] - // and returns the new score. - /* - score: result => { - const [docname, title, anchor, descr, score, filename, kind] = result - return score - }, - */ - - // query matches the full name of an object - objNameMatch: 11, - // or matches in the last dotted part of the object name - objPartialMatch: 6, - // Additive scores depending on the priority of the object - objPrio: { - 0: 15, // used to be importantResults - 1: 5, // used to be objectResults - 2: -5, // used to be unimportantResults - }, - // Used when the priority is not in the mapping. - objPrioDefault: 0, - - // query found in title - title: 15, - partialTitle: 7, - // query found in terms - term: 5, - partialTerm: 2, - }; -} - -// Global search result kind enum, used by themes to style search results. -class SearchResultKind { - static get index() { return "index"; } - static get object() { return "object"; } - static get text() { return "text"; } - static get title() { return "title"; } -} - -const _removeChildren = (element) => { - while (element && element.lastChild) element.removeChild(element.lastChild); -}; - -/** - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping - */ -const _escapeRegExp = (string) => - string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string - -const _displayItem = (item, searchTerms, highlightTerms) => { - const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; - const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; - const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; - const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; - const contentRoot = document.documentElement.dataset.content_root; - - const [docName, title, anchor, descr, score, _filename, kind] = item; - - let listItem = document.createElement("li"); - // Add a class representing the item's type: - // can be used by a theme's CSS selector for styling - // See SearchResultKind for the class names. - listItem.classList.add(`kind-${kind}`); - let requestUrl; - let linkUrl; - if (docBuilder === "dirhtml") { - // dirhtml builder - let dirname = docName + "/"; - if (dirname.match(/\/index\/$/)) - dirname = dirname.substring(0, dirname.length - 6); - else if (dirname === "index/") dirname = ""; - requestUrl = contentRoot + dirname; - linkUrl = requestUrl; - } else { - // normal html builders - requestUrl = contentRoot + docName + docFileSuffix; - linkUrl = docName + docLinkSuffix; - } - let linkEl = listItem.appendChild(document.createElement("a")); - linkEl.href = linkUrl + anchor; - linkEl.dataset.score = score; - linkEl.innerHTML = title; - if (descr) { - listItem.appendChild(document.createElement("span")).innerHTML = - " (" + descr + ")"; - // highlight search terms in the description - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - } - else if (showSearchSummary) - fetch(requestUrl) - .then((responseData) => responseData.text()) - .then((data) => { - if (data) - listItem.appendChild( - Search.makeSearchSummary(data, searchTerms, anchor) - ); - // highlight search terms in the summary - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - }); - Search.output.appendChild(listItem); -}; -const _finishSearch = (resultCount) => { - Search.stopPulse(); - Search.title.innerText = _("Search Results"); - if (!resultCount) - Search.status.innerText = Documentation.gettext( - "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." - ); - else - Search.status.innerText = Documentation.ngettext( - "Search finished, found one page matching the search query.", - "Search finished, found ${resultCount} pages matching the search query.", - resultCount, - ).replace('${resultCount}', resultCount); -}; -const _displayNextItem = ( - results, - resultCount, - searchTerms, - highlightTerms, -) => { - // results left, load the summary and display it - // this is intended to be dynamic (don't sub resultsCount) - if (results.length) { - _displayItem(results.pop(), searchTerms, highlightTerms); - setTimeout( - () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), - 5 - ); - } - // search finished, update title and status message - else _finishSearch(resultCount); -}; -// Helper function used by query() to order search results. -// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. -// Order the results by score (in opposite order of appearance, since the -// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. -const _orderResultsByScoreThenName = (a, b) => { - const leftScore = a[4]; - const rightScore = b[4]; - if (leftScore === rightScore) { - // same score: sort alphabetically - const leftTitle = a[1].toLowerCase(); - const rightTitle = b[1].toLowerCase(); - if (leftTitle === rightTitle) return 0; - return leftTitle > rightTitle ? -1 : 1; // inverted is intentional - } - return leftScore > rightScore ? 1 : -1; -}; - -/** - * Default splitQuery function. Can be overridden in ``sphinx.search`` with a - * custom function per language. - * - * The regular expression works by splitting the string on consecutive characters - * that are not Unicode letters, numbers, underscores, or emoji characters. - * This is the same as ``\W+`` in Python, preserving the surrogate pair area. - */ -if (typeof splitQuery === "undefined") { - var splitQuery = (query) => query - .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) - .filter(term => term) // remove remaining empty strings -} - -/** - * Search Module - */ -const Search = { - _index: null, - _queued_query: null, - _pulse_status: -1, - - htmlToText: (htmlString, anchor) => { - const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - for (const removalQuery of [".headerlink", "script", "style"]) { - htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); - } - if (anchor) { - const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); - if (anchorContent) return anchorContent.textContent; - - console.warn( - `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` - ); - } - - // if anchor not specified or not found, fall back to main content - const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent) return docContent.textContent; - - console.warn( - "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." - ); - return ""; - }, - - init: () => { - const query = new URLSearchParams(window.location.search).get("q"); - document - .querySelectorAll('input[name="q"]') - .forEach((el) => (el.value = query)); - if (query) Search.performSearch(query); - }, - - loadIndex: (url) => - (document.body.appendChild(document.createElement("script")).src = url), - - setIndex: (index) => { - Search._index = index; - if (Search._queued_query !== null) { - const query = Search._queued_query; - Search._queued_query = null; - Search.query(query); - } - }, - - hasIndex: () => Search._index !== null, - - deferQuery: (query) => (Search._queued_query = query), - - stopPulse: () => (Search._pulse_status = -1), - - startPulse: () => { - if (Search._pulse_status >= 0) return; - - const pulse = () => { - Search._pulse_status = (Search._pulse_status + 1) % 4; - Search.dots.innerText = ".".repeat(Search._pulse_status); - if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); - }; - pulse(); - }, - - /** - * perform a search for something (or wait until index is loaded) - */ - performSearch: (query) => { - // create the required interface elements - const searchText = document.createElement("h2"); - searchText.textContent = _("Searching"); - const searchSummary = document.createElement("p"); - searchSummary.classList.add("search-summary"); - searchSummary.innerText = ""; - const searchList = document.createElement("ul"); - searchList.setAttribute("role", "list"); - searchList.classList.add("search"); - - const out = document.getElementById("search-results"); - Search.title = out.appendChild(searchText); - Search.dots = Search.title.appendChild(document.createElement("span")); - Search.status = out.appendChild(searchSummary); - Search.output = out.appendChild(searchList); - - const searchProgress = document.getElementById("search-progress"); - // Some themes don't use the search progress node - if (searchProgress) { - searchProgress.innerText = _("Preparing search..."); - } - Search.startPulse(); - - // index already loaded, the browser was quick! - if (Search.hasIndex()) Search.query(query); - else Search.deferQuery(query); - }, - - _parseQuery: (query) => { - // stem the search terms and add them to the correct list - const stemmer = new Stemmer(); - const searchTerms = new Set(); - const excludedTerms = new Set(); - const highlightTerms = new Set(); - const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); - splitQuery(query.trim()).forEach((queryTerm) => { - const queryTermLower = queryTerm.toLowerCase(); - - // maybe skip this "word" - // stopwords array is from language_data.js - if ( - stopwords.indexOf(queryTermLower) !== -1 || - queryTerm.match(/^\d+$/) - ) - return; - - // stem the word - let word = stemmer.stemWord(queryTermLower); - // select the correct list - if (word[0] === "-") excludedTerms.add(word.substr(1)); - else { - searchTerms.add(word); - highlightTerms.add(queryTermLower); - } - }); - - if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js - localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) - } - - // console.debug("SEARCH: searching for:"); - // console.info("required: ", [...searchTerms]); - // console.info("excluded: ", [...excludedTerms]); - - return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; - }, - - /** - * execute search (requires search index to be loaded) - */ - _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - - // Collect multiple result groups to be sorted separately and then ordered. - // Each is an array of [docname, title, anchor, descr, score, filename, kind]. - const normalResults = []; - const nonMainIndexResults = []; - - _removeChildren(document.getElementById("search-progress")); - - const queryLower = query.toLowerCase().trim(); - for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { - for (const [file, id] of foundTitles) { - const score = Math.round(Scorer.title * queryLower.length / title.length); - const boost = titles[file] === title ? 1 : 0; // add a boost for document titles - normalResults.push([ - docNames[file], - titles[file] !== title ? `${titles[file]} > ${title}` : title, - id !== null ? "#" + id : "", - null, - score + boost, - filenames[file], - SearchResultKind.title, - ]); - } - } - } - - // search for explicit entries in index directives - for (const [entry, foundEntries] of Object.entries(indexEntries)) { - if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id, isMain] of foundEntries) { - const score = Math.round(100 * queryLower.length / entry.length); - const result = [ - docNames[file], - titles[file], - id ? "#" + id : "", - null, - score, - filenames[file], - SearchResultKind.index, - ]; - if (isMain) { - normalResults.push(result); - } else { - nonMainIndexResults.push(result); - } - } - } - } - - // lookup as object - objectTerms.forEach((term) => - normalResults.push(...Search.performObjectSearch(term, objectTerms)) - ); - - // lookup as search terms in fulltext - normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); - - // let the scorer override scores with a custom scoring function - if (Scorer.score) { - normalResults.forEach((item) => (item[4] = Scorer.score(item))); - nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); - } - - // Sort each group of results by score and then alphabetically by name. - normalResults.sort(_orderResultsByScoreThenName); - nonMainIndexResults.sort(_orderResultsByScoreThenName); - - // Combine the result groups in (reverse) order. - // Non-main index entries are typically arbitrary cross-references, - // so display them after other results. - let results = [...nonMainIndexResults, ...normalResults]; - - // remove duplicate search results - // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept - let seen = new Set(); - results = results.reverse().reduce((acc, result) => { - let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); - if (!seen.has(resultStr)) { - acc.push(result); - seen.add(resultStr); - } - return acc; - }, []); - - return results.reverse(); - }, - - query: (query) => { - const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); - const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); - - // for debugging - //Search.lastresults = results.slice(); // a copy - // console.info("search results:", Search.lastresults); - - // print the results - _displayNextItem(results, results.length, searchTerms, highlightTerms); - }, - - /** - * search for object names - */ - performObjectSearch: (object, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const objects = Search._index.objects; - const objNames = Search._index.objnames; - const titles = Search._index.titles; - - const results = []; - - const objectSearchCallback = (prefix, match) => { - const name = match[4] - const fullname = (prefix ? prefix + "." : "") + name; - const fullnameLower = fullname.toLowerCase(); - if (fullnameLower.indexOf(object) < 0) return; - - let score = 0; - const parts = fullnameLower.split("."); - - // check for different match types: exact matches of full name or - // "last name" (i.e. last dotted part) - if (fullnameLower === object || parts.slice(-1)[0] === object) - score += Scorer.objNameMatch; - else if (parts.slice(-1)[0].indexOf(object) > -1) - score += Scorer.objPartialMatch; // matches in last name - - const objName = objNames[match[1]][2]; - const title = titles[match[0]]; - - // If more than one term searched for, we require other words to be - // found in the name/title/description - const otherTerms = new Set(objectTerms); - otherTerms.delete(object); - if (otherTerms.size > 0) { - const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); - if ( - [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) - ) - return; - } - - let anchor = match[3]; - if (anchor === "") anchor = fullname; - else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; - - const descr = objName + _(", in ") + title; - - // add custom score for some objects according to scorer - if (Scorer.objPrio.hasOwnProperty(match[2])) - score += Scorer.objPrio[match[2]]; - else score += Scorer.objPrioDefault; - - results.push([ - docNames[match[0]], - fullname, - "#" + anchor, - descr, - score, - filenames[match[0]], - SearchResultKind.object, - ]); - }; - Object.keys(objects).forEach((prefix) => - objects[prefix].forEach((array) => - objectSearchCallback(prefix, array) - ) - ); - return results; - }, - - /** - * search for full-text terms in the index - */ - performTermsSearch: (searchTerms, excludedTerms) => { - // prepare search - const terms = Search._index.terms; - const titleTerms = Search._index.titleterms; - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - - const scoreMap = new Map(); - const fileMap = new Map(); - - // perform the search on the required terms - searchTerms.forEach((word) => { - const files = []; - const arr = [ - { files: terms[word], score: Scorer.term }, - { files: titleTerms[word], score: Scorer.title }, - ]; - // add support for partial matches - if (word.length > 2) { - const escapedWord = _escapeRegExp(word); - if (!terms.hasOwnProperty(word)) { - Object.keys(terms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: terms[term], score: Scorer.partialTerm }); - }); - } - if (!titleTerms.hasOwnProperty(word)) { - Object.keys(titleTerms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); - }); - } - } - - // no match but word was a required one - if (arr.every((record) => record.files === undefined)) return; - - // found search word in contents - arr.forEach((record) => { - if (record.files === undefined) return; - - let recordFiles = record.files; - if (recordFiles.length === undefined) recordFiles = [recordFiles]; - files.push(...recordFiles); - - // set score for the word in each file - recordFiles.forEach((file) => { - if (!scoreMap.has(file)) scoreMap.set(file, {}); - scoreMap.get(file)[word] = record.score; - }); - }); - - // create the mapping - files.forEach((file) => { - if (!fileMap.has(file)) fileMap.set(file, [word]); - else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); - }); - }); - - // now check if the files don't contain excluded terms - const results = []; - for (const [file, wordList] of fileMap) { - // check if all requirements are matched - - // as search terms with length < 3 are discarded - const filteredTermCount = [...searchTerms].filter( - (term) => term.length > 2 - ).length; - if ( - wordList.length !== searchTerms.size && - wordList.length !== filteredTermCount - ) - continue; - - // ensure that none of the excluded terms is in the search result - if ( - [...excludedTerms].some( - (term) => - terms[term] === file || - titleTerms[term] === file || - (terms[term] || []).includes(file) || - (titleTerms[term] || []).includes(file) - ) - ) - break; - - // select one (max) score for the file. - const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); - // add result to the result list - results.push([ - docNames[file], - titles[file], - "", - null, - score, - filenames[file], - SearchResultKind.text, - ]); - } - return results; - }, - - /** - * helper function to return a node containing the - * search summary for a given text. keywords is a list - * of stemmed words. - */ - makeSearchSummary: (htmlText, keywords, anchor) => { - const text = Search.htmlToText(htmlText, anchor); - if (text === "") return null; - - const textLower = text.toLowerCase(); - const actualStartPosition = [...keywords] - .map((k) => textLower.indexOf(k.toLowerCase())) - .filter((i) => i > -1) - .slice(-1)[0]; - const startWithContext = Math.max(actualStartPosition - 120, 0); - - const top = startWithContext === 0 ? "" : "..."; - const tail = startWithContext + 240 < text.length ? "..." : ""; - - let summary = document.createElement("p"); - summary.classList.add("context"); - summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; - - return summary; - }, -}; - -_ready(Search.init); diff --git a/docs/0.4.7/_static/sphinx_highlight.js b/docs/0.4.7/_static/sphinx_highlight.js deleted file mode 100644 index 8a96c69a..00000000 --- a/docs/0.4.7/_static/sphinx_highlight.js +++ /dev/null @@ -1,154 +0,0 @@ -/* Highlighting utilities for Sphinx HTML documentation. */ -"use strict"; - -const SPHINX_HIGHLIGHT_ENABLED = true - -/** - * highlight a given string on a node by wrapping it in - * span elements with the given class name. - */ -const _highlight = (node, addItems, text, className) => { - if (node.nodeType === Node.TEXT_NODE) { - const val = node.nodeValue; - const parent = node.parentNode; - const pos = val.toLowerCase().indexOf(text); - if ( - pos >= 0 && - !parent.classList.contains(className) && - !parent.classList.contains("nohighlight") - ) { - let span; - - const closestNode = parent.closest("body, svg, foreignObject"); - const isInSVG = closestNode && closestNode.matches("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.classList.add(className); - } - - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - const rest = document.createTextNode(val.substr(pos + text.length)); - parent.insertBefore( - span, - parent.insertBefore( - rest, - node.nextSibling - ) - ); - node.nodeValue = val.substr(0, pos); - /* There may be more occurrences of search term in this node. So call this - * function recursively on the remaining fragment. - */ - _highlight(rest, addItems, text, className); - - if (isInSVG) { - const rect = document.createElementNS( - "http://www.w3.org/2000/svg", - "rect" - ); - const bbox = parent.getBBox(); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute("class", className); - addItems.push({ parent: parent, target: rect }); - } - } - } else if (node.matches && !node.matches("button, select, textarea")) { - node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); - } -}; -const _highlightText = (thisNode, text, className) => { - let addItems = []; - _highlight(thisNode, addItems, text, className); - addItems.forEach((obj) => - obj.parent.insertAdjacentElement("beforebegin", obj.target) - ); -}; - -/** - * Small JavaScript module for the documentation. - */ -const SphinxHighlight = { - - /** - * highlight the search words provided in localstorage in the text - */ - highlightSearchWords: () => { - if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight - - // get and clear terms from localstorage - const url = new URL(window.location); - const highlight = - localStorage.getItem("sphinx_highlight_terms") - || url.searchParams.get("highlight") - || ""; - localStorage.removeItem("sphinx_highlight_terms") - url.searchParams.delete("highlight"); - window.history.replaceState({}, "", url); - - // get individual terms from highlight string - const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); - if (terms.length === 0) return; // nothing to do - - // There should never be more than one element matching "div.body" - const divBody = document.querySelectorAll("div.body"); - const body = divBody.length ? divBody[0] : document.querySelector("body"); - window.setTimeout(() => { - terms.forEach((term) => _highlightText(body, term, "highlighted")); - }, 10); - - const searchBox = document.getElementById("searchbox"); - if (searchBox === null) return; - searchBox.appendChild( - document - .createRange() - .createContextualFragment( - '

' + - '' + - _("Hide Search Matches") + - "

" - ) - ); - }, - - /** - * helper function to hide the search marks again - */ - hideSearchWords: () => { - document - .querySelectorAll("#searchbox .highlight-link") - .forEach((el) => el.remove()); - document - .querySelectorAll("span.highlighted") - .forEach((el) => el.classList.remove("highlighted")); - localStorage.removeItem("sphinx_highlight_terms") - }, - - initEscapeListener: () => { - // only install a listener if it is really needed - if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; - - document.addEventListener("keydown", (event) => { - // bail for input elements - if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; - // bail with special keys - if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; - if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { - SphinxHighlight.hideSearchWords(); - event.preventDefault(); - } - }); - }, -}; - -_ready(() => { - /* Do not call highlightSearchWords() when we are on the search page. - * It will highlight words from the *previous* search query. - */ - if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); - SphinxHighlight.initEscapeListener(); -}); diff --git a/docs/0.4.7/autodoc/mmif.serialize.html b/docs/0.4.7/autodoc/mmif.serialize.html deleted file mode 100644 index f1b38699..00000000 --- a/docs/0.4.7/autodoc/mmif.serialize.html +++ /dev/null @@ -1,1148 +0,0 @@ - - - - - - - - - mmif.serialize module — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.serialize module

-
-

mmif.serialize.model module

-

The model module contains the classes used to represent an -abstract MMIF object as a live Python object.

-

The MmifObject class or one of its derivatives is subclassed by -all other classes defined in this SDK, except for MmifObjectEncoder.

-

These objects are generally instantiated from JSON, either as a string -or as an already-loaded Python dictionary. This base class provides the -core functionality for deserializing MMIF JSON data into live objects -and serializing live objects into MMIF JSON data. Specialized behavior -for the different components of MMIF is added in the subclasses.

-
-
-class mmif.serialize.model.DataDict(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject, Generic[T, S]

-
-
-empty()[source]
-
- -
-
-get(key: T, default=None) → S | None[source]
-
- -
-
-items()[source]
-
- -
-
-keys()[source]
-
- -
-
-update(other, overwrite)[source]
-
- -
-
-values()[source]
-
- -
- -
-
-class mmif.serialize.model.DataList(mmif_obj: bytes | str | list | None = None)[source]
-

Bases: MmifObject, Generic[T]

-

The DataList class is an abstraction that represents the -various lists found in a MMIF file, such as documents, subdocuments, -views, and annotations.

-
-
Parameters:
-

mmif_obj (Union[str, list]) – the data that the list contains

-
-
-
-
-append(value, overwrite)[source]
-
- -
-
-deserialize(mmif_json: str | list) → None[source]
-

Passes the input data into the internal deserializer.

-
- -
-
-empty()[source]
-
- -
-
-get(key: str) → T | None[source]
-

Standard dictionary-style get() method, albeit with no default -parameter. Relies on the implementation of __getitem__.

-

Will return None if the key is not found.

-
-
Parameters:
-

key – the key to search for

-
-
Returns:
-

the value matching that key

-
-
-
- -
- -
-
-class mmif.serialize.model.MmifObject(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: object

-

Abstract superclass for MMIF related key-value pair objects.

-

Any MMIF object can be initialized as an empty placeholder or -an actual representation with a JSON formatted string or equivalent -dict object argument.

-

This superclass has three specially designed instance variables, and these -variable names cannot be used as attribute names for MMIF objects.

-
    -

  1. _unnamed_attributes: -Only can be either None or an empty dictionary. If it’s set to None, -it means the class won’t take any Additional Attributes in the JSON -schema sense. If it’s a dict, users can throw any k-v pairs to the -class, EXCEPT for the reserved two key names.

    2. -

  2. _attribute_classes: -This is a dict from a key name to a specific python class to use for -deserialize the value. Note that a key name in this dict does NOT -have to be a named attribute, but is recommended to be one.

    3. -

  3. _required_attributes: -This is a simple list of names of attributes that are required in the object. -When serialize, an object will skip its empty (e.g. zero-length, or None) -attributes unless they are in this list. Otherwise, the serialized JSON -string would have empty representations (e.g. "", []).

    4. -
-

# TODO (krim @ 8/17/20): this dict is however, a duplicate with the type hints in the class definition. -Maybe there is a better way to utilize type hints (e.g. getting them as a programmatically), but for now -developers should be careful to add types to hints as well as to this dict.

-

Also note that those two special attributes MUST be set in the __init__() -before calling super method, otherwise deserialization will not work.

-

And also, a subclass that has one or more named attributes, it must -set those attributes in the __init__() before calling super method. When -serializing a MmifObject, all empty attributes will be ignored, so for -optional named attributes, you must leave the values empty (len == 0), but -NOT None. Any None-valued named attributes will cause issues with current -implementation.

-
-
Parameters:
-

mmif_obj – JSON string or dict to initialize an object. -If not given, an empty object will be initialized, sometimes with -an ID value automatically generated, based on its parent object.

-
-
-
-
-deserialize(mmif_json: str | dict) → None[source]
-

Takes a JSON-formatted string or a simple dict that’s json-loaded from -such a string as an input and populates object’s fields with the values -specified in the input.

-
-
Parameters:
-

mmif_json – JSON-formatted string or dict from such a string -that represents a MMIF object

-
-
-
- -
-
-disallow_additional_properties() → None[source]
-

Call this method in __init__() to prevent the insertion -of unnamed attributes after initialization.

-
- -
-
-static is_empty(obj) → bool[source]
-

return True if the obj is None or “emtpy”. The emptiness first defined as -having zero length. But for objects that lack __len__ method, we need -additional check.

-
- -
-
-reserved_names: Set = {'_attribute_classes', '_id_counts', '_parent_view_id', '_required_attributes', '_unnamed_attributes', 'reserved_names'}[source]
-
- -
-
-serialize(pretty: bool = False) → str[source]
-

Generates JSON representation of an object.

-
-
Parameters:
-

pretty – If True, returns string representation with indentation.

-
-
Returns:
-

JSON string of the object.

-
-
-
- -
-
-set_additional_property(key: str, value: Any) → None[source]
-

Method to set values in _unnamed_attributes.

-
-
Parameters:
-
    -

  • key – the attribute name

    • -

  • value – the desired value

    • -
-
-
Returns:
-

None

-
-
Raise:
-

AttributeError if additional properties are disallowed by disallow_additional_properties()

-
-
-
- -
- -
-
-class mmif.serialize.model.MmifObjectEncoder(*, skipkeys=False, ensure_ascii=True, check_circular=True, allow_nan=True, sort_keys=False, indent=None, separators=None, default=None)[source]
-

Bases: JSONEncoder

-

Encoder class to define behaviors of de-/serialization

-
-
-default(obj: MmifObject)[source]
-

Overrides default encoding behavior to prioritize MmifObject.serialize().

-
- -
- -
-
-

mmif.serialize.mmif module

-

The mmif module contains the classes used to represent a full MMIF -file as a live Python object.

-

See the specification docs and the JSON Schema file for more information.

-
-
-class mmif.serialize.mmif.Mmif(mmif_obj: bytes | str | dict | None = None, *, validate: bool = True)[source]
-

Bases: MmifObject

-

MmifObject that represents a full MMIF file.

-
-
Parameters:
-
    -

  • mmif_obj – the JSON data

    • -

  • validate – whether to validate the data against the MMIF JSON schema.

    • -
-
-
-
-
-add_document(document: Document, overwrite=False) → None[source]
-

Appends a Document object to the documents list.

-

Fails if there is already a document with the same ID in the MMIF object.

-
-
Parameters:
-
    -

  • document – the Document object to add

    • -

  • overwrite – if set to True, will overwrite -an existing view with the same ID

    • -
-
-
Returns:
-

None

-
-
-
- -
-
-add_view(view: View, overwrite=False) → None[source]
-

Appends a View object to the views list.

-

Fails if there is already a view with the same ID in the MMIF object.

-
-
Parameters:
-
    -

  • view – the Document object to add

    • -

  • overwrite – if set to True, will overwrite -an existing view with the same ID

    • -
-
-
Returns:
-

None

-
-
-
- -
-
-get_alignments(at_type1: str | TypesBase, at_type2: str | TypesBase) → Dict[str, List[Annotation]][source]
-

Finds views where alignments between two given annotation types occurred.

-
-
Returns:
-

a dict that keyed by view IDs (str) and has lists of alignment Annotation objects as values.

-
-
-
- -
-
-get_all_views_contain(at_types: TypesBase | str | List[str | TypesBase]) → List[View][source]
-

Returns the list of all views in the MMIF if given types -are present in that view’s ‘contains’ metadata.

-
-
Parameters:
-

at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

-
-
Returns:
-

the list of views that contain the type

-
-
-
- -
-
-get_document_by_id(doc_id: str) → Document[source]
-

Finds a Document object with the given ID.

-
-
Parameters:
-

doc_id – the ID to search for

-
-
Returns:
-

a reference to the corresponding document, if it exists

-
-
Raises:
-

Exception – if there is no corresponding document

-
-
-
- -
-
-get_document_location(m_type: DocumentTypes | str, path_only=False) → str | None[source]
-

Method to get the location of first document of given type.

-
-
Parameters:
-

m_type – the type to search for

-
-
Returns:
-

the value of the location field in the corresponding document

-
-
-
- -
-
-get_documents_by_app(app_id: str) → List[Document][source]
-

Method to get all documents object queries by its originated app name.

-
-
Parameters:
-

app_id – the app name to search for

-
-
Returns:
-

a list of documents matching the requested app name, or an empty list if the app not found

-
-
-
- -
-
-get_documents_by_property(prop_key: str, prop_value: str) → List[Document][source]
-

Method to retrieve documents by an arbitrary key-value pair in the document properties objects.

-
-
Parameters:
-
    -

  • prop_key – the metadata key to search for

    • -

  • prop_value – the metadata value to match

    • -
-
-
Returns:
-

a list of documents matching the requested metadata key-value pair

-
-
-
- -
-
-get_documents_by_type(doc_type: str | DocumentTypes) → List[Document][source]
-

Method to get all documents where the type matches a particular document type, which should be one of the CLAMS document types.

-
-
Parameters:
-

doc_type – the type of documents to search for, must be one of Document type defined in the CLAMS vocabulary.

-
-
Returns:
-

a list of documents matching the requested type, or an empty list if none found.

-
-
-
- -
-
-get_documents_in_view(vid: str | None = None) → List[Document][source]
-

Method to get all documents object queries by a view id.

-
-
Parameters:
-

vid – the source view ID to search for

-
-
Returns:
-

a list of documents matching the requested source view ID, or an empty list if the view not found

-
-
-
- -
-
-get_documents_locations(m_type: DocumentTypes | str, path_only=False) → List[str | None][source]
-

This method returns the file paths of documents of given type. -Only top-level documents have locations, so we only check them.

-
-
Parameters:
-

m_type – the type to search for

-
-
Returns:
-

a list of the values of the location fields in the corresponding documents

-
-
-
- -
-
-get_view_by_id(req_view_id: str) → View[source]
-

Finds a View object with the given ID.

-
-
Parameters:
-

req_view_id – the ID to search for

-
-
Returns:
-

a reference to the corresponding view, if it exists

-
-
Raises:
-

Exception – if there is no corresponding view

-
-
-
- -
-
-get_view_contains(at_types: TypesBase | str | List[str | TypesBase]) → View | None[source]
-

Returns the last view appended that contains the given -types in its ‘contains’ metadata.

-
-
Parameters:
-

at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

-
-
Returns:
-

the view, or None if the type is not found

-
-
-
- -
-
-get_views_contain(at_types: TypesBase | str | List[str | TypesBase]) → List[View][source]
-

An alias to get_all_views_contain method.

-
- -
-
-get_views_for_document(doc_id: str)[source]
-

Returns the list of all views that have annotations anchored on a particular document. -Note that when the document is insids a view (generated during the pipeline’s running), -doc_id must be prefixed with the view_id.

-
- -
-
-id_delimiter: ClassVar[str] = ':'[source]
-
- -
-
-new_view() → View[source]
-

Creates an empty view with a new ID and appends it to the views list.

-
-
Returns:
-

a reference to the new View object

-
-
-
- -
-
-new_view_id() → str[source]
-

Fetches an ID for a new view.

-
-
Returns:
-

the ID

-
-
-
- -
-
-static validate(json_str: bytes | str | dict) → None[source]
-

Validates a MMIF JSON object against the MMIF Schema. -Note that this method operates before processing by MmifObject._load_str, -so it expects @ and not _ for the JSON-LD @-keys.

-
-
Raises:
-

jsonschema.exceptions.ValidationError – if the input fails validation

-
-
Parameters:
-

json_str – a MMIF JSON dict or string

-
-
Returns:
-

None

-
-
-
- -
-
-view_prefix: ClassVar[str] = 'v_'[source]
-
- -
- -
-
-

mmif.serialize.view module

-

The view module contains the classes used to represent a MMIF view -as a live Python object.

-

In MMIF, views are created by apps in a pipeline that are annotating -data that was previously present in the MMIF file.

-
-
-class mmif.serialize.view.Contain(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-

Contain object that represents the metadata of a single -annotation type in the contains metadata of a MMIF view.

-
- -
-
-class mmif.serialize.view.View(view_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-

View object that represents a single view in a MMIF file.

-

A view is identified by an ID, and contains certain metadata, -a list of annotations, and potentially a JSON-LD @context -IRI.

-

If view_obj is not provided, an empty View will be generated.

-
-
Parameters:
-

view_obj – the JSON data that defines the view

-
-
-
-
-add_annotation(annotation: Annotation, overwrite=False) → Annotation[source]
-

Adds an annotation to the current view.

-

Fails if there is already an annotation with the same ID -in the view, unless overwrite is set to True.

-
-
Parameters:
-
-
-
Raises:
-

KeyError – if overwrite is set to False and -an annotation with the same ID exists -in the view

-
-
Returns:
-

the same Annotation object passed in as annotation

-
-
-
- -
-
-add_document(document: Document, overwrite=False) → Annotation[source]
-

Appends a Document object to the annotations list.

-

Fails if there is already a document with the same ID in the annotations list.

-
-
Parameters:
-
    -

  • document – the Document object to add

    • -

  • overwrite – if set to True, will overwrite -an existing view with the same ID

    • -
-
-
Returns:
-

None

-
-
-
- -
-
-get_annotation_by_id(ann_id)[source]
-
- -
-
-get_annotations(at_type: str | TypesBase | None = None, **properties) → Generator[Annotation, None, None][source]
-

Look for certain annotations in this view, specified by parameters

-
-
Parameters:
-
    -

  • at_type – @type of the annotations to look for. When this is None, any @type will match.

    • -

  • properties – properties of the annotations to look for. When given more than one property, all properties must match. Note that annotation type metadata are specified in the contains view metadata, not in individual annotation objects.

    • -
-
-
-
- -
-
-get_document_by_id(doc_id) → Document[source]
-
- -
-
-get_documents() → List[Document][source]
-
- -
-
-new_annotation(at_type: str | TypesBase, aid: str | None = None, overwrite=False, **properties) → Annotation[source]
-

Generates a new mmif.serialize.annotation.Annotation -object and adds it to the current view.

-

Fails if there is already an annotation with the same ID -in the view, unless overwrite is set to True.

-
-
Parameters:
-
    -

  • at_type – the desired @type of the annotation.

    • -

  • aid – the desired ID of the annotation, when not given, -the mmif SDK tries to automatically generate an ID based on -Annotation type and existing annotations in the view.

    • -

  • overwrite – if set to True, will overwrite an -existing annotation with the same ID.

    • -
-
-
Raises:
-

KeyError – if overwrite is set to False and -an annotation with the same ID exists -in the view.

-
-
Returns:
-

the generated mmif.serialize.annotation.Annotation

-
-
-
- -
-
-new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
-

Adds a new element to the contains metadata.

-
-
Parameters:
-
    -

  • at_type – the @type of the annotation type being added

    • -

  • contains_metadata – any metadata associated with the annotation type

    • -
-
-
Returns:
-

the generated Contain object

-
-
-
- -
-
-new_textdocument(text: str, lang: str = 'en', did: str | None = None, overwrite=False, **properties) → Document[source]
-

Generates a new mmif.serialize.annotation.Document -object, particularly typed as TextDocument and adds it to the current view.

-

Fails if there is already a text document with the same ID -in the view, unless overwrite is set to True.

-
-
Parameters:
-
    -

  • text – text content of the new document

    • -

  • lang – ISO 639-1 code of the language used in the new document

    • -

  • did – the desired ID of the document, when not given, -the mmif SDK tries to automatically generate an ID based on -Annotation type and existing documents in the view.

    • -

  • overwrite – if set to True, will overwrite an -existing document with the same ID

    • -
-
-
Raises:
-

KeyError – if overwrite is set to False and -an document with the same ID exists -in the view

-
-
Returns:
-

the generated mmif.serialize.annotation.Document

-
-
-
- -
-
-set_error(err_message: str, err_trace: str) → None[source]
-
- -
- -
-
-class mmif.serialize.view.ViewMetadata(viewmetadata_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-

ViewMetadata object that represents the metadata object within a MMIF view.

-
-
Parameters:
-

viewmetadata_obj – the JSON data that defines the metadata

-
-
-
-
-add_parameter(param_key, param_value)[source]
-
- -
-
-add_parameters(**runtime_params)[source]
-
- -
-
-add_warnings(*warnings: Warning)[source]
-
- -
-
-emtpy_warnings()[source]
-
- -
-
-get_parameter(param_key)[source]
-
- -
-
-new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
-

Adds a new element to the contains dictionary.

-
-
Parameters:
-
    -

  • at_type – the @type of the annotation type being added

    • -

  • contains_metadata – any metadata associated with the annotation type

    • -
-
-
Returns:
-

the generated Contain object

-
-
-
- -
-
-set_error(message: str, stack_trace: str)[source]
-
- -
- -
-
-

mmif.serialize.annotation module

-

The annotation module contains the classes used to represent a -MMIF annotation as a live Python object.

-

In MMIF, annotations are created by apps in a pipeline as a part -of a view. For documentation on how views are represented, see -mmif.serialize.view.

-
-
-class mmif.serialize.annotation.Annotation(anno_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-

MmifObject that represents an annotation in a MMIF view.

-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]]) → None[source]
-

Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

-
- -
-
-property at_type: TypesBase[source]
-
- -
-
-property id: str[source]
-
- -
-
-is_document()[source]
-
- -
-
-is_type(at_type: str | TypesBase) → bool[source]
-

Check if the @type of this object matches.

-
- -
- -
-
-class mmif.serialize.annotation.AnnotationProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject, MutableMapping[str, T]

-

AnnotationProperties object that represents the -properties object within a MMIF annotation.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
- -
-
-class mmif.serialize.annotation.Document(doc_obj: bytes | str | dict | None = None)[source]
-

Bases: Annotation

-

Document object that represents a single document in a MMIF file.

-

A document is identified by an ID, and contains certain attributes -and potentially contains the contents of the document itself, -metadata about how the document was created, and/or a list of -subdocuments grouped together logically.

-

If document_obj is not provided, an empty Document will be generated.

-
-
Parameters:
-

document_obj – the JSON data that defines the document

-
-
-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None]) → None[source]
-

Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

-
- -
-
-property location: str | None[source]
-

location property must be a legitimate URI. That is, should the document be a local file -then the file:// scheme must be used. -Returns None when no location is set.

-
- -
-
-location_address() → str | None[source]
-

Retrieves the full address from the document location URI. -Returns None when no location is set.

-
- -
-
-location_path() → str | None[source]
-

Retrieves only path name of the document location (hostname is ignored). -Useful to get a path of a local file. -Returns None when no location is set.

-
- -
-
-location_scheme() → str | None[source]
-

Retrieves URI scheme of the document location. -Returns None when no location is set.

-
- -
-
-property parent: str[source]
-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.DocumentProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: AnnotationProperties

-

DocumentProperties object that represents the -properties object within a MMIF document.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
-
-property location: str | None[source]
-

location property must be a legitimate URI. That is, should the document be a local file -then the file:// scheme must be used. -Returns None when no location is set.

-
- -
-
-location_address() → str | None[source]
-

Retrieves the full address from the document location URI. -Returns None when no location is set.

-
- -
-
-location_path() → str | None[source]
-

Retrieves only path name of the document location (hostname is ignored). -Useful to get a path of a local file. -Returns None when no location is set.

-
- -
-
-location_scheme() → str | None[source]
-

Retrieves URI scheme of the document location. -Returns None when no location is set.

-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.Text(text_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-
-
-property lang: str[source]
-
- -
-
-property value: str[source]
-
- -
- -
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.4.7 - - -
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- -
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- - - \ No newline at end of file diff --git a/docs/0.4.7/autodoc/mmif.vocabulary.html b/docs/0.4.7/autodoc/mmif.vocabulary.html deleted file mode 100644 index 2d869c19..00000000 --- a/docs/0.4.7/autodoc/mmif.vocabulary.html +++ /dev/null @@ -1,285 +0,0 @@ - - - - - - - - - mmif.vocabulary module — mmif-python documentation - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.vocabulary module

-
-

mmif.vocabulary.annotation_types module

-
-
-class mmif.vocabulary.annotation_types.AnnotationTypes(type_uri: str)[source]
-

Bases: AnnotationTypesBase

-

This class contains the CLAMS annotation types -defined in the spec version 0.4.2 as class variables.

-
-
-Alignment = http://mmif.clams.ai/0.4.2/vocabulary/Alignment[source]
-
- -
-
-Annotation = http://mmif.clams.ai/0.4.2/vocabulary/Annotation[source]
-
- -
-
-BoundingBox = http://mmif.clams.ai/0.4.2/vocabulary/BoundingBox[source]
-
- -
-
-Chapter = http://mmif.clams.ai/0.4.2/vocabulary/Chapter[source]
-
- -
-
-Interval = http://mmif.clams.ai/0.4.2/vocabulary/Interval[source]
-
- -
-
-Polygon = http://mmif.clams.ai/0.4.2/vocabulary/Polygon[source]
-
- -
-
-Region = http://mmif.clams.ai/0.4.2/vocabulary/Region[source]
-
- -
-
-Relation = http://mmif.clams.ai/0.4.2/vocabulary/Relation[source]
-
- -
-
-Span = http://mmif.clams.ai/0.4.2/vocabulary/Span[source]
-
- -
-
-TimeFrame = http://mmif.clams.ai/0.4.2/vocabulary/TimeFrame[source]
-
- -
-
-TimePoint = http://mmif.clams.ai/0.4.2/vocabulary/TimePoint[source]
-
- -
-
-VideoObject = http://mmif.clams.ai/0.4.2/vocabulary/VideoObject[source]
-
- -
- -
-
-

mmif.vocabulary.document_types module

-
-
-class mmif.vocabulary.document_types.DocumentTypes(type_uri: str)[source]
-

Bases: DocumentTypesBase

-

This class contains the CLAMS document types -defined in the spec version 0.4.2 as class variables.

-
-
-AudioDocument = http://mmif.clams.ai/0.4.2/vocabulary/AudioDocument[source]
-
- -
-
-Document = http://mmif.clams.ai/0.4.2/vocabulary/Document[source]
-
- -
-
-ImageDocument = http://mmif.clams.ai/0.4.2/vocabulary/ImageDocument[source]
-
- -
-
-TextDocument = http://mmif.clams.ai/0.4.2/vocabulary/TextDocument[source]
-
- -
-
-VideoDocument = http://mmif.clams.ai/0.4.2/vocabulary/VideoDocument[source]
-
- -
- -
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.4.7 - - -
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- - - \ No newline at end of file diff --git a/docs/0.4.7/consumer-tutorial.html b/docs/0.4.7/consumer-tutorial.html deleted file mode 100644 index 01d1d1ab..00000000 --- a/docs/0.4.7/consumer-tutorial.html +++ /dev/null @@ -1,176 +0,0 @@ - - - - - - - - - MMIF consumer — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • MMIF consumer
    • -
  • -
    • -
-
-
-
-
- -
-

MMIF consumer

-

A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the appliance documentation to learn more about the appliance.

-

MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance.

-
    -

  1. The code must be hosted on a public git repository (e.g. Github, Gitlab, …)

    2. -

  2. Must listen to 5000 port.

    3. -

  3. Must expose /display route .

    4. -

  4. /display router should response to GET requests.

    5. -

  5. In the GET request, a public URL of the input MMIF file is passed via file URL parameter.

    6. -

  6. On the codebase root, there must be a Dockerfile that can build a docker image that runs the web app.

    7. -
-

We provide an example consumer at https://github.com/clamsproject/mmif-visualizer.

-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.4.7 - - -
-
- -
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- - -
- -
-
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    -
    • -
  • Index
    • -
  • -
    • -
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Index

- -
- A - | B - | C - | D - | E - | G - | I - | K - | L - | M - | N - | P - | R - | S - | T - | U - | V - -
-

A

- - - -
- -

B

- - -
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C

- - - -
- -

D

- - - -
- -

E

- - - -
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G

- - - -
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I

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K

- - -
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L

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M

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N

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P

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R

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S

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T

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U

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V

- - - -
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- - Other Versions - v: 0.4.7 - - -
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0.3.4
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- - -
- -
-
-
-
    -
    • -
  • Welcome to mmif-python’s documentation!
    • -
  • -
    • -
-
-
-
-
- -
-

Welcome to mmif-python’s documentation!

-
-
-

MMIF for python

-

NOTE that this project is in pre-alpha and being actively developed. Nothing is guaranteed to reliably work for the moment and developer need to be very careful when using APIs implemented here. Please use the issue track to report bugs and malfunctions.

-
-

MultiMedia Interchange Format

-

MMIF is a JSON(-LD)-based data format designed for transferring annotation data between computational analysis applications in CLAMS project.

-
-

Contents

- -
-
-

API documentation:

- -
-
-
-
-

Indices and tables

- -
- - -
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- -
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- -
- - Other Versions - v: 0.4.7 - - -
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0.3.0
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- - - \ No newline at end of file diff --git a/docs/0.4.7/introduction.html b/docs/0.4.7/introduction.html deleted file mode 100644 index 966a1637..00000000 --- a/docs/0.4.7/introduction.html +++ /dev/null @@ -1,236 +0,0 @@ - - - - - - - - - Getting Started — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
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  • Getting Started
    • -
  • -
    • -
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Getting Started

-
-

Overview

-

MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF wbesite. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports de-/serialization of MMIF objects, as well as many navigation and manipulation helpers for MMIF objects.

-
-
-

Prerequisites

-
    -

  • Python: mmif-python requires Python 3.6 or newer. We have no plan to support Python 2.7.

    • -
-
-
-

Installation

-

Package mmif-python is distributed via the official PyPI. Users are supposed to pip-install to get latest release.

-
pip install mmif-python
-
-
-

This will install a package mmif to local python.

-

The MMIF format and specification is evolving over time, and mmif-python package will be updated along with the changes in MMIF format.

-
-

Note

-

MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and mmif-python versions, please take time to read our decision on the subject here. If you need to know which python SDK supports which specification version, see Target MMIF Versions page.

-
-
-
-

MMIF Serialization

-

mmif.serialize.mmif.Mmif represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of mmif.serialize.model.MmifObject, including the mmif.serialize.mmif.Mmif. To start with an existing MMIF str, simple initiate a new Mmif object with the file.

-
import mmif
-from mmif import Mmif
-
-mmif_str = """{
-"metadata": {
-  "mmif": "http://mmif.clams.ai/0.2.0"
-},
-"documents": [
-  {
-    "@type": "http://mmif.clams.ai/0.2.0/vocabulary/VideoDocument",
-    "properties": {
-      "id": "m1",
-      "mime": "video/mp4",
-      "location": "file:///var/archive/video-0012.mp4"
-    }
-  },
-  {
-    "@type": "http://mmif.clams.ai/0.2.0/vocabulary/TextDocument",
-    "properties": {
-      "id": "m2",
-      "mime": "text/plain",
-      "location": "file:///var/archive/video-0012-transcript.txt"
-    }
-  }
-],
-"views": []}"""
-mmif_obj = Mmif(mmif_str)
-
-
-

Few notes;

-
    -

  1. MMIF does not carry the primary source files in it.

    2. -

  2. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version mmif-python implementation of the MMIF might not be able to load an unsupported version of MMIF string.

    3. -
-

When serializing back to str, call .serialize() (mmif.serialize.model.MmifObject.serialize()) on the object.

-

To get subcomponents, you can use various getters implemented in subclasses. For more details, the API documentation (mmif package) will help.

-
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.4.7 - - -
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0.3.1
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- - - \ No newline at end of file diff --git a/docs/0.4.7/modules.html b/docs/0.4.7/modules.html deleted file mode 100644 index 39c0306f..00000000 --- a/docs/0.4.7/modules.html +++ /dev/null @@ -1,330 +0,0 @@ - - - - - - - - - mmif package — mmif-python documentation - - - - - - - - - - - - - - - - - -
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  • mmif package
    • -
  • -
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mmif package

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1, 2, 3, 4, 5, 6], "model": 0, "modul": [0, 1], "multimedia": 3, "overview": 4, "packag": 5, "prerequisit": 4, "python": 3, "serial": [0, 4], "specif": 6, "start": 4, "tabl": 3, "target": 6, "version": 6, "view": 0, "vocabulari": 1, "welcom": 3}}) \ No newline at end of file diff --git a/docs/0.4.7/target-versions.html b/docs/0.4.7/target-versions.html deleted file mode 100644 index 4a532252..00000000 --- a/docs/0.4.7/target-versions.html +++ /dev/null @@ -1,227 +0,0 @@ - - - - - - - - - Target MMIF Versions — mmif-python documentation - - - - - - - - - - - - - - - - - -
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Target MMIF Versions

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This article provides targeting MMIF specification versions of different versions of mmif-python SDK.

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Target Specification Versions

mmif-python version

Target MMIF Specification

0.4.7

0.4.2

0.4.6

0.4.0

0.4.5

0.4.0

0.4.4

0.4.0

0.4.3

0.4.0

0.4.2

0.4.0

0.4.1

0.4.0

0.4.0

0.4.0

0.3.5

0.3.1

0.3.4

0.3.1

0.3.3

0.3.1

0.3.2

0.3.1

0.3.1

0.3.0

0.3.0

0.3.0

0.2.2

0.2.1

0.2.1

0.2.1

0.2.0

0.2.1

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0.3.0
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0.3.1
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0.3.2
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0.3.3
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0.3.4
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0.3.5
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0.4.0
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0.4.1
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0.4.2
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0.4.3
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0.4.4
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0.4.5
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0.4.6
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0.4.7
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0.4.8
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0.5.0
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0.5.1
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0.5.2
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1.0.0
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1.0.1
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1.0.10
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1.0.11
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1.0.12
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1.0.13
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1.0.14
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1.0.15
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1.0.16
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1.0.17
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1.0.18
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1.0.19
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1.0.2
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1.0.3
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1.0.4
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1.0.5
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1.0.6
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1.0.7
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1.0.8
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1.0.9
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1.1.0
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The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the `appliance documentation `_ to learn more about the appliance. - -MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance. - -#. The code must be hosted on a public git repository (e.g. Github, Gitlab, ...) -#. Must listen to ``5000`` port. -#. Must expose ``/display`` route . -#. ``/display`` router should response to ``GET`` requests. -#. In the ``GET`` request, a public URL of the input MMIF file is passed via ``file`` URL parameter. -#. On the codebase root, there must be a ``Dockerfile`` that can build a `docker `_ image that runs the web app. - -We provide an example consumer at https://github.com/clamsproject/mmif-visualizer. diff --git a/docs/0.4.8/_sources/index.rst.txt b/docs/0.4.8/_sources/index.rst.txt deleted file mode 100644 index 9b90b38e..00000000 --- a/docs/0.4.8/_sources/index.rst.txt +++ /dev/null @@ -1,26 +0,0 @@ -Welcome to mmif-python's documentation! -======================================= - -.. mdinclude:: ../README.md - -.. toctree:: - :maxdepth: 2 - :caption: Contents - - introduction - target-versions - consumer-tutorial - -.. toctree:: - :maxdepth: 2 - :caption: API documentation: - - modules - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/docs/0.4.8/_sources/introduction.rst.txt b/docs/0.4.8/_sources/introduction.rst.txt deleted file mode 100644 index 6fea3a3c..00000000 --- a/docs/0.4.8/_sources/introduction.rst.txt +++ /dev/null @@ -1,78 +0,0 @@ -.. _instroduction: - -Getting Started -=============== - - -Overview ---------- - -MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF wbesite `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports de-/serialization of MMIF objects, as well as many navigation and manipulation helpers for MMIF objects. - -Prerequisites -------------- - -* `Python `_: ``mmif-python`` requires Python 3.6 or newer. We have no plan to support `Python 2.7 `_. - -Installation ---------------- - -Package ``mmif-python`` is distributed via the official PyPI. Users are supposed to pip-install to get latest release. - -.. code-block:: bash - - pip install mmif-python - -This will install a package `mmif` to local python. - -The MMIF format and specification is evolving over time, and ``mmif-python`` package will be updated along with the changes in MMIF format. - -.. note:: MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and ``mmif-python`` versions, please take time to read our decision on the subject `here `_. If you need to know which python SDK supports which specification version, see :ref:`target-versions` page. - -MMIF Serialization ---------------------------- - -:class:`mmif.serialize.mmif.Mmif` represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of :class:`mmif.serialize.model.MmifObject`, including the :class:`mmif.serialize.mmif.Mmif`. To start with an existing MMIF :class:`str`, simple initiate a new ``Mmif`` object with the file. - -.. code-block:: python - - import mmif - from mmif import Mmif - - mmif_str = """{ - "metadata": { - "mmif": "http://mmif.clams.ai/0.2.0" - }, - "documents": [ - { - "@type": "http://mmif.clams.ai/0.2.0/vocabulary/VideoDocument", - "properties": { - "id": "m1", - "mime": "video/mp4", - "location": "file:///var/archive/video-0012.mp4" - } - }, - { - "@type": "http://mmif.clams.ai/0.2.0/vocabulary/TextDocument", - "properties": { - "id": "m2", - "mime": "text/plain", - "location": "file:///var/archive/video-0012-transcript.txt" - } - } - ], - "views": []}""" - mmif_obj = Mmif(mmif_str) - - -Few notes; - -#. MMIF does not carry the primary source files in it. -#. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version ``mmif-python`` implementation of the MMIF might not be able to load an unsupported version of MMIF string. - -When serializing back to :class:`str`, call ``.serialize()`` (:meth:`mmif.serialize.model.MmifObject.serialize`) on the object. - -To get subcomponents, you can use various getters implemented in subclasses. For more details, the API documentation (:ref:`apidoc`) will help. - diff --git a/docs/0.4.8/_sources/modules.rst.txt b/docs/0.4.8/_sources/modules.rst.txt deleted file mode 100644 index e4269c6d..00000000 --- a/docs/0.4.8/_sources/modules.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _apidoc: - -mmif package -============ - -.. toctree:: - :maxdepth: 4 - - autodoc/mmif.serialize - autodoc/mmif.vocabulary diff --git a/docs/0.4.8/_sources/target-versions.rst.txt b/docs/0.4.8/_sources/target-versions.rst.txt deleted file mode 100644 index 34216d3e..00000000 --- a/docs/0.4.8/_sources/target-versions.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _target-versions: - -Target MMIF Versions -==================== - -This article provides targeting MMIF specification versions of different versions of ``mmif-python`` SDK. - -.. csv-table:: Target Specification Versions - :file: target-versions.csv - :header-rows: 1 diff --git a/docs/0.4.8/_static/_sphinx_javascript_frameworks_compat.js b/docs/0.4.8/_static/_sphinx_javascript_frameworks_compat.js deleted file mode 100644 index 81415803..00000000 --- a/docs/0.4.8/_static/_sphinx_javascript_frameworks_compat.js +++ /dev/null @@ -1,123 +0,0 @@ -/* Compatability shim for jQuery and underscores.js. - * - * Copyright Sphinx contributors - * Released under the two clause BSD licence - */ - -/** - * small helper function to urldecode strings - * - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL - */ -jQuery.urldecode = function(x) { - if (!x) { - return x - } - return decodeURIComponent(x.replace(/\+/g, ' ')); -}; - -/** - * small helper function to urlencode strings - */ -jQuery.urlencode = encodeURIComponent; - -/** - * This function returns the parsed url parameters of the - * current request. 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- -/** - * Simple result scoring code. - */ -if (typeof Scorer === "undefined") { - var Scorer = { - // Implement the following function to further tweak the score for each result - // The function takes a result array [docname, title, anchor, descr, score, filename] - // and returns the new score. - /* - score: result => { - const [docname, title, anchor, descr, score, filename, kind] = result - return score - }, - */ - - // query matches the full name of an object - objNameMatch: 11, - // or matches in the last dotted part of the object name - objPartialMatch: 6, - // Additive scores depending on the priority of the object - objPrio: { - 0: 15, // used to be importantResults - 1: 5, // used to be objectResults - 2: -5, // used to be unimportantResults - }, - // Used when the priority is not in the mapping. - objPrioDefault: 0, - - // query found in title - title: 15, - partialTitle: 7, - // query found in terms - term: 5, - partialTerm: 2, - }; -} - -// Global search result kind enum, used by themes to style search results. -class SearchResultKind { - static get index() { return "index"; } - static get object() { return "object"; } - static get text() { return "text"; } - static get title() { return "title"; } -} - -const _removeChildren = (element) => { - while (element && element.lastChild) element.removeChild(element.lastChild); -}; - -/** - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping - */ -const _escapeRegExp = (string) => - string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string - -const _displayItem = (item, searchTerms, highlightTerms) => { - const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; - const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; - const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; - const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; - const contentRoot = document.documentElement.dataset.content_root; - - const [docName, title, anchor, descr, score, _filename, kind] = item; - - let listItem = document.createElement("li"); - // Add a class representing the item's type: - // can be used by a theme's CSS selector for styling - // See SearchResultKind for the class names. - listItem.classList.add(`kind-${kind}`); - let requestUrl; - let linkUrl; - if (docBuilder === "dirhtml") { - // dirhtml builder - let dirname = docName + "/"; - if (dirname.match(/\/index\/$/)) - dirname = dirname.substring(0, dirname.length - 6); - else if (dirname === "index/") dirname = ""; - requestUrl = contentRoot + dirname; - linkUrl = requestUrl; - } else { - // normal html builders - requestUrl = contentRoot + docName + docFileSuffix; - linkUrl = docName + docLinkSuffix; - } - let linkEl = listItem.appendChild(document.createElement("a")); - linkEl.href = linkUrl + anchor; - linkEl.dataset.score = score; - linkEl.innerHTML = title; - if (descr) { - listItem.appendChild(document.createElement("span")).innerHTML = - " (" + descr + ")"; - // highlight search terms in the description - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - } - else if (showSearchSummary) - fetch(requestUrl) - .then((responseData) => responseData.text()) - .then((data) => { - if (data) - listItem.appendChild( - Search.makeSearchSummary(data, searchTerms, anchor) - ); - // highlight search terms in the summary - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - }); - Search.output.appendChild(listItem); -}; -const _finishSearch = (resultCount) => { - Search.stopPulse(); - Search.title.innerText = _("Search Results"); - if (!resultCount) - Search.status.innerText = Documentation.gettext( - "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." - ); - else - Search.status.innerText = Documentation.ngettext( - "Search finished, found one page matching the search query.", - "Search finished, found ${resultCount} pages matching the search query.", - resultCount, - ).replace('${resultCount}', resultCount); -}; -const _displayNextItem = ( - results, - resultCount, - searchTerms, - highlightTerms, -) => { - // results left, load the summary and display it - // this is intended to be dynamic (don't sub resultsCount) - if (results.length) { - _displayItem(results.pop(), searchTerms, highlightTerms); - setTimeout( - () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), - 5 - ); - } - // search finished, update title and status message - else _finishSearch(resultCount); -}; -// Helper function used by query() to order search results. -// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. -// Order the results by score (in opposite order of appearance, since the -// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. -const _orderResultsByScoreThenName = (a, b) => { - const leftScore = a[4]; - const rightScore = b[4]; - if (leftScore === rightScore) { - // same score: sort alphabetically - const leftTitle = a[1].toLowerCase(); - const rightTitle = b[1].toLowerCase(); - if (leftTitle === rightTitle) return 0; - return leftTitle > rightTitle ? -1 : 1; // inverted is intentional - } - return leftScore > rightScore ? 1 : -1; -}; - -/** - * Default splitQuery function. Can be overridden in ``sphinx.search`` with a - * custom function per language. - * - * The regular expression works by splitting the string on consecutive characters - * that are not Unicode letters, numbers, underscores, or emoji characters. - * This is the same as ``\W+`` in Python, preserving the surrogate pair area. - */ -if (typeof splitQuery === "undefined") { - var splitQuery = (query) => query - .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) - .filter(term => term) // remove remaining empty strings -} - -/** - * Search Module - */ -const Search = { - _index: null, - _queued_query: null, - _pulse_status: -1, - - htmlToText: (htmlString, anchor) => { - const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - for (const removalQuery of [".headerlink", "script", "style"]) { - htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); - } - if (anchor) { - const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); - if (anchorContent) return anchorContent.textContent; - - console.warn( - `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` - ); - } - - // if anchor not specified or not found, fall back to main content - const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent) return docContent.textContent; - - console.warn( - "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." - ); - return ""; - }, - - init: () => { - const query = new URLSearchParams(window.location.search).get("q"); - document - .querySelectorAll('input[name="q"]') - .forEach((el) => (el.value = query)); - if (query) Search.performSearch(query); - }, - - loadIndex: (url) => - (document.body.appendChild(document.createElement("script")).src = url), - - setIndex: (index) => { - Search._index = index; - if (Search._queued_query !== null) { - const query = Search._queued_query; - Search._queued_query = null; - Search.query(query); - } - }, - - hasIndex: () => Search._index !== null, - - deferQuery: (query) => (Search._queued_query = query), - - stopPulse: () => (Search._pulse_status = -1), - - startPulse: () => { - if (Search._pulse_status >= 0) return; - - const pulse = () => { - Search._pulse_status = (Search._pulse_status + 1) % 4; - Search.dots.innerText = ".".repeat(Search._pulse_status); - if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); - }; - pulse(); - }, - - /** - * perform a search for something (or wait until index is loaded) - */ - performSearch: (query) => { - // create the required interface elements - const searchText = document.createElement("h2"); - searchText.textContent = _("Searching"); - const searchSummary = document.createElement("p"); - searchSummary.classList.add("search-summary"); - searchSummary.innerText = ""; - const searchList = document.createElement("ul"); - searchList.setAttribute("role", "list"); - searchList.classList.add("search"); - - const out = document.getElementById("search-results"); - Search.title = out.appendChild(searchText); - Search.dots = Search.title.appendChild(document.createElement("span")); - Search.status = out.appendChild(searchSummary); - Search.output = out.appendChild(searchList); - - const searchProgress = document.getElementById("search-progress"); - // Some themes don't use the search progress node - if (searchProgress) { - searchProgress.innerText = _("Preparing search..."); - } - Search.startPulse(); - - // index already loaded, the browser was quick! - if (Search.hasIndex()) Search.query(query); - else Search.deferQuery(query); - }, - - _parseQuery: (query) => { - // stem the search terms and add them to the correct list - const stemmer = new Stemmer(); - const searchTerms = new Set(); - const excludedTerms = new Set(); - const highlightTerms = new Set(); - const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); - splitQuery(query.trim()).forEach((queryTerm) => { - const queryTermLower = queryTerm.toLowerCase(); - - // maybe skip this "word" - // stopwords array is from language_data.js - if ( - stopwords.indexOf(queryTermLower) !== -1 || - queryTerm.match(/^\d+$/) - ) - return; - - // stem the word - let word = stemmer.stemWord(queryTermLower); - // select the correct list - if (word[0] === "-") excludedTerms.add(word.substr(1)); - else { - searchTerms.add(word); - highlightTerms.add(queryTermLower); - } - }); - - if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js - localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) - } - - // console.debug("SEARCH: searching for:"); - // console.info("required: ", [...searchTerms]); - // console.info("excluded: ", [...excludedTerms]); - - return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; - }, - - /** - * execute search (requires search index to be loaded) - */ - _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - - // Collect multiple result groups to be sorted separately and then ordered. - // Each is an array of [docname, title, anchor, descr, score, filename, kind]. - const normalResults = []; - const nonMainIndexResults = []; - - _removeChildren(document.getElementById("search-progress")); - - const queryLower = query.toLowerCase().trim(); - for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { - for (const [file, id] of foundTitles) { - const score = Math.round(Scorer.title * queryLower.length / title.length); - const boost = titles[file] === title ? 1 : 0; // add a boost for document titles - normalResults.push([ - docNames[file], - titles[file] !== title ? `${titles[file]} > ${title}` : title, - id !== null ? "#" + id : "", - null, - score + boost, - filenames[file], - SearchResultKind.title, - ]); - } - } - } - - // search for explicit entries in index directives - for (const [entry, foundEntries] of Object.entries(indexEntries)) { - if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id, isMain] of foundEntries) { - const score = Math.round(100 * queryLower.length / entry.length); - const result = [ - docNames[file], - titles[file], - id ? "#" + id : "", - null, - score, - filenames[file], - SearchResultKind.index, - ]; - if (isMain) { - normalResults.push(result); - } else { - nonMainIndexResults.push(result); - } - } - } - } - - // lookup as object - objectTerms.forEach((term) => - normalResults.push(...Search.performObjectSearch(term, objectTerms)) - ); - - // lookup as search terms in fulltext - normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); - - // let the scorer override scores with a custom scoring function - if (Scorer.score) { - normalResults.forEach((item) => (item[4] = Scorer.score(item))); - nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); - } - - // Sort each group of results by score and then alphabetically by name. - normalResults.sort(_orderResultsByScoreThenName); - nonMainIndexResults.sort(_orderResultsByScoreThenName); - - // Combine the result groups in (reverse) order. - // Non-main index entries are typically arbitrary cross-references, - // so display them after other results. - let results = [...nonMainIndexResults, ...normalResults]; - - // remove duplicate search results - // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept - let seen = new Set(); - results = results.reverse().reduce((acc, result) => { - let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); - if (!seen.has(resultStr)) { - acc.push(result); - seen.add(resultStr); - } - return acc; - }, []); - - return results.reverse(); - }, - - query: (query) => { - const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); - const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); - - // for debugging - //Search.lastresults = results.slice(); // a copy - // console.info("search results:", Search.lastresults); - - // print the results - _displayNextItem(results, results.length, searchTerms, highlightTerms); - }, - - /** - * search for object names - */ - performObjectSearch: (object, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const objects = Search._index.objects; - const objNames = Search._index.objnames; - const titles = Search._index.titles; - - const results = []; - - const objectSearchCallback = (prefix, match) => { - const name = match[4] - const fullname = (prefix ? prefix + "." : "") + name; - const fullnameLower = fullname.toLowerCase(); - if (fullnameLower.indexOf(object) < 0) return; - - let score = 0; - const parts = fullnameLower.split("."); - - // check for different match types: exact matches of full name or - // "last name" (i.e. last dotted part) - if (fullnameLower === object || parts.slice(-1)[0] === object) - score += Scorer.objNameMatch; - else if (parts.slice(-1)[0].indexOf(object) > -1) - score += Scorer.objPartialMatch; // matches in last name - - const objName = objNames[match[1]][2]; - const title = titles[match[0]]; - - // If more than one term searched for, we require other words to be - // found in the name/title/description - const otherTerms = new Set(objectTerms); - otherTerms.delete(object); - if (otherTerms.size > 0) { - const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); - if ( - [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) - ) - return; - } - - let anchor = match[3]; - if (anchor === "") anchor = fullname; - else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; - - const descr = objName + _(", in ") + title; - - // add custom score for some objects according to scorer - if (Scorer.objPrio.hasOwnProperty(match[2])) - score += Scorer.objPrio[match[2]]; - else score += Scorer.objPrioDefault; - - results.push([ - docNames[match[0]], - fullname, - "#" + anchor, - descr, - score, - filenames[match[0]], - SearchResultKind.object, - ]); - }; - Object.keys(objects).forEach((prefix) => - objects[prefix].forEach((array) => - objectSearchCallback(prefix, array) - ) - ); - return results; - }, - - /** - * search for full-text terms in the index - */ - performTermsSearch: (searchTerms, excludedTerms) => { - // prepare search - const terms = Search._index.terms; - const titleTerms = Search._index.titleterms; - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - - const scoreMap = new Map(); - const fileMap = new Map(); - - // perform the search on the required terms - searchTerms.forEach((word) => { - const files = []; - const arr = [ - { files: terms[word], score: Scorer.term }, - { files: titleTerms[word], score: Scorer.title }, - ]; - // add support for partial matches - if (word.length > 2) { - const escapedWord = _escapeRegExp(word); - if (!terms.hasOwnProperty(word)) { - Object.keys(terms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: terms[term], score: Scorer.partialTerm }); - }); - } - if (!titleTerms.hasOwnProperty(word)) { - Object.keys(titleTerms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); - }); - } - } - - // no match but word was a required one - if (arr.every((record) => record.files === undefined)) return; - - // found search word in contents - arr.forEach((record) => { - if (record.files === undefined) return; - - let recordFiles = record.files; - if (recordFiles.length === undefined) recordFiles = [recordFiles]; - files.push(...recordFiles); - - // set score for the word in each file - recordFiles.forEach((file) => { - if (!scoreMap.has(file)) scoreMap.set(file, {}); - scoreMap.get(file)[word] = record.score; - }); - }); - - // create the mapping - files.forEach((file) => { - if (!fileMap.has(file)) fileMap.set(file, [word]); - else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); - }); - }); - - // now check if the files don't contain excluded terms - const results = []; - for (const [file, wordList] of fileMap) { - // check if all requirements are matched - - // as search terms with length < 3 are discarded - const filteredTermCount = [...searchTerms].filter( - (term) => term.length > 2 - ).length; - if ( - wordList.length !== searchTerms.size && - wordList.length !== filteredTermCount - ) - continue; - - // ensure that none of the excluded terms is in the search result - if ( - [...excludedTerms].some( - (term) => - terms[term] === file || - titleTerms[term] === file || - (terms[term] || []).includes(file) || - (titleTerms[term] || []).includes(file) - ) - ) - break; - - // select one (max) score for the file. - const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); - // add result to the result list - results.push([ - docNames[file], - titles[file], - "", - null, - score, - filenames[file], - SearchResultKind.text, - ]); - } - return results; - }, - - /** - * helper function to return a node containing the - * search summary for a given text. keywords is a list - * of stemmed words. - */ - makeSearchSummary: (htmlText, keywords, anchor) => { - const text = Search.htmlToText(htmlText, anchor); - if (text === "") return null; - - const textLower = text.toLowerCase(); - const actualStartPosition = [...keywords] - .map((k) => textLower.indexOf(k.toLowerCase())) - .filter((i) => i > -1) - .slice(-1)[0]; - const startWithContext = Math.max(actualStartPosition - 120, 0); - - const top = startWithContext === 0 ? "" : "..."; - const tail = startWithContext + 240 < text.length ? "..." : ""; - - let summary = document.createElement("p"); - summary.classList.add("context"); - summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; - - return summary; - }, -}; - -_ready(Search.init); diff --git a/docs/0.4.8/_static/sphinx_highlight.js b/docs/0.4.8/_static/sphinx_highlight.js deleted file mode 100644 index 8a96c69a..00000000 --- a/docs/0.4.8/_static/sphinx_highlight.js +++ /dev/null @@ -1,154 +0,0 @@ -/* Highlighting utilities for Sphinx HTML documentation. */ -"use strict"; - -const SPHINX_HIGHLIGHT_ENABLED = true - -/** - * highlight a given string on a node by wrapping it in - * span elements with the given class name. - */ -const _highlight = (node, addItems, text, className) => { - if (node.nodeType === Node.TEXT_NODE) { - const val = node.nodeValue; - const parent = node.parentNode; - const pos = val.toLowerCase().indexOf(text); - if ( - pos >= 0 && - !parent.classList.contains(className) && - !parent.classList.contains("nohighlight") - ) { - let span; - - const closestNode = parent.closest("body, svg, foreignObject"); - const isInSVG = closestNode && closestNode.matches("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.classList.add(className); - } - - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - const rest = document.createTextNode(val.substr(pos + text.length)); - parent.insertBefore( - span, - parent.insertBefore( - rest, - node.nextSibling - ) - ); - node.nodeValue = val.substr(0, pos); - /* There may be more occurrences of search term in this node. So call this - * function recursively on the remaining fragment. - */ - _highlight(rest, addItems, text, className); - - if (isInSVG) { - const rect = document.createElementNS( - "http://www.w3.org/2000/svg", - "rect" - ); - const bbox = parent.getBBox(); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute("class", className); - addItems.push({ parent: parent, target: rect }); - } - } - } else if (node.matches && !node.matches("button, select, textarea")) { - node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); - } -}; -const _highlightText = (thisNode, text, className) => { - let addItems = []; - _highlight(thisNode, addItems, text, className); - addItems.forEach((obj) => - obj.parent.insertAdjacentElement("beforebegin", obj.target) - ); -}; - -/** - * Small JavaScript module for the documentation. - */ -const SphinxHighlight = { - - /** - * highlight the search words provided in localstorage in the text - */ - highlightSearchWords: () => { - if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight - - // get and clear terms from localstorage - const url = new URL(window.location); - const highlight = - localStorage.getItem("sphinx_highlight_terms") - || url.searchParams.get("highlight") - || ""; - localStorage.removeItem("sphinx_highlight_terms") - url.searchParams.delete("highlight"); - window.history.replaceState({}, "", url); - - // get individual terms from highlight string - const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); - if (terms.length === 0) return; // nothing to do - - // There should never be more than one element matching "div.body" - const divBody = document.querySelectorAll("div.body"); - const body = divBody.length ? divBody[0] : document.querySelector("body"); - window.setTimeout(() => { - terms.forEach((term) => _highlightText(body, term, "highlighted")); - }, 10); - - const searchBox = document.getElementById("searchbox"); - if (searchBox === null) return; - searchBox.appendChild( - document - .createRange() - .createContextualFragment( - '

' + - '' + - _("Hide Search Matches") + - "

" - ) - ); - }, - - /** - * helper function to hide the search marks again - */ - hideSearchWords: () => { - document - .querySelectorAll("#searchbox .highlight-link") - .forEach((el) => el.remove()); - document - .querySelectorAll("span.highlighted") - .forEach((el) => el.classList.remove("highlighted")); - localStorage.removeItem("sphinx_highlight_terms") - }, - - initEscapeListener: () => { - // only install a listener if it is really needed - if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; - - document.addEventListener("keydown", (event) => { - // bail for input elements - if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; - // bail with special keys - if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; - if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { - SphinxHighlight.hideSearchWords(); - event.preventDefault(); - } - }); - }, -}; - -_ready(() => { - /* Do not call highlightSearchWords() when we are on the search page. - * It will highlight words from the *previous* search query. - */ - if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); - SphinxHighlight.initEscapeListener(); -}); diff --git a/docs/0.4.8/autodoc/mmif.serialize.html b/docs/0.4.8/autodoc/mmif.serialize.html deleted file mode 100644 index d6120045..00000000 --- a/docs/0.4.8/autodoc/mmif.serialize.html +++ /dev/null @@ -1,1148 +0,0 @@ - - - - - - - - - mmif.serialize module — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.serialize module

-
-

mmif.serialize.model module

-

The model module contains the classes used to represent an -abstract MMIF object as a live Python object.

-

The MmifObject class or one of its derivatives is subclassed by -all other classes defined in this SDK, except for MmifObjectEncoder.

-

These objects are generally instantiated from JSON, either as a string -or as an already-loaded Python dictionary. This base class provides the -core functionality for deserializing MMIF JSON data into live objects -and serializing live objects into MMIF JSON data. Specialized behavior -for the different components of MMIF is added in the subclasses.

-
-
-class mmif.serialize.model.DataDict(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject, Generic[T, S]

-
-
-empty()[source]
-
- -
-
-get(key: T, default=None) → S | None[source]
-
- -
-
-items()[source]
-
- -
-
-keys()[source]
-
- -
-
-update(other, overwrite)[source]
-
- -
-
-values()[source]
-
- -
- -
-
-class mmif.serialize.model.DataList(mmif_obj: bytes | str | list | None = None)[source]
-

Bases: MmifObject, Generic[T]

-

The DataList class is an abstraction that represents the -various lists found in a MMIF file, such as documents, subdocuments, -views, and annotations.

-
-
Parameters:
-

mmif_obj (Union[str, list]) – the data that the list contains

-
-
-
-
-append(value, overwrite)[source]
-
- -
-
-deserialize(mmif_json: str | list) → None[source]
-

Passes the input data into the internal deserializer.

-
- -
-
-empty()[source]
-
- -
-
-get(key: str) → T | None[source]
-

Standard dictionary-style get() method, albeit with no default -parameter. Relies on the implementation of __getitem__.

-

Will return None if the key is not found.

-
-
Parameters:
-

key – the key to search for

-
-
Returns:
-

the value matching that key

-
-
-
- -
- -
-
-class mmif.serialize.model.MmifObject(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: object

-

Abstract superclass for MMIF related key-value pair objects.

-

Any MMIF object can be initialized as an empty placeholder or -an actual representation with a JSON formatted string or equivalent -dict object argument.

-

This superclass has three specially designed instance variables, and these -variable names cannot be used as attribute names for MMIF objects.

-
    -

  1. _unnamed_attributes: -Only can be either None or an empty dictionary. If it’s set to None, -it means the class won’t take any Additional Attributes in the JSON -schema sense. If it’s a dict, users can throw any k-v pairs to the -class, EXCEPT for the reserved two key names.

    2. -

  2. _attribute_classes: -This is a dict from a key name to a specific python class to use for -deserialize the value. Note that a key name in this dict does NOT -have to be a named attribute, but is recommended to be one.

    3. -

  3. _required_attributes: -This is a simple list of names of attributes that are required in the object. -When serialize, an object will skip its empty (e.g. zero-length, or None) -attributes unless they are in this list. Otherwise, the serialized JSON -string would have empty representations (e.g. "", []).

    4. -
-

# TODO (krim @ 8/17/20): this dict is however, a duplicate with the type hints in the class definition. -Maybe there is a better way to utilize type hints (e.g. getting them as a programmatically), but for now -developers should be careful to add types to hints as well as to this dict.

-

Also note that those two special attributes MUST be set in the __init__() -before calling super method, otherwise deserialization will not work.

-

And also, a subclass that has one or more named attributes, it must -set those attributes in the __init__() before calling super method. When -serializing a MmifObject, all empty attributes will be ignored, so for -optional named attributes, you must leave the values empty (len == 0), but -NOT None. Any None-valued named attributes will cause issues with current -implementation.

-
-
Parameters:
-

mmif_obj – JSON string or dict to initialize an object. -If not given, an empty object will be initialized, sometimes with -an ID value automatically generated, based on its parent object.

-
-
-
-
-deserialize(mmif_json: str | dict) → None[source]
-

Takes a JSON-formatted string or a simple dict that’s json-loaded from -such a string as an input and populates object’s fields with the values -specified in the input.

-
-
Parameters:
-

mmif_json – JSON-formatted string or dict from such a string -that represents a MMIF object

-
-
-
- -
-
-disallow_additional_properties() → None[source]
-

Call this method in __init__() to prevent the insertion -of unnamed attributes after initialization.

-
- -
-
-static is_empty(obj) → bool[source]
-

return True if the obj is None or “emtpy”. The emptiness first defined as -having zero length. But for objects that lack __len__ method, we need -additional check.

-
- -
-
-reserved_names: Set = {'_attribute_classes', '_id_counts', '_parent_view_id', '_required_attributes', '_unnamed_attributes', 'reserved_names'}[source]
-
- -
-
-serialize(pretty: bool = False) → str[source]
-

Generates JSON representation of an object.

-
-
Parameters:
-

pretty – If True, returns string representation with indentation.

-
-
Returns:
-

JSON string of the object.

-
-
-
- -
-
-set_additional_property(key: str, value: Any) → None[source]
-

Method to set values in _unnamed_attributes.

-
-
Parameters:
-
    -

  • key – the attribute name

    • -

  • value – the desired value

    • -
-
-
Returns:
-

None

-
-
Raise:
-

AttributeError if additional properties are disallowed by disallow_additional_properties()

-
-
-
- -
- -
-
-class mmif.serialize.model.MmifObjectEncoder(*, skipkeys=False, ensure_ascii=True, check_circular=True, allow_nan=True, sort_keys=False, indent=None, separators=None, default=None)[source]
-

Bases: JSONEncoder

-

Encoder class to define behaviors of de-/serialization

-
-
-default(obj: MmifObject)[source]
-

Overrides default encoding behavior to prioritize MmifObject.serialize().

-
- -
- -
-
-

mmif.serialize.mmif module

-

The mmif module contains the classes used to represent a full MMIF -file as a live Python object.

-

See the specification docs and the JSON Schema file for more information.

-
-
-class mmif.serialize.mmif.Mmif(mmif_obj: bytes | str | dict | None = None, *, validate: bool = True)[source]
-

Bases: MmifObject

-

MmifObject that represents a full MMIF file.

-
-
Parameters:
-
    -

  • mmif_obj – the JSON data

    • -

  • validate – whether to validate the data against the MMIF JSON schema.

    • -
-
-
-
-
-add_document(document: Document, overwrite=False) → None[source]
-

Appends a Document object to the documents list.

-

Fails if there is already a document with the same ID in the MMIF object.

-
-
Parameters:
-
    -

  • document – the Document object to add

    • -

  • overwrite – if set to True, will overwrite -an existing view with the same ID

    • -
-
-
Returns:
-

None

-
-
-
- -
-
-add_view(view: View, overwrite=False) → None[source]
-

Appends a View object to the views list.

-

Fails if there is already a view with the same ID in the MMIF object.

-
-
Parameters:
-
    -

  • view – the Document object to add

    • -

  • overwrite – if set to True, will overwrite -an existing view with the same ID

    • -
-
-
Returns:
-

None

-
-
-
- -
-
-get_alignments(at_type1: str | TypesBase, at_type2: str | TypesBase) → Dict[str, List[Annotation]][source]
-

Finds views where alignments between two given annotation types occurred.

-
-
Returns:
-

a dict that keyed by view IDs (str) and has lists of alignment Annotation objects as values.

-
-
-
- -
-
-get_all_views_contain(at_types: TypesBase | str | List[str | TypesBase]) → List[View][source]
-

Returns the list of all views in the MMIF if given types -are present in that view’s ‘contains’ metadata.

-
-
Parameters:
-

at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

-
-
Returns:
-

the list of views that contain the type

-
-
-
- -
-
-get_document_by_id(doc_id: str) → Document[source]
-

Finds a Document object with the given ID.

-
-
Parameters:
-

doc_id – the ID to search for

-
-
Returns:
-

a reference to the corresponding document, if it exists

-
-
Raises:
-

Exception – if there is no corresponding document

-
-
-
- -
-
-get_document_location(m_type: DocumentTypes | str, path_only=False) → str | None[source]
-

Method to get the location of first document of given type.

-
-
Parameters:
-

m_type – the type to search for

-
-
Returns:
-

the value of the location field in the corresponding document

-
-
-
- -
-
-get_documents_by_app(app_id: str) → List[Document][source]
-

Method to get all documents object queries by its originated app name.

-
-
Parameters:
-

app_id – the app name to search for

-
-
Returns:
-

a list of documents matching the requested app name, or an empty list if the app not found

-
-
-
- -
-
-get_documents_by_property(prop_key: str, prop_value: str) → List[Document][source]
-

Method to retrieve documents by an arbitrary key-value pair in the document properties objects.

-
-
Parameters:
-
    -

  • prop_key – the metadata key to search for

    • -

  • prop_value – the metadata value to match

    • -
-
-
Returns:
-

a list of documents matching the requested metadata key-value pair

-
-
-
- -
-
-get_documents_by_type(doc_type: str | DocumentTypes) → List[Document][source]
-

Method to get all documents where the type matches a particular document type, which should be one of the CLAMS document types.

-
-
Parameters:
-

doc_type – the type of documents to search for, must be one of Document type defined in the CLAMS vocabulary.

-
-
Returns:
-

a list of documents matching the requested type, or an empty list if none found.

-
-
-
- -
-
-get_documents_in_view(vid: str | None = None) → List[Document][source]
-

Method to get all documents object queries by a view id.

-
-
Parameters:
-

vid – the source view ID to search for

-
-
Returns:
-

a list of documents matching the requested source view ID, or an empty list if the view not found

-
-
-
- -
-
-get_documents_locations(m_type: DocumentTypes | str, path_only=False) → List[str | None][source]
-

This method returns the file paths of documents of given type. -Only top-level documents have locations, so we only check them.

-
-
Parameters:
-

m_type – the type to search for

-
-
Returns:
-

a list of the values of the location fields in the corresponding documents

-
-
-
- -
-
-get_view_by_id(req_view_id: str) → View[source]
-

Finds a View object with the given ID.

-
-
Parameters:
-

req_view_id – the ID to search for

-
-
Returns:
-

a reference to the corresponding view, if it exists

-
-
Raises:
-

Exception – if there is no corresponding view

-
-
-
- -
-
-get_view_contains(at_types: TypesBase | str | List[str | TypesBase]) → View | None[source]
-

Returns the last view appended that contains the given -types in its ‘contains’ metadata.

-
-
Parameters:
-

at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

-
-
Returns:
-

the view, or None if the type is not found

-
-
-
- -
-
-get_views_contain(at_types: TypesBase | str | List[str | TypesBase]) → List[View][source]
-

An alias to get_all_views_contain method.

-
- -
-
-get_views_for_document(doc_id: str)[source]
-

Returns the list of all views that have annotations anchored on a particular document. -Note that when the document is insids a view (generated during the pipeline’s running), -doc_id must be prefixed with the view_id.

-
- -
-
-id_delimiter: ClassVar[str] = ':'[source]
-
- -
-
-new_view() → View[source]
-

Creates an empty view with a new ID and appends it to the views list.

-
-
Returns:
-

a reference to the new View object

-
-
-
- -
-
-new_view_id() → str[source]
-

Fetches an ID for a new view.

-
-
Returns:
-

the ID

-
-
-
- -
-
-static validate(json_str: bytes | str | dict) → None[source]
-

Validates a MMIF JSON object against the MMIF Schema. -Note that this method operates before processing by MmifObject._load_str, -so it expects @ and not _ for the JSON-LD @-keys.

-
-
Raises:
-

jsonschema.exceptions.ValidationError – if the input fails validation

-
-
Parameters:
-

json_str – a MMIF JSON dict or string

-
-
Returns:
-

None

-
-
-
- -
-
-view_prefix: ClassVar[str] = 'v_'[source]
-
- -
- -
-
-

mmif.serialize.view module

-

The view module contains the classes used to represent a MMIF view -as a live Python object.

-

In MMIF, views are created by apps in a pipeline that are annotating -data that was previously present in the MMIF file.

-
-
-class mmif.serialize.view.Contain(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-

Contain object that represents the metadata of a single -annotation type in the contains metadata of a MMIF view.

-
- -
-
-class mmif.serialize.view.View(view_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-

View object that represents a single view in a MMIF file.

-

A view is identified by an ID, and contains certain metadata, -a list of annotations, and potentially a JSON-LD @context -IRI.

-

If view_obj is not provided, an empty View will be generated.

-
-
Parameters:
-

view_obj – the JSON data that defines the view

-
-
-
-
-add_annotation(annotation: Annotation, overwrite=False) → Annotation[source]
-

Adds an annotation to the current view.

-

Fails if there is already an annotation with the same ID -in the view, unless overwrite is set to True.

-
-
Parameters:
-
-
-
Raises:
-

KeyError – if overwrite is set to False and -an annotation with the same ID exists -in the view

-
-
Returns:
-

the same Annotation object passed in as annotation

-
-
-
- -
-
-add_document(document: Document, overwrite=False) → Annotation[source]
-

Appends a Document object to the annotations list.

-

Fails if there is already a document with the same ID in the annotations list.

-
-
Parameters:
-
    -

  • document – the Document object to add

    • -

  • overwrite – if set to True, will overwrite -an existing view with the same ID

    • -
-
-
Returns:
-

None

-
-
-
- -
-
-get_annotation_by_id(ann_id)[source]
-
- -
-
-get_annotations(at_type: str | TypesBase | None = None, **properties) → Generator[Annotation, None, None][source]
-

Look for certain annotations in this view, specified by parameters

-
-
Parameters:
-
    -

  • at_type – @type of the annotations to look for. When this is None, any @type will match.

    • -

  • properties – properties of the annotations to look for. When given more than one property, all properties must match. Note that annotation type metadata are specified in the contains view metadata, not in individual annotation objects.

    • -
-
-
-
- -
-
-get_document_by_id(doc_id) → Document[source]
-
- -
-
-get_documents() → List[Document][source]
-
- -
-
-new_annotation(at_type: str | TypesBase, aid: str | None = None, overwrite=False, **properties) → Annotation[source]
-

Generates a new mmif.serialize.annotation.Annotation -object and adds it to the current view.

-

Fails if there is already an annotation with the same ID -in the view, unless overwrite is set to True.

-
-
Parameters:
-
    -

  • at_type – the desired @type of the annotation.

    • -

  • aid – the desired ID of the annotation, when not given, -the mmif SDK tries to automatically generate an ID based on -Annotation type and existing annotations in the view.

    • -

  • overwrite – if set to True, will overwrite an -existing annotation with the same ID.

    • -
-
-
Raises:
-

KeyError – if overwrite is set to False and -an annotation with the same ID exists -in the view.

-
-
Returns:
-

the generated mmif.serialize.annotation.Annotation

-
-
-
- -
-
-new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
-

Adds a new element to the contains metadata.

-
-
Parameters:
-
    -

  • at_type – the @type of the annotation type being added

    • -

  • contains_metadata – any metadata associated with the annotation type

    • -
-
-
Returns:
-

the generated Contain object

-
-
-
- -
-
-new_textdocument(text: str, lang: str = 'en', did: str | None = None, overwrite=False, **properties) → Document[source]
-

Generates a new mmif.serialize.annotation.Document -object, particularly typed as TextDocument and adds it to the current view.

-

Fails if there is already a text document with the same ID -in the view, unless overwrite is set to True.

-
-
Parameters:
-
    -

  • text – text content of the new document

    • -

  • lang – ISO 639-1 code of the language used in the new document

    • -

  • did – the desired ID of the document, when not given, -the mmif SDK tries to automatically generate an ID based on -Annotation type and existing documents in the view.

    • -

  • overwrite – if set to True, will overwrite an -existing document with the same ID

    • -
-
-
Raises:
-

KeyError – if overwrite is set to False and -an document with the same ID exists -in the view

-
-
Returns:
-

the generated mmif.serialize.annotation.Document

-
-
-
- -
-
-set_error(err_message: str, err_trace: str) → None[source]
-
- -
- -
-
-class mmif.serialize.view.ViewMetadata(viewmetadata_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-

ViewMetadata object that represents the metadata object within a MMIF view.

-
-
Parameters:
-

viewmetadata_obj – the JSON data that defines the metadata

-
-
-
-
-add_parameter(param_key, param_value)[source]
-
- -
-
-add_parameters(**runtime_params)[source]
-
- -
-
-add_warnings(*warnings: Warning)[source]
-
- -
-
-emtpy_warnings()[source]
-
- -
-
-get_parameter(param_key)[source]
-
- -
-
-new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
-

Adds a new element to the contains dictionary.

-
-
Parameters:
-
    -

  • at_type – the @type of the annotation type being added

    • -

  • contains_metadata – any metadata associated with the annotation type

    • -
-
-
Returns:
-

the generated Contain object

-
-
-
- -
-
-set_error(message: str, stack_trace: str)[source]
-
- -
- -
-
-

mmif.serialize.annotation module

-

The annotation module contains the classes used to represent a -MMIF annotation as a live Python object.

-

In MMIF, annotations are created by apps in a pipeline as a part -of a view. For documentation on how views are represented, see -mmif.serialize.view.

-
-
-class mmif.serialize.annotation.Annotation(anno_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-

MmifObject that represents an annotation in a MMIF view.

-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]]) → None[source]
-

Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

-
- -
-
-property at_type: TypesBase[source]
-
- -
-
-property id: str[source]
-
- -
-
-is_document()[source]
-
- -
-
-is_type(at_type: str | TypesBase) → bool[source]
-

Check if the @type of this object matches.

-
- -
- -
-
-class mmif.serialize.annotation.AnnotationProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject, MutableMapping[str, T]

-

AnnotationProperties object that represents the -properties object within a MMIF annotation.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
- -
-
-class mmif.serialize.annotation.Document(doc_obj: bytes | str | dict | None = None)[source]
-

Bases: Annotation

-

Document object that represents a single document in a MMIF file.

-

A document is identified by an ID, and contains certain attributes -and potentially contains the contents of the document itself, -metadata about how the document was created, and/or a list of -subdocuments grouped together logically.

-

If document_obj is not provided, an empty Document will be generated.

-
-
Parameters:
-

document_obj – the JSON data that defines the document

-
-
-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None]) → None[source]
-

Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

-
- -
-
-property location: str | None[source]
-

location property must be a legitimate URI. That is, should the document be a local file -then the file:// scheme must be used. -Returns None when no location is set.

-
- -
-
-location_address() → str | None[source]
-

Retrieves the full address from the document location URI. -Returns None when no location is set.

-
- -
-
-location_path() → str | None[source]
-

Retrieves only path name of the document location (hostname is ignored). -Useful to get a path of a local file. -Returns None when no location is set.

-
- -
-
-location_scheme() → str | None[source]
-

Retrieves URI scheme of the document location. -Returns None when no location is set.

-
- -
-
-property parent: str[source]
-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.DocumentProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: AnnotationProperties

-

DocumentProperties object that represents the -properties object within a MMIF document.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
-
-property location: str | None[source]
-

location property must be a legitimate URI. That is, should the document be a local file -then the file:// scheme must be used. -Returns None when no location is set.

-
- -
-
-location_address() → str | None[source]
-

Retrieves the full address from the document location URI. -Returns None when no location is set.

-
- -
-
-location_path() → str | None[source]
-

Retrieves only path name of the document location (hostname is ignored). -Useful to get a path of a local file. -Returns None when no location is set.

-
- -
-
-location_scheme() → str | None[source]
-

Retrieves URI scheme of the document location. -Returns None when no location is set.

-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.Text(text_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-
-
-property lang: str[source]
-
- -
-
-property value: str[source]
-
- -
- -
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.4.8 - - -
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0.3.2
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- - - \ No newline at end of file diff --git a/docs/0.4.8/autodoc/mmif.vocabulary.html b/docs/0.4.8/autodoc/mmif.vocabulary.html deleted file mode 100644 index 7b894fb5..00000000 --- a/docs/0.4.8/autodoc/mmif.vocabulary.html +++ /dev/null @@ -1,285 +0,0 @@ - - - - - - - - - mmif.vocabulary module — mmif-python documentation - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.vocabulary module

-
-

mmif.vocabulary.annotation_types module

-
-
-class mmif.vocabulary.annotation_types.AnnotationTypes(type_uri: str)[source]
-

Bases: AnnotationTypesBase

-

This class contains the CLAMS annotation types -defined in the spec version 0.4.2 as class variables.

-
-
-Alignment = http://mmif.clams.ai/0.4.2/vocabulary/Alignment[source]
-
- -
-
-Annotation = http://mmif.clams.ai/0.4.2/vocabulary/Annotation[source]
-
- -
-
-BoundingBox = http://mmif.clams.ai/0.4.2/vocabulary/BoundingBox[source]
-
- -
-
-Chapter = http://mmif.clams.ai/0.4.2/vocabulary/Chapter[source]
-
- -
-
-Interval = http://mmif.clams.ai/0.4.2/vocabulary/Interval[source]
-
- -
-
-Polygon = http://mmif.clams.ai/0.4.2/vocabulary/Polygon[source]
-
- -
-
-Region = http://mmif.clams.ai/0.4.2/vocabulary/Region[source]
-
- -
-
-Relation = http://mmif.clams.ai/0.4.2/vocabulary/Relation[source]
-
- -
-
-Span = http://mmif.clams.ai/0.4.2/vocabulary/Span[source]
-
- -
-
-TimeFrame = http://mmif.clams.ai/0.4.2/vocabulary/TimeFrame[source]
-
- -
-
-TimePoint = http://mmif.clams.ai/0.4.2/vocabulary/TimePoint[source]
-
- -
-
-VideoObject = http://mmif.clams.ai/0.4.2/vocabulary/VideoObject[source]
-
- -
- -
-
-

mmif.vocabulary.document_types module

-
-
-class mmif.vocabulary.document_types.DocumentTypes(type_uri: str)[source]
-

Bases: DocumentTypesBase

-

This class contains the CLAMS document types -defined in the spec version 0.4.2 as class variables.

-
-
-AudioDocument = http://mmif.clams.ai/0.4.2/vocabulary/AudioDocument[source]
-
- -
-
-Document = http://mmif.clams.ai/0.4.2/vocabulary/Document[source]
-
- -
-
-ImageDocument = http://mmif.clams.ai/0.4.2/vocabulary/ImageDocument[source]
-
- -
-
-TextDocument = http://mmif.clams.ai/0.4.2/vocabulary/TextDocument[source]
-
- -
-
-VideoDocument = http://mmif.clams.ai/0.4.2/vocabulary/VideoDocument[source]
-
- -
- -
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.4.8 - - -
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- - - \ No newline at end of file diff --git a/docs/0.4.8/consumer-tutorial.html b/docs/0.4.8/consumer-tutorial.html deleted file mode 100644 index 21aa3d04..00000000 --- a/docs/0.4.8/consumer-tutorial.html +++ /dev/null @@ -1,176 +0,0 @@ - - - - - - - - - MMIF consumer — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • MMIF consumer
    • -
  • -
    • -
-
-
-
-
- -
-

MMIF consumer

-

A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the appliance documentation to learn more about the appliance.

-

MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance.

-
    -

  1. The code must be hosted on a public git repository (e.g. Github, Gitlab, …)

    2. -

  2. Must listen to 5000 port.

    3. -

  3. Must expose /display route .

    4. -

  4. /display router should response to GET requests.

    5. -

  5. In the GET request, a public URL of the input MMIF file is passed via file URL parameter.

    6. -

  6. On the codebase root, there must be a Dockerfile that can build a docker image that runs the web app.

    7. -
-

We provide an example consumer at https://github.com/clamsproject/mmif-visualizer.

-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.4.8 - - -
-
- -
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- - -
- -
-
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-
    -
    • -
  • Index
    • -
  • -
    • -
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- - -

Index

- -
- A - | B - | C - | D - | E - | G - | I - | K - | L - | M - | N - | P - | R - | S - | T - | U - | V - -
-

A

- - - -
- -

B

- - -
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C

- - - -
- -

D

- - - -
- -

E

- - - -
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G

- - - -
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K

- - -
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L

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M

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N

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P

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R

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S

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T

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U

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V

- - - -
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- - Other Versions - v: 0.4.8 - - -
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- - -
- -
-
-
-
    -
    • -
  • Welcome to mmif-python’s documentation!
    • -
  • -
    • -
-
-
-
-
- -
-

Welcome to mmif-python’s documentation!

-
-
-

MMIF for python

-

NOTE that this project is in pre-alpha and being actively developed. Nothing is guaranteed to reliably work for the moment and developer need to be very careful when using APIs implemented here. Please use the issue track to report bugs and malfunctions.

-
-

MultiMedia Interchange Format

-

MMIF is a JSON(-LD)-based data format designed for transferring annotation data between computational analysis applications in CLAMS project.

-
-

Contents

- -
-
-

API documentation:

- -
-
-
-
-

Indices and tables

- -
- - -
-
- -
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- -
- - Other Versions - v: 0.4.8 - - -
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0.3.0
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- - - \ No newline at end of file diff --git a/docs/0.4.8/introduction.html b/docs/0.4.8/introduction.html deleted file mode 100644 index 9fc58f51..00000000 --- a/docs/0.4.8/introduction.html +++ /dev/null @@ -1,236 +0,0 @@ - - - - - - - - - Getting Started — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
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  • Getting Started
    • -
  • -
    • -
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Getting Started

-
-

Overview

-

MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF wbesite. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports de-/serialization of MMIF objects, as well as many navigation and manipulation helpers for MMIF objects.

-
-
-

Prerequisites

-
    -

  • Python: mmif-python requires Python 3.6 or newer. We have no plan to support Python 2.7.

    • -
-
-
-

Installation

-

Package mmif-python is distributed via the official PyPI. Users are supposed to pip-install to get latest release.

-
pip install mmif-python
-
-
-

This will install a package mmif to local python.

-

The MMIF format and specification is evolving over time, and mmif-python package will be updated along with the changes in MMIF format.

-
-

Note

-

MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and mmif-python versions, please take time to read our decision on the subject here. If you need to know which python SDK supports which specification version, see Target MMIF Versions page.

-
-
-
-

MMIF Serialization

-

mmif.serialize.mmif.Mmif represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of mmif.serialize.model.MmifObject, including the mmif.serialize.mmif.Mmif. To start with an existing MMIF str, simple initiate a new Mmif object with the file.

-
import mmif
-from mmif import Mmif
-
-mmif_str = """{
-"metadata": {
-  "mmif": "http://mmif.clams.ai/0.2.0"
-},
-"documents": [
-  {
-    "@type": "http://mmif.clams.ai/0.2.0/vocabulary/VideoDocument",
-    "properties": {
-      "id": "m1",
-      "mime": "video/mp4",
-      "location": "file:///var/archive/video-0012.mp4"
-    }
-  },
-  {
-    "@type": "http://mmif.clams.ai/0.2.0/vocabulary/TextDocument",
-    "properties": {
-      "id": "m2",
-      "mime": "text/plain",
-      "location": "file:///var/archive/video-0012-transcript.txt"
-    }
-  }
-],
-"views": []}"""
-mmif_obj = Mmif(mmif_str)
-
-
-

Few notes;

-
    -

  1. MMIF does not carry the primary source files in it.

    2. -

  2. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version mmif-python implementation of the MMIF might not be able to load an unsupported version of MMIF string.

    3. -
-

When serializing back to str, call .serialize() (mmif.serialize.model.MmifObject.serialize()) on the object.

-

To get subcomponents, you can use various getters implemented in subclasses. For more details, the API documentation (mmif package) will help.

-
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.4.8 - - -
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- - - \ No newline at end of file diff --git a/docs/0.4.8/modules.html b/docs/0.4.8/modules.html deleted file mode 100644 index a67d39af..00000000 --- a/docs/0.4.8/modules.html +++ /dev/null @@ -1,330 +0,0 @@ - - - - - - - - - mmif package — mmif-python documentation - - - - - - - - - - - - - - - - - -
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- -
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  • mmif package
    • -
  • -
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mmif package

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- - - - - - - - \ No newline at end of file diff --git a/docs/0.4.8/searchindex.js b/docs/0.4.8/searchindex.js deleted file mode 100644 index 9c527daa..00000000 --- a/docs/0.4.8/searchindex.js +++ /dev/null @@ -1 +0,0 @@ -Search.setIndex({"alltitles": {"API documentation:": [[3, null]], "Contents": [[3, null]], "Getting Started": [[4, null]], "Indices and tables": [[3, "indices-and-tables"]], "Installation": [[4, "installation"]], "MMIF Serialization": [[4, "mmif-serialization"]], "MMIF consumer": [[2, null]], "MMIF for python": [[3, "mmif-for-python"]], "MultiMedia Interchange Format": [[3, "multimedia-interchange-format"]], "Overview": [[4, "overview"]], "Prerequisites": [[4, "prerequisites"]], "Target MMIF Versions": [[6, null]], "Target Specification Versions": [[6, "id1"]], "Welcome to mmif-python\u2019s documentation!": [[3, null]], "mmif package": [[5, null]], "mmif.serialize module": [[0, null]], "mmif.serialize.annotation module": [[0, "module-mmif.serialize.annotation"]], 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1, 2, 3, 4, 5, 6], "model": 0, "modul": [0, 1], "multimedia": 3, "overview": 4, "packag": 5, "prerequisit": 4, "python": 3, "serial": [0, 4], "specif": 6, "start": 4, "tabl": 3, "target": 6, "version": 6, "view": 0, "vocabulari": 1, "welcom": 3}}) \ No newline at end of file diff --git a/docs/0.4.8/target-versions.html b/docs/0.4.8/target-versions.html deleted file mode 100644 index 16c95d46..00000000 --- a/docs/0.4.8/target-versions.html +++ /dev/null @@ -1,230 +0,0 @@ - - - - - - - - - Target MMIF Versions — mmif-python documentation - - - - - - - - - - - - - - - - - -
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  • Target MMIF Versions
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Target MMIF Versions

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This article provides targeting MMIF specification versions of different versions of mmif-python SDK.

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Target Specification Versions

mmif-python version

Target MMIF Specification

0.4.8

0.4.2

0.4.7

0.4.1

0.4.6

0.4.0

0.4.5

0.4.0

0.4.4

0.4.0

0.4.3

0.4.0

0.4.2

0.4.0

0.4.1

0.4.0

0.4.0

0.4.0

0.3.5

0.3.1

0.3.4

0.3.1

0.3.3

0.3.1

0.3.2

0.3.1

0.3.1

0.3.0

0.3.0

0.3.0

0.2.2

0.2.1

0.2.1

0.2.1

0.2.0

0.2.1

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0.3.0
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0.3.1
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0.3.2
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0.3.3
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0.3.4
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0.3.5
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0.4.0
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0.4.1
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0.4.2
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0.4.3
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0.4.4
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0.4.5
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0.4.6
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0.4.7
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0.4.8
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0.5.0
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0.5.1
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0.5.2
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1.0.0
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1.0.1
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1.0.10
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1.0.11
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1.0.12
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1.0.13
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1.0.14
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1.0.15
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1.0.16
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1.0.17
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1.0.18
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1.0.19
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1.0.2
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1.0.3
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1.0.4
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1.0.5
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1.0.6
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1.0.7
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1.0.8
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1.0.9
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1.1.0
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The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the `appliance documentation `_ to learn more about the appliance. - -MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance. - -#. The code must be hosted on a public git repository (e.g. Github, Gitlab, ...) -#. Must listen to ``5000`` port. -#. Must expose ``/display`` route . -#. ``/display`` router should response to ``GET`` requests. -#. In the ``GET`` request, a public URL of the input MMIF file is passed via ``file`` URL parameter. -#. On the codebase root, there must be a ``Dockerfile`` that can build a `docker `_ image that runs the web app. - -We provide an example consumer at https://github.com/clamsproject/mmif-visualizer. diff --git a/docs/0.5.0/_sources/index.rst.txt b/docs/0.5.0/_sources/index.rst.txt deleted file mode 100644 index 9b90b38e..00000000 --- a/docs/0.5.0/_sources/index.rst.txt +++ /dev/null @@ -1,26 +0,0 @@ -Welcome to mmif-python's documentation! -======================================= - -.. mdinclude:: ../README.md - -.. toctree:: - :maxdepth: 2 - :caption: Contents - - introduction - target-versions - consumer-tutorial - -.. toctree:: - :maxdepth: 2 - :caption: API documentation: - - modules - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/docs/0.5.0/_sources/introduction.rst.txt b/docs/0.5.0/_sources/introduction.rst.txt deleted file mode 100644 index 6fea3a3c..00000000 --- a/docs/0.5.0/_sources/introduction.rst.txt +++ /dev/null @@ -1,78 +0,0 @@ -.. _instroduction: - -Getting Started -=============== - - -Overview ---------- - -MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF wbesite `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports de-/serialization of MMIF objects, as well as many navigation and manipulation helpers for MMIF objects. - -Prerequisites -------------- - -* `Python `_: ``mmif-python`` requires Python 3.6 or newer. We have no plan to support `Python 2.7 `_. - -Installation ---------------- - -Package ``mmif-python`` is distributed via the official PyPI. Users are supposed to pip-install to get latest release. - -.. code-block:: bash - - pip install mmif-python - -This will install a package `mmif` to local python. - -The MMIF format and specification is evolving over time, and ``mmif-python`` package will be updated along with the changes in MMIF format. - -.. note:: MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and ``mmif-python`` versions, please take time to read our decision on the subject `here `_. If you need to know which python SDK supports which specification version, see :ref:`target-versions` page. - -MMIF Serialization ---------------------------- - -:class:`mmif.serialize.mmif.Mmif` represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of :class:`mmif.serialize.model.MmifObject`, including the :class:`mmif.serialize.mmif.Mmif`. To start with an existing MMIF :class:`str`, simple initiate a new ``Mmif`` object with the file. - -.. code-block:: python - - import mmif - from mmif import Mmif - - mmif_str = """{ - "metadata": { - "mmif": "http://mmif.clams.ai/0.2.0" - }, - "documents": [ - { - "@type": "http://mmif.clams.ai/0.2.0/vocabulary/VideoDocument", - "properties": { - "id": "m1", - "mime": "video/mp4", - "location": "file:///var/archive/video-0012.mp4" - } - }, - { - "@type": "http://mmif.clams.ai/0.2.0/vocabulary/TextDocument", - "properties": { - "id": "m2", - "mime": "text/plain", - "location": "file:///var/archive/video-0012-transcript.txt" - } - } - ], - "views": []}""" - mmif_obj = Mmif(mmif_str) - - -Few notes; - -#. MMIF does not carry the primary source files in it. -#. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version ``mmif-python`` implementation of the MMIF might not be able to load an unsupported version of MMIF string. - -When serializing back to :class:`str`, call ``.serialize()`` (:meth:`mmif.serialize.model.MmifObject.serialize`) on the object. - -To get subcomponents, you can use various getters implemented in subclasses. For more details, the API documentation (:ref:`apidoc`) will help. - diff --git a/docs/0.5.0/_sources/modules.rst.txt b/docs/0.5.0/_sources/modules.rst.txt deleted file mode 100644 index e4269c6d..00000000 --- a/docs/0.5.0/_sources/modules.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _apidoc: - -mmif package -============ - -.. toctree:: - :maxdepth: 4 - - autodoc/mmif.serialize - autodoc/mmif.vocabulary diff --git a/docs/0.5.0/_sources/target-versions.rst.txt b/docs/0.5.0/_sources/target-versions.rst.txt deleted file mode 100644 index 34216d3e..00000000 --- a/docs/0.5.0/_sources/target-versions.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _target-versions: - -Target MMIF Versions -==================== - -This article provides targeting MMIF specification versions of different versions of ``mmif-python`` SDK. - -.. csv-table:: Target Specification Versions - :file: target-versions.csv - :header-rows: 1 diff --git a/docs/0.5.0/_static/_sphinx_javascript_frameworks_compat.js b/docs/0.5.0/_static/_sphinx_javascript_frameworks_compat.js deleted file mode 100644 index 81415803..00000000 --- a/docs/0.5.0/_static/_sphinx_javascript_frameworks_compat.js +++ /dev/null @@ -1,123 +0,0 @@ -/* Compatability shim for jQuery and underscores.js. - * - * Copyright Sphinx contributors - * Released under the two clause BSD licence - */ - -/** - * small helper function to urldecode strings - * - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL - */ -jQuery.urldecode = function(x) { - if (!x) { - return x - } - return decodeURIComponent(x.replace(/\+/g, ' ')); -}; - -/** - * small helper function to urlencode strings - */ -jQuery.urlencode = encodeURIComponent; - -/** - * This function returns the parsed url parameters of the - * current request. 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- -/** - * Simple result scoring code. - */ -if (typeof Scorer === "undefined") { - var Scorer = { - // Implement the following function to further tweak the score for each result - // The function takes a result array [docname, title, anchor, descr, score, filename] - // and returns the new score. - /* - score: result => { - const [docname, title, anchor, descr, score, filename, kind] = result - return score - }, - */ - - // query matches the full name of an object - objNameMatch: 11, - // or matches in the last dotted part of the object name - objPartialMatch: 6, - // Additive scores depending on the priority of the object - objPrio: { - 0: 15, // used to be importantResults - 1: 5, // used to be objectResults - 2: -5, // used to be unimportantResults - }, - // Used when the priority is not in the mapping. - objPrioDefault: 0, - - // query found in title - title: 15, - partialTitle: 7, - // query found in terms - term: 5, - partialTerm: 2, - }; -} - -// Global search result kind enum, used by themes to style search results. -class SearchResultKind { - static get index() { return "index"; } - static get object() { return "object"; } - static get text() { return "text"; } - static get title() { return "title"; } -} - -const _removeChildren = (element) => { - while (element && element.lastChild) element.removeChild(element.lastChild); -}; - -/** - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping - */ -const _escapeRegExp = (string) => - string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string - -const _displayItem = (item, searchTerms, highlightTerms) => { - const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; - const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; - const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; - const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; - const contentRoot = document.documentElement.dataset.content_root; - - const [docName, title, anchor, descr, score, _filename, kind] = item; - - let listItem = document.createElement("li"); - // Add a class representing the item's type: - // can be used by a theme's CSS selector for styling - // See SearchResultKind for the class names. - listItem.classList.add(`kind-${kind}`); - let requestUrl; - let linkUrl; - if (docBuilder === "dirhtml") { - // dirhtml builder - let dirname = docName + "/"; - if (dirname.match(/\/index\/$/)) - dirname = dirname.substring(0, dirname.length - 6); - else if (dirname === "index/") dirname = ""; - requestUrl = contentRoot + dirname; - linkUrl = requestUrl; - } else { - // normal html builders - requestUrl = contentRoot + docName + docFileSuffix; - linkUrl = docName + docLinkSuffix; - } - let linkEl = listItem.appendChild(document.createElement("a")); - linkEl.href = linkUrl + anchor; - linkEl.dataset.score = score; - linkEl.innerHTML = title; - if (descr) { - listItem.appendChild(document.createElement("span")).innerHTML = - " (" + descr + ")"; - // highlight search terms in the description - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - } - else if (showSearchSummary) - fetch(requestUrl) - .then((responseData) => responseData.text()) - .then((data) => { - if (data) - listItem.appendChild( - Search.makeSearchSummary(data, searchTerms, anchor) - ); - // highlight search terms in the summary - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - }); - Search.output.appendChild(listItem); -}; -const _finishSearch = (resultCount) => { - Search.stopPulse(); - Search.title.innerText = _("Search Results"); - if (!resultCount) - Search.status.innerText = Documentation.gettext( - "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." - ); - else - Search.status.innerText = Documentation.ngettext( - "Search finished, found one page matching the search query.", - "Search finished, found ${resultCount} pages matching the search query.", - resultCount, - ).replace('${resultCount}', resultCount); -}; -const _displayNextItem = ( - results, - resultCount, - searchTerms, - highlightTerms, -) => { - // results left, load the summary and display it - // this is intended to be dynamic (don't sub resultsCount) - if (results.length) { - _displayItem(results.pop(), searchTerms, highlightTerms); - setTimeout( - () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), - 5 - ); - } - // search finished, update title and status message - else _finishSearch(resultCount); -}; -// Helper function used by query() to order search results. -// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. -// Order the results by score (in opposite order of appearance, since the -// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. -const _orderResultsByScoreThenName = (a, b) => { - const leftScore = a[4]; - const rightScore = b[4]; - if (leftScore === rightScore) { - // same score: sort alphabetically - const leftTitle = a[1].toLowerCase(); - const rightTitle = b[1].toLowerCase(); - if (leftTitle === rightTitle) return 0; - return leftTitle > rightTitle ? -1 : 1; // inverted is intentional - } - return leftScore > rightScore ? 1 : -1; -}; - -/** - * Default splitQuery function. Can be overridden in ``sphinx.search`` with a - * custom function per language. - * - * The regular expression works by splitting the string on consecutive characters - * that are not Unicode letters, numbers, underscores, or emoji characters. - * This is the same as ``\W+`` in Python, preserving the surrogate pair area. - */ -if (typeof splitQuery === "undefined") { - var splitQuery = (query) => query - .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) - .filter(term => term) // remove remaining empty strings -} - -/** - * Search Module - */ -const Search = { - _index: null, - _queued_query: null, - _pulse_status: -1, - - htmlToText: (htmlString, anchor) => { - const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - for (const removalQuery of [".headerlink", "script", "style"]) { - htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); - } - if (anchor) { - const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); - if (anchorContent) return anchorContent.textContent; - - console.warn( - `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` - ); - } - - // if anchor not specified or not found, fall back to main content - const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent) return docContent.textContent; - - console.warn( - "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." - ); - return ""; - }, - - init: () => { - const query = new URLSearchParams(window.location.search).get("q"); - document - .querySelectorAll('input[name="q"]') - .forEach((el) => (el.value = query)); - if (query) Search.performSearch(query); - }, - - loadIndex: (url) => - (document.body.appendChild(document.createElement("script")).src = url), - - setIndex: (index) => { - Search._index = index; - if (Search._queued_query !== null) { - const query = Search._queued_query; - Search._queued_query = null; - Search.query(query); - } - }, - - hasIndex: () => Search._index !== null, - - deferQuery: (query) => (Search._queued_query = query), - - stopPulse: () => (Search._pulse_status = -1), - - startPulse: () => { - if (Search._pulse_status >= 0) return; - - const pulse = () => { - Search._pulse_status = (Search._pulse_status + 1) % 4; - Search.dots.innerText = ".".repeat(Search._pulse_status); - if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); - }; - pulse(); - }, - - /** - * perform a search for something (or wait until index is loaded) - */ - performSearch: (query) => { - // create the required interface elements - const searchText = document.createElement("h2"); - searchText.textContent = _("Searching"); - const searchSummary = document.createElement("p"); - searchSummary.classList.add("search-summary"); - searchSummary.innerText = ""; - const searchList = document.createElement("ul"); - searchList.setAttribute("role", "list"); - searchList.classList.add("search"); - - const out = document.getElementById("search-results"); - Search.title = out.appendChild(searchText); - Search.dots = Search.title.appendChild(document.createElement("span")); - Search.status = out.appendChild(searchSummary); - Search.output = out.appendChild(searchList); - - const searchProgress = document.getElementById("search-progress"); - // Some themes don't use the search progress node - if (searchProgress) { - searchProgress.innerText = _("Preparing search..."); - } - Search.startPulse(); - - // index already loaded, the browser was quick! - if (Search.hasIndex()) Search.query(query); - else Search.deferQuery(query); - }, - - _parseQuery: (query) => { - // stem the search terms and add them to the correct list - const stemmer = new Stemmer(); - const searchTerms = new Set(); - const excludedTerms = new Set(); - const highlightTerms = new Set(); - const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); - splitQuery(query.trim()).forEach((queryTerm) => { - const queryTermLower = queryTerm.toLowerCase(); - - // maybe skip this "word" - // stopwords array is from language_data.js - if ( - stopwords.indexOf(queryTermLower) !== -1 || - queryTerm.match(/^\d+$/) - ) - return; - - // stem the word - let word = stemmer.stemWord(queryTermLower); - // select the correct list - if (word[0] === "-") excludedTerms.add(word.substr(1)); - else { - searchTerms.add(word); - highlightTerms.add(queryTermLower); - } - }); - - if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js - localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) - } - - // console.debug("SEARCH: searching for:"); - // console.info("required: ", [...searchTerms]); - // console.info("excluded: ", [...excludedTerms]); - - return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; - }, - - /** - * execute search (requires search index to be loaded) - */ - _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - - // Collect multiple result groups to be sorted separately and then ordered. - // Each is an array of [docname, title, anchor, descr, score, filename, kind]. - const normalResults = []; - const nonMainIndexResults = []; - - _removeChildren(document.getElementById("search-progress")); - - const queryLower = query.toLowerCase().trim(); - for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { - for (const [file, id] of foundTitles) { - const score = Math.round(Scorer.title * queryLower.length / title.length); - const boost = titles[file] === title ? 1 : 0; // add a boost for document titles - normalResults.push([ - docNames[file], - titles[file] !== title ? `${titles[file]} > ${title}` : title, - id !== null ? "#" + id : "", - null, - score + boost, - filenames[file], - SearchResultKind.title, - ]); - } - } - } - - // search for explicit entries in index directives - for (const [entry, foundEntries] of Object.entries(indexEntries)) { - if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id, isMain] of foundEntries) { - const score = Math.round(100 * queryLower.length / entry.length); - const result = [ - docNames[file], - titles[file], - id ? "#" + id : "", - null, - score, - filenames[file], - SearchResultKind.index, - ]; - if (isMain) { - normalResults.push(result); - } else { - nonMainIndexResults.push(result); - } - } - } - } - - // lookup as object - objectTerms.forEach((term) => - normalResults.push(...Search.performObjectSearch(term, objectTerms)) - ); - - // lookup as search terms in fulltext - normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); - - // let the scorer override scores with a custom scoring function - if (Scorer.score) { - normalResults.forEach((item) => (item[4] = Scorer.score(item))); - nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); - } - - // Sort each group of results by score and then alphabetically by name. - normalResults.sort(_orderResultsByScoreThenName); - nonMainIndexResults.sort(_orderResultsByScoreThenName); - - // Combine the result groups in (reverse) order. - // Non-main index entries are typically arbitrary cross-references, - // so display them after other results. - let results = [...nonMainIndexResults, ...normalResults]; - - // remove duplicate search results - // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept - let seen = new Set(); - results = results.reverse().reduce((acc, result) => { - let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); - if (!seen.has(resultStr)) { - acc.push(result); - seen.add(resultStr); - } - return acc; - }, []); - - return results.reverse(); - }, - - query: (query) => { - const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); - const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); - - // for debugging - //Search.lastresults = results.slice(); // a copy - // console.info("search results:", Search.lastresults); - - // print the results - _displayNextItem(results, results.length, searchTerms, highlightTerms); - }, - - /** - * search for object names - */ - performObjectSearch: (object, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const objects = Search._index.objects; - const objNames = Search._index.objnames; - const titles = Search._index.titles; - - const results = []; - - const objectSearchCallback = (prefix, match) => { - const name = match[4] - const fullname = (prefix ? prefix + "." : "") + name; - const fullnameLower = fullname.toLowerCase(); - if (fullnameLower.indexOf(object) < 0) return; - - let score = 0; - const parts = fullnameLower.split("."); - - // check for different match types: exact matches of full name or - // "last name" (i.e. last dotted part) - if (fullnameLower === object || parts.slice(-1)[0] === object) - score += Scorer.objNameMatch; - else if (parts.slice(-1)[0].indexOf(object) > -1) - score += Scorer.objPartialMatch; // matches in last name - - const objName = objNames[match[1]][2]; - const title = titles[match[0]]; - - // If more than one term searched for, we require other words to be - // found in the name/title/description - const otherTerms = new Set(objectTerms); - otherTerms.delete(object); - if (otherTerms.size > 0) { - const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); - if ( - [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) - ) - return; - } - - let anchor = match[3]; - if (anchor === "") anchor = fullname; - else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; - - const descr = objName + _(", in ") + title; - - // add custom score for some objects according to scorer - if (Scorer.objPrio.hasOwnProperty(match[2])) - score += Scorer.objPrio[match[2]]; - else score += Scorer.objPrioDefault; - - results.push([ - docNames[match[0]], - fullname, - "#" + anchor, - descr, - score, - filenames[match[0]], - SearchResultKind.object, - ]); - }; - Object.keys(objects).forEach((prefix) => - objects[prefix].forEach((array) => - objectSearchCallback(prefix, array) - ) - ); - return results; - }, - - /** - * search for full-text terms in the index - */ - performTermsSearch: (searchTerms, excludedTerms) => { - // prepare search - const terms = Search._index.terms; - const titleTerms = Search._index.titleterms; - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - - const scoreMap = new Map(); - const fileMap = new Map(); - - // perform the search on the required terms - searchTerms.forEach((word) => { - const files = []; - const arr = [ - { files: terms[word], score: Scorer.term }, - { files: titleTerms[word], score: Scorer.title }, - ]; - // add support for partial matches - if (word.length > 2) { - const escapedWord = _escapeRegExp(word); - if (!terms.hasOwnProperty(word)) { - Object.keys(terms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: terms[term], score: Scorer.partialTerm }); - }); - } - if (!titleTerms.hasOwnProperty(word)) { - Object.keys(titleTerms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); - }); - } - } - - // no match but word was a required one - if (arr.every((record) => record.files === undefined)) return; - - // found search word in contents - arr.forEach((record) => { - if (record.files === undefined) return; - - let recordFiles = record.files; - if (recordFiles.length === undefined) recordFiles = [recordFiles]; - files.push(...recordFiles); - - // set score for the word in each file - recordFiles.forEach((file) => { - if (!scoreMap.has(file)) scoreMap.set(file, {}); - scoreMap.get(file)[word] = record.score; - }); - }); - - // create the mapping - files.forEach((file) => { - if (!fileMap.has(file)) fileMap.set(file, [word]); - else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); - }); - }); - - // now check if the files don't contain excluded terms - const results = []; - for (const [file, wordList] of fileMap) { - // check if all requirements are matched - - // as search terms with length < 3 are discarded - const filteredTermCount = [...searchTerms].filter( - (term) => term.length > 2 - ).length; - if ( - wordList.length !== searchTerms.size && - wordList.length !== filteredTermCount - ) - continue; - - // ensure that none of the excluded terms is in the search result - if ( - [...excludedTerms].some( - (term) => - terms[term] === file || - titleTerms[term] === file || - (terms[term] || []).includes(file) || - (titleTerms[term] || []).includes(file) - ) - ) - break; - - // select one (max) score for the file. - const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); - // add result to the result list - results.push([ - docNames[file], - titles[file], - "", - null, - score, - filenames[file], - SearchResultKind.text, - ]); - } - return results; - }, - - /** - * helper function to return a node containing the - * search summary for a given text. keywords is a list - * of stemmed words. - */ - makeSearchSummary: (htmlText, keywords, anchor) => { - const text = Search.htmlToText(htmlText, anchor); - if (text === "") return null; - - const textLower = text.toLowerCase(); - const actualStartPosition = [...keywords] - .map((k) => textLower.indexOf(k.toLowerCase())) - .filter((i) => i > -1) - .slice(-1)[0]; - const startWithContext = Math.max(actualStartPosition - 120, 0); - - const top = startWithContext === 0 ? "" : "..."; - const tail = startWithContext + 240 < text.length ? "..." : ""; - - let summary = document.createElement("p"); - summary.classList.add("context"); - summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; - - return summary; - }, -}; - -_ready(Search.init); diff --git a/docs/0.5.0/_static/sphinx_highlight.js b/docs/0.5.0/_static/sphinx_highlight.js deleted file mode 100644 index 8a96c69a..00000000 --- a/docs/0.5.0/_static/sphinx_highlight.js +++ /dev/null @@ -1,154 +0,0 @@ -/* Highlighting utilities for Sphinx HTML documentation. */ -"use strict"; - -const SPHINX_HIGHLIGHT_ENABLED = true - -/** - * highlight a given string on a node by wrapping it in - * span elements with the given class name. - */ -const _highlight = (node, addItems, text, className) => { - if (node.nodeType === Node.TEXT_NODE) { - const val = node.nodeValue; - const parent = node.parentNode; - const pos = val.toLowerCase().indexOf(text); - if ( - pos >= 0 && - !parent.classList.contains(className) && - !parent.classList.contains("nohighlight") - ) { - let span; - - const closestNode = parent.closest("body, svg, foreignObject"); - const isInSVG = closestNode && closestNode.matches("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.classList.add(className); - } - - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - const rest = document.createTextNode(val.substr(pos + text.length)); - parent.insertBefore( - span, - parent.insertBefore( - rest, - node.nextSibling - ) - ); - node.nodeValue = val.substr(0, pos); - /* There may be more occurrences of search term in this node. So call this - * function recursively on the remaining fragment. - */ - _highlight(rest, addItems, text, className); - - if (isInSVG) { - const rect = document.createElementNS( - "http://www.w3.org/2000/svg", - "rect" - ); - const bbox = parent.getBBox(); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute("class", className); - addItems.push({ parent: parent, target: rect }); - } - } - } else if (node.matches && !node.matches("button, select, textarea")) { - node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); - } -}; -const _highlightText = (thisNode, text, className) => { - let addItems = []; - _highlight(thisNode, addItems, text, className); - addItems.forEach((obj) => - obj.parent.insertAdjacentElement("beforebegin", obj.target) - ); -}; - -/** - * Small JavaScript module for the documentation. - */ -const SphinxHighlight = { - - /** - * highlight the search words provided in localstorage in the text - */ - highlightSearchWords: () => { - if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight - - // get and clear terms from localstorage - const url = new URL(window.location); - const highlight = - localStorage.getItem("sphinx_highlight_terms") - || url.searchParams.get("highlight") - || ""; - localStorage.removeItem("sphinx_highlight_terms") - url.searchParams.delete("highlight"); - window.history.replaceState({}, "", url); - - // get individual terms from highlight string - const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); - if (terms.length === 0) return; // nothing to do - - // There should never be more than one element matching "div.body" - const divBody = document.querySelectorAll("div.body"); - const body = divBody.length ? divBody[0] : document.querySelector("body"); - window.setTimeout(() => { - terms.forEach((term) => _highlightText(body, term, "highlighted")); - }, 10); - - const searchBox = document.getElementById("searchbox"); - if (searchBox === null) return; - searchBox.appendChild( - document - .createRange() - .createContextualFragment( - '

' + - '' + - _("Hide Search Matches") + - "

" - ) - ); - }, - - /** - * helper function to hide the search marks again - */ - hideSearchWords: () => { - document - .querySelectorAll("#searchbox .highlight-link") - .forEach((el) => el.remove()); - document - .querySelectorAll("span.highlighted") - .forEach((el) => el.classList.remove("highlighted")); - localStorage.removeItem("sphinx_highlight_terms") - }, - - initEscapeListener: () => { - // only install a listener if it is really needed - if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; - - document.addEventListener("keydown", (event) => { - // bail for input elements - if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; - // bail with special keys - if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; - if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { - SphinxHighlight.hideSearchWords(); - event.preventDefault(); - } - }); - }, -}; - -_ready(() => { - /* Do not call highlightSearchWords() when we are on the search page. - * It will highlight words from the *previous* search query. - */ - if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); - SphinxHighlight.initEscapeListener(); -}); diff --git a/docs/0.5.0/autodoc/mmif.serialize.html b/docs/0.5.0/autodoc/mmif.serialize.html deleted file mode 100644 index 486a8d97..00000000 --- a/docs/0.5.0/autodoc/mmif.serialize.html +++ /dev/null @@ -1,1148 +0,0 @@ - - - - - - - - - mmif.serialize module — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.serialize module

-
-

mmif.serialize.model module

-

The model module contains the classes used to represent an -abstract MMIF object as a live Python object.

-

The MmifObject class or one of its derivatives is subclassed by -all other classes defined in this SDK, except for MmifObjectEncoder.

-

These objects are generally instantiated from JSON, either as a string -or as an already-loaded Python dictionary. This base class provides the -core functionality for deserializing MMIF JSON data into live objects -and serializing live objects into MMIF JSON data. Specialized behavior -for the different components of MMIF is added in the subclasses.

-
-
-class mmif.serialize.model.DataDict(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject, Generic[T, S]

-
-
-empty()[source]
-
- -
-
-get(key: T, default=None) → S | None[source]
-
- -
-
-items()[source]
-
- -
-
-keys()[source]
-
- -
-
-update(other, overwrite)[source]
-
- -
-
-values()[source]
-
- -
- -
-
-class mmif.serialize.model.DataList(mmif_obj: bytes | str | list | None = None)[source]
-

Bases: MmifObject, Generic[T]

-

The DataList class is an abstraction that represents the -various lists found in a MMIF file, such as documents, subdocuments, -views, and annotations.

-
-
Parameters:
-

mmif_obj (Union[str, list]) – the data that the list contains

-
-
-
-
-append(value, overwrite)[source]
-
- -
-
-deserialize(mmif_json: str | list) → None[source]
-

Passes the input data into the internal deserializer.

-
- -
-
-empty()[source]
-
- -
-
-get(key: str) → T | None[source]
-

Standard dictionary-style get() method, albeit with no default -parameter. Relies on the implementation of __getitem__.

-

Will return None if the key is not found.

-
-
Parameters:
-

key – the key to search for

-
-
Returns:
-

the value matching that key

-
-
-
- -
- -
-
-class mmif.serialize.model.MmifObject(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: object

-

Abstract superclass for MMIF related key-value pair objects.

-

Any MMIF object can be initialized as an empty placeholder or -an actual representation with a JSON formatted string or equivalent -dict object argument.

-

This superclass has three specially designed instance variables, and these -variable names cannot be used as attribute names for MMIF objects.

-
    -

  1. _unnamed_attributes: -Only can be either None or an empty dictionary. If it’s set to None, -it means the class won’t take any Additional Attributes in the JSON -schema sense. If it’s a dict, users can throw any k-v pairs to the -class, EXCEPT for the reserved two key names.

    2. -

  2. _attribute_classes: -This is a dict from a key name to a specific python class to use for -deserialize the value. Note that a key name in this dict does NOT -have to be a named attribute, but is recommended to be one.

    3. -

  3. _required_attributes: -This is a simple list of names of attributes that are required in the object. -When serialize, an object will skip its empty (e.g. zero-length, or None) -attributes unless they are in this list. Otherwise, the serialized JSON -string would have empty representations (e.g. "", []).

    4. -
-

# TODO (krim @ 8/17/20): this dict is however, a duplicate with the type hints in the class definition. -Maybe there is a better way to utilize type hints (e.g. getting them as a programmatically), but for now -developers should be careful to add types to hints as well as to this dict.

-

Also note that those two special attributes MUST be set in the __init__() -before calling super method, otherwise deserialization will not work.

-

And also, a subclass that has one or more named attributes, it must -set those attributes in the __init__() before calling super method. When -serializing a MmifObject, all empty attributes will be ignored, so for -optional named attributes, you must leave the values empty (len == 0), but -NOT None. Any None-valued named attributes will cause issues with current -implementation.

-
-
Parameters:
-

mmif_obj – JSON string or dict to initialize an object. -If not given, an empty object will be initialized, sometimes with -an ID value automatically generated, based on its parent object.

-
-
-
-
-deserialize(mmif_json: str | dict) → None[source]
-

Takes a JSON-formatted string or a simple dict that’s json-loaded from -such a string as an input and populates object’s fields with the values -specified in the input.

-
-
Parameters:
-

mmif_json – JSON-formatted string or dict from such a string -that represents a MMIF object

-
-
-
- -
-
-disallow_additional_properties() → None[source]
-

Call this method in __init__() to prevent the insertion -of unnamed attributes after initialization.

-
- -
-
-static is_empty(obj) → bool[source]
-

return True if the obj is None or “emtpy”. The emptiness first defined as -having zero length. But for objects that lack __len__ method, we need -additional check.

-
- -
-
-reserved_names: Set = {'_attribute_classes', '_id_counts', '_parent_view_id', '_required_attributes', '_unnamed_attributes', 'reserved_names'}[source]
-
- -
-
-serialize(pretty: bool = False) → str[source]
-

Generates JSON representation of an object.

-
-
Parameters:
-

pretty – If True, returns string representation with indentation.

-
-
Returns:
-

JSON string of the object.

-
-
-
- -
-
-set_additional_property(key: str, value: Any) → None[source]
-

Method to set values in _unnamed_attributes.

-
-
Parameters:
-
    -

  • key – the attribute name

    • -

  • value – the desired value

    • -
-
-
Returns:
-

None

-
-
Raise:
-

AttributeError if additional properties are disallowed by disallow_additional_properties()

-
-
-
- -
- -
-
-class mmif.serialize.model.MmifObjectEncoder(*, skipkeys=False, ensure_ascii=True, check_circular=True, allow_nan=True, sort_keys=False, indent=None, separators=None, default=None)[source]
-

Bases: JSONEncoder

-

Encoder class to define behaviors of de-/serialization

-
-
-default(obj: MmifObject)[source]
-

Overrides default encoding behavior to prioritize MmifObject.serialize().

-
- -
- -
-
-

mmif.serialize.mmif module

-

The mmif module contains the classes used to represent a full MMIF -file as a live Python object.

-

See the specification docs and the JSON Schema file for more information.

-
-
-class mmif.serialize.mmif.Mmif(mmif_obj: bytes | str | dict | None = None, *, validate: bool = True)[source]
-

Bases: MmifObject

-

MmifObject that represents a full MMIF file.

-
-
Parameters:
-
    -

  • mmif_obj – the JSON data

    • -

  • validate – whether to validate the data against the MMIF JSON schema.

    • -
-
-
-
-
-add_document(document: Document, overwrite=False) → None[source]
-

Appends a Document object to the documents list.

-

Fails if there is already a document with the same ID in the MMIF object.

-
-
Parameters:
-
    -

  • document – the Document object to add

    • -

  • overwrite – if set to True, will overwrite -an existing view with the same ID

    • -
-
-
Returns:
-

None

-
-
-
- -
-
-add_view(view: View, overwrite=False) → None[source]
-

Appends a View object to the views list.

-

Fails if there is already a view with the same ID in the MMIF object.

-
-
Parameters:
-
    -

  • view – the Document object to add

    • -

  • overwrite – if set to True, will overwrite -an existing view with the same ID

    • -
-
-
Returns:
-

None

-
-
-
- -
-
-get_alignments(at_type1: str | TypesBase, at_type2: str | TypesBase) → Dict[str, List[Annotation]][source]
-

Finds views where alignments between two given annotation types occurred.

-
-
Returns:
-

a dict that keyed by view IDs (str) and has lists of alignment Annotation objects as values.

-
-
-
- -
-
-get_all_views_contain(at_types: TypesBase | str | List[str | TypesBase]) → List[View][source]
-

Returns the list of all views in the MMIF if given types -are present in that view’s ‘contains’ metadata.

-
-
Parameters:
-

at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

-
-
Returns:
-

the list of views that contain the type

-
-
-
- -
-
-get_document_by_id(doc_id: str) → Document[source]
-

Finds a Document object with the given ID.

-
-
Parameters:
-

doc_id – the ID to search for

-
-
Returns:
-

a reference to the corresponding document, if it exists

-
-
Raises:
-

Exception – if there is no corresponding document

-
-
-
- -
-
-get_document_location(m_type: DocumentTypes | str, path_only=False) → str | None[source]
-

Method to get the location of first document of given type.

-
-
Parameters:
-

m_type – the type to search for

-
-
Returns:
-

the value of the location field in the corresponding document

-
-
-
- -
-
-get_documents_by_app(app_id: str) → List[Document][source]
-

Method to get all documents object queries by its originated app name.

-
-
Parameters:
-

app_id – the app name to search for

-
-
Returns:
-

a list of documents matching the requested app name, or an empty list if the app not found

-
-
-
- -
-
-get_documents_by_property(prop_key: str, prop_value: str) → List[Document][source]
-

Method to retrieve documents by an arbitrary key-value pair in the document properties objects.

-
-
Parameters:
-
    -

  • prop_key – the metadata key to search for

    • -

  • prop_value – the metadata value to match

    • -
-
-
Returns:
-

a list of documents matching the requested metadata key-value pair

-
-
-
- -
-
-get_documents_by_type(doc_type: str | DocumentTypes) → List[Document][source]
-

Method to get all documents where the type matches a particular document type, which should be one of the CLAMS document types.

-
-
Parameters:
-

doc_type – the type of documents to search for, must be one of Document type defined in the CLAMS vocabulary.

-
-
Returns:
-

a list of documents matching the requested type, or an empty list if none found.

-
-
-
- -
-
-get_documents_in_view(vid: str | None = None) → List[Document][source]
-

Method to get all documents object queries by a view id.

-
-
Parameters:
-

vid – the source view ID to search for

-
-
Returns:
-

a list of documents matching the requested source view ID, or an empty list if the view not found

-
-
-
- -
-
-get_documents_locations(m_type: DocumentTypes | str, path_only=False) → List[str | None][source]
-

This method returns the file paths of documents of given type. -Only top-level documents have locations, so we only check them.

-
-
Parameters:
-

m_type – the type to search for

-
-
Returns:
-

a list of the values of the location fields in the corresponding documents

-
-
-
- -
-
-get_view_by_id(req_view_id: str) → View[source]
-

Finds a View object with the given ID.

-
-
Parameters:
-

req_view_id – the ID to search for

-
-
Returns:
-

a reference to the corresponding view, if it exists

-
-
Raises:
-

Exception – if there is no corresponding view

-
-
-
- -
-
-get_view_contains(at_types: TypesBase | str | List[str | TypesBase]) → View | None[source]
-

Returns the last view appended that contains the given -types in its ‘contains’ metadata.

-
-
Parameters:
-

at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

-
-
Returns:
-

the view, or None if the type is not found

-
-
-
- -
-
-get_views_contain(at_types: TypesBase | str | List[str | TypesBase]) → List[View][source]
-

An alias to get_all_views_contain method.

-
- -
-
-get_views_for_document(doc_id: str)[source]
-

Returns the list of all views that have annotations anchored on a particular document. -Note that when the document is insids a view (generated during the pipeline’s running), -doc_id must be prefixed with the view_id.

-
- -
-
-id_delimiter: ClassVar[str] = ':'[source]
-
- -
-
-new_view() → View[source]
-

Creates an empty view with a new ID and appends it to the views list.

-
-
Returns:
-

a reference to the new View object

-
-
-
- -
-
-new_view_id() → str[source]
-

Fetches an ID for a new view.

-
-
Returns:
-

the ID

-
-
-
- -
-
-static validate(json_str: bytes | str | dict) → None[source]
-

Validates a MMIF JSON object against the MMIF Schema. -Note that this method operates before processing by MmifObject._load_str, -so it expects @ and not _ for the JSON-LD @-keys.

-
-
Raises:
-

jsonschema.exceptions.ValidationError – if the input fails validation

-
-
Parameters:
-

json_str – a MMIF JSON dict or string

-
-
Returns:
-

None

-
-
-
- -
-
-view_prefix: ClassVar[str] = 'v_'[source]
-
- -
- -
-
-

mmif.serialize.view module

-

The view module contains the classes used to represent a MMIF view -as a live Python object.

-

In MMIF, views are created by apps in a pipeline that are annotating -data that was previously present in the MMIF file.

-
-
-class mmif.serialize.view.Contain(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-

Contain object that represents the metadata of a single -annotation type in the contains metadata of a MMIF view.

-
- -
-
-class mmif.serialize.view.View(view_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-

View object that represents a single view in a MMIF file.

-

A view is identified by an ID, and contains certain metadata, -a list of annotations, and potentially a JSON-LD @context -IRI.

-

If view_obj is not provided, an empty View will be generated.

-
-
Parameters:
-

view_obj – the JSON data that defines the view

-
-
-
-
-add_annotation(annotation: Annotation, overwrite=False) → Annotation[source]
-

Adds an annotation to the current view.

-

Fails if there is already an annotation with the same ID -in the view, unless overwrite is set to True.

-
-
Parameters:
-
-
-
Raises:
-

KeyError – if overwrite is set to False and -an annotation with the same ID exists -in the view

-
-
Returns:
-

the same Annotation object passed in as annotation

-
-
-
- -
-
-add_document(document: Document, overwrite=False) → Annotation[source]
-

Appends a Document object to the annotations list.

-

Fails if there is already a document with the same ID in the annotations list.

-
-
Parameters:
-
    -

  • document – the Document object to add

    • -

  • overwrite – if set to True, will overwrite -an existing view with the same ID

    • -
-
-
Returns:
-

None

-
-
-
- -
-
-get_annotation_by_id(ann_id)[source]
-
- -
-
-get_annotations(at_type: str | TypesBase | None = None, **properties) → Generator[Annotation, None, None][source]
-

Look for certain annotations in this view, specified by parameters

-
-
Parameters:
-
    -

  • at_type – @type of the annotations to look for. When this is None, any @type will match.

    • -

  • properties – properties of the annotations to look for. When given more than one property, all properties must match. Note that annotation type metadata are specified in the contains view metadata, not in individual annotation objects.

    • -
-
-
-
- -
-
-get_document_by_id(doc_id) → Document[source]
-
- -
-
-get_documents() → List[Document][source]
-
- -
-
-new_annotation(at_type: str | TypesBase, aid: str | None = None, overwrite=False, **properties) → Annotation[source]
-

Generates a new mmif.serialize.annotation.Annotation -object and adds it to the current view.

-

Fails if there is already an annotation with the same ID -in the view, unless overwrite is set to True.

-
-
Parameters:
-
    -

  • at_type – the desired @type of the annotation.

    • -

  • aid – the desired ID of the annotation, when not given, -the mmif SDK tries to automatically generate an ID based on -Annotation type and existing annotations in the view.

    • -

  • overwrite – if set to True, will overwrite an -existing annotation with the same ID.

    • -
-
-
Raises:
-

KeyError – if overwrite is set to False and -an annotation with the same ID exists -in the view.

-
-
Returns:
-

the generated mmif.serialize.annotation.Annotation

-
-
-
- -
-
-new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
-

Adds a new element to the contains metadata.

-
-
Parameters:
-
    -

  • at_type – the @type of the annotation type being added

    • -

  • contains_metadata – any metadata associated with the annotation type

    • -
-
-
Returns:
-

the generated Contain object

-
-
-
- -
-
-new_textdocument(text: str, lang: str = 'en', did: str | None = None, overwrite=False, **properties) → Document[source]
-

Generates a new mmif.serialize.annotation.Document -object, particularly typed as TextDocument and adds it to the current view.

-

Fails if there is already a text document with the same ID -in the view, unless overwrite is set to True.

-
-
Parameters:
-
    -

  • text – text content of the new document

    • -

  • lang – ISO 639-1 code of the language used in the new document

    • -

  • did – the desired ID of the document, when not given, -the mmif SDK tries to automatically generate an ID based on -Annotation type and existing documents in the view.

    • -

  • overwrite – if set to True, will overwrite an -existing document with the same ID

    • -
-
-
Raises:
-

KeyError – if overwrite is set to False and -an document with the same ID exists -in the view

-
-
Returns:
-

the generated mmif.serialize.annotation.Document

-
-
-
- -
-
-set_error(err_message: str, err_trace: str) → None[source]
-
- -
- -
-
-class mmif.serialize.view.ViewMetadata(viewmetadata_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-

ViewMetadata object that represents the metadata object within a MMIF view.

-
-
Parameters:
-

viewmetadata_obj – the JSON data that defines the metadata

-
-
-
-
-add_parameter(param_key, param_value)[source]
-
- -
-
-add_parameters(**runtime_params)[source]
-
- -
-
-add_warnings(*warnings: Warning)[source]
-
- -
-
-emtpy_warnings()[source]
-
- -
-
-get_parameter(param_key)[source]
-
- -
-
-new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
-

Adds a new element to the contains dictionary.

-
-
Parameters:
-
    -

  • at_type – the @type of the annotation type being added

    • -

  • contains_metadata – any metadata associated with the annotation type

    • -
-
-
Returns:
-

the generated Contain object

-
-
-
- -
-
-set_error(message: str, stack_trace: str)[source]
-
- -
- -
-
-

mmif.serialize.annotation module

-

The annotation module contains the classes used to represent a -MMIF annotation as a live Python object.

-

In MMIF, annotations are created by apps in a pipeline as a part -of a view. For documentation on how views are represented, see -mmif.serialize.view.

-
-
-class mmif.serialize.annotation.Annotation(anno_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-

MmifObject that represents an annotation in a MMIF view.

-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]]) → None[source]
-

Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

-
- -
-
-property at_type: TypesBase[source]
-
- -
-
-property id: str[source]
-
- -
-
-is_document()[source]
-
- -
-
-is_type(at_type: str | TypesBase) → bool[source]
-

Check if the @type of this object matches.

-
- -
- -
-
-class mmif.serialize.annotation.AnnotationProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject, MutableMapping[str, T]

-

AnnotationProperties object that represents the -properties object within a MMIF annotation.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
- -
-
-class mmif.serialize.annotation.Document(doc_obj: bytes | str | dict | None = None)[source]
-

Bases: Annotation

-

Document object that represents a single document in a MMIF file.

-

A document is identified by an ID, and contains certain attributes -and potentially contains the contents of the document itself, -metadata about how the document was created, and/or a list of -subdocuments grouped together logically.

-

If document_obj is not provided, an empty Document will be generated.

-
-
Parameters:
-

document_obj – the JSON data that defines the document

-
-
-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None]) → None[source]
-

Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

-
- -
-
-property location: str | None[source]
-

location property must be a legitimate URI. That is, should the document be a local file -then the file:// scheme must be used. -Returns None when no location is set.

-
- -
-
-location_address() → str | None[source]
-

Retrieves the full address from the document location URI. -Returns None when no location is set.

-
- -
-
-location_path() → str | None[source]
-

Retrieves only path name of the document location (hostname is ignored). -Useful to get a path of a local file. -Returns None when no location is set.

-
- -
-
-location_scheme() → str | None[source]
-

Retrieves URI scheme of the document location. -Returns None when no location is set.

-
- -
-
-property parent: str[source]
-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.DocumentProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: AnnotationProperties

-

DocumentProperties object that represents the -properties object within a MMIF document.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
-
-property location: str | None[source]
-

location property must be a legitimate URI. That is, should the document be a local file -then the file:// scheme must be used. -Returns None when no location is set.

-
- -
-
-location_address() → str | None[source]
-

Retrieves the full address from the document location URI. -Returns None when no location is set.

-
- -
-
-location_path() → str | None[source]
-

Retrieves only path name of the document location (hostname is ignored). -Useful to get a path of a local file. -Returns None when no location is set.

-
- -
-
-location_scheme() → str | None[source]
-

Retrieves URI scheme of the document location. -Returns None when no location is set.

-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.Text(text_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-
-
-property lang: str[source]
-
- -
-
-property value: str[source]
-
- -
- -
-
- - -
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- -
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- - Other Versions - v: 0.5.0 - - -
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0.3.2
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- - - \ No newline at end of file diff --git a/docs/0.5.0/autodoc/mmif.vocabulary.html b/docs/0.5.0/autodoc/mmif.vocabulary.html deleted file mode 100644 index 02ef6097..00000000 --- a/docs/0.5.0/autodoc/mmif.vocabulary.html +++ /dev/null @@ -1,325 +0,0 @@ - - - - - - - - - mmif.vocabulary module — mmif-python documentation - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.vocabulary module

-
-

mmif.vocabulary.annotation_types module

-
-
-class mmif.vocabulary.annotation_types.AnnotationTypes(type_uri: str)[source]
-

Bases: AnnotationTypesBase

-

This class contains the CLAMS annotation types -defined in the spec version 1.1.0 as class variables.

-
-
-Alignment = http://mmif.clams.ai/vocabulary/Alignment/v1[source]
-
- -
-
-Annotation = http://mmif.clams.ai/vocabulary/Annotation/v6[source]
-
- -
-
-BoundingBox = http://mmif.clams.ai/vocabulary/BoundingBox/v5[source]
-
- -
-
-Chapter = http://mmif.clams.ai/vocabulary/Chapter/v6[source]
-
- -
-
-Interval = http://mmif.clams.ai/vocabulary/Interval/v5[source]
-
- -
-
-NamedEntity = http://mmif.clams.ai/vocabulary/NamedEntity/v1[source]
-
- -
-
-NounChunk = http://mmif.clams.ai/vocabulary/NounChunk/v1[source]
-
- -
-
-Paragraph = http://mmif.clams.ai/vocabulary/Paragraph/v1[source]
-
- -
-
-Polygon = http://mmif.clams.ai/vocabulary/Polygon/v5[source]
-
- -
-
-Region = http://mmif.clams.ai/vocabulary/Region/v5[source]
-
- -
-
-Relation = http://mmif.clams.ai/vocabulary/Relation/v5[source]
-
- -
-
-Sentence = http://mmif.clams.ai/vocabulary/Sentence/v1[source]
-
- -
-
-Span = http://mmif.clams.ai/vocabulary/Span/v5[source]
-
- -
-
-TimeFrame = http://mmif.clams.ai/vocabulary/TimeFrame/v6[source]
-
- -
-
-TimePoint = http://mmif.clams.ai/vocabulary/TimePoint/v5[source]
-
- -
-
-Token = http://mmif.clams.ai/vocabulary/Token/v1[source]
-
- -
-
-VerbChunk = http://mmif.clams.ai/vocabulary/VerbChunk/v1[source]
-
- -
-
-VideoObject = http://mmif.clams.ai/vocabulary/VideoObject/v5[source]
-
- -
-
-typevers = {'Alignment': 'v1', 'Annotation': 'v6', 'BoundingBox': 'v5', 'Chapter': 'v6', 'Interval': 'v5', 'NamedEntity': 'v1', 'NounChunk': 'v1', 'Paragraph': 'v1', 'Polygon': 'v5', 'Region': 'v5', 'Relation': 'v5', 'Sentence': 'v1', 'Span': 'v5', 'TimeFrame': 'v6', 'TimePoint': 'v5', 'Token': 'v1', 'VerbChunk': 'v1', 'VideoObject': 'v5'}[source]
-
- -
- -
-
-

mmif.vocabulary.document_types module

-
-
-class mmif.vocabulary.document_types.DocumentTypes(type_uri: str)[source]
-

Bases: DocumentTypesBase

-

This class contains the CLAMS document types -defined in the spec version 1.1.0 as class variables.

-
-
-AudioDocument = http://mmif.clams.ai/vocabulary/AudioDocument/v1[source]
-
- -
-
-Document = http://mmif.clams.ai/vocabulary/Document/v1[source]
-
- -
-
-ImageDocument = http://mmif.clams.ai/vocabulary/ImageDocument/v1[source]
-
- -
-
-TextDocument = http://mmif.clams.ai/vocabulary/TextDocument/v1[source]
-
- -
-
-VideoDocument = http://mmif.clams.ai/vocabulary/VideoDocument/v1[source]
-
- -
-
-typevers = {'AudioDocument': 'v1', 'Document': 'v1', 'ImageDocument': 'v1', 'TextDocument': 'v1', 'VideoDocument': 'v1'}[source]
-
- -
- -
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.5.0 - - -
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- -
0.3.0
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- - - \ No newline at end of file diff --git a/docs/0.5.0/consumer-tutorial.html b/docs/0.5.0/consumer-tutorial.html deleted file mode 100644 index d2bb6d39..00000000 --- a/docs/0.5.0/consumer-tutorial.html +++ /dev/null @@ -1,176 +0,0 @@ - - - - - - - - - MMIF consumer — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • MMIF consumer
    • -
  • -
    • -
-
-
-
-
- -
-

MMIF consumer

-

A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the appliance documentation to learn more about the appliance.

-

MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance.

-
    -

  1. The code must be hosted on a public git repository (e.g. Github, Gitlab, …)

    2. -

  2. Must listen to 5000 port.

    3. -

  3. Must expose /display route .

    4. -

  4. /display router should response to GET requests.

    5. -

  5. In the GET request, a public URL of the input MMIF file is passed via file URL parameter.

    6. -

  6. On the codebase root, there must be a Dockerfile that can build a docker image that runs the web app.

    7. -
-

We provide an example consumer at https://github.com/clamsproject/mmif-visualizer.

-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.5.0 - - -
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- -
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- - - \ No newline at end of file diff --git a/docs/0.5.0/genindex.html b/docs/0.5.0/genindex.html deleted file mode 100644 index f9560184..00000000 --- a/docs/0.5.0/genindex.html +++ /dev/null @@ -1,632 +0,0 @@ - - - - - - - - Index — mmif-python documentation - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • Index
    • -
  • -
    • -
-
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-
-
- - -

Index

- -
- A - | B - | C - | D - | E - | G - | I - | K - | L - | M - | N - | P - | R - | S - | T - | U - | V - -
-

A

- - - -
- -

B

- - -
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C

- - - -
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D

- - - -
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V

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- - -
- -
-
-
-
    -
    • -
  • Welcome to mmif-python’s documentation!
    • -
  • -
    • -
-
-
-
-
- -
-

Welcome to mmif-python’s documentation!

-
-
-

MMIF for python

-

NOTE that this project is in pre-alpha and being actively developed. Nothing is guaranteed to reliably work for the moment and developer need to be very careful when using APIs implemented here. Please use the issue track to report bugs and malfunctions.

-
-

MultiMedia Interchange Format

-

MMIF is a JSON(-LD)-based data format designed for transferring annotation data between computational analysis applications in CLAMS project.

-
-

Contents

- -
-
-

API documentation:

- -
-
-
-
-

Indices and tables

- -
- - -
-
- -
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-
- -
- - Other Versions - v: 0.5.0 - - -
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- - - \ No newline at end of file diff --git a/docs/0.5.0/introduction.html b/docs/0.5.0/introduction.html deleted file mode 100644 index d421d3bc..00000000 --- a/docs/0.5.0/introduction.html +++ /dev/null @@ -1,236 +0,0 @@ - - - - - - - - - Getting Started — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
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    -
    • -
  • Getting Started
    • -
  • -
    • -
-
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- -
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Getting Started

-
-

Overview

-

MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF wbesite. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports de-/serialization of MMIF objects, as well as many navigation and manipulation helpers for MMIF objects.

-
-
-

Prerequisites

-
    -

  • Python: mmif-python requires Python 3.6 or newer. We have no plan to support Python 2.7.

    • -
-
-
-

Installation

-

Package mmif-python is distributed via the official PyPI. Users are supposed to pip-install to get latest release.

-
pip install mmif-python
-
-
-

This will install a package mmif to local python.

-

The MMIF format and specification is evolving over time, and mmif-python package will be updated along with the changes in MMIF format.

-
-

Note

-

MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and mmif-python versions, please take time to read our decision on the subject here. If you need to know which python SDK supports which specification version, see Target MMIF Versions page.

-
-
-
-

MMIF Serialization

-

mmif.serialize.mmif.Mmif represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of mmif.serialize.model.MmifObject, including the mmif.serialize.mmif.Mmif. To start with an existing MMIF str, simple initiate a new Mmif object with the file.

-
import mmif
-from mmif import Mmif
-
-mmif_str = """{
-"metadata": {
-  "mmif": "http://mmif.clams.ai/0.2.0"
-},
-"documents": [
-  {
-    "@type": "http://mmif.clams.ai/0.2.0/vocabulary/VideoDocument",
-    "properties": {
-      "id": "m1",
-      "mime": "video/mp4",
-      "location": "file:///var/archive/video-0012.mp4"
-    }
-  },
-  {
-    "@type": "http://mmif.clams.ai/0.2.0/vocabulary/TextDocument",
-    "properties": {
-      "id": "m2",
-      "mime": "text/plain",
-      "location": "file:///var/archive/video-0012-transcript.txt"
-    }
-  }
-],
-"views": []}"""
-mmif_obj = Mmif(mmif_str)
-
-
-

Few notes;

-
    -

  1. MMIF does not carry the primary source files in it.

    2. -

  2. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version mmif-python implementation of the MMIF might not be able to load an unsupported version of MMIF string.

    3. -
-

When serializing back to str, call .serialize() (mmif.serialize.model.MmifObject.serialize()) on the object.

-

To get subcomponents, you can use various getters implemented in subclasses. For more details, the API documentation (mmif package) will help.

-
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.5.0 - - -
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0.3.0
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0.3.2
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0.3.3
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0.3.4
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mode 100644 index aaf8ca84..00000000 --- a/docs/0.5.0/target-versions.html +++ /dev/null @@ -1,233 +0,0 @@ - - - - - - - - - Target MMIF Versions — mmif-python documentation - - - - - - - - - - - - - - - - - -
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  • Target MMIF Versions
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Target MMIF Versions

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This article provides targeting MMIF specification versions of different versions of mmif-python SDK.

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Target Specification Versions

mmif-python version

Target MMIF Specification

0.5.0

1.1.0

0.4.8

0.4.2

0.4.7

0.4.1

0.4.6

0.4.0

0.4.5

0.4.0

0.4.4

0.4.0

0.4.3

0.4.0

0.4.2

0.4.0

0.4.1

0.4.0

0.4.0

0.4.0

0.3.5

0.3.1

0.3.4

0.3.1

0.3.3

0.3.1

0.3.2

0.3.1

0.3.1

0.3.0

0.3.0

0.3.0

0.2.2

0.2.1

0.2.1

0.2.1

0.2.0

0.2.1

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0.3.0
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0.3.1
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0.3.2
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0.3.3
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0.3.4
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0.3.5
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0.4.0
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0.4.1
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0.4.2
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0.4.3
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0.4.4
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0.4.5
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0.4.6
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0.4.7
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0.4.8
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0.5.0
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0.5.1
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0.5.2
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1.0.0
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1.0.1
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1.0.10
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1.0.11
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1.0.12
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1.0.13
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1.0.14
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1.0.15
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1.0.16
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1.0.17
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1.0.18
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1.0.19
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1.0.2
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1.0.3
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1.0.4
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1.0.5
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1.0.6
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1.0.7
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1.0.8
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1.0.9
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1.1.0
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The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the `appliance documentation `_ to learn more about the appliance. - -MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance. - -#. The code must be hosted on a public git repository (e.g. Github, Gitlab, ...) -#. Must listen to ``5000`` port. -#. Must expose ``/display`` route . -#. ``/display`` router should response to ``GET`` requests. -#. In the ``GET`` request, a public URL of the input MMIF file is passed via ``file`` URL parameter. -#. On the codebase root, there must be a ``Dockerfile`` that can build a `docker `_ image that runs the web app. - -We provide an example consumer at https://github.com/clamsproject/mmif-visualizer. diff --git a/docs/0.5.1/_sources/index.rst.txt b/docs/0.5.1/_sources/index.rst.txt deleted file mode 100644 index 9b90b38e..00000000 --- a/docs/0.5.1/_sources/index.rst.txt +++ /dev/null @@ -1,26 +0,0 @@ -Welcome to mmif-python's documentation! -======================================= - -.. mdinclude:: ../README.md - -.. toctree:: - :maxdepth: 2 - :caption: Contents - - introduction - target-versions - consumer-tutorial - -.. toctree:: - :maxdepth: 2 - :caption: API documentation: - - modules - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/docs/0.5.1/_sources/introduction.rst.txt b/docs/0.5.1/_sources/introduction.rst.txt deleted file mode 100644 index 6fea3a3c..00000000 --- a/docs/0.5.1/_sources/introduction.rst.txt +++ /dev/null @@ -1,78 +0,0 @@ -.. _instroduction: - -Getting Started -=============== - - -Overview ---------- - -MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF wbesite `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports de-/serialization of MMIF objects, as well as many navigation and manipulation helpers for MMIF objects. - -Prerequisites -------------- - -* `Python `_: ``mmif-python`` requires Python 3.6 or newer. We have no plan to support `Python 2.7 `_. - -Installation ---------------- - -Package ``mmif-python`` is distributed via the official PyPI. Users are supposed to pip-install to get latest release. - -.. code-block:: bash - - pip install mmif-python - -This will install a package `mmif` to local python. - -The MMIF format and specification is evolving over time, and ``mmif-python`` package will be updated along with the changes in MMIF format. - -.. note:: MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and ``mmif-python`` versions, please take time to read our decision on the subject `here `_. If you need to know which python SDK supports which specification version, see :ref:`target-versions` page. - -MMIF Serialization ---------------------------- - -:class:`mmif.serialize.mmif.Mmif` represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of :class:`mmif.serialize.model.MmifObject`, including the :class:`mmif.serialize.mmif.Mmif`. To start with an existing MMIF :class:`str`, simple initiate a new ``Mmif`` object with the file. - -.. code-block:: python - - import mmif - from mmif import Mmif - - mmif_str = """{ - "metadata": { - "mmif": "http://mmif.clams.ai/0.2.0" - }, - "documents": [ - { - "@type": "http://mmif.clams.ai/0.2.0/vocabulary/VideoDocument", - "properties": { - "id": "m1", - "mime": "video/mp4", - "location": "file:///var/archive/video-0012.mp4" - } - }, - { - "@type": "http://mmif.clams.ai/0.2.0/vocabulary/TextDocument", - "properties": { - "id": "m2", - "mime": "text/plain", - "location": "file:///var/archive/video-0012-transcript.txt" - } - } - ], - "views": []}""" - mmif_obj = Mmif(mmif_str) - - -Few notes; - -#. MMIF does not carry the primary source files in it. -#. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version ``mmif-python`` implementation of the MMIF might not be able to load an unsupported version of MMIF string. - -When serializing back to :class:`str`, call ``.serialize()`` (:meth:`mmif.serialize.model.MmifObject.serialize`) on the object. - -To get subcomponents, you can use various getters implemented in subclasses. For more details, the API documentation (:ref:`apidoc`) will help. - diff --git a/docs/0.5.1/_sources/modules.rst.txt b/docs/0.5.1/_sources/modules.rst.txt deleted file mode 100644 index e4269c6d..00000000 --- a/docs/0.5.1/_sources/modules.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _apidoc: - -mmif package -============ - -.. toctree:: - :maxdepth: 4 - - autodoc/mmif.serialize - autodoc/mmif.vocabulary diff --git a/docs/0.5.1/_sources/target-versions.rst.txt b/docs/0.5.1/_sources/target-versions.rst.txt deleted file mode 100644 index 34216d3e..00000000 --- a/docs/0.5.1/_sources/target-versions.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _target-versions: - -Target MMIF Versions -==================== - -This article provides targeting MMIF specification versions of different versions of ``mmif-python`` SDK. - -.. csv-table:: Target Specification Versions - :file: target-versions.csv - :header-rows: 1 diff --git a/docs/0.5.1/_static/_sphinx_javascript_frameworks_compat.js b/docs/0.5.1/_static/_sphinx_javascript_frameworks_compat.js deleted file mode 100644 index 81415803..00000000 --- a/docs/0.5.1/_static/_sphinx_javascript_frameworks_compat.js +++ /dev/null @@ -1,123 +0,0 @@ -/* Compatability shim for jQuery and underscores.js. - * - * Copyright Sphinx contributors - * Released under the two clause BSD licence - */ - -/** - * small helper function to urldecode strings - * - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL - */ -jQuery.urldecode = function(x) { - if (!x) { - return x - } - return decodeURIComponent(x.replace(/\+/g, ' ')); -}; - -/** - * small helper function to urlencode strings - */ -jQuery.urlencode = encodeURIComponent; - -/** - * This function returns the parsed url parameters of the - * current request. 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- -/** - * Simple result scoring code. - */ -if (typeof Scorer === "undefined") { - var Scorer = { - // Implement the following function to further tweak the score for each result - // The function takes a result array [docname, title, anchor, descr, score, filename] - // and returns the new score. - /* - score: result => { - const [docname, title, anchor, descr, score, filename, kind] = result - return score - }, - */ - - // query matches the full name of an object - objNameMatch: 11, - // or matches in the last dotted part of the object name - objPartialMatch: 6, - // Additive scores depending on the priority of the object - objPrio: { - 0: 15, // used to be importantResults - 1: 5, // used to be objectResults - 2: -5, // used to be unimportantResults - }, - // Used when the priority is not in the mapping. - objPrioDefault: 0, - - // query found in title - title: 15, - partialTitle: 7, - // query found in terms - term: 5, - partialTerm: 2, - }; -} - -// Global search result kind enum, used by themes to style search results. -class SearchResultKind { - static get index() { return "index"; } - static get object() { return "object"; } - static get text() { return "text"; } - static get title() { return "title"; } -} - -const _removeChildren = (element) => { - while (element && element.lastChild) element.removeChild(element.lastChild); -}; - -/** - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping - */ -const _escapeRegExp = (string) => - string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string - -const _displayItem = (item, searchTerms, highlightTerms) => { - const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; - const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; - const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; - const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; - const contentRoot = document.documentElement.dataset.content_root; - - const [docName, title, anchor, descr, score, _filename, kind] = item; - - let listItem = document.createElement("li"); - // Add a class representing the item's type: - // can be used by a theme's CSS selector for styling - // See SearchResultKind for the class names. - listItem.classList.add(`kind-${kind}`); - let requestUrl; - let linkUrl; - if (docBuilder === "dirhtml") { - // dirhtml builder - let dirname = docName + "/"; - if (dirname.match(/\/index\/$/)) - dirname = dirname.substring(0, dirname.length - 6); - else if (dirname === "index/") dirname = ""; - requestUrl = contentRoot + dirname; - linkUrl = requestUrl; - } else { - // normal html builders - requestUrl = contentRoot + docName + docFileSuffix; - linkUrl = docName + docLinkSuffix; - } - let linkEl = listItem.appendChild(document.createElement("a")); - linkEl.href = linkUrl + anchor; - linkEl.dataset.score = score; - linkEl.innerHTML = title; - if (descr) { - listItem.appendChild(document.createElement("span")).innerHTML = - " (" + descr + ")"; - // highlight search terms in the description - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - } - else if (showSearchSummary) - fetch(requestUrl) - .then((responseData) => responseData.text()) - .then((data) => { - if (data) - listItem.appendChild( - Search.makeSearchSummary(data, searchTerms, anchor) - ); - // highlight search terms in the summary - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - }); - Search.output.appendChild(listItem); -}; -const _finishSearch = (resultCount) => { - Search.stopPulse(); - Search.title.innerText = _("Search Results"); - if (!resultCount) - Search.status.innerText = Documentation.gettext( - "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." - ); - else - Search.status.innerText = Documentation.ngettext( - "Search finished, found one page matching the search query.", - "Search finished, found ${resultCount} pages matching the search query.", - resultCount, - ).replace('${resultCount}', resultCount); -}; -const _displayNextItem = ( - results, - resultCount, - searchTerms, - highlightTerms, -) => { - // results left, load the summary and display it - // this is intended to be dynamic (don't sub resultsCount) - if (results.length) { - _displayItem(results.pop(), searchTerms, highlightTerms); - setTimeout( - () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), - 5 - ); - } - // search finished, update title and status message - else _finishSearch(resultCount); -}; -// Helper function used by query() to order search results. -// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. -// Order the results by score (in opposite order of appearance, since the -// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. -const _orderResultsByScoreThenName = (a, b) => { - const leftScore = a[4]; - const rightScore = b[4]; - if (leftScore === rightScore) { - // same score: sort alphabetically - const leftTitle = a[1].toLowerCase(); - const rightTitle = b[1].toLowerCase(); - if (leftTitle === rightTitle) return 0; - return leftTitle > rightTitle ? -1 : 1; // inverted is intentional - } - return leftScore > rightScore ? 1 : -1; -}; - -/** - * Default splitQuery function. Can be overridden in ``sphinx.search`` with a - * custom function per language. - * - * The regular expression works by splitting the string on consecutive characters - * that are not Unicode letters, numbers, underscores, or emoji characters. - * This is the same as ``\W+`` in Python, preserving the surrogate pair area. - */ -if (typeof splitQuery === "undefined") { - var splitQuery = (query) => query - .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) - .filter(term => term) // remove remaining empty strings -} - -/** - * Search Module - */ -const Search = { - _index: null, - _queued_query: null, - _pulse_status: -1, - - htmlToText: (htmlString, anchor) => { - const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - for (const removalQuery of [".headerlink", "script", "style"]) { - htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); - } - if (anchor) { - const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); - if (anchorContent) return anchorContent.textContent; - - console.warn( - `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` - ); - } - - // if anchor not specified or not found, fall back to main content - const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent) return docContent.textContent; - - console.warn( - "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." - ); - return ""; - }, - - init: () => { - const query = new URLSearchParams(window.location.search).get("q"); - document - .querySelectorAll('input[name="q"]') - .forEach((el) => (el.value = query)); - if (query) Search.performSearch(query); - }, - - loadIndex: (url) => - (document.body.appendChild(document.createElement("script")).src = url), - - setIndex: (index) => { - Search._index = index; - if (Search._queued_query !== null) { - const query = Search._queued_query; - Search._queued_query = null; - Search.query(query); - } - }, - - hasIndex: () => Search._index !== null, - - deferQuery: (query) => (Search._queued_query = query), - - stopPulse: () => (Search._pulse_status = -1), - - startPulse: () => { - if (Search._pulse_status >= 0) return; - - const pulse = () => { - Search._pulse_status = (Search._pulse_status + 1) % 4; - Search.dots.innerText = ".".repeat(Search._pulse_status); - if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); - }; - pulse(); - }, - - /** - * perform a search for something (or wait until index is loaded) - */ - performSearch: (query) => { - // create the required interface elements - const searchText = document.createElement("h2"); - searchText.textContent = _("Searching"); - const searchSummary = document.createElement("p"); - searchSummary.classList.add("search-summary"); - searchSummary.innerText = ""; - const searchList = document.createElement("ul"); - searchList.setAttribute("role", "list"); - searchList.classList.add("search"); - - const out = document.getElementById("search-results"); - Search.title = out.appendChild(searchText); - Search.dots = Search.title.appendChild(document.createElement("span")); - Search.status = out.appendChild(searchSummary); - Search.output = out.appendChild(searchList); - - const searchProgress = document.getElementById("search-progress"); - // Some themes don't use the search progress node - if (searchProgress) { - searchProgress.innerText = _("Preparing search..."); - } - Search.startPulse(); - - // index already loaded, the browser was quick! - if (Search.hasIndex()) Search.query(query); - else Search.deferQuery(query); - }, - - _parseQuery: (query) => { - // stem the search terms and add them to the correct list - const stemmer = new Stemmer(); - const searchTerms = new Set(); - const excludedTerms = new Set(); - const highlightTerms = new Set(); - const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); - splitQuery(query.trim()).forEach((queryTerm) => { - const queryTermLower = queryTerm.toLowerCase(); - - // maybe skip this "word" - // stopwords array is from language_data.js - if ( - stopwords.indexOf(queryTermLower) !== -1 || - queryTerm.match(/^\d+$/) - ) - return; - - // stem the word - let word = stemmer.stemWord(queryTermLower); - // select the correct list - if (word[0] === "-") excludedTerms.add(word.substr(1)); - else { - searchTerms.add(word); - highlightTerms.add(queryTermLower); - } - }); - - if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js - localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) - } - - // console.debug("SEARCH: searching for:"); - // console.info("required: ", [...searchTerms]); - // console.info("excluded: ", [...excludedTerms]); - - return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; - }, - - /** - * execute search (requires search index to be loaded) - */ - _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - - // Collect multiple result groups to be sorted separately and then ordered. - // Each is an array of [docname, title, anchor, descr, score, filename, kind]. - const normalResults = []; - const nonMainIndexResults = []; - - _removeChildren(document.getElementById("search-progress")); - - const queryLower = query.toLowerCase().trim(); - for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { - for (const [file, id] of foundTitles) { - const score = Math.round(Scorer.title * queryLower.length / title.length); - const boost = titles[file] === title ? 1 : 0; // add a boost for document titles - normalResults.push([ - docNames[file], - titles[file] !== title ? `${titles[file]} > ${title}` : title, - id !== null ? "#" + id : "", - null, - score + boost, - filenames[file], - SearchResultKind.title, - ]); - } - } - } - - // search for explicit entries in index directives - for (const [entry, foundEntries] of Object.entries(indexEntries)) { - if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id, isMain] of foundEntries) { - const score = Math.round(100 * queryLower.length / entry.length); - const result = [ - docNames[file], - titles[file], - id ? "#" + id : "", - null, - score, - filenames[file], - SearchResultKind.index, - ]; - if (isMain) { - normalResults.push(result); - } else { - nonMainIndexResults.push(result); - } - } - } - } - - // lookup as object - objectTerms.forEach((term) => - normalResults.push(...Search.performObjectSearch(term, objectTerms)) - ); - - // lookup as search terms in fulltext - normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); - - // let the scorer override scores with a custom scoring function - if (Scorer.score) { - normalResults.forEach((item) => (item[4] = Scorer.score(item))); - nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); - } - - // Sort each group of results by score and then alphabetically by name. - normalResults.sort(_orderResultsByScoreThenName); - nonMainIndexResults.sort(_orderResultsByScoreThenName); - - // Combine the result groups in (reverse) order. - // Non-main index entries are typically arbitrary cross-references, - // so display them after other results. - let results = [...nonMainIndexResults, ...normalResults]; - - // remove duplicate search results - // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept - let seen = new Set(); - results = results.reverse().reduce((acc, result) => { - let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); - if (!seen.has(resultStr)) { - acc.push(result); - seen.add(resultStr); - } - return acc; - }, []); - - return results.reverse(); - }, - - query: (query) => { - const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); - const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); - - // for debugging - //Search.lastresults = results.slice(); // a copy - // console.info("search results:", Search.lastresults); - - // print the results - _displayNextItem(results, results.length, searchTerms, highlightTerms); - }, - - /** - * search for object names - */ - performObjectSearch: (object, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const objects = Search._index.objects; - const objNames = Search._index.objnames; - const titles = Search._index.titles; - - const results = []; - - const objectSearchCallback = (prefix, match) => { - const name = match[4] - const fullname = (prefix ? prefix + "." : "") + name; - const fullnameLower = fullname.toLowerCase(); - if (fullnameLower.indexOf(object) < 0) return; - - let score = 0; - const parts = fullnameLower.split("."); - - // check for different match types: exact matches of full name or - // "last name" (i.e. last dotted part) - if (fullnameLower === object || parts.slice(-1)[0] === object) - score += Scorer.objNameMatch; - else if (parts.slice(-1)[0].indexOf(object) > -1) - score += Scorer.objPartialMatch; // matches in last name - - const objName = objNames[match[1]][2]; - const title = titles[match[0]]; - - // If more than one term searched for, we require other words to be - // found in the name/title/description - const otherTerms = new Set(objectTerms); - otherTerms.delete(object); - if (otherTerms.size > 0) { - const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); - if ( - [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) - ) - return; - } - - let anchor = match[3]; - if (anchor === "") anchor = fullname; - else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; - - const descr = objName + _(", in ") + title; - - // add custom score for some objects according to scorer - if (Scorer.objPrio.hasOwnProperty(match[2])) - score += Scorer.objPrio[match[2]]; - else score += Scorer.objPrioDefault; - - results.push([ - docNames[match[0]], - fullname, - "#" + anchor, - descr, - score, - filenames[match[0]], - SearchResultKind.object, - ]); - }; - Object.keys(objects).forEach((prefix) => - objects[prefix].forEach((array) => - objectSearchCallback(prefix, array) - ) - ); - return results; - }, - - /** - * search for full-text terms in the index - */ - performTermsSearch: (searchTerms, excludedTerms) => { - // prepare search - const terms = Search._index.terms; - const titleTerms = Search._index.titleterms; - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - - const scoreMap = new Map(); - const fileMap = new Map(); - - // perform the search on the required terms - searchTerms.forEach((word) => { - const files = []; - const arr = [ - { files: terms[word], score: Scorer.term }, - { files: titleTerms[word], score: Scorer.title }, - ]; - // add support for partial matches - if (word.length > 2) { - const escapedWord = _escapeRegExp(word); - if (!terms.hasOwnProperty(word)) { - Object.keys(terms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: terms[term], score: Scorer.partialTerm }); - }); - } - if (!titleTerms.hasOwnProperty(word)) { - Object.keys(titleTerms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); - }); - } - } - - // no match but word was a required one - if (arr.every((record) => record.files === undefined)) return; - - // found search word in contents - arr.forEach((record) => { - if (record.files === undefined) return; - - let recordFiles = record.files; - if (recordFiles.length === undefined) recordFiles = [recordFiles]; - files.push(...recordFiles); - - // set score for the word in each file - recordFiles.forEach((file) => { - if (!scoreMap.has(file)) scoreMap.set(file, {}); - scoreMap.get(file)[word] = record.score; - }); - }); - - // create the mapping - files.forEach((file) => { - if (!fileMap.has(file)) fileMap.set(file, [word]); - else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); - }); - }); - - // now check if the files don't contain excluded terms - const results = []; - for (const [file, wordList] of fileMap) { - // check if all requirements are matched - - // as search terms with length < 3 are discarded - const filteredTermCount = [...searchTerms].filter( - (term) => term.length > 2 - ).length; - if ( - wordList.length !== searchTerms.size && - wordList.length !== filteredTermCount - ) - continue; - - // ensure that none of the excluded terms is in the search result - if ( - [...excludedTerms].some( - (term) => - terms[term] === file || - titleTerms[term] === file || - (terms[term] || []).includes(file) || - (titleTerms[term] || []).includes(file) - ) - ) - break; - - // select one (max) score for the file. - const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); - // add result to the result list - results.push([ - docNames[file], - titles[file], - "", - null, - score, - filenames[file], - SearchResultKind.text, - ]); - } - return results; - }, - - /** - * helper function to return a node containing the - * search summary for a given text. keywords is a list - * of stemmed words. - */ - makeSearchSummary: (htmlText, keywords, anchor) => { - const text = Search.htmlToText(htmlText, anchor); - if (text === "") return null; - - const textLower = text.toLowerCase(); - const actualStartPosition = [...keywords] - .map((k) => textLower.indexOf(k.toLowerCase())) - .filter((i) => i > -1) - .slice(-1)[0]; - const startWithContext = Math.max(actualStartPosition - 120, 0); - - const top = startWithContext === 0 ? "" : "..."; - const tail = startWithContext + 240 < text.length ? "..." : ""; - - let summary = document.createElement("p"); - summary.classList.add("context"); - summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; - - return summary; - }, -}; - -_ready(Search.init); diff --git a/docs/0.5.1/_static/sphinx_highlight.js b/docs/0.5.1/_static/sphinx_highlight.js deleted file mode 100644 index 8a96c69a..00000000 --- a/docs/0.5.1/_static/sphinx_highlight.js +++ /dev/null @@ -1,154 +0,0 @@ -/* Highlighting utilities for Sphinx HTML documentation. */ -"use strict"; - -const SPHINX_HIGHLIGHT_ENABLED = true - -/** - * highlight a given string on a node by wrapping it in - * span elements with the given class name. - */ -const _highlight = (node, addItems, text, className) => { - if (node.nodeType === Node.TEXT_NODE) { - const val = node.nodeValue; - const parent = node.parentNode; - const pos = val.toLowerCase().indexOf(text); - if ( - pos >= 0 && - !parent.classList.contains(className) && - !parent.classList.contains("nohighlight") - ) { - let span; - - const closestNode = parent.closest("body, svg, foreignObject"); - const isInSVG = closestNode && closestNode.matches("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.classList.add(className); - } - - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - const rest = document.createTextNode(val.substr(pos + text.length)); - parent.insertBefore( - span, - parent.insertBefore( - rest, - node.nextSibling - ) - ); - node.nodeValue = val.substr(0, pos); - /* There may be more occurrences of search term in this node. So call this - * function recursively on the remaining fragment. - */ - _highlight(rest, addItems, text, className); - - if (isInSVG) { - const rect = document.createElementNS( - "http://www.w3.org/2000/svg", - "rect" - ); - const bbox = parent.getBBox(); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute("class", className); - addItems.push({ parent: parent, target: rect }); - } - } - } else if (node.matches && !node.matches("button, select, textarea")) { - node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); - } -}; -const _highlightText = (thisNode, text, className) => { - let addItems = []; - _highlight(thisNode, addItems, text, className); - addItems.forEach((obj) => - obj.parent.insertAdjacentElement("beforebegin", obj.target) - ); -}; - -/** - * Small JavaScript module for the documentation. - */ -const SphinxHighlight = { - - /** - * highlight the search words provided in localstorage in the text - */ - highlightSearchWords: () => { - if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight - - // get and clear terms from localstorage - const url = new URL(window.location); - const highlight = - localStorage.getItem("sphinx_highlight_terms") - || url.searchParams.get("highlight") - || ""; - localStorage.removeItem("sphinx_highlight_terms") - url.searchParams.delete("highlight"); - window.history.replaceState({}, "", url); - - // get individual terms from highlight string - const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); - if (terms.length === 0) return; // nothing to do - - // There should never be more than one element matching "div.body" - const divBody = document.querySelectorAll("div.body"); - const body = divBody.length ? divBody[0] : document.querySelector("body"); - window.setTimeout(() => { - terms.forEach((term) => _highlightText(body, term, "highlighted")); - }, 10); - - const searchBox = document.getElementById("searchbox"); - if (searchBox === null) return; - searchBox.appendChild( - document - .createRange() - .createContextualFragment( - '

' + - '' + - _("Hide Search Matches") + - "

" - ) - ); - }, - - /** - * helper function to hide the search marks again - */ - hideSearchWords: () => { - document - .querySelectorAll("#searchbox .highlight-link") - .forEach((el) => el.remove()); - document - .querySelectorAll("span.highlighted") - .forEach((el) => el.classList.remove("highlighted")); - localStorage.removeItem("sphinx_highlight_terms") - }, - - initEscapeListener: () => { - // only install a listener if it is really needed - if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; - - document.addEventListener("keydown", (event) => { - // bail for input elements - if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; - // bail with special keys - if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; - if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { - SphinxHighlight.hideSearchWords(); - event.preventDefault(); - } - }); - }, -}; - -_ready(() => { - /* Do not call highlightSearchWords() when we are on the search page. - * It will highlight words from the *previous* search query. - */ - if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); - SphinxHighlight.initEscapeListener(); -}); diff --git a/docs/0.5.1/autodoc/mmif.serialize.html b/docs/0.5.1/autodoc/mmif.serialize.html deleted file mode 100644 index 010343ea..00000000 --- a/docs/0.5.1/autodoc/mmif.serialize.html +++ /dev/null @@ -1,1173 +0,0 @@ - - - - - - - - - mmif.serialize module — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.serialize module

-
-

mmif.serialize.model module

-

The model module contains the classes used to represent an -abstract MMIF object as a live Python object.

-

The MmifObject class or one of its derivatives is subclassed by -all other classes defined in this SDK, except for MmifObjectEncoder.

-

These objects are generally instantiated from JSON, either as a string -or as an already-loaded Python dictionary. This base class provides the -core functionality for deserializing MMIF JSON data into live objects -and serializing live objects into MMIF JSON data. Specialized behavior -for the different components of MMIF is added in the subclasses.

-
-
-class mmif.serialize.model.DataDict(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject, Generic[T, S]

-
-
-empty()[source]
-
- -
-
-get(key: T, default=None) → S | None[source]
-
- -
-
-items()[source]
-
- -
-
-keys()[source]
-
- -
-
-update(other, overwrite)[source]
-
- -
-
-values()[source]
-
- -
- -
-
-class mmif.serialize.model.DataList(mmif_obj: bytes | str | list | None = None)[source]
-

Bases: MmifObject, Generic[T]

-

The DataList class is an abstraction that represents the -various lists found in a MMIF file, such as documents, subdocuments, -views, and annotations.

-
-
Parameters:
-

mmif_obj (Union[str, list]) – the data that the list contains

-
-
-
-
-append(value, overwrite)[source]
-
- -
-
-deserialize(mmif_json: str | list) → None[source]
-

Passes the input data into the internal deserializer.

-
- -
-
-empty()[source]
-
- -
-
-get(key: str) → T | None[source]
-

Standard dictionary-style get() method, albeit with no default -parameter. Relies on the implementation of __getitem__.

-

Will return None if the key is not found.

-
-
Parameters:
-

key – the key to search for

-
-
Returns:
-

the value matching that key

-
-
-
- -
- -
-
-class mmif.serialize.model.MmifObject(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: object

-

Abstract superclass for MMIF related key-value pair objects.

-

Any MMIF object can be initialized as an empty placeholder or -an actual representation with a JSON formatted string or equivalent -dict object argument.

-

This superclass has three specially designed instance variables, and these -variable names cannot be used as attribute names for MMIF objects.

-
    -

  1. _unnamed_attributes: -Only can be either None or an empty dictionary. If it’s set to None, -it means the class won’t take any Additional Attributes in the JSON -schema sense. If it’s a dict, users can throw any k-v pairs to the -class, EXCEPT for the reserved two key names.

    2. -

  2. _attribute_classes: -This is a dict from a key name to a specific python class to use for -deserialize the value. Note that a key name in this dict does NOT -have to be a named attribute, but is recommended to be one.

    3. -

  3. _required_attributes: -This is a simple list of names of attributes that are required in the object. -When serialize, an object will skip its empty (e.g. zero-length, or None) -attributes unless they are in this list. Otherwise, the serialized JSON -string would have empty representations (e.g. "", []).

    4. -
-

# TODO (krim @ 8/17/20): this dict is however, a duplicate with the type hints in the class definition. -Maybe there is a better way to utilize type hints (e.g. getting them as a programmatically), but for now -developers should be careful to add types to hints as well as to this dict.

-

Also note that those two special attributes MUST be set in the __init__() -before calling super method, otherwise deserialization will not work.

-

And also, a subclass that has one or more named attributes, it must -set those attributes in the __init__() before calling super method. When -serializing a MmifObject, all empty attributes will be ignored, so for -optional named attributes, you must leave the values empty (len == 0), but -NOT None. Any None-valued named attributes will cause issues with current -implementation.

-
-
Parameters:
-

mmif_obj – JSON string or dict to initialize an object. -If not given, an empty object will be initialized, sometimes with -an ID value automatically generated, based on its parent object.

-
-
-
-
-deserialize(mmif_json: str | dict) → None[source]
-

Takes a JSON-formatted string or a simple dict that’s json-loaded from -such a string as an input and populates object’s fields with the values -specified in the input.

-
-
Parameters:
-

mmif_json – JSON-formatted string or dict from such a string -that represents a MMIF object

-
-
-
- -
-
-disallow_additional_properties() → None[source]
-

Call this method in __init__() to prevent the insertion -of unnamed attributes after initialization.

-
- -
-
-static is_empty(obj) → bool[source]
-

return True if the obj is None or “emtpy”. The emptiness first defined as -having zero length. But for objects that lack __len__ method, we need -additional check.

-
- -
-
-reserved_names: Set = {'_attribute_classes', '_id_counts', '_parent_view_id', '_required_attributes', '_unnamed_attributes', 'reserved_names'}[source]
-
- -
-
-serialize(pretty: bool = False) → str[source]
-

Generates JSON representation of an object.

-
-
Parameters:
-

pretty – If True, returns string representation with indentation.

-
-
Returns:
-

JSON string of the object.

-
-
-
- -
-
-set_additional_property(key: str, value: Any) → None[source]
-

Method to set values in _unnamed_attributes.

-
-
Parameters:
-
    -

  • key – the attribute name

    • -

  • value – the desired value

    • -
-
-
Returns:
-

None

-
-
Raise:
-

AttributeError if additional properties are disallowed by disallow_additional_properties()

-
-
-
- -
- -
-
-class mmif.serialize.model.MmifObjectEncoder(*, skipkeys=False, ensure_ascii=True, check_circular=True, allow_nan=True, sort_keys=False, indent=None, separators=None, default=None)[source]
-

Bases: JSONEncoder

-

Encoder class to define behaviors of de-/serialization

-
-
-default(obj: MmifObject)[source]
-

Overrides default encoding behavior to prioritize MmifObject.serialize().

-
- -
- -
-
-

mmif.serialize.mmif module

-

The mmif module contains the classes used to represent a full MMIF -file as a live Python object.

-

See the specification docs and the JSON Schema file for more information.

-
-
-class mmif.serialize.mmif.Mmif(mmif_obj: bytes | str | dict | None = None, *, validate: bool = True)[source]
-

Bases: MmifObject

-

MmifObject that represents a full MMIF file.

-
-
Parameters:
-
    -

  • mmif_obj – the JSON data

    • -

  • validate – whether to validate the data against the MMIF JSON schema.

    • -
-
-
-
-
-add_document(document: Document, overwrite=False) → None[source]
-

Appends a Document object to the documents list.

-

Fails if there is already a document with the same ID in the MMIF object.

-
-
Parameters:
-
    -

  • document – the Document object to add

    • -

  • overwrite – if set to True, will overwrite -an existing view with the same ID

    • -
-
-
Returns:
-

None

-
-
-
- -
-
-add_view(view: View, overwrite=False) → None[source]
-

Appends a View object to the views list.

-

Fails if there is already a view with the same ID in the MMIF object.

-
-
Parameters:
-
    -

  • view – the Document object to add

    • -

  • overwrite – if set to True, will overwrite -an existing view with the same ID

    • -
-
-
Returns:
-

None

-
-
-
- -
-
-get_alignments(at_type1: str | TypesBase, at_type2: str | TypesBase) → Dict[str, List[Annotation]][source]
-

Finds views where alignments between two given annotation types occurred.

-
-
Returns:
-

a dict that keyed by view IDs (str) and has lists of alignment Annotation objects as values.

-
-
-
- -
-
-get_all_views_contain(at_types: TypesBase | str | List[str | TypesBase]) → List[View][source]
-

Returns the list of all views in the MMIF if given types -are present in that view’s ‘contains’ metadata.

-
-
Parameters:
-

at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

-
-
Returns:
-

the list of views that contain the type

-
-
-
- -
-
-get_document_by_id(doc_id: str) → Document[source]
-

Finds a Document object with the given ID.

-
-
Parameters:
-

doc_id – the ID to search for

-
-
Returns:
-

a reference to the corresponding document, if it exists

-
-
Raises:
-

Exception – if there is no corresponding document

-
-
-
- -
-
-get_document_location(m_type: DocumentTypes | str, path_only=False) → str | None[source]
-

Method to get the location of first document of given type.

-
-
Parameters:
-

m_type – the type to search for

-
-
Returns:
-

the value of the location field in the corresponding document

-
-
-
- -
-
-get_documents_by_app(app_id: str) → List[Document][source]
-

Method to get all documents object queries by its originated app name.

-
-
Parameters:
-

app_id – the app name to search for

-
-
Returns:
-

a list of documents matching the requested app name, or an empty list if the app not found

-
-
-
- -
-
-get_documents_by_property(prop_key: str, prop_value: str) → List[Document][source]
-

Method to retrieve documents by an arbitrary key-value pair in the document properties objects.

-
-
Parameters:
-
    -

  • prop_key – the metadata key to search for

    • -

  • prop_value – the metadata value to match

    • -
-
-
Returns:
-

a list of documents matching the requested metadata key-value pair

-
-
-
- -
-
-get_documents_by_type(doc_type: str | DocumentTypes) → List[Document][source]
-

Method to get all documents where the type matches a particular document type, which should be one of the CLAMS document types.

-
-
Parameters:
-

doc_type – the type of documents to search for, must be one of Document type defined in the CLAMS vocabulary.

-
-
Returns:
-

a list of documents matching the requested type, or an empty list if none found.

-
-
-
- -
-
-get_documents_in_view(vid: str | None = None) → List[Document][source]
-

Method to get all documents object queries by a view id.

-
-
Parameters:
-

vid – the source view ID to search for

-
-
Returns:
-

a list of documents matching the requested source view ID, or an empty list if the view not found

-
-
-
- -
-
-get_documents_locations(m_type: DocumentTypes | str, path_only=False) → List[str | None][source]
-

This method returns the file paths of documents of given type. -Only top-level documents have locations, so we only check them.

-
-
Parameters:
-

m_type – the type to search for

-
-
Returns:
-

a list of the values of the location fields in the corresponding documents

-
-
-
- -
-
-get_view_by_id(req_view_id: str) → View[source]
-

Finds a View object with the given ID.

-
-
Parameters:
-

req_view_id – the ID to search for

-
-
Returns:
-

a reference to the corresponding view, if it exists

-
-
Raises:
-

Exception – if there is no corresponding view

-
-
-
- -
-
-get_view_contains(at_types: TypesBase | str | List[str | TypesBase]) → View | None[source]
-

Returns the last view appended that contains the given -types in its ‘contains’ metadata.

-
-
Parameters:
-

at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

-
-
Returns:
-

the view, or None if the type is not found

-
-
-
- -
-
-get_views_contain(at_types: TypesBase | str | List[str | TypesBase]) → List[View][source]
-

An alias to get_all_views_contain method.

-
- -
-
-get_views_for_document(doc_id: str)[source]
-

Returns the list of all views that have annotations anchored on a particular document. -Note that when the document is insids a view (generated during the pipeline’s running), -doc_id must be prefixed with the view_id.

-
- -
-
-id_delimiter: ClassVar[str] = ':'[source]
-
- -
-
-new_view() → View[source]
-

Creates an empty view with a new ID and appends it to the views list.

-
-
Returns:
-

a reference to the new View object

-
-
-
- -
-
-new_view_id() → str[source]
-

Fetches an ID for a new view.

-
-
Returns:
-

the ID

-
-
-
- -
-
-sanitize()[source]
-

Sanitizes a Mmif object by running some safeguards. -Concretely, it performs the following before returning the JSON string.

-
    -

  1. validating output using built-in MMIF jsonschema

    2. -

  2. remove non-existing annotation types from contains metadata

    3. -
-
- -
-
-serialize(pretty: bool = False, sanitize: bool = False) → str[source]
-

Generates JSON representation of an object.

-
-
Parameters:
-

pretty – If True, returns string representation with indentation.

-
-
Returns:
-

JSON string of the object.

-
-
-
- -
-
-static validate(json_str: bytes | str | dict) → None[source]
-

Validates a MMIF JSON object against the MMIF Schema. -Note that this method operates before processing by MmifObject._load_str, -so it expects @ and not _ for the JSON-LD @-keys.

-
-
Raises:
-

jsonschema.exceptions.ValidationError – if the input fails validation

-
-
Parameters:
-

json_str – a MMIF JSON dict or string

-
-
Returns:
-

None

-
-
-
- -
-
-view_prefix: ClassVar[str] = 'v_'[source]
-
- -
- -
-
-

mmif.serialize.view module

-

The view module contains the classes used to represent a MMIF view -as a live Python object.

-

In MMIF, views are created by apps in a pipeline that are annotating -data that was previously present in the MMIF file.

-
-
-class mmif.serialize.view.Contain(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-

Contain object that represents the metadata of a single -annotation type in the contains metadata of a MMIF view.

-
- -
-
-class mmif.serialize.view.View(view_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-

View object that represents a single view in a MMIF file.

-

A view is identified by an ID, and contains certain metadata, -a list of annotations, and potentially a JSON-LD @context -IRI.

-

If view_obj is not provided, an empty View will be generated.

-
-
Parameters:
-

view_obj – the JSON data that defines the view

-
-
-
-
-add_annotation(annotation: Annotation, overwrite=False) → Annotation[source]
-

Adds an annotation to the current view.

-

Fails if there is already an annotation with the same ID -in the view, unless overwrite is set to True.

-
-
Parameters:
-
-
-
Raises:
-

KeyError – if overwrite is set to False and -an annotation with the same ID exists -in the view

-
-
Returns:
-

the same Annotation object passed in as annotation

-
-
-
- -
-
-add_document(document: Document, overwrite=False) → Annotation[source]
-

Appends a Document object to the annotations list.

-

Fails if there is already a document with the same ID in the annotations list.

-
-
Parameters:
-
    -

  • document – the Document object to add

    • -

  • overwrite – if set to True, will overwrite -an existing view with the same ID

    • -
-
-
Returns:
-

None

-
-
-
- -
-
-get_annotation_by_id(ann_id)[source]
-
- -
-
-get_annotations(at_type: str | TypesBase | None = None, **properties) → Generator[Annotation, None, None][source]
-

Look for certain annotations in this view, specified by parameters

-
-
Parameters:
-
    -

  • at_type – @type of the annotations to look for. When this is None, any @type will match.

    • -

  • properties – properties of the annotations to look for. When given more than one property, all properties must match. Note that annotation type metadata are specified in the contains view metadata, not in individual annotation objects.

    • -
-
-
-
- -
-
-get_document_by_id(doc_id) → Document[source]
-
- -
-
-get_documents() → List[Document][source]
-
- -
-
-new_annotation(at_type: str | TypesBase, aid: str | None = None, overwrite=False, **properties) → Annotation[source]
-

Generates a new mmif.serialize.annotation.Annotation -object and adds it to the current view.

-

Fails if there is already an annotation with the same ID -in the view, unless overwrite is set to True.

-
-
Parameters:
-
    -

  • at_type – the desired @type of the annotation.

    • -

  • aid – the desired ID of the annotation, when not given, -the mmif SDK tries to automatically generate an ID based on -Annotation type and existing annotations in the view.

    • -

  • overwrite – if set to True, will overwrite an -existing annotation with the same ID.

    • -
-
-
Raises:
-

KeyError – if overwrite is set to False and -an annotation with the same ID exists -in the view.

-
-
Returns:
-

the generated mmif.serialize.annotation.Annotation

-
-
-
- -
-
-new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
-

Adds a new element to the contains metadata.

-
-
Parameters:
-
    -

  • at_type – the @type of the annotation type being added

    • -

  • contains_metadata – any metadata associated with the annotation type

    • -
-
-
Returns:
-

the generated Contain object

-
-
-
- -
-
-new_textdocument(text: str, lang: str = 'en', did: str | None = None, overwrite=False, **properties) → Document[source]
-

Generates a new mmif.serialize.annotation.Document -object, particularly typed as TextDocument and adds it to the current view.

-

Fails if there is already a text document with the same ID -in the view, unless overwrite is set to True.

-
-
Parameters:
-
    -

  • text – text content of the new document

    • -

  • lang – ISO 639-1 code of the language used in the new document

    • -

  • did – the desired ID of the document, when not given, -the mmif SDK tries to automatically generate an ID based on -Annotation type and existing documents in the view.

    • -

  • overwrite – if set to True, will overwrite an -existing document with the same ID

    • -
-
-
Raises:
-

KeyError – if overwrite is set to False and -an document with the same ID exists -in the view

-
-
Returns:
-

the generated mmif.serialize.annotation.Document

-
-
-
- -
-
-set_error(err_message: str, err_trace: str) → None[source]
-
- -
- -
-
-class mmif.serialize.view.ViewMetadata(viewmetadata_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-

ViewMetadata object that represents the metadata object within a MMIF view.

-
-
Parameters:
-

viewmetadata_obj – the JSON data that defines the metadata

-
-
-
-
-add_parameter(param_key, param_value)[source]
-
- -
-
-add_parameters(**runtime_params)[source]
-
- -
-
-add_warnings(*warnings: Warning)[source]
-
- -
-
-emtpy_warnings()[source]
-
- -
-
-get_parameter(param_key)[source]
-
- -
-
-new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
-

Adds a new element to the contains dictionary.

-
-
Parameters:
-
    -

  • at_type – the @type of the annotation type being added

    • -

  • contains_metadata – any metadata associated with the annotation type

    • -
-
-
Returns:
-

the generated Contain object

-
-
-
- -
-
-set_error(message: str, stack_trace: str)[source]
-
- -
- -
-
-

mmif.serialize.annotation module

-

The annotation module contains the classes used to represent a -MMIF annotation as a live Python object.

-

In MMIF, annotations are created by apps in a pipeline as a part -of a view. For documentation on how views are represented, see -mmif.serialize.view.

-
-
-class mmif.serialize.annotation.Annotation(anno_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-

MmifObject that represents an annotation in a MMIF view.

-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]]) → None[source]
-

Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

-
- -
-
-property at_type: TypesBase[source]
-
- -
-
-property id: str[source]
-
- -
-
-is_document()[source]
-
- -
-
-is_type(at_type: str | TypesBase) → bool[source]
-

Check if the @type of this object matches.

-
- -
- -
-
-class mmif.serialize.annotation.AnnotationProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject, MutableMapping[str, T]

-

AnnotationProperties object that represents the -properties object within a MMIF annotation.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
- -
-
-class mmif.serialize.annotation.Document(doc_obj: bytes | str | dict | None = None)[source]
-

Bases: Annotation

-

Document object that represents a single document in a MMIF file.

-

A document is identified by an ID, and contains certain attributes -and potentially contains the contents of the document itself, -metadata about how the document was created, and/or a list of -subdocuments grouped together logically.

-

If document_obj is not provided, an empty Document will be generated.

-
-
Parameters:
-

document_obj – the JSON data that defines the document

-
-
-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None]) → None[source]
-

Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

-
- -
-
-property location: str | None[source]
-

location property must be a legitimate URI. That is, should the document be a local file -then the file:// scheme must be used. -Returns None when no location is set.

-
- -
-
-location_address() → str | None[source]
-

Retrieves the full address from the document location URI. -Returns None when no location is set.

-
- -
-
-location_path() → str | None[source]
-

Retrieves only path name of the document location (hostname is ignored). -Useful to get a path of a local file. -Returns None when no location is set.

-
- -
-
-location_scheme() → str | None[source]
-

Retrieves URI scheme of the document location. -Returns None when no location is set.

-
- -
-
-property parent: str[source]
-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.DocumentProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: AnnotationProperties

-

DocumentProperties object that represents the -properties object within a MMIF document.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
-
-property location: str | None[source]
-

location property must be a legitimate URI. That is, should the document be a local file -then the file:// scheme must be used. -Returns None when no location is set.

-
- -
-
-location_address() → str | None[source]
-

Retrieves the full address from the document location URI. -Returns None when no location is set.

-
- -
-
-location_path() → str | None[source]
-

Retrieves only path name of the document location (hostname is ignored). -Useful to get a path of a local file. -Returns None when no location is set.

-
- -
-
-location_scheme() → str | None[source]
-

Retrieves URI scheme of the document location. -Returns None when no location is set.

-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.Text(text_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-
-
-property lang: str[source]
-
- -
-
-property value: str[source]
-
- -
- -
-
- - -
-
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- - Other Versions - v: 0.5.1 - - -
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- - - \ No newline at end of file diff --git a/docs/0.5.1/autodoc/mmif.vocabulary.html b/docs/0.5.1/autodoc/mmif.vocabulary.html deleted file mode 100644 index aa983ee2..00000000 --- a/docs/0.5.1/autodoc/mmif.vocabulary.html +++ /dev/null @@ -1,325 +0,0 @@ - - - - - - - - - mmif.vocabulary module — mmif-python documentation - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.vocabulary module

-
-

mmif.vocabulary.annotation_types module

-
-
-class mmif.vocabulary.annotation_types.AnnotationTypes(type_uri, fuzzymode=True)[source]
-

Bases: AnnotationTypesBase

-

This class contains the CLAMS annotation types -defined in the spec version 1.1.0 as class variables.

-
-
-Alignment = http://mmif.clams.ai/vocabulary/Alignment/v1[source]
-
- -
-
-Annotation = http://mmif.clams.ai/vocabulary/Annotation/v6[source]
-
- -
-
-BoundingBox = http://mmif.clams.ai/vocabulary/BoundingBox/v5[source]
-
- -
-
-Chapter = http://mmif.clams.ai/vocabulary/Chapter/v6[source]
-
- -
-
-Interval = http://mmif.clams.ai/vocabulary/Interval/v5[source]
-
- -
-
-NamedEntity = http://mmif.clams.ai/vocabulary/NamedEntity/v1[source]
-
- -
-
-NounChunk = http://mmif.clams.ai/vocabulary/NounChunk/v1[source]
-
- -
-
-Paragraph = http://mmif.clams.ai/vocabulary/Paragraph/v1[source]
-
- -
-
-Polygon = http://mmif.clams.ai/vocabulary/Polygon/v5[source]
-
- -
-
-Region = http://mmif.clams.ai/vocabulary/Region/v5[source]
-
- -
-
-Relation = http://mmif.clams.ai/vocabulary/Relation/v5[source]
-
- -
-
-Sentence = http://mmif.clams.ai/vocabulary/Sentence/v1[source]
-
- -
-
-Span = http://mmif.clams.ai/vocabulary/Span/v5[source]
-
- -
-
-TimeFrame = http://mmif.clams.ai/vocabulary/TimeFrame/v6[source]
-
- -
-
-TimePoint = http://mmif.clams.ai/vocabulary/TimePoint/v5[source]
-
- -
-
-Token = http://mmif.clams.ai/vocabulary/Token/v1[source]
-
- -
-
-VerbChunk = http://mmif.clams.ai/vocabulary/VerbChunk/v1[source]
-
- -
-
-VideoObject = http://mmif.clams.ai/vocabulary/VideoObject/v5[source]
-
- -
-
-typevers = {'Alignment': 'v1', 'Annotation': 'v6', 'BoundingBox': 'v5', 'Chapter': 'v6', 'Interval': 'v5', 'NamedEntity': 'v1', 'NounChunk': 'v1', 'Paragraph': 'v1', 'Polygon': 'v5', 'Region': 'v5', 'Relation': 'v5', 'Sentence': 'v1', 'Span': 'v5', 'TimeFrame': 'v6', 'TimePoint': 'v5', 'Token': 'v1', 'VerbChunk': 'v1', 'VideoObject': 'v5'}[source]
-
- -
- -
-
-

mmif.vocabulary.document_types module

-
-
-class mmif.vocabulary.document_types.DocumentTypes(type_uri, fuzzymode=True)[source]
-

Bases: DocumentTypesBase

-

This class contains the CLAMS document types -defined in the spec version 1.1.0 as class variables.

-
-
-AudioDocument = http://mmif.clams.ai/vocabulary/AudioDocument/v1[source]
-
- -
-
-Document = http://mmif.clams.ai/vocabulary/Document/v1[source]
-
- -
-
-ImageDocument = http://mmif.clams.ai/vocabulary/ImageDocument/v1[source]
-
- -
-
-TextDocument = http://mmif.clams.ai/vocabulary/TextDocument/v1[source]
-
- -
-
-VideoDocument = http://mmif.clams.ai/vocabulary/VideoDocument/v1[source]
-
- -
-
-typevers = {'AudioDocument': 'v1', 'Document': 'v1', 'ImageDocument': 'v1', 'TextDocument': 'v1', 'VideoDocument': 'v1'}[source]
-
- -
- -
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.5.1 - - -
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- -
0.3.0
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0.3.2
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0.3.3
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0.4.0
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0.4.3
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0.4.7
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0.5.2
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- - - \ No newline at end of file diff --git a/docs/0.5.1/consumer-tutorial.html b/docs/0.5.1/consumer-tutorial.html deleted file mode 100644 index 918bc788..00000000 --- a/docs/0.5.1/consumer-tutorial.html +++ /dev/null @@ -1,176 +0,0 @@ - - - - - - - - - MMIF consumer — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • MMIF consumer
    • -
  • -
    • -
-
-
-
-
- -
-

MMIF consumer

-

A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the appliance documentation to learn more about the appliance.

-

MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance.

-
    -

  1. The code must be hosted on a public git repository (e.g. Github, Gitlab, …)

    2. -

  2. Must listen to 5000 port.

    3. -

  3. Must expose /display route .

    4. -

  4. /display router should response to GET requests.

    5. -

  5. In the GET request, a public URL of the input MMIF file is passed via file URL parameter.

    6. -

  6. On the codebase root, there must be a Dockerfile that can build a docker image that runs the web app.

    7. -
-

We provide an example consumer at https://github.com/clamsproject/mmif-visualizer.

-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.5.1 - - -
-
- -
0.3.0
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- - - \ No newline at end of file diff --git a/docs/0.5.1/genindex.html b/docs/0.5.1/genindex.html deleted file mode 100644 index 07b43444..00000000 --- a/docs/0.5.1/genindex.html +++ /dev/null @@ -1,638 +0,0 @@ - - - - - - - - Index — mmif-python documentation - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • Index
    • -
  • -
    • -
-
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-
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- - -

Index

- -
- A - | B - | C - | D - | E - | G - | I - | K - | L - | M - | N - | P - | R - | S - | T - | U - | V - -
-

A

- - - -
- -

B

- - -
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C

- - - -
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D

- - - -
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E

- - - -
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G

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I

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K

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M

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N

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P

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R

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S

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U

- - -
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V

- - - -
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- - -
- -
-
-
-
    -
    • -
  • Welcome to mmif-python’s documentation!
    • -
  • -
    • -
-
-
-
-
- -
-

Welcome to mmif-python’s documentation!

-
-
-

MMIF for python

-

NOTE that this project is in pre-alpha and being actively developed. Nothing is guaranteed to reliably work for the moment and developer need to be very careful when using APIs implemented here. Please use the issue track to report bugs and malfunctions.

-
-

MultiMedia Interchange Format

-

MMIF is a JSON(-LD)-based data format designed for transferring annotation data between computational analysis applications in CLAMS project.

-
-

Contents

- -
-
-

API documentation:

- -
-
-
-
-

Indices and tables

- -
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.5.1 - - -
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0.3.2
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- - - \ No newline at end of file diff --git a/docs/0.5.1/introduction.html b/docs/0.5.1/introduction.html deleted file mode 100644 index fefb2902..00000000 --- a/docs/0.5.1/introduction.html +++ /dev/null @@ -1,236 +0,0 @@ - - - - - - - - - Getting Started — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
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-
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    • -
  • Getting Started
    • -
  • -
    • -
-
-
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- -
-

Getting Started

-
-

Overview

-

MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF wbesite. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports de-/serialization of MMIF objects, as well as many navigation and manipulation helpers for MMIF objects.

-
-
-

Prerequisites

-
    -

  • Python: mmif-python requires Python 3.6 or newer. We have no plan to support Python 2.7.

    • -
-
-
-

Installation

-

Package mmif-python is distributed via the official PyPI. Users are supposed to pip-install to get latest release.

-
pip install mmif-python
-
-
-

This will install a package mmif to local python.

-

The MMIF format and specification is evolving over time, and mmif-python package will be updated along with the changes in MMIF format.

-
-

Note

-

MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and mmif-python versions, please take time to read our decision on the subject here. If you need to know which python SDK supports which specification version, see Target MMIF Versions page.

-
-
-
-

MMIF Serialization

-

mmif.serialize.mmif.Mmif represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of mmif.serialize.model.MmifObject, including the mmif.serialize.mmif.Mmif. To start with an existing MMIF str, simple initiate a new Mmif object with the file.

-
import mmif
-from mmif import Mmif
-
-mmif_str = """{
-"metadata": {
-  "mmif": "http://mmif.clams.ai/0.2.0"
-},
-"documents": [
-  {
-    "@type": "http://mmif.clams.ai/0.2.0/vocabulary/VideoDocument",
-    "properties": {
-      "id": "m1",
-      "mime": "video/mp4",
-      "location": "file:///var/archive/video-0012.mp4"
-    }
-  },
-  {
-    "@type": "http://mmif.clams.ai/0.2.0/vocabulary/TextDocument",
-    "properties": {
-      "id": "m2",
-      "mime": "text/plain",
-      "location": "file:///var/archive/video-0012-transcript.txt"
-    }
-  }
-],
-"views": []}"""
-mmif_obj = Mmif(mmif_str)
-
-
-

Few notes;

-
    -

  1. MMIF does not carry the primary source files in it.

    2. -

  2. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version mmif-python implementation of the MMIF might not be able to load an unsupported version of MMIF string.

    3. -
-

When serializing back to str, call .serialize() (mmif.serialize.model.MmifObject.serialize()) on the object.

-

To get subcomponents, you can use various getters implemented in subclasses. For more details, the API documentation (mmif package) will help.

-
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.5.1 - - -
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0.3.0
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0.3.1
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0.3.2
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0.3.3
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0.3.4
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0.3.5
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0.4.0
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0.4.1
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"interchang": 3, "mmif": [0, 1, 2, 3, 4, 5, 6], "model": 0, "modul": [0, 1], "multimedia": 3, "overview": 4, "packag": 5, "prerequisit": 4, "python": 3, "serial": [0, 4], "specif": 6, "start": 4, "tabl": 3, "target": 6, "version": 6, "view": 0, "vocabulari": 1, "welcom": 3}}) \ No newline at end of file diff --git a/docs/0.5.1/target-versions.html b/docs/0.5.1/target-versions.html deleted file mode 100644 index e4207473..00000000 --- a/docs/0.5.1/target-versions.html +++ /dev/null @@ -1,236 +0,0 @@ - - - - - - - - - Target MMIF Versions — mmif-python documentation - - - - - - - - - - - - - - - - - -
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  • Target MMIF Versions
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Target MMIF Versions

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This article provides targeting MMIF specification versions of different versions of mmif-python SDK.

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Target Specification Versions

mmif-python version

Target MMIF Specification

0.5.1

1.1.0

0.5.0

0.5.0

0.4.8

0.4.2

0.4.7

0.4.1

0.4.6

0.4.0

0.4.5

0.4.0

0.4.4

0.4.0

0.4.3

0.4.0

0.4.2

0.4.0

0.4.1

0.4.0

0.4.0

0.4.0

0.3.5

0.3.1

0.3.4

0.3.1

0.3.3

0.3.1

0.3.2

0.3.1

0.3.1

0.3.0

0.3.0

0.3.0

0.2.2

0.2.1

0.2.1

0.2.1

0.2.0

0.2.1

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0.3.0
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0.3.1
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0.3.2
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0.3.3
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0.3.4
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0.3.5
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0.4.0
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0.4.1
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0.4.2
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0.4.3
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0.4.4
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0.4.5
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0.4.6
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0.4.7
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0.4.8
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0.5.0
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0.5.1
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0.5.2
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1.0.0
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1.0.1
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1.0.10
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1.0.11
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1.0.12
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1.0.13
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1.0.14
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1.0.15
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1.0.16
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1.0.17
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1.0.18
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1.0.19
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1.0.2
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1.0.3
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1.0.4
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1.0.5
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1.0.6
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1.0.7
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1.0.8
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1.0.9
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1.1.0
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The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the `appliance documentation `_ to learn more about the appliance. - -MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance. - -#. The code must be hosted on a public git repository (e.g. Github, Gitlab, ...) -#. Must listen to ``5000`` port. -#. Must expose ``/display`` route . -#. ``/display`` router should response to ``GET`` requests. -#. In the ``GET`` request, a public URL of the input MMIF file is passed via ``file`` URL parameter. -#. On the codebase root, there must be a ``Dockerfile`` that can build a `docker `_ image that runs the web app. - -We provide an example consumer at https://github.com/clamsproject/mmif-visualizer. diff --git a/docs/0.5.2/_sources/index.rst.txt b/docs/0.5.2/_sources/index.rst.txt deleted file mode 100644 index 1f6c350c..00000000 --- a/docs/0.5.2/_sources/index.rst.txt +++ /dev/null @@ -1,25 +0,0 @@ -Welcome to mmif-python's documentation! -======================================= - -.. mdinclude:: ../README.md - -.. toctree:: - :maxdepth: 2 - :caption: Contents - - introduction - target-versions - -.. toctree:: - :maxdepth: 2 - :caption: API documentation: - - modules - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/docs/0.5.2/_sources/introduction.rst.txt b/docs/0.5.2/_sources/introduction.rst.txt deleted file mode 100644 index b1070185..00000000 --- a/docs/0.5.2/_sources/introduction.rst.txt +++ /dev/null @@ -1,89 +0,0 @@ -.. _instroduction: - -Getting Started -=============== - - -Overview ---------- - -MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for reproducibility, transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF website `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects. - -Prerequisites -------------- - -* `Python `_: the latest ``mmif-python`` requires Python 3.8 or newer. We have no plan to support `Python 2.7 `_. - -Installation ---------------- - -Package ``mmif-python`` is distributed via the official PyPI. Users are supposed to pip-install to get latest release. - -.. code-block:: bash - - pip install mmif-python - -This will install a package `mmif` to local python. - -The MMIF format and specification is evolving over time, and ``mmif-python`` package will be updated along with the changes in MMIF format. - -.. note:: MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and ``mmif-python`` versions, please take time to read our decision on the subject `here `_. If you need to know which python SDK supports which specification version, see :ref:`target-versions` page. - -MMIF Serialization ---------------------------- - -:class:`mmif.serialize.mmif.Mmif` represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of :class:`mmif.serialize.model.MmifObject`, including the :class:`mmif.serialize.mmif.Mmif`. To start with an existing MMIF :class:`str`, simple initiate a new ``Mmif`` object with the file. - -.. code-block:: python - - import mmif - from mmif import Mmif - - mmif_str = """{ - "metadata": { - "mmif": "http://mmif.clams.ai/1.0.0" - }, - "documents": [ - { - "@type": "http://mmif.clams.ai/vocabulary/VideoDocument/v1", - "properties": { - "id": "m1", - "mime": "video/mp4", - "location": "file:///var/archive/video-0012.mp4" - } - }, - { - "@type": "http://mmif.clams.ai/vocabulary/TextDocument/v1", - "properties": { - "id": "m2", - "mime": "text/plain", - "location": "file:///var/archive/video-0012-transcript.txt" - } - } - ], - "views": []}""" - mmif_obj = Mmif(mmif_str) - - -Few notes; - -#. MMIF does not carry the primary source files in it. -#. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version ``mmif-python`` implementation of the MMIF might not be able to load an unsupported version of MMIF string. - -When serializing back to :class:`str`, call :meth:`mmif.serialize.model.MmifObject.serialize` on the object. - -To get subcomponents, you can use various getters implemented in subclasses. For example; - -.. code-block:: python - - from mmif.vocabulary.document_types import DocumentTypes - - for video in mmif_obj.Mmif.get_documents_by_type(DocumentTypes.VideoDocument): - with open(video.location_path(), 'b') as in_video: - # do something with the video file - - -For a full list of available helper methods, please refer to :ref:`the API documentation `. - diff --git a/docs/0.5.2/_sources/modules.rst.txt b/docs/0.5.2/_sources/modules.rst.txt deleted file mode 100644 index e4269c6d..00000000 --- a/docs/0.5.2/_sources/modules.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _apidoc: - -mmif package -============ - -.. toctree:: - :maxdepth: 4 - - autodoc/mmif.serialize - autodoc/mmif.vocabulary diff --git a/docs/0.5.2/_sources/target-versions.rst.txt b/docs/0.5.2/_sources/target-versions.rst.txt deleted file mode 100644 index 34216d3e..00000000 --- a/docs/0.5.2/_sources/target-versions.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _target-versions: - -Target MMIF Versions -==================== - -This article provides targeting MMIF specification versions of different versions of ``mmif-python`` SDK. - -.. csv-table:: Target Specification Versions - :file: target-versions.csv - :header-rows: 1 diff --git a/docs/0.5.2/_static/_sphinx_javascript_frameworks_compat.js b/docs/0.5.2/_static/_sphinx_javascript_frameworks_compat.js deleted file mode 100644 index 81415803..00000000 --- a/docs/0.5.2/_static/_sphinx_javascript_frameworks_compat.js +++ /dev/null @@ -1,123 +0,0 @@ -/* Compatability shim for jQuery and underscores.js. - * - * Copyright Sphinx contributors - * Released under the two clause BSD licence - */ - -/** - * small helper function to urldecode strings - * - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL - */ -jQuery.urldecode = function(x) { - if (!x) { - return x - } - return decodeURIComponent(x.replace(/\+/g, ' ')); -}; - -/** - * small helper function to urlencode strings - */ -jQuery.urlencode = encodeURIComponent; - -/** - * This function returns the parsed url parameters of the - * current request. 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- -/** - * Simple result scoring code. - */ -if (typeof Scorer === "undefined") { - var Scorer = { - // Implement the following function to further tweak the score for each result - // The function takes a result array [docname, title, anchor, descr, score, filename] - // and returns the new score. - /* - score: result => { - const [docname, title, anchor, descr, score, filename, kind] = result - return score - }, - */ - - // query matches the full name of an object - objNameMatch: 11, - // or matches in the last dotted part of the object name - objPartialMatch: 6, - // Additive scores depending on the priority of the object - objPrio: { - 0: 15, // used to be importantResults - 1: 5, // used to be objectResults - 2: -5, // used to be unimportantResults - }, - // Used when the priority is not in the mapping. - objPrioDefault: 0, - - // query found in title - title: 15, - partialTitle: 7, - // query found in terms - term: 5, - partialTerm: 2, - }; -} - -// Global search result kind enum, used by themes to style search results. -class SearchResultKind { - static get index() { return "index"; } - static get object() { return "object"; } - static get text() { return "text"; } - static get title() { return "title"; } -} - -const _removeChildren = (element) => { - while (element && element.lastChild) element.removeChild(element.lastChild); -}; - -/** - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping - */ -const _escapeRegExp = (string) => - string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string - -const _displayItem = (item, searchTerms, highlightTerms) => { - const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; - const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; - const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; - const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; - const contentRoot = document.documentElement.dataset.content_root; - - const [docName, title, anchor, descr, score, _filename, kind] = item; - - let listItem = document.createElement("li"); - // Add a class representing the item's type: - // can be used by a theme's CSS selector for styling - // See SearchResultKind for the class names. - listItem.classList.add(`kind-${kind}`); - let requestUrl; - let linkUrl; - if (docBuilder === "dirhtml") { - // dirhtml builder - let dirname = docName + "/"; - if (dirname.match(/\/index\/$/)) - dirname = dirname.substring(0, dirname.length - 6); - else if (dirname === "index/") dirname = ""; - requestUrl = contentRoot + dirname; - linkUrl = requestUrl; - } else { - // normal html builders - requestUrl = contentRoot + docName + docFileSuffix; - linkUrl = docName + docLinkSuffix; - } - let linkEl = listItem.appendChild(document.createElement("a")); - linkEl.href = linkUrl + anchor; - linkEl.dataset.score = score; - linkEl.innerHTML = title; - if (descr) { - listItem.appendChild(document.createElement("span")).innerHTML = - " (" + descr + ")"; - // highlight search terms in the description - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - } - else if (showSearchSummary) - fetch(requestUrl) - .then((responseData) => responseData.text()) - .then((data) => { - if (data) - listItem.appendChild( - Search.makeSearchSummary(data, searchTerms, anchor) - ); - // highlight search terms in the summary - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - }); - Search.output.appendChild(listItem); -}; -const _finishSearch = (resultCount) => { - Search.stopPulse(); - Search.title.innerText = _("Search Results"); - if (!resultCount) - Search.status.innerText = Documentation.gettext( - "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." - ); - else - Search.status.innerText = Documentation.ngettext( - "Search finished, found one page matching the search query.", - "Search finished, found ${resultCount} pages matching the search query.", - resultCount, - ).replace('${resultCount}', resultCount); -}; -const _displayNextItem = ( - results, - resultCount, - searchTerms, - highlightTerms, -) => { - // results left, load the summary and display it - // this is intended to be dynamic (don't sub resultsCount) - if (results.length) { - _displayItem(results.pop(), searchTerms, highlightTerms); - setTimeout( - () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), - 5 - ); - } - // search finished, update title and status message - else _finishSearch(resultCount); -}; -// Helper function used by query() to order search results. -// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. -// Order the results by score (in opposite order of appearance, since the -// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. -const _orderResultsByScoreThenName = (a, b) => { - const leftScore = a[4]; - const rightScore = b[4]; - if (leftScore === rightScore) { - // same score: sort alphabetically - const leftTitle = a[1].toLowerCase(); - const rightTitle = b[1].toLowerCase(); - if (leftTitle === rightTitle) return 0; - return leftTitle > rightTitle ? -1 : 1; // inverted is intentional - } - return leftScore > rightScore ? 1 : -1; -}; - -/** - * Default splitQuery function. Can be overridden in ``sphinx.search`` with a - * custom function per language. - * - * The regular expression works by splitting the string on consecutive characters - * that are not Unicode letters, numbers, underscores, or emoji characters. - * This is the same as ``\W+`` in Python, preserving the surrogate pair area. - */ -if (typeof splitQuery === "undefined") { - var splitQuery = (query) => query - .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) - .filter(term => term) // remove remaining empty strings -} - -/** - * Search Module - */ -const Search = { - _index: null, - _queued_query: null, - _pulse_status: -1, - - htmlToText: (htmlString, anchor) => { - const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - for (const removalQuery of [".headerlink", "script", "style"]) { - htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); - } - if (anchor) { - const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); - if (anchorContent) return anchorContent.textContent; - - console.warn( - `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` - ); - } - - // if anchor not specified or not found, fall back to main content - const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent) return docContent.textContent; - - console.warn( - "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." - ); - return ""; - }, - - init: () => { - const query = new URLSearchParams(window.location.search).get("q"); - document - .querySelectorAll('input[name="q"]') - .forEach((el) => (el.value = query)); - if (query) Search.performSearch(query); - }, - - loadIndex: (url) => - (document.body.appendChild(document.createElement("script")).src = url), - - setIndex: (index) => { - Search._index = index; - if (Search._queued_query !== null) { - const query = Search._queued_query; - Search._queued_query = null; - Search.query(query); - } - }, - - hasIndex: () => Search._index !== null, - - deferQuery: (query) => (Search._queued_query = query), - - stopPulse: () => (Search._pulse_status = -1), - - startPulse: () => { - if (Search._pulse_status >= 0) return; - - const pulse = () => { - Search._pulse_status = (Search._pulse_status + 1) % 4; - Search.dots.innerText = ".".repeat(Search._pulse_status); - if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); - }; - pulse(); - }, - - /** - * perform a search for something (or wait until index is loaded) - */ - performSearch: (query) => { - // create the required interface elements - const searchText = document.createElement("h2"); - searchText.textContent = _("Searching"); - const searchSummary = document.createElement("p"); - searchSummary.classList.add("search-summary"); - searchSummary.innerText = ""; - const searchList = document.createElement("ul"); - searchList.setAttribute("role", "list"); - searchList.classList.add("search"); - - const out = document.getElementById("search-results"); - Search.title = out.appendChild(searchText); - Search.dots = Search.title.appendChild(document.createElement("span")); - Search.status = out.appendChild(searchSummary); - Search.output = out.appendChild(searchList); - - const searchProgress = document.getElementById("search-progress"); - // Some themes don't use the search progress node - if (searchProgress) { - searchProgress.innerText = _("Preparing search..."); - } - Search.startPulse(); - - // index already loaded, the browser was quick! - if (Search.hasIndex()) Search.query(query); - else Search.deferQuery(query); - }, - - _parseQuery: (query) => { - // stem the search terms and add them to the correct list - const stemmer = new Stemmer(); - const searchTerms = new Set(); - const excludedTerms = new Set(); - const highlightTerms = new Set(); - const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); - splitQuery(query.trim()).forEach((queryTerm) => { - const queryTermLower = queryTerm.toLowerCase(); - - // maybe skip this "word" - // stopwords array is from language_data.js - if ( - stopwords.indexOf(queryTermLower) !== -1 || - queryTerm.match(/^\d+$/) - ) - return; - - // stem the word - let word = stemmer.stemWord(queryTermLower); - // select the correct list - if (word[0] === "-") excludedTerms.add(word.substr(1)); - else { - searchTerms.add(word); - highlightTerms.add(queryTermLower); - } - }); - - if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js - localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) - } - - // console.debug("SEARCH: searching for:"); - // console.info("required: ", [...searchTerms]); - // console.info("excluded: ", [...excludedTerms]); - - return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; - }, - - /** - * execute search (requires search index to be loaded) - */ - _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - - // Collect multiple result groups to be sorted separately and then ordered. - // Each is an array of [docname, title, anchor, descr, score, filename, kind]. - const normalResults = []; - const nonMainIndexResults = []; - - _removeChildren(document.getElementById("search-progress")); - - const queryLower = query.toLowerCase().trim(); - for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { - for (const [file, id] of foundTitles) { - const score = Math.round(Scorer.title * queryLower.length / title.length); - const boost = titles[file] === title ? 1 : 0; // add a boost for document titles - normalResults.push([ - docNames[file], - titles[file] !== title ? `${titles[file]} > ${title}` : title, - id !== null ? "#" + id : "", - null, - score + boost, - filenames[file], - SearchResultKind.title, - ]); - } - } - } - - // search for explicit entries in index directives - for (const [entry, foundEntries] of Object.entries(indexEntries)) { - if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id, isMain] of foundEntries) { - const score = Math.round(100 * queryLower.length / entry.length); - const result = [ - docNames[file], - titles[file], - id ? "#" + id : "", - null, - score, - filenames[file], - SearchResultKind.index, - ]; - if (isMain) { - normalResults.push(result); - } else { - nonMainIndexResults.push(result); - } - } - } - } - - // lookup as object - objectTerms.forEach((term) => - normalResults.push(...Search.performObjectSearch(term, objectTerms)) - ); - - // lookup as search terms in fulltext - normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); - - // let the scorer override scores with a custom scoring function - if (Scorer.score) { - normalResults.forEach((item) => (item[4] = Scorer.score(item))); - nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); - } - - // Sort each group of results by score and then alphabetically by name. - normalResults.sort(_orderResultsByScoreThenName); - nonMainIndexResults.sort(_orderResultsByScoreThenName); - - // Combine the result groups in (reverse) order. - // Non-main index entries are typically arbitrary cross-references, - // so display them after other results. - let results = [...nonMainIndexResults, ...normalResults]; - - // remove duplicate search results - // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept - let seen = new Set(); - results = results.reverse().reduce((acc, result) => { - let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); - if (!seen.has(resultStr)) { - acc.push(result); - seen.add(resultStr); - } - return acc; - }, []); - - return results.reverse(); - }, - - query: (query) => { - const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); - const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); - - // for debugging - //Search.lastresults = results.slice(); // a copy - // console.info("search results:", Search.lastresults); - - // print the results - _displayNextItem(results, results.length, searchTerms, highlightTerms); - }, - - /** - * search for object names - */ - performObjectSearch: (object, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const objects = Search._index.objects; - const objNames = Search._index.objnames; - const titles = Search._index.titles; - - const results = []; - - const objectSearchCallback = (prefix, match) => { - const name = match[4] - const fullname = (prefix ? prefix + "." : "") + name; - const fullnameLower = fullname.toLowerCase(); - if (fullnameLower.indexOf(object) < 0) return; - - let score = 0; - const parts = fullnameLower.split("."); - - // check for different match types: exact matches of full name or - // "last name" (i.e. last dotted part) - if (fullnameLower === object || parts.slice(-1)[0] === object) - score += Scorer.objNameMatch; - else if (parts.slice(-1)[0].indexOf(object) > -1) - score += Scorer.objPartialMatch; // matches in last name - - const objName = objNames[match[1]][2]; - const title = titles[match[0]]; - - // If more than one term searched for, we require other words to be - // found in the name/title/description - const otherTerms = new Set(objectTerms); - otherTerms.delete(object); - if (otherTerms.size > 0) { - const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); - if ( - [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) - ) - return; - } - - let anchor = match[3]; - if (anchor === "") anchor = fullname; - else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; - - const descr = objName + _(", in ") + title; - - // add custom score for some objects according to scorer - if (Scorer.objPrio.hasOwnProperty(match[2])) - score += Scorer.objPrio[match[2]]; - else score += Scorer.objPrioDefault; - - results.push([ - docNames[match[0]], - fullname, - "#" + anchor, - descr, - score, - filenames[match[0]], - SearchResultKind.object, - ]); - }; - Object.keys(objects).forEach((prefix) => - objects[prefix].forEach((array) => - objectSearchCallback(prefix, array) - ) - ); - return results; - }, - - /** - * search for full-text terms in the index - */ - performTermsSearch: (searchTerms, excludedTerms) => { - // prepare search - const terms = Search._index.terms; - const titleTerms = Search._index.titleterms; - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - - const scoreMap = new Map(); - const fileMap = new Map(); - - // perform the search on the required terms - searchTerms.forEach((word) => { - const files = []; - const arr = [ - { files: terms[word], score: Scorer.term }, - { files: titleTerms[word], score: Scorer.title }, - ]; - // add support for partial matches - if (word.length > 2) { - const escapedWord = _escapeRegExp(word); - if (!terms.hasOwnProperty(word)) { - Object.keys(terms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: terms[term], score: Scorer.partialTerm }); - }); - } - if (!titleTerms.hasOwnProperty(word)) { - Object.keys(titleTerms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); - }); - } - } - - // no match but word was a required one - if (arr.every((record) => record.files === undefined)) return; - - // found search word in contents - arr.forEach((record) => { - if (record.files === undefined) return; - - let recordFiles = record.files; - if (recordFiles.length === undefined) recordFiles = [recordFiles]; - files.push(...recordFiles); - - // set score for the word in each file - recordFiles.forEach((file) => { - if (!scoreMap.has(file)) scoreMap.set(file, {}); - scoreMap.get(file)[word] = record.score; - }); - }); - - // create the mapping - files.forEach((file) => { - if (!fileMap.has(file)) fileMap.set(file, [word]); - else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); - }); - }); - - // now check if the files don't contain excluded terms - const results = []; - for (const [file, wordList] of fileMap) { - // check if all requirements are matched - - // as search terms with length < 3 are discarded - const filteredTermCount = [...searchTerms].filter( - (term) => term.length > 2 - ).length; - if ( - wordList.length !== searchTerms.size && - wordList.length !== filteredTermCount - ) - continue; - - // ensure that none of the excluded terms is in the search result - if ( - [...excludedTerms].some( - (term) => - terms[term] === file || - titleTerms[term] === file || - (terms[term] || []).includes(file) || - (titleTerms[term] || []).includes(file) - ) - ) - break; - - // select one (max) score for the file. - const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); - // add result to the result list - results.push([ - docNames[file], - titles[file], - "", - null, - score, - filenames[file], - SearchResultKind.text, - ]); - } - return results; - }, - - /** - * helper function to return a node containing the - * search summary for a given text. keywords is a list - * of stemmed words. - */ - makeSearchSummary: (htmlText, keywords, anchor) => { - const text = Search.htmlToText(htmlText, anchor); - if (text === "") return null; - - const textLower = text.toLowerCase(); - const actualStartPosition = [...keywords] - .map((k) => textLower.indexOf(k.toLowerCase())) - .filter((i) => i > -1) - .slice(-1)[0]; - const startWithContext = Math.max(actualStartPosition - 120, 0); - - const top = startWithContext === 0 ? "" : "..."; - const tail = startWithContext + 240 < text.length ? "..." : ""; - - let summary = document.createElement("p"); - summary.classList.add("context"); - summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; - - return summary; - }, -}; - -_ready(Search.init); diff --git a/docs/0.5.2/_static/sphinx_highlight.js b/docs/0.5.2/_static/sphinx_highlight.js deleted file mode 100644 index 8a96c69a..00000000 --- a/docs/0.5.2/_static/sphinx_highlight.js +++ /dev/null @@ -1,154 +0,0 @@ -/* Highlighting utilities for Sphinx HTML documentation. */ -"use strict"; - -const SPHINX_HIGHLIGHT_ENABLED = true - -/** - * highlight a given string on a node by wrapping it in - * span elements with the given class name. - */ -const _highlight = (node, addItems, text, className) => { - if (node.nodeType === Node.TEXT_NODE) { - const val = node.nodeValue; - const parent = node.parentNode; - const pos = val.toLowerCase().indexOf(text); - if ( - pos >= 0 && - !parent.classList.contains(className) && - !parent.classList.contains("nohighlight") - ) { - let span; - - const closestNode = parent.closest("body, svg, foreignObject"); - const isInSVG = closestNode && closestNode.matches("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.classList.add(className); - } - - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - const rest = document.createTextNode(val.substr(pos + text.length)); - parent.insertBefore( - span, - parent.insertBefore( - rest, - node.nextSibling - ) - ); - node.nodeValue = val.substr(0, pos); - /* There may be more occurrences of search term in this node. So call this - * function recursively on the remaining fragment. - */ - _highlight(rest, addItems, text, className); - - if (isInSVG) { - const rect = document.createElementNS( - "http://www.w3.org/2000/svg", - "rect" - ); - const bbox = parent.getBBox(); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute("class", className); - addItems.push({ parent: parent, target: rect }); - } - } - } else if (node.matches && !node.matches("button, select, textarea")) { - node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); - } -}; -const _highlightText = (thisNode, text, className) => { - let addItems = []; - _highlight(thisNode, addItems, text, className); - addItems.forEach((obj) => - obj.parent.insertAdjacentElement("beforebegin", obj.target) - ); -}; - -/** - * Small JavaScript module for the documentation. - */ -const SphinxHighlight = { - - /** - * highlight the search words provided in localstorage in the text - */ - highlightSearchWords: () => { - if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight - - // get and clear terms from localstorage - const url = new URL(window.location); - const highlight = - localStorage.getItem("sphinx_highlight_terms") - || url.searchParams.get("highlight") - || ""; - localStorage.removeItem("sphinx_highlight_terms") - url.searchParams.delete("highlight"); - window.history.replaceState({}, "", url); - - // get individual terms from highlight string - const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); - if (terms.length === 0) return; // nothing to do - - // There should never be more than one element matching "div.body" - const divBody = document.querySelectorAll("div.body"); - const body = divBody.length ? divBody[0] : document.querySelector("body"); - window.setTimeout(() => { - terms.forEach((term) => _highlightText(body, term, "highlighted")); - }, 10); - - const searchBox = document.getElementById("searchbox"); - if (searchBox === null) return; - searchBox.appendChild( - document - .createRange() - .createContextualFragment( - '

' + - '' + - _("Hide Search Matches") + - "

" - ) - ); - }, - - /** - * helper function to hide the search marks again - */ - hideSearchWords: () => { - document - .querySelectorAll("#searchbox .highlight-link") - .forEach((el) => el.remove()); - document - .querySelectorAll("span.highlighted") - .forEach((el) => el.classList.remove("highlighted")); - localStorage.removeItem("sphinx_highlight_terms") - }, - - initEscapeListener: () => { - // only install a listener if it is really needed - if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; - - document.addEventListener("keydown", (event) => { - // bail for input elements - if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; - // bail with special keys - if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; - if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { - SphinxHighlight.hideSearchWords(); - event.preventDefault(); - } - }); - }, -}; - -_ready(() => { - /* Do not call highlightSearchWords() when we are on the search page. - * It will highlight words from the *previous* search query. - */ - if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); - SphinxHighlight.initEscapeListener(); -}); diff --git a/docs/0.5.2/autodoc/mmif.serialize.html b/docs/0.5.2/autodoc/mmif.serialize.html deleted file mode 100644 index 1cdfbc5a..00000000 --- a/docs/0.5.2/autodoc/mmif.serialize.html +++ /dev/null @@ -1,1175 +0,0 @@ - - - - - - - - - mmif.serialize module — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.serialize module

-
-

mmif.serialize.model module

-

The model module contains the classes used to represent an -abstract MMIF object as a live Python object.

-

The MmifObject class or one of its derivatives is subclassed by -all other classes defined in this SDK, except for MmifObjectEncoder.

-

These objects are generally instantiated from JSON, either as a string -or as an already-loaded Python dictionary. This base class provides the -core functionality for deserializing MMIF JSON data into live objects -and serializing live objects into MMIF JSON data. Specialized behavior -for the different components of MMIF is added in the subclasses.

-
-
-class mmif.serialize.model.DataDict(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject, Generic[T, S]

-
-
-empty()[source]
-
- -
-
-get(key: T, default=None) → S | None[source]
-
- -
-
-items()[source]
-
- -
-
-keys()[source]
-
- -
-
-update(other, overwrite)[source]
-
- -
-
-values()[source]
-
- -
- -
-
-class mmif.serialize.model.DataList(mmif_obj: bytes | str | list | None = None)[source]
-

Bases: MmifObject, Generic[T]

-

The DataList class is an abstraction that represents the -various lists found in a MMIF file, such as documents, subdocuments, -views, and annotations.

-
-
Parameters:
-

mmif_obj (Union[str, list]) – the data that the list contains

-
-
-
-
-append(value, overwrite)[source]
-
- -
-
-deserialize(mmif_json: str | list) → None[source]
-

Passes the input data into the internal deserializer.

-
- -
-
-empty()[source]
-
- -
-
-get(key: str) → T | None[source]
-

Standard dictionary-style get() method, albeit with no default -parameter. Relies on the implementation of __getitem__.

-

Will return None if the key is not found.

-
-
Parameters:
-

key – the key to search for

-
-
Returns:
-

the value matching that key

-
-
-
- -
- -
-
-class mmif.serialize.model.MmifObject(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: object

-

Abstract superclass for MMIF related key-value pair objects.

-

Any MMIF object can be initialized as an empty placeholder or -an actual representation with a JSON formatted string or equivalent -dict object argument.

-

This superclass has four specially designed instance variables, and these -variable names cannot be used as attribute names for MMIF objects.

-
    -

  1. _unnamed_attributes: -Only can be either None or an empty dictionary. If it’s set to None, -it means the class won’t take any Additional Attributes in the JSON -schema sense. If it’s a dict, users can throw any k-v pairs to the -class, EXCEPT for the reserved two key names.

    2. -

  2. _attribute_classes: -This is a dict from a key name to a specific python class to use for -deserialize the value. Note that a key name in this dict does NOT -have to be a named attribute, but is recommended to be one.

    3. -

  3. _required_attributes: -This is a simple list of names of attributes that are required in the object. -When serialize, an object will skip its empty (e.g. zero-length, or None) -attributes unless they are in this list. Otherwise, the serialized JSON -string would have empty representations (e.g. "", []).

    4. -

  4. _exclude_from_diff: -This is a simple list of names of attributes that should be excluded from -the diff calculation in __eq__.

    5. -
-

# TODO (krim @ 8/17/20): this dict is however, a duplicate with the type hints in the class definition. -Maybe there is a better way to utilize type hints (e.g. getting them as a programmatically), but for now -developers should be careful to add types to hints as well as to this dict.

-

Also note that those special attributes MUST be set in the __init__() -before calling super method, otherwise deserialization will not work.

-

And also, a subclass that has one or more named attributes, it must -set those attributes in the __init__() before calling super method. When -serializing a MmifObject, all empty attributes will be ignored, so for -optional named attributes, you must leave the values empty (len == 0), but -NOT None. Any None-valued named attributes will cause issues with current -implementation.

-
-
Parameters:
-

mmif_obj – JSON string or dict to initialize an object. -If not given, an empty object will be initialized, sometimes with -an ID value automatically generated, based on its parent object.

-
-
-
-
-deserialize(mmif_json: str | dict) → None[source]
-

Takes a JSON-formatted string or a simple dict that’s json-loaded from -such a string as an input and populates object’s fields with the values -specified in the input.

-
-
Parameters:
-

mmif_json – JSON-formatted string or dict from such a string -that represents a MMIF object

-
-
-
- -
-
-disallow_additional_properties() → None[source]
-

Call this method in __init__() to prevent the insertion -of unnamed attributes after initialization.

-
- -
-
-static is_empty(obj) → bool[source]
-

return True if the obj is None or “emtpy”. The emptiness first defined as -having zero length. But for objects that lack __len__ method, we need -additional check.

-
- -
-
-reserved_names: Set[str] = {'_attribute_classes', '_exclude_from_diff', '_required_attributes', '_unnamed_attributes', 'reserved_names'}[source]
-
- -
-
-serialize(pretty: bool = False) → str[source]
-

Generates JSON representation of an object.

-
-
Parameters:
-

pretty – If True, returns string representation with indentation.

-
-
Returns:
-

JSON string of the object.

-
-
-
- -
-
-set_additional_property(key: str, value: Any) → None[source]
-

Method to set values in _unnamed_attributes.

-
-
Parameters:
-
    -

  • key – the attribute name

    • -

  • value – the desired value

    • -
-
-
Returns:
-

None

-
-
Raise:
-

AttributeError if additional properties are disallowed by disallow_additional_properties()

-
-
-
- -
- -
-
-class mmif.serialize.model.MmifObjectEncoder(*, skipkeys=False, ensure_ascii=True, check_circular=True, allow_nan=True, sort_keys=False, indent=None, separators=None, default=None)[source]
-

Bases: JSONEncoder

-

Encoder class to define behaviors of de-/serialization

-
-
-default(obj: MmifObject)[source]
-

Overrides default encoding behavior to prioritize MmifObject.serialize().

-
- -
- -
-
-

mmif.serialize.mmif module

-

The mmif module contains the classes used to represent a full MMIF -file as a live Python object.

-

See the specification docs and the JSON Schema file for more information.

-
-
-class mmif.serialize.mmif.Mmif(mmif_obj: bytes | str | dict | None = None, *, validate: bool = True)[source]
-

Bases: MmifObject

-

MmifObject that represents a full MMIF file.

-
-
Parameters:
-
    -

  • mmif_obj – the JSON data

    • -

  • validate – whether to validate the data against the MMIF JSON schema.

    • -
-
-
-
-
-add_document(document: Document, overwrite=False) → None[source]
-

Appends a Document object to the documents list.

-

Fails if there is already a document with the same ID in the MMIF object.

-
-
Parameters:
-
    -

  • document – the Document object to add

    • -

  • overwrite – if set to True, will overwrite -an existing view with the same ID

    • -
-
-
Returns:
-

None

-
-
-
- -
-
-add_view(view: View, overwrite=False) → None[source]
-

Appends a View object to the views list.

-

Fails if there is already a view with the same ID in the MMIF object.

-
-
Parameters:
-
    -

  • view – the Document object to add

    • -

  • overwrite – if set to True, will overwrite -an existing view with the same ID

    • -
-
-
Returns:
-

None

-
-
-
- -
-
-get_alignments(at_type1: str | TypesBase, at_type2: str | TypesBase) → Dict[str, List[Annotation]][source]
-

Finds views where alignments between two given annotation types occurred.

-
-
Returns:
-

a dict that keyed by view IDs (str) and has lists of alignment Annotation objects as values.

-
-
-
- -
-
-get_all_views_contain(at_types: TypesBase | str | List[str | TypesBase]) → List[View][source]
-

Returns the list of all views in the MMIF if given types -are present in that view’s ‘contains’ metadata.

-
-
Parameters:
-

at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

-
-
Returns:
-

the list of views that contain the type

-
-
-
- -
-
-get_document_by_id(doc_id: str) → Document[source]
-

Finds a Document object with the given ID.

-
-
Parameters:
-

doc_id – the ID to search for

-
-
Returns:
-

a reference to the corresponding document, if it exists

-
-
Raises:
-

Exception – if there is no corresponding document

-
-
-
- -
-
-get_document_location(m_type: DocumentTypes | str, path_only=False) → str | None[source]
-

Method to get the location of first document of given type.

-
-
Parameters:
-

m_type – the type to search for

-
-
Returns:
-

the value of the location field in the corresponding document

-
-
-
- -
-
-get_documents_by_app(app_id: str) → List[Document][source]
-

Method to get all documents object queries by its originated app name.

-
-
Parameters:
-

app_id – the app name to search for

-
-
Returns:
-

a list of documents matching the requested app name, or an empty list if the app not found

-
-
-
- -
-
-get_documents_by_property(prop_key: str, prop_value: str) → List[Document][source]
-

Method to retrieve documents by an arbitrary key-value pair in the document properties objects.

-
-
Parameters:
-
    -

  • prop_key – the metadata key to search for

    • -

  • prop_value – the metadata value to match

    • -
-
-
Returns:
-

a list of documents matching the requested metadata key-value pair

-
-
-
- -
-
-get_documents_by_type(doc_type: str | DocumentTypes) → List[Document][source]
-

Method to get all documents where the type matches a particular document type, which should be one of the CLAMS document types.

-
-
Parameters:
-

doc_type – the type of documents to search for, must be one of Document type defined in the CLAMS vocabulary.

-
-
Returns:
-

a list of documents matching the requested type, or an empty list if none found.

-
-
-
- -
-
-get_documents_in_view(vid: str | None = None) → List[Document][source]
-

Method to get all documents object queries by a view id.

-
-
Parameters:
-

vid – the source view ID to search for

-
-
Returns:
-

a list of documents matching the requested source view ID, or an empty list if the view not found

-
-
-
- -
-
-get_documents_locations(m_type: DocumentTypes | str, path_only=False) → List[str | None][source]
-

This method returns the file paths of documents of given type. -Only top-level documents have locations, so we only check them.

-
-
Parameters:
-

m_type – the type to search for

-
-
Returns:
-

a list of the values of the location fields in the corresponding documents

-
-
-
- -
-
-get_view_by_id(req_view_id: str) → View[source]
-

Finds a View object with the given ID.

-
-
Parameters:
-

req_view_id – the ID to search for

-
-
Returns:
-

a reference to the corresponding view, if it exists

-
-
Raises:
-

Exception – if there is no corresponding view

-
-
-
- -
-
-get_view_contains(at_types: TypesBase | str | List[str | TypesBase]) → View | None[source]
-

Returns the last view appended that contains the given -types in its ‘contains’ metadata.

-
-
Parameters:
-

at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

-
-
Returns:
-

the view, or None if the type is not found

-
-
-
- -
-
-get_views_contain(at_types: TypesBase | str | List[str | TypesBase]) → List[View][source]
-

An alias to get_all_views_contain method.

-
- -
-
-get_views_for_document(doc_id: str)[source]
-

Returns the list of all views that have annotations anchored on a particular document. -Note that when the document is insids a view (generated during the pipeline’s running), -doc_id must be prefixed with the view_id.

-
- -
-
-id_delimiter: ClassVar[str] = ':'[source]
-
- -
-
-new_view() → View[source]
-

Creates an empty view with a new ID and appends it to the views list.

-
-
Returns:
-

a reference to the new View object

-
-
-
- -
-
-new_view_id() → str[source]
-

Fetches an ID for a new view.

-
-
Returns:
-

the ID

-
-
-
- -
-
-sanitize()[source]
-

Sanitizes a Mmif object by running some safeguards. -Concretely, it performs the following before returning the JSON string.

-
    -

  1. validating output using built-in MMIF jsonschema

    2. -

  2. remove non-existing annotation types from contains metadata

    3. -
-
- -
-
-serialize(pretty: bool = False, sanitize: bool = False) → str[source]
-

Generates JSON representation of an object.

-
-
Parameters:
-

pretty – If True, returns string representation with indentation.

-
-
Returns:
-

JSON string of the object.

-
-
-
- -
-
-static validate(json_str: bytes | str | dict) → None[source]
-

Validates a MMIF JSON object against the MMIF Schema. -Note that this method operates before processing by MmifObject._load_str, -so it expects @ and not _ for the JSON-LD @-keys.

-
-
Raises:
-

jsonschema.exceptions.ValidationError – if the input fails validation

-
-
Parameters:
-

json_str – a MMIF JSON dict or string

-
-
Returns:
-

None

-
-
-
- -
-
-view_prefix: ClassVar[str] = 'v_'[source]
-
- -
- -
-
-

mmif.serialize.view module

-

The view module contains the classes used to represent a MMIF view -as a live Python object.

-

In MMIF, views are created by apps in a pipeline that are annotating -data that was previously present in the MMIF file.

-
-
-class mmif.serialize.view.Contain(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-

Contain object that represents the metadata of a single -annotation type in the contains metadata of a MMIF view.

-
- -
-
-class mmif.serialize.view.View(view_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-

View object that represents a single view in a MMIF file.

-

A view is identified by an ID, and contains certain metadata, -a list of annotations, and potentially a JSON-LD @context -IRI.

-

If view_obj is not provided, an empty View will be generated.

-
-
Parameters:
-

view_obj – the JSON data that defines the view

-
-
-
-
-add_annotation(annotation: Annotation, overwrite=False) → Annotation[source]
-

Adds an annotation to the current view.

-

Fails if there is already an annotation with the same ID -in the view, unless overwrite is set to True.

-
-
Parameters:
-
-
-
Raises:
-

KeyError – if overwrite is set to False and -an annotation with the same ID exists -in the view

-
-
Returns:
-

the same Annotation object passed in as annotation

-
-
-
- -
-
-add_document(document: Document, overwrite=False) → Annotation[source]
-

Appends a Document object to the annotations list.

-

Fails if there is already a document with the same ID in the annotations list.

-
-
Parameters:
-
    -

  • document – the Document object to add

    • -

  • overwrite – if set to True, will overwrite -an existing view with the same ID

    • -
-
-
Returns:
-

None

-
-
-
- -
-
-get_annotation_by_id(ann_id)[source]
-
- -
-
-get_annotations(at_type: str | TypesBase | None = None, **properties) → Generator[Annotation, None, None][source]
-

Look for certain annotations in this view, specified by parameters

-
-
Parameters:
-
    -

  • at_type – @type of the annotations to look for. When this is None, any @type will match.

    • -

  • properties – properties of the annotations to look for. When given more than one property, all properties must match. Note that annotation type metadata are specified in the contains view metadata, not in individual annotation objects.

    • -
-
-
-
- -
-
-get_document_by_id(doc_id) → Document[source]
-
- -
-
-get_documents() → List[Document][source]
-
- -
-
-new_annotation(at_type: str | TypesBase, aid: str | None = None, overwrite=False, **properties) → Annotation[source]
-

Generates a new mmif.serialize.annotation.Annotation -object and adds it to the current view.

-

Fails if there is already an annotation with the same ID -in the view, unless overwrite is set to True.

-
-
Parameters:
-
    -

  • at_type – the desired @type of the annotation.

    • -

  • aid – the desired ID of the annotation, when not given, -the mmif SDK tries to automatically generate an ID based on -Annotation type and existing annotations in the view.

    • -

  • overwrite – if set to True, will overwrite an -existing annotation with the same ID.

    • -
-
-
Raises:
-

KeyError – if overwrite is set to False and -an annotation with the same ID exists -in the view.

-
-
Returns:
-

the generated mmif.serialize.annotation.Annotation

-
-
-
- -
-
-new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
-

Adds a new element to the contains metadata.

-
-
Parameters:
-
    -

  • at_type – the @type of the annotation type being added

    • -

  • contains_metadata – any metadata associated with the annotation type

    • -
-
-
Returns:
-

the generated Contain object

-
-
-
- -
-
-new_textdocument(text: str, lang: str = 'en', did: str | None = None, overwrite=False, **properties) → Document[source]
-

Generates a new mmif.serialize.annotation.Document -object, particularly typed as TextDocument and adds it to the current view.

-

Fails if there is already a text document with the same ID -in the view, unless overwrite is set to True.

-
-
Parameters:
-
    -

  • text – text content of the new document

    • -

  • lang – ISO 639-1 code of the language used in the new document

    • -

  • did – the desired ID of the document, when not given, -the mmif SDK tries to automatically generate an ID based on -Annotation type and existing documents in the view.

    • -

  • overwrite – if set to True, will overwrite an -existing document with the same ID

    • -
-
-
Raises:
-

KeyError – if overwrite is set to False and -an document with the same ID exists -in the view

-
-
Returns:
-

the generated mmif.serialize.annotation.Document

-
-
-
- -
-
-set_error(err_message: str, err_trace: str) → None[source]
-
- -
- -
-
-class mmif.serialize.view.ViewMetadata(viewmetadata_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-

ViewMetadata object that represents the metadata object within a MMIF view.

-
-
Parameters:
-

viewmetadata_obj – the JSON data that defines the metadata

-
-
-
-
-add_parameter(param_key, param_value)[source]
-
- -
-
-add_parameters(**runtime_params)[source]
-
- -
-
-add_warnings(*warnings: Warning)[source]
-
- -
-
-emtpy_warnings()[source]
-
- -
-
-get_parameter(param_key)[source]
-
- -
-
-new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
-

Adds a new element to the contains dictionary.

-
-
Parameters:
-
    -

  • at_type – the @type of the annotation type being added

    • -

  • contains_metadata – any metadata associated with the annotation type

    • -
-
-
Returns:
-

the generated Contain object

-
-
-
- -
-
-set_error(message: str, stack_trace: str)[source]
-
- -
- -
-
-

mmif.serialize.annotation module

-

The annotation module contains the classes used to represent a -MMIF annotation as a live Python object.

-

In MMIF, annotations are created by apps in a pipeline as a part -of a view. For documentation on how views are represented, see -mmif.serialize.view.

-
-
-class mmif.serialize.annotation.Annotation(anno_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-

MmifObject that represents an annotation in a MMIF view.

-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]]) → None[source]
-

Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

-
- -
-
-property at_type: TypesBase[source]
-
- -
-
-property id: str[source]
-
- -
-
-is_document()[source]
-
- -
-
-is_type(at_type: str | TypesBase) → bool[source]
-

Check if the @type of this object matches.

-
- -
- -
-
-class mmif.serialize.annotation.AnnotationProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject, MutableMapping[str, T]

-

AnnotationProperties object that represents the -properties object within a MMIF annotation.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
- -
-
-class mmif.serialize.annotation.Document(doc_obj: bytes | str | dict | None = None)[source]
-

Bases: Annotation

-

Document object that represents a single document in a MMIF file.

-

A document is identified by an ID, and contains certain attributes -and potentially contains the contents of the document itself, -metadata about how the document was created, and/or a list of -subdocuments grouped together logically.

-

If document_obj is not provided, an empty Document will be generated.

-
-
Parameters:
-

document_obj – the JSON data that defines the document

-
-
-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None]) → None[source]
-

Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

-
- -
-
-property location: str | None[source]
-

location property must be a legitimate URI. That is, should the document be a local file -then the file:// scheme must be used. -Returns None when no location is set.

-
- -
-
-location_address() → str | None[source]
-

Retrieves the full address from the document location URI. -Returns None when no location is set.

-
- -
-
-location_path() → str | None[source]
-

Retrieves only path name of the document location (hostname is ignored). -Useful to get a path of a local file. -Returns None when no location is set.

-
- -
-
-location_scheme() → str | None[source]
-

Retrieves URI scheme of the document location. -Returns None when no location is set.

-
- -
-
-property parent: str[source]
-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.DocumentProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: AnnotationProperties

-

DocumentProperties object that represents the -properties object within a MMIF document.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
-
-property location: str | None[source]
-

location property must be a legitimate URI. That is, should the document be a local file -then the file:// scheme must be used. -Returns None when no location is set.

-
- -
-
-location_address() → str | None[source]
-

Retrieves the full address from the document location URI. -Returns None when no location is set.

-
- -
-
-location_path() → str | None[source]
-

Retrieves only path name of the document location (hostname is ignored). -Useful to get a path of a local file. -Returns None when no location is set.

-
- -
-
-location_scheme() → str | None[source]
-

Retrieves URI scheme of the document location. -Returns None when no location is set.

-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.Text(text_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-
-
-property lang: str[source]
-
- -
-
-property value: str[source]
-
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- - - \ No newline at end of file diff --git a/docs/0.5.2/autodoc/mmif.vocabulary.html b/docs/0.5.2/autodoc/mmif.vocabulary.html deleted file mode 100644 index ce31e984..00000000 --- a/docs/0.5.2/autodoc/mmif.vocabulary.html +++ /dev/null @@ -1,324 +0,0 @@ - - - - - - - - - mmif.vocabulary module — mmif-python documentation - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.vocabulary module

-
-

mmif.vocabulary.annotation_types module

-
-
-class mmif.vocabulary.annotation_types.AnnotationTypes(type_uri, fuzzymode=True)[source]
-

Bases: AnnotationTypesBase

-

This class contains the CLAMS annotation types -defined in the spec version 1.1.0 as class variables.

-
-
-Alignment = http://mmif.clams.ai/vocabulary/Alignment/v1[source]
-
- -
-
-Annotation = http://mmif.clams.ai/vocabulary/Annotation/v6[source]
-
- -
-
-BoundingBox = http://mmif.clams.ai/vocabulary/BoundingBox/v5[source]
-
- -
-
-Chapter = http://mmif.clams.ai/vocabulary/Chapter/v6[source]
-
- -
-
-Interval = http://mmif.clams.ai/vocabulary/Interval/v5[source]
-
- -
-
-NamedEntity = http://mmif.clams.ai/vocabulary/NamedEntity/v1[source]
-
- -
-
-NounChunk = http://mmif.clams.ai/vocabulary/NounChunk/v1[source]
-
- -
-
-Paragraph = http://mmif.clams.ai/vocabulary/Paragraph/v1[source]
-
- -
-
-Polygon = http://mmif.clams.ai/vocabulary/Polygon/v5[source]
-
- -
-
-Region = http://mmif.clams.ai/vocabulary/Region/v5[source]
-
- -
-
-Relation = http://mmif.clams.ai/vocabulary/Relation/v5[source]
-
- -
-
-Sentence = http://mmif.clams.ai/vocabulary/Sentence/v1[source]
-
- -
-
-Span = http://mmif.clams.ai/vocabulary/Span/v5[source]
-
- -
-
-TimeFrame = http://mmif.clams.ai/vocabulary/TimeFrame/v6[source]
-
- -
-
-TimePoint = http://mmif.clams.ai/vocabulary/TimePoint/v5[source]
-
- -
-
-Token = http://mmif.clams.ai/vocabulary/Token/v1[source]
-
- -
-
-VerbChunk = http://mmif.clams.ai/vocabulary/VerbChunk/v1[source]
-
- -
-
-VideoObject = http://mmif.clams.ai/vocabulary/VideoObject/v5[source]
-
- -
-
-typevers = {'Alignment': 'v1', 'Annotation': 'v6', 'BoundingBox': 'v5', 'Chapter': 'v6', 'Interval': 'v5', 'NamedEntity': 'v1', 'NounChunk': 'v1', 'Paragraph': 'v1', 'Polygon': 'v5', 'Region': 'v5', 'Relation': 'v5', 'Sentence': 'v1', 'Span': 'v5', 'TimeFrame': 'v6', 'TimePoint': 'v5', 'Token': 'v1', 'VerbChunk': 'v1', 'VideoObject': 'v5'}[source]
-
- -
- -
-
-

mmif.vocabulary.document_types module

-
-
-class mmif.vocabulary.document_types.DocumentTypes(type_uri, fuzzymode=True)[source]
-

Bases: DocumentTypesBase

-

This class contains the CLAMS document types -defined in the spec version 1.1.0 as class variables.

-
-
-AudioDocument = http://mmif.clams.ai/vocabulary/AudioDocument/v1[source]
-
- -
-
-Document = http://mmif.clams.ai/vocabulary/Document/v1[source]
-
- -
-
-ImageDocument = http://mmif.clams.ai/vocabulary/ImageDocument/v1[source]
-
- -
-
-TextDocument = http://mmif.clams.ai/vocabulary/TextDocument/v1[source]
-
- -
-
-VideoDocument = http://mmif.clams.ai/vocabulary/VideoDocument/v1[source]
-
- -
-
-typevers = {'AudioDocument': 'v1', 'Document': 'v1', 'ImageDocument': 'v1', 'TextDocument': 'v1', 'VideoDocument': 'v1'}[source]
-
- -
- -
-
- - -
-
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-
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- -
- - Other Versions - v: 0.5.2 - - -
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- - - \ No newline at end of file diff --git a/docs/0.5.2/consumer-tutorial.html b/docs/0.5.2/consumer-tutorial.html deleted file mode 100644 index cacec782..00000000 --- a/docs/0.5.2/consumer-tutorial.html +++ /dev/null @@ -1,170 +0,0 @@ - - - - - - - - - MMIF consumer — mmif-python documentation - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • MMIF consumer
    • -
  • -
    • -
-
-
-
-
- -
-

MMIF consumer

-

A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the appliance documentation to learn more about the appliance.

-

MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance.

-
    -

  1. The code must be hosted on a public git repository (e.g. Github, Gitlab, …)

    2. -

  2. Must listen to 5000 port.

    3. -

  3. Must expose /display route .

    4. -

  4. /display router should response to GET requests.

    5. -

  5. In the GET request, a public URL of the input MMIF file is passed via file URL parameter.

    6. -

  6. On the codebase root, there must be a Dockerfile that can build a docker image that runs the web app.

    7. -
-

We provide an example consumer at https://github.com/clamsproject/mmif-visualizer.

-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 0.5.2 - - -
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- - -
- -
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    -
    • -
  • Index
    • -
  • -
    • -
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Index

- -
- A - | B - | C - | D - | E - | G - | I - | K - | L - | M - | N - | P - | R - | S - | T - | U - | V - -
-

A

- - - -
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- - - -
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- - -
- -
-
-
-
    -
    • -
  • Welcome to mmif-python’s documentation!
    • -
  • -
    • -
-
-
-
-
- -
-

Welcome to mmif-python’s documentation!

-
-

MultiMedia Interchange Format

-

MMIF is a JSON(-LD)-based data format designed for transferring annotation data between computational analysis applications in CLAMS project.

-
-

Contents

- -
-
-

API documentation:

- -
-
-
-
-

Indices and tables

- -
- - -
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- -
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- - Other Versions - v: 0.5.2 - - -
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- - -
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  • Getting Started
    • -
  • -
    • -
-
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Getting Started

-
-

Overview

-

MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for reproducibility, transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF website. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects.

-
-
-

Prerequisites

-
    -

  • Python: the latest mmif-python requires Python 3.8 or newer. We have no plan to support Python 2.7.

    • -
-
-
-

Installation

-

Package mmif-python is distributed via the official PyPI. Users are supposed to pip-install to get latest release.

-
pip install mmif-python
-
-
-

This will install a package mmif to local python.

-

The MMIF format and specification is evolving over time, and mmif-python package will be updated along with the changes in MMIF format.

-
-

Note

-

MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and mmif-python versions, please take time to read our decision on the subject here. If you need to know which python SDK supports which specification version, see Target MMIF Versions page.

-
-
-
-

MMIF Serialization

-

mmif.serialize.mmif.Mmif represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of mmif.serialize.model.MmifObject, including the mmif.serialize.mmif.Mmif. To start with an existing MMIF str, simple initiate a new Mmif object with the file.

-
import mmif
-from mmif import Mmif
-
-mmif_str = """{
-"metadata": {
-  "mmif": "http://mmif.clams.ai/1.0.0"
-},
-"documents": [
-  {
-    "@type": "http://mmif.clams.ai/vocabulary/VideoDocument/v1",
-    "properties": {
-      "id": "m1",
-      "mime": "video/mp4",
-      "location": "file:///var/archive/video-0012.mp4"
-    }
-  },
-  {
-    "@type": "http://mmif.clams.ai/vocabulary/TextDocument/v1",
-    "properties": {
-      "id": "m2",
-      "mime": "text/plain",
-      "location": "file:///var/archive/video-0012-transcript.txt"
-    }
-  }
-],
-"views": []}"""
-mmif_obj = Mmif(mmif_str)
-
-
-

Few notes;

-
    -

  1. MMIF does not carry the primary source files in it.

    2. -

  2. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version mmif-python implementation of the MMIF might not be able to load an unsupported version of MMIF string.

    3. -
-

When serializing back to str, call mmif.serialize.model.MmifObject.serialize() on the object.

-

To get subcomponents, you can use various getters implemented in subclasses. For example;

-
from mmif.vocabulary.document_types import DocumentTypes
-
-for video in mmif_obj.Mmif.get_documents_by_type(DocumentTypes.VideoDocument):
-  with open(video.location_path(), 'b') as in_video:
-    # do something with the video file
-
-
-

For a full list of available helper methods, please refer to the API documentation.

-
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- - Other Versions - v: 0.5.2 - - -
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- - - - - - - - \ No newline at end of file diff --git a/docs/0.5.2/searchindex.js b/docs/0.5.2/searchindex.js deleted file mode 100644 index 31d8afa4..00000000 --- a/docs/0.5.2/searchindex.js +++ /dev/null @@ -1 +0,0 @@ -Search.setIndex({"alltitles": {"API documentation:": [[3, null]], "Contents": [[3, null]], "Getting Started": [[4, null]], "Indices and tables": [[3, "indices-and-tables"]], "Installation": [[4, "installation"]], "MMIF Serialization": [[4, "mmif-serialization"]], "MMIF consumer": [[2, null]], "MultiMedia Interchange Format": [[3, "multimedia-interchange-format"]], "Overview": [[4, "overview"]], "Prerequisites": [[4, "prerequisites"]], "Target MMIF Versions": [[6, null]], "Target Specification Versions": [[6, "id1"]], "Welcome to mmif-python\u2019s documentation!": [[3, null]], "mmif package": [[5, null]], "mmif.serialize module": [[0, null]], "mmif.serialize.annotation module": [[0, "module-mmif.serialize.annotation"]], "mmif.serialize.mmif module": [[0, 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[0, 4], "specif": 6, "start": 4, "tabl": 3, "target": 6, "version": 6, "view": 0, "vocabulari": 1, "welcom": 3}}) \ No newline at end of file diff --git a/docs/0.5.2/target-versions.html b/docs/0.5.2/target-versions.html deleted file mode 100644 index 2ffa3853..00000000 --- a/docs/0.5.2/target-versions.html +++ /dev/null @@ -1,238 +0,0 @@ - - - - - - - - - Target MMIF Versions — mmif-python documentation - - - - - - - - - - - - - - - - - -
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  • Target MMIF Versions
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Target MMIF Versions

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This article provides targeting MMIF specification versions of different versions of mmif-python SDK.

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Target Specification Versions

mmif-python version

Target MMIF Specification

0.5.2

1.1.0

0.5.1

0.5.0

0.5.0

0.5.0

0.4.8

0.4.2

0.4.7

0.4.1

0.4.6

0.4.0

0.4.5

0.4.0

0.4.4

0.4.0

0.4.3

0.4.0

0.4.2

0.4.0

0.4.1

0.4.0

0.4.0

0.4.0

0.3.5

0.3.1

0.3.4

0.3.1

0.3.3

0.3.1

0.3.2

0.3.1

0.3.1

0.3.0

0.3.0

0.3.0

0.2.2

0.2.1

0.2.1

0.2.1

0.2.0

0.2.1

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0.3.0
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0.3.1
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0.3.2
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0.3.3
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0.3.4
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0.3.5
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0.4.0
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0.4.1
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0.4.2
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0.4.3
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0.4.4
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0.4.5
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0.4.6
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0.4.7
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0.4.8
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0.5.0
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0.5.1
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0.5.2
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1.0.0
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1.0.1
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1.0.10
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1.0.11
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1.0.12
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1.0.13
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1.0.14
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1.0.15
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1.0.16
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1.0.17
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1.0.18
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1.0.19
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1.0.2
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1.0.3
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1.0.4
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1.0.5
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1.0.6
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1.0.7
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1.0.8
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1.0.9
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1.1.0
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The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the `appliance documentation `_ to learn more about the appliance. - -MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance. - -#. The code must be hosted on a public git repository (e.g. Github, Gitlab, ...) -#. Must listen to ``5000`` port. -#. Must expose ``/display`` route . -#. ``/display`` router should response to ``GET`` requests. -#. In the ``GET`` request, a public URL of the input MMIF file is passed via ``file`` URL parameter. -#. On the codebase root, there must be a ``Dockerfile`` that can build a `docker `_ image that runs the web app. - -We provide an example consumer at https://github.com/clamsproject/mmif-visualizer. diff --git a/docs/1.0.0/_sources/index.rst.txt b/docs/1.0.0/_sources/index.rst.txt deleted file mode 100644 index 1f6c350c..00000000 --- a/docs/1.0.0/_sources/index.rst.txt +++ /dev/null @@ -1,25 +0,0 @@ -Welcome to mmif-python's documentation! -======================================= - -.. mdinclude:: ../README.md - -.. toctree:: - :maxdepth: 2 - :caption: Contents - - introduction - target-versions - -.. toctree:: - :maxdepth: 2 - :caption: API documentation: - - modules - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/docs/1.0.0/_sources/introduction.rst.txt b/docs/1.0.0/_sources/introduction.rst.txt deleted file mode 100644 index b1070185..00000000 --- a/docs/1.0.0/_sources/introduction.rst.txt +++ /dev/null @@ -1,89 +0,0 @@ -.. _instroduction: - -Getting Started -=============== - - -Overview ---------- - -MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for reproducibility, transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF website `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects. - -Prerequisites -------------- - -* `Python `_: the latest ``mmif-python`` requires Python 3.8 or newer. We have no plan to support `Python 2.7 `_. - -Installation ---------------- - -Package ``mmif-python`` is distributed via the official PyPI. Users are supposed to pip-install to get latest release. - -.. code-block:: bash - - pip install mmif-python - -This will install a package `mmif` to local python. - -The MMIF format and specification is evolving over time, and ``mmif-python`` package will be updated along with the changes in MMIF format. - -.. note:: MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and ``mmif-python`` versions, please take time to read our decision on the subject `here `_. If you need to know which python SDK supports which specification version, see :ref:`target-versions` page. - -MMIF Serialization ---------------------------- - -:class:`mmif.serialize.mmif.Mmif` represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of :class:`mmif.serialize.model.MmifObject`, including the :class:`mmif.serialize.mmif.Mmif`. To start with an existing MMIF :class:`str`, simple initiate a new ``Mmif`` object with the file. - -.. code-block:: python - - import mmif - from mmif import Mmif - - mmif_str = """{ - "metadata": { - "mmif": "http://mmif.clams.ai/1.0.0" - }, - "documents": [ - { - "@type": "http://mmif.clams.ai/vocabulary/VideoDocument/v1", - "properties": { - "id": "m1", - "mime": "video/mp4", - "location": "file:///var/archive/video-0012.mp4" - } - }, - { - "@type": "http://mmif.clams.ai/vocabulary/TextDocument/v1", - "properties": { - "id": "m2", - "mime": "text/plain", - "location": "file:///var/archive/video-0012-transcript.txt" - } - } - ], - "views": []}""" - mmif_obj = Mmif(mmif_str) - - -Few notes; - -#. MMIF does not carry the primary source files in it. -#. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version ``mmif-python`` implementation of the MMIF might not be able to load an unsupported version of MMIF string. - -When serializing back to :class:`str`, call :meth:`mmif.serialize.model.MmifObject.serialize` on the object. - -To get subcomponents, you can use various getters implemented in subclasses. For example; - -.. code-block:: python - - from mmif.vocabulary.document_types import DocumentTypes - - for video in mmif_obj.Mmif.get_documents_by_type(DocumentTypes.VideoDocument): - with open(video.location_path(), 'b') as in_video: - # do something with the video file - - -For a full list of available helper methods, please refer to :ref:`the API documentation `. - diff --git a/docs/1.0.0/_sources/modules.rst.txt b/docs/1.0.0/_sources/modules.rst.txt deleted file mode 100644 index e4269c6d..00000000 --- a/docs/1.0.0/_sources/modules.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _apidoc: - -mmif package -============ - -.. toctree:: - :maxdepth: 4 - - autodoc/mmif.serialize - autodoc/mmif.vocabulary diff --git a/docs/1.0.0/_sources/target-versions.rst.txt b/docs/1.0.0/_sources/target-versions.rst.txt deleted file mode 100644 index 34216d3e..00000000 --- a/docs/1.0.0/_sources/target-versions.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _target-versions: - -Target MMIF Versions -==================== - -This article provides targeting MMIF specification versions of different versions of ``mmif-python`` SDK. - -.. csv-table:: Target Specification Versions - :file: target-versions.csv - :header-rows: 1 diff --git a/docs/1.0.0/_static/_sphinx_javascript_frameworks_compat.js b/docs/1.0.0/_static/_sphinx_javascript_frameworks_compat.js deleted file mode 100644 index 81415803..00000000 --- a/docs/1.0.0/_static/_sphinx_javascript_frameworks_compat.js +++ /dev/null @@ -1,123 +0,0 @@ -/* Compatability shim for jQuery and underscores.js. - * - * Copyright Sphinx contributors - * Released under the two clause BSD licence - */ - -/** - * small helper function to urldecode strings - * - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL - */ -jQuery.urldecode = function(x) { - if (!x) { - return x - } - return decodeURIComponent(x.replace(/\+/g, ' ')); -}; - -/** - * small helper function to urlencode strings - */ -jQuery.urlencode = encodeURIComponent; - -/** - * This function returns the parsed url parameters of the - * current request. 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- -/** - * Simple result scoring code. - */ -if (typeof Scorer === "undefined") { - var Scorer = { - // Implement the following function to further tweak the score for each result - // The function takes a result array [docname, title, anchor, descr, score, filename] - // and returns the new score. - /* - score: result => { - const [docname, title, anchor, descr, score, filename, kind] = result - return score - }, - */ - - // query matches the full name of an object - objNameMatch: 11, - // or matches in the last dotted part of the object name - objPartialMatch: 6, - // Additive scores depending on the priority of the object - objPrio: { - 0: 15, // used to be importantResults - 1: 5, // used to be objectResults - 2: -5, // used to be unimportantResults - }, - // Used when the priority is not in the mapping. - objPrioDefault: 0, - - // query found in title - title: 15, - partialTitle: 7, - // query found in terms - term: 5, - partialTerm: 2, - }; -} - -// Global search result kind enum, used by themes to style search results. -class SearchResultKind { - static get index() { return "index"; } - static get object() { return "object"; } - static get text() { return "text"; } - static get title() { return "title"; } -} - -const _removeChildren = (element) => { - while (element && element.lastChild) element.removeChild(element.lastChild); -}; - -/** - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping - */ -const _escapeRegExp = (string) => - string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string - -const _displayItem = (item, searchTerms, highlightTerms) => { - const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; - const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; - const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; - const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; - const contentRoot = document.documentElement.dataset.content_root; - - const [docName, title, anchor, descr, score, _filename, kind] = item; - - let listItem = document.createElement("li"); - // Add a class representing the item's type: - // can be used by a theme's CSS selector for styling - // See SearchResultKind for the class names. - listItem.classList.add(`kind-${kind}`); - let requestUrl; - let linkUrl; - if (docBuilder === "dirhtml") { - // dirhtml builder - let dirname = docName + "/"; - if (dirname.match(/\/index\/$/)) - dirname = dirname.substring(0, dirname.length - 6); - else if (dirname === "index/") dirname = ""; - requestUrl = contentRoot + dirname; - linkUrl = requestUrl; - } else { - // normal html builders - requestUrl = contentRoot + docName + docFileSuffix; - linkUrl = docName + docLinkSuffix; - } - let linkEl = listItem.appendChild(document.createElement("a")); - linkEl.href = linkUrl + anchor; - linkEl.dataset.score = score; - linkEl.innerHTML = title; - if (descr) { - listItem.appendChild(document.createElement("span")).innerHTML = - " (" + descr + ")"; - // highlight search terms in the description - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - } - else if (showSearchSummary) - fetch(requestUrl) - .then((responseData) => responseData.text()) - .then((data) => { - if (data) - listItem.appendChild( - Search.makeSearchSummary(data, searchTerms, anchor) - ); - // highlight search terms in the summary - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - }); - Search.output.appendChild(listItem); -}; -const _finishSearch = (resultCount) => { - Search.stopPulse(); - Search.title.innerText = _("Search Results"); - if (!resultCount) - Search.status.innerText = Documentation.gettext( - "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." - ); - else - Search.status.innerText = Documentation.ngettext( - "Search finished, found one page matching the search query.", - "Search finished, found ${resultCount} pages matching the search query.", - resultCount, - ).replace('${resultCount}', resultCount); -}; -const _displayNextItem = ( - results, - resultCount, - searchTerms, - highlightTerms, -) => { - // results left, load the summary and display it - // this is intended to be dynamic (don't sub resultsCount) - if (results.length) { - _displayItem(results.pop(), searchTerms, highlightTerms); - setTimeout( - () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), - 5 - ); - } - // search finished, update title and status message - else _finishSearch(resultCount); -}; -// Helper function used by query() to order search results. -// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. -// Order the results by score (in opposite order of appearance, since the -// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. -const _orderResultsByScoreThenName = (a, b) => { - const leftScore = a[4]; - const rightScore = b[4]; - if (leftScore === rightScore) { - // same score: sort alphabetically - const leftTitle = a[1].toLowerCase(); - const rightTitle = b[1].toLowerCase(); - if (leftTitle === rightTitle) return 0; - return leftTitle > rightTitle ? -1 : 1; // inverted is intentional - } - return leftScore > rightScore ? 1 : -1; -}; - -/** - * Default splitQuery function. Can be overridden in ``sphinx.search`` with a - * custom function per language. - * - * The regular expression works by splitting the string on consecutive characters - * that are not Unicode letters, numbers, underscores, or emoji characters. - * This is the same as ``\W+`` in Python, preserving the surrogate pair area. - */ -if (typeof splitQuery === "undefined") { - var splitQuery = (query) => query - .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) - .filter(term => term) // remove remaining empty strings -} - -/** - * Search Module - */ -const Search = { - _index: null, - _queued_query: null, - _pulse_status: -1, - - htmlToText: (htmlString, anchor) => { - const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - for (const removalQuery of [".headerlink", "script", "style"]) { - htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); - } - if (anchor) { - const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); - if (anchorContent) return anchorContent.textContent; - - console.warn( - `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` - ); - } - - // if anchor not specified or not found, fall back to main content - const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent) return docContent.textContent; - - console.warn( - "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." - ); - return ""; - }, - - init: () => { - const query = new URLSearchParams(window.location.search).get("q"); - document - .querySelectorAll('input[name="q"]') - .forEach((el) => (el.value = query)); - if (query) Search.performSearch(query); - }, - - loadIndex: (url) => - (document.body.appendChild(document.createElement("script")).src = url), - - setIndex: (index) => { - Search._index = index; - if (Search._queued_query !== null) { - const query = Search._queued_query; - Search._queued_query = null; - Search.query(query); - } - }, - - hasIndex: () => Search._index !== null, - - deferQuery: (query) => (Search._queued_query = query), - - stopPulse: () => (Search._pulse_status = -1), - - startPulse: () => { - if (Search._pulse_status >= 0) return; - - const pulse = () => { - Search._pulse_status = (Search._pulse_status + 1) % 4; - Search.dots.innerText = ".".repeat(Search._pulse_status); - if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); - }; - pulse(); - }, - - /** - * perform a search for something (or wait until index is loaded) - */ - performSearch: (query) => { - // create the required interface elements - const searchText = document.createElement("h2"); - searchText.textContent = _("Searching"); - const searchSummary = document.createElement("p"); - searchSummary.classList.add("search-summary"); - searchSummary.innerText = ""; - const searchList = document.createElement("ul"); - searchList.setAttribute("role", "list"); - searchList.classList.add("search"); - - const out = document.getElementById("search-results"); - Search.title = out.appendChild(searchText); - Search.dots = Search.title.appendChild(document.createElement("span")); - Search.status = out.appendChild(searchSummary); - Search.output = out.appendChild(searchList); - - const searchProgress = document.getElementById("search-progress"); - // Some themes don't use the search progress node - if (searchProgress) { - searchProgress.innerText = _("Preparing search..."); - } - Search.startPulse(); - - // index already loaded, the browser was quick! - if (Search.hasIndex()) Search.query(query); - else Search.deferQuery(query); - }, - - _parseQuery: (query) => { - // stem the search terms and add them to the correct list - const stemmer = new Stemmer(); - const searchTerms = new Set(); - const excludedTerms = new Set(); - const highlightTerms = new Set(); - const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); - splitQuery(query.trim()).forEach((queryTerm) => { - const queryTermLower = queryTerm.toLowerCase(); - - // maybe skip this "word" - // stopwords array is from language_data.js - if ( - stopwords.indexOf(queryTermLower) !== -1 || - queryTerm.match(/^\d+$/) - ) - return; - - // stem the word - let word = stemmer.stemWord(queryTermLower); - // select the correct list - if (word[0] === "-") excludedTerms.add(word.substr(1)); - else { - searchTerms.add(word); - highlightTerms.add(queryTermLower); - } - }); - - if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js - localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) - } - - // console.debug("SEARCH: searching for:"); - // console.info("required: ", [...searchTerms]); - // console.info("excluded: ", [...excludedTerms]); - - return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; - }, - - /** - * execute search (requires search index to be loaded) - */ - _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - - // Collect multiple result groups to be sorted separately and then ordered. - // Each is an array of [docname, title, anchor, descr, score, filename, kind]. - const normalResults = []; - const nonMainIndexResults = []; - - _removeChildren(document.getElementById("search-progress")); - - const queryLower = query.toLowerCase().trim(); - for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { - for (const [file, id] of foundTitles) { - const score = Math.round(Scorer.title * queryLower.length / title.length); - const boost = titles[file] === title ? 1 : 0; // add a boost for document titles - normalResults.push([ - docNames[file], - titles[file] !== title ? `${titles[file]} > ${title}` : title, - id !== null ? "#" + id : "", - null, - score + boost, - filenames[file], - SearchResultKind.title, - ]); - } - } - } - - // search for explicit entries in index directives - for (const [entry, foundEntries] of Object.entries(indexEntries)) { - if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id, isMain] of foundEntries) { - const score = Math.round(100 * queryLower.length / entry.length); - const result = [ - docNames[file], - titles[file], - id ? "#" + id : "", - null, - score, - filenames[file], - SearchResultKind.index, - ]; - if (isMain) { - normalResults.push(result); - } else { - nonMainIndexResults.push(result); - } - } - } - } - - // lookup as object - objectTerms.forEach((term) => - normalResults.push(...Search.performObjectSearch(term, objectTerms)) - ); - - // lookup as search terms in fulltext - normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); - - // let the scorer override scores with a custom scoring function - if (Scorer.score) { - normalResults.forEach((item) => (item[4] = Scorer.score(item))); - nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); - } - - // Sort each group of results by score and then alphabetically by name. - normalResults.sort(_orderResultsByScoreThenName); - nonMainIndexResults.sort(_orderResultsByScoreThenName); - - // Combine the result groups in (reverse) order. - // Non-main index entries are typically arbitrary cross-references, - // so display them after other results. - let results = [...nonMainIndexResults, ...normalResults]; - - // remove duplicate search results - // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept - let seen = new Set(); - results = results.reverse().reduce((acc, result) => { - let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); - if (!seen.has(resultStr)) { - acc.push(result); - seen.add(resultStr); - } - return acc; - }, []); - - return results.reverse(); - }, - - query: (query) => { - const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); - const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); - - // for debugging - //Search.lastresults = results.slice(); // a copy - // console.info("search results:", Search.lastresults); - - // print the results - _displayNextItem(results, results.length, searchTerms, highlightTerms); - }, - - /** - * search for object names - */ - performObjectSearch: (object, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const objects = Search._index.objects; - const objNames = Search._index.objnames; - const titles = Search._index.titles; - - const results = []; - - const objectSearchCallback = (prefix, match) => { - const name = match[4] - const fullname = (prefix ? prefix + "." : "") + name; - const fullnameLower = fullname.toLowerCase(); - if (fullnameLower.indexOf(object) < 0) return; - - let score = 0; - const parts = fullnameLower.split("."); - - // check for different match types: exact matches of full name or - // "last name" (i.e. last dotted part) - if (fullnameLower === object || parts.slice(-1)[0] === object) - score += Scorer.objNameMatch; - else if (parts.slice(-1)[0].indexOf(object) > -1) - score += Scorer.objPartialMatch; // matches in last name - - const objName = objNames[match[1]][2]; - const title = titles[match[0]]; - - // If more than one term searched for, we require other words to be - // found in the name/title/description - const otherTerms = new Set(objectTerms); - otherTerms.delete(object); - if (otherTerms.size > 0) { - const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); - if ( - [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) - ) - return; - } - - let anchor = match[3]; - if (anchor === "") anchor = fullname; - else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; - - const descr = objName + _(", in ") + title; - - // add custom score for some objects according to scorer - if (Scorer.objPrio.hasOwnProperty(match[2])) - score += Scorer.objPrio[match[2]]; - else score += Scorer.objPrioDefault; - - results.push([ - docNames[match[0]], - fullname, - "#" + anchor, - descr, - score, - filenames[match[0]], - SearchResultKind.object, - ]); - }; - Object.keys(objects).forEach((prefix) => - objects[prefix].forEach((array) => - objectSearchCallback(prefix, array) - ) - ); - return results; - }, - - /** - * search for full-text terms in the index - */ - performTermsSearch: (searchTerms, excludedTerms) => { - // prepare search - const terms = Search._index.terms; - const titleTerms = Search._index.titleterms; - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - - const scoreMap = new Map(); - const fileMap = new Map(); - - // perform the search on the required terms - searchTerms.forEach((word) => { - const files = []; - const arr = [ - { files: terms[word], score: Scorer.term }, - { files: titleTerms[word], score: Scorer.title }, - ]; - // add support for partial matches - if (word.length > 2) { - const escapedWord = _escapeRegExp(word); - if (!terms.hasOwnProperty(word)) { - Object.keys(terms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: terms[term], score: Scorer.partialTerm }); - }); - } - if (!titleTerms.hasOwnProperty(word)) { - Object.keys(titleTerms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); - }); - } - } - - // no match but word was a required one - if (arr.every((record) => record.files === undefined)) return; - - // found search word in contents - arr.forEach((record) => { - if (record.files === undefined) return; - - let recordFiles = record.files; - if (recordFiles.length === undefined) recordFiles = [recordFiles]; - files.push(...recordFiles); - - // set score for the word in each file - recordFiles.forEach((file) => { - if (!scoreMap.has(file)) scoreMap.set(file, {}); - scoreMap.get(file)[word] = record.score; - }); - }); - - // create the mapping - files.forEach((file) => { - if (!fileMap.has(file)) fileMap.set(file, [word]); - else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); - }); - }); - - // now check if the files don't contain excluded terms - const results = []; - for (const [file, wordList] of fileMap) { - // check if all requirements are matched - - // as search terms with length < 3 are discarded - const filteredTermCount = [...searchTerms].filter( - (term) => term.length > 2 - ).length; - if ( - wordList.length !== searchTerms.size && - wordList.length !== filteredTermCount - ) - continue; - - // ensure that none of the excluded terms is in the search result - if ( - [...excludedTerms].some( - (term) => - terms[term] === file || - titleTerms[term] === file || - (terms[term] || []).includes(file) || - (titleTerms[term] || []).includes(file) - ) - ) - break; - - // select one (max) score for the file. - const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); - // add result to the result list - results.push([ - docNames[file], - titles[file], - "", - null, - score, - filenames[file], - SearchResultKind.text, - ]); - } - return results; - }, - - /** - * helper function to return a node containing the - * search summary for a given text. keywords is a list - * of stemmed words. - */ - makeSearchSummary: (htmlText, keywords, anchor) => { - const text = Search.htmlToText(htmlText, anchor); - if (text === "") return null; - - const textLower = text.toLowerCase(); - const actualStartPosition = [...keywords] - .map((k) => textLower.indexOf(k.toLowerCase())) - .filter((i) => i > -1) - .slice(-1)[0]; - const startWithContext = Math.max(actualStartPosition - 120, 0); - - const top = startWithContext === 0 ? "" : "..."; - const tail = startWithContext + 240 < text.length ? "..." : ""; - - let summary = document.createElement("p"); - summary.classList.add("context"); - summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; - - return summary; - }, -}; - -_ready(Search.init); diff --git a/docs/1.0.0/_static/sphinx_highlight.js b/docs/1.0.0/_static/sphinx_highlight.js deleted file mode 100644 index 8a96c69a..00000000 --- a/docs/1.0.0/_static/sphinx_highlight.js +++ /dev/null @@ -1,154 +0,0 @@ -/* Highlighting utilities for Sphinx HTML documentation. */ -"use strict"; - -const SPHINX_HIGHLIGHT_ENABLED = true - -/** - * highlight a given string on a node by wrapping it in - * span elements with the given class name. - */ -const _highlight = (node, addItems, text, className) => { - if (node.nodeType === Node.TEXT_NODE) { - const val = node.nodeValue; - const parent = node.parentNode; - const pos = val.toLowerCase().indexOf(text); - if ( - pos >= 0 && - !parent.classList.contains(className) && - !parent.classList.contains("nohighlight") - ) { - let span; - - const closestNode = parent.closest("body, svg, foreignObject"); - const isInSVG = closestNode && closestNode.matches("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.classList.add(className); - } - - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - const rest = document.createTextNode(val.substr(pos + text.length)); - parent.insertBefore( - span, - parent.insertBefore( - rest, - node.nextSibling - ) - ); - node.nodeValue = val.substr(0, pos); - /* There may be more occurrences of search term in this node. So call this - * function recursively on the remaining fragment. - */ - _highlight(rest, addItems, text, className); - - if (isInSVG) { - const rect = document.createElementNS( - "http://www.w3.org/2000/svg", - "rect" - ); - const bbox = parent.getBBox(); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute("class", className); - addItems.push({ parent: parent, target: rect }); - } - } - } else if (node.matches && !node.matches("button, select, textarea")) { - node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); - } -}; -const _highlightText = (thisNode, text, className) => { - let addItems = []; - _highlight(thisNode, addItems, text, className); - addItems.forEach((obj) => - obj.parent.insertAdjacentElement("beforebegin", obj.target) - ); -}; - -/** - * Small JavaScript module for the documentation. - */ -const SphinxHighlight = { - - /** - * highlight the search words provided in localstorage in the text - */ - highlightSearchWords: () => { - if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight - - // get and clear terms from localstorage - const url = new URL(window.location); - const highlight = - localStorage.getItem("sphinx_highlight_terms") - || url.searchParams.get("highlight") - || ""; - localStorage.removeItem("sphinx_highlight_terms") - url.searchParams.delete("highlight"); - window.history.replaceState({}, "", url); - - // get individual terms from highlight string - const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); - if (terms.length === 0) return; // nothing to do - - // There should never be more than one element matching "div.body" - const divBody = document.querySelectorAll("div.body"); - const body = divBody.length ? divBody[0] : document.querySelector("body"); - window.setTimeout(() => { - terms.forEach((term) => _highlightText(body, term, "highlighted")); - }, 10); - - const searchBox = document.getElementById("searchbox"); - if (searchBox === null) return; - searchBox.appendChild( - document - .createRange() - .createContextualFragment( - '

' + - '' + - _("Hide Search Matches") + - "

" - ) - ); - }, - - /** - * helper function to hide the search marks again - */ - hideSearchWords: () => { - document - .querySelectorAll("#searchbox .highlight-link") - .forEach((el) => el.remove()); - document - .querySelectorAll("span.highlighted") - .forEach((el) => el.classList.remove("highlighted")); - localStorage.removeItem("sphinx_highlight_terms") - }, - - initEscapeListener: () => { - // only install a listener if it is really needed - if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; - - document.addEventListener("keydown", (event) => { - // bail for input elements - if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; - // bail with special keys - if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; - if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { - SphinxHighlight.hideSearchWords(); - event.preventDefault(); - } - }); - }, -}; - -_ready(() => { - /* Do not call highlightSearchWords() when we are on the search page. - * It will highlight words from the *previous* search query. - */ - if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); - SphinxHighlight.initEscapeListener(); -}); diff --git a/docs/1.0.0/autodoc/mmif.serialize.html b/docs/1.0.0/autodoc/mmif.serialize.html deleted file mode 100644 index 18cda8e7..00000000 --- a/docs/1.0.0/autodoc/mmif.serialize.html +++ /dev/null @@ -1,1175 +0,0 @@ - - - - - - - - - mmif.serialize module — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.serialize module

-
-

mmif.serialize.model module

-

The model module contains the classes used to represent an -abstract MMIF object as a live Python object.

-

The MmifObject class or one of its derivatives is subclassed by -all other classes defined in this SDK, except for MmifObjectEncoder.

-

These objects are generally instantiated from JSON, either as a string -or as an already-loaded Python dictionary. This base class provides the -core functionality for deserializing MMIF JSON data into live objects -and serializing live objects into MMIF JSON data. Specialized behavior -for the different components of MMIF is added in the subclasses.

-
-
-class mmif.serialize.model.DataDict(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject, Generic[T, S]

-
-
-empty()[source]
-
- -
-
-get(key: T, default=None) → S | None[source]
-
- -
-
-items()[source]
-
- -
-
-keys()[source]
-
- -
-
-update(other, overwrite)[source]
-
- -
-
-values()[source]
-
- -
- -
-
-class mmif.serialize.model.DataList(mmif_obj: bytes | str | list | None = None)[source]
-

Bases: MmifObject, Generic[T]

-

The DataList class is an abstraction that represents the -various lists found in a MMIF file, such as documents, subdocuments, -views, and annotations.

-
-
Parameters:
-

mmif_obj (Union[str, list]) – the data that the list contains

-
-
-
-
-append(value, overwrite)[source]
-
- -
-
-deserialize(mmif_json: str | list) → None[source]
-

Passes the input data into the internal deserializer.

-
- -
-
-empty()[source]
-
- -
-
-get(key: str) → T | None[source]
-

Standard dictionary-style get() method, albeit with no default -parameter. Relies on the implementation of __getitem__.

-

Will return None if the key is not found.

-
-
Parameters:
-

key – the key to search for

-
-
Returns:
-

the value matching that key

-
-
-
- -
- -
-
-class mmif.serialize.model.MmifObject(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: object

-

Abstract superclass for MMIF related key-value pair objects.

-

Any MMIF object can be initialized as an empty placeholder or -an actual representation with a JSON formatted string or equivalent -dict object argument.

-

This superclass has four specially designed instance variables, and these -variable names cannot be used as attribute names for MMIF objects.

-
    -

  1. _unnamed_attributes: -Only can be either None or an empty dictionary. If it’s set to None, -it means the class won’t take any Additional Attributes in the JSON -schema sense. If it’s a dict, users can throw any k-v pairs to the -class, EXCEPT for the reserved two key names.

    2. -

  2. _attribute_classes: -This is a dict from a key name to a specific python class to use for -deserialize the value. Note that a key name in this dict does NOT -have to be a named attribute, but is recommended to be one.

    3. -

  3. _required_attributes: -This is a simple list of names of attributes that are required in the object. -When serialize, an object will skip its empty (e.g. zero-length, or None) -attributes unless they are in this list. Otherwise, the serialized JSON -string would have empty representations (e.g. "", []).

    4. -

  4. _exclude_from_diff: -This is a simple list of names of attributes that should be excluded from -the diff calculation in __eq__.

    5. -
-

# TODO (krim @ 8/17/20): this dict is however, a duplicate with the type hints in the class definition. -Maybe there is a better way to utilize type hints (e.g. getting them as a programmatically), but for now -developers should be careful to add types to hints as well as to this dict.

-

Also note that those special attributes MUST be set in the __init__() -before calling super method, otherwise deserialization will not work.

-

And also, a subclass that has one or more named attributes, it must -set those attributes in the __init__() before calling super method. When -serializing a MmifObject, all empty attributes will be ignored, so for -optional named attributes, you must leave the values empty (len == 0), but -NOT None. Any None-valued named attributes will cause issues with current -implementation.

-
-
Parameters:
-

mmif_obj – JSON string or dict to initialize an object. -If not given, an empty object will be initialized, sometimes with -an ID value automatically generated, based on its parent object.

-
-
-
-
-deserialize(mmif_json: str | dict) → None[source]
-

Takes a JSON-formatted string or a simple dict that’s json-loaded from -such a string as an input and populates object’s fields with the values -specified in the input.

-
-
Parameters:
-

mmif_json – JSON-formatted string or dict from such a string -that represents a MMIF object

-
-
-
- -
-
-disallow_additional_properties() → None[source]
-

Call this method in __init__() to prevent the insertion -of unnamed attributes after initialization.

-
- -
-
-static is_empty(obj) → bool[source]
-

return True if the obj is None or “emtpy”. The emptiness first defined as -having zero length. But for objects that lack __len__ method, we need -additional check.

-
- -
-
-reserved_names: Set[str] = {'_attribute_classes', '_exclude_from_diff', '_required_attributes', '_unnamed_attributes', 'reserved_names'}[source]
-
- -
-
-serialize(pretty: bool = False) → str[source]
-

Generates JSON representation of an object.

-
-
Parameters:
-

pretty – If True, returns string representation with indentation.

-
-
Returns:
-

JSON string of the object.

-
-
-
- -
-
-set_additional_property(key: str, value: Any) → None[source]
-

Method to set values in _unnamed_attributes.

-
-
Parameters:
-
    -

  • key – the attribute name

    • -

  • value – the desired value

    • -
-
-
Returns:
-

None

-
-
Raise:
-

AttributeError if additional properties are disallowed by disallow_additional_properties()

-
-
-
- -
- -
-
-class mmif.serialize.model.MmifObjectEncoder(*, skipkeys=False, ensure_ascii=True, check_circular=True, allow_nan=True, sort_keys=False, indent=None, separators=None, default=None)[source]
-

Bases: JSONEncoder

-

Encoder class to define behaviors of de-/serialization

-
-
-default(obj: MmifObject)[source]
-

Overrides default encoding behavior to prioritize MmifObject.serialize().

-
- -
- -
-
-

mmif.serialize.mmif module

-

The mmif module contains the classes used to represent a full MMIF -file as a live Python object.

-

See the specification docs and the JSON Schema file for more information.

-
-
-class mmif.serialize.mmif.Mmif(mmif_obj: bytes | str | dict | None = None, *, validate: bool = True)[source]
-

Bases: MmifObject

-

MmifObject that represents a full MMIF file.

-
-
Parameters:
-
    -

  • mmif_obj – the JSON data

    • -

  • validate – whether to validate the data against the MMIF JSON schema.

    • -
-
-
-
-
-add_document(document: Document, overwrite=False) → None[source]
-

Appends a Document object to the documents list.

-

Fails if there is already a document with the same ID in the MMIF object.

-
-
Parameters:
-
    -

  • document – the Document object to add

    • -

  • overwrite – if set to True, will overwrite -an existing view with the same ID

    • -
-
-
Returns:
-

None

-
-
-
- -
-
-add_view(view: View, overwrite=False) → None[source]
-

Appends a View object to the views list.

-

Fails if there is already a view with the same ID in the MMIF object.

-
-
Parameters:
-
    -

  • view – the Document object to add

    • -

  • overwrite – if set to True, will overwrite -an existing view with the same ID

    • -
-
-
Returns:
-

None

-
-
-
- -
-
-get_alignments(at_type1: str | TypesBase, at_type2: str | TypesBase) → Dict[str, List[Annotation]][source]
-

Finds views where alignments between two given annotation types occurred.

-
-
Returns:
-

a dict that keyed by view IDs (str) and has lists of alignment Annotation objects as values.

-
-
-
- -
-
-get_all_views_contain(at_types: TypesBase | str | List[str | TypesBase]) → List[View][source]
-

Returns the list of all views in the MMIF if given types -are present in that view’s ‘contains’ metadata.

-
-
Parameters:
-

at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

-
-
Returns:
-

the list of views that contain the type

-
-
-
- -
-
-get_document_by_id(doc_id: str) → Document[source]
-

Finds a Document object with the given ID.

-
-
Parameters:
-

doc_id – the ID to search for

-
-
Returns:
-

a reference to the corresponding document, if it exists

-
-
Raises:
-

Exception – if there is no corresponding document

-
-
-
- -
-
-get_document_location(m_type: DocumentTypes | str, path_only=False) → str | None[source]
-

Method to get the location of first document of given type.

-
-
Parameters:
-

m_type – the type to search for

-
-
Returns:
-

the value of the location field in the corresponding document

-
-
-
- -
-
-get_documents_by_app(app_id: str) → List[Document][source]
-

Method to get all documents object queries by its originated app name.

-
-
Parameters:
-

app_id – the app name to search for

-
-
Returns:
-

a list of documents matching the requested app name, or an empty list if the app not found

-
-
-
- -
-
-get_documents_by_property(prop_key: str, prop_value: str) → List[Document][source]
-

Method to retrieve documents by an arbitrary key-value pair in the document properties objects.

-
-
Parameters:
-
    -

  • prop_key – the metadata key to search for

    • -

  • prop_value – the metadata value to match

    • -
-
-
Returns:
-

a list of documents matching the requested metadata key-value pair

-
-
-
- -
-
-get_documents_by_type(doc_type: str | DocumentTypes) → List[Document][source]
-

Method to get all documents where the type matches a particular document type, which should be one of the CLAMS document types.

-
-
Parameters:
-

doc_type – the type of documents to search for, must be one of Document type defined in the CLAMS vocabulary.

-
-
Returns:
-

a list of documents matching the requested type, or an empty list if none found.

-
-
-
- -
-
-get_documents_in_view(vid: str | None = None) → List[Document][source]
-

Method to get all documents object queries by a view id.

-
-
Parameters:
-

vid – the source view ID to search for

-
-
Returns:
-

a list of documents matching the requested source view ID, or an empty list if the view not found

-
-
-
- -
-
-get_documents_locations(m_type: DocumentTypes | str, path_only=False) → List[str | None][source]
-

This method returns the file paths of documents of given type. -Only top-level documents have locations, so we only check them.

-
-
Parameters:
-

m_type – the type to search for

-
-
Returns:
-

a list of the values of the location fields in the corresponding documents

-
-
-
- -
-
-get_view_by_id(req_view_id: str) → View[source]
-

Finds a View object with the given ID.

-
-
Parameters:
-

req_view_id – the ID to search for

-
-
Returns:
-

a reference to the corresponding view, if it exists

-
-
Raises:
-

Exception – if there is no corresponding view

-
-
-
- -
-
-get_view_contains(at_types: TypesBase | str | List[str | TypesBase]) → View | None[source]
-

Returns the last view appended that contains the given -types in its ‘contains’ metadata.

-
-
Parameters:
-

at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

-
-
Returns:
-

the view, or None if the type is not found

-
-
-
- -
-
-get_views_contain(at_types: TypesBase | str | List[str | TypesBase]) → List[View][source]
-

An alias to get_all_views_contain method.

-
- -
-
-get_views_for_document(doc_id: str)[source]
-

Returns the list of all views that have annotations anchored on a particular document. -Note that when the document is insids a view (generated during the pipeline’s running), -doc_id must be prefixed with the view_id.

-
- -
-
-id_delimiter: ClassVar[str] = ':'[source]
-
- -
-
-new_view() → View[source]
-

Creates an empty view with a new ID and appends it to the views list.

-
-
Returns:
-

a reference to the new View object

-
-
-
- -
-
-new_view_id() → str[source]
-

Fetches an ID for a new view.

-
-
Returns:
-

the ID

-
-
-
- -
-
-sanitize()[source]
-

Sanitizes a Mmif object by running some safeguards. -Concretely, it performs the following before returning the JSON string.

-
    -

  1. validating output using built-in MMIF jsonschema

    2. -

  2. remove non-existing annotation types from contains metadata

    3. -
-
- -
-
-serialize(pretty: bool = False, sanitize: bool = False) → str[source]
-

Generates JSON representation of an object.

-
-
Parameters:
-

pretty – If True, returns string representation with indentation.

-
-
Returns:
-

JSON string of the object.

-
-
-
- -
-
-static validate(json_str: bytes | str | dict) → None[source]
-

Validates a MMIF JSON object against the MMIF Schema. -Note that this method operates before processing by MmifObject._load_str, -so it expects @ and not _ for the JSON-LD @-keys.

-
-
Raises:
-

jsonschema.exceptions.ValidationError – if the input fails validation

-
-
Parameters:
-

json_str – a MMIF JSON dict or string

-
-
Returns:
-

None

-
-
-
- -
-
-view_prefix: ClassVar[str] = 'v_'[source]
-
- -
- -
-
-

mmif.serialize.view module

-

The view module contains the classes used to represent a MMIF view -as a live Python object.

-

In MMIF, views are created by apps in a pipeline that are annotating -data that was previously present in the MMIF file.

-
-
-class mmif.serialize.view.Contain(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-

Contain object that represents the metadata of a single -annotation type in the contains metadata of a MMIF view.

-
- -
-
-class mmif.serialize.view.View(view_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-

View object that represents a single view in a MMIF file.

-

A view is identified by an ID, and contains certain metadata, -a list of annotations, and potentially a JSON-LD @context -IRI.

-

If view_obj is not provided, an empty View will be generated.

-
-
Parameters:
-

view_obj – the JSON data that defines the view

-
-
-
-
-add_annotation(annotation: Annotation, overwrite=False) → Annotation[source]
-

Adds an annotation to the current view.

-

Fails if there is already an annotation with the same ID -in the view, unless overwrite is set to True.

-
-
Parameters:
-
-
-
Raises:
-

KeyError – if overwrite is set to False and -an annotation with the same ID exists -in the view

-
-
Returns:
-

the same Annotation object passed in as annotation

-
-
-
- -
-
-add_document(document: Document, overwrite=False) → Annotation[source]
-

Appends a Document object to the annotations list.

-

Fails if there is already a document with the same ID in the annotations list.

-
-
Parameters:
-
    -

  • document – the Document object to add

    • -

  • overwrite – if set to True, will overwrite -an existing view with the same ID

    • -
-
-
Returns:
-

None

-
-
-
- -
-
-get_annotation_by_id(ann_id)[source]
-
- -
-
-get_annotations(at_type: str | TypesBase | None = None, **properties) → Generator[Annotation, None, None][source]
-

Look for certain annotations in this view, specified by parameters

-
-
Parameters:
-
    -

  • at_type – @type of the annotations to look for. When this is None, any @type will match.

    • -

  • properties – properties of the annotations to look for. When given more than one property, all properties must match. Note that annotation type metadata are specified in the contains view metadata, not in individual annotation objects.

    • -
-
-
-
- -
-
-get_document_by_id(doc_id) → Document[source]
-
- -
-
-get_documents() → List[Document][source]
-
- -
-
-new_annotation(at_type: str | TypesBase, aid: str | None = None, overwrite=False, **properties) → Annotation[source]
-

Generates a new mmif.serialize.annotation.Annotation -object and adds it to the current view.

-

Fails if there is already an annotation with the same ID -in the view, unless overwrite is set to True.

-
-
Parameters:
-
    -

  • at_type – the desired @type of the annotation.

    • -

  • aid – the desired ID of the annotation, when not given, -the mmif SDK tries to automatically generate an ID based on -Annotation type and existing annotations in the view.

    • -

  • overwrite – if set to True, will overwrite an -existing annotation with the same ID.

    • -
-
-
Raises:
-

KeyError – if overwrite is set to False and -an annotation with the same ID exists -in the view.

-
-
Returns:
-

the generated mmif.serialize.annotation.Annotation

-
-
-
- -
-
-new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
-

Adds a new element to the contains metadata.

-
-
Parameters:
-
    -

  • at_type – the @type of the annotation type being added

    • -

  • contains_metadata – any metadata associated with the annotation type

    • -
-
-
Returns:
-

the generated Contain object

-
-
-
- -
-
-new_textdocument(text: str, lang: str = 'en', did: str | None = None, overwrite=False, **properties) → Document[source]
-

Generates a new mmif.serialize.annotation.Document -object, particularly typed as TextDocument and adds it to the current view.

-

Fails if there is already a text document with the same ID -in the view, unless overwrite is set to True.

-
-
Parameters:
-
    -

  • text – text content of the new document

    • -

  • lang – ISO 639-1 code of the language used in the new document

    • -

  • did – the desired ID of the document, when not given, -the mmif SDK tries to automatically generate an ID based on -Annotation type and existing documents in the view.

    • -

  • overwrite – if set to True, will overwrite an -existing document with the same ID

    • -
-
-
Raises:
-

KeyError – if overwrite is set to False and -an document with the same ID exists -in the view

-
-
Returns:
-

the generated mmif.serialize.annotation.Document

-
-
-
- -
-
-set_error(err_message: str, err_trace: str) → None[source]
-
- -
- -
-
-class mmif.serialize.view.ViewMetadata(viewmetadata_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-

ViewMetadata object that represents the metadata object within a MMIF view.

-
-
Parameters:
-

viewmetadata_obj – the JSON data that defines the metadata

-
-
-
-
-add_parameter(param_key, param_value)[source]
-
- -
-
-add_parameters(**runtime_params)[source]
-
- -
-
-add_warnings(*warnings: Warning)[source]
-
- -
-
-emtpy_warnings()[source]
-
- -
-
-get_parameter(param_key)[source]
-
- -
-
-new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
-

Adds a new element to the contains dictionary.

-
-
Parameters:
-
    -

  • at_type – the @type of the annotation type being added

    • -

  • contains_metadata – any metadata associated with the annotation type

    • -
-
-
Returns:
-

the generated Contain object

-
-
-
- -
-
-set_error(message: str, stack_trace: str)[source]
-
- -
- -
-
-

mmif.serialize.annotation module

-

The annotation module contains the classes used to represent a -MMIF annotation as a live Python object.

-

In MMIF, annotations are created by apps in a pipeline as a part -of a view. For documentation on how views are represented, see -mmif.serialize.view.

-
-
-class mmif.serialize.annotation.Annotation(anno_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-

MmifObject that represents an annotation in a MMIF view.

-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]]) → None[source]
-

Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

-
- -
-
-property at_type: TypesBase[source]
-
- -
-
-property id: str[source]
-
- -
-
-is_document()[source]
-
- -
-
-is_type(at_type: str | TypesBase) → bool[source]
-

Check if the @type of this object matches.

-
- -
- -
-
-class mmif.serialize.annotation.AnnotationProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject, MutableMapping[str, T]

-

AnnotationProperties object that represents the -properties object within a MMIF annotation.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
- -
-
-class mmif.serialize.annotation.Document(doc_obj: bytes | str | dict | None = None)[source]
-

Bases: Annotation

-

Document object that represents a single document in a MMIF file.

-

A document is identified by an ID, and contains certain attributes -and potentially contains the contents of the document itself, -metadata about how the document was created, and/or a list of -subdocuments grouped together logically.

-

If document_obj is not provided, an empty Document will be generated.

-
-
Parameters:
-

document_obj – the JSON data that defines the document

-
-
-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None]) → None[source]
-

Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

-
- -
-
-property location: str | None[source]
-

location property must be a legitimate URI. That is, should the document be a local file -then the file:// scheme must be used. -Returns None when no location is set.

-
- -
-
-location_address() → str | None[source]
-

Retrieves the full address from the document location URI. -Returns None when no location is set.

-
- -
-
-location_path() → str | None[source]
-

Retrieves only path name of the document location (hostname is ignored). -Useful to get a path of a local file. -Returns None when no location is set.

-
- -
-
-location_scheme() → str | None[source]
-

Retrieves URI scheme of the document location. -Returns None when no location is set.

-
- -
-
-property parent: str[source]
-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.DocumentProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: AnnotationProperties

-

DocumentProperties object that represents the -properties object within a MMIF document.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
-
-property location: str | None[source]
-

location property must be a legitimate URI. That is, should the document be a local file -then the file:// scheme must be used. -Returns None when no location is set.

-
- -
-
-location_address() → str | None[source]
-

Retrieves the full address from the document location URI. -Returns None when no location is set.

-
- -
-
-location_path() → str | None[source]
-

Retrieves only path name of the document location (hostname is ignored). -Useful to get a path of a local file. -Returns None when no location is set.

-
- -
-
-location_scheme() → str | None[source]
-

Retrieves URI scheme of the document location. -Returns None when no location is set.

-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.Text(text_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-
-
-property lang: str[source]
-
- -
-
-property value: str[source]
-
- -
- -
-
- - -
-
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- - Other Versions - v: 1.0.0 - - -
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- - - \ No newline at end of file diff --git a/docs/1.0.0/autodoc/mmif.vocabulary.html b/docs/1.0.0/autodoc/mmif.vocabulary.html deleted file mode 100644 index dbf55964..00000000 --- a/docs/1.0.0/autodoc/mmif.vocabulary.html +++ /dev/null @@ -1,324 +0,0 @@ - - - - - - - - - mmif.vocabulary module — mmif-python documentation - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.vocabulary module

-
-

mmif.vocabulary.annotation_types module

-
-
-class mmif.vocabulary.annotation_types.AnnotationTypes(type_uri, fuzzymode=True)[source]
-

Bases: AnnotationTypesBase

-

This class contains the CLAMS annotation types -defined in the spec version 1.1.0 as class variables.

-
-
-Alignment = http://mmif.clams.ai/vocabulary/Alignment/v1[source]
-
- -
-
-Annotation = http://mmif.clams.ai/vocabulary/Annotation/v6[source]
-
- -
-
-BoundingBox = http://mmif.clams.ai/vocabulary/BoundingBox/v5[source]
-
- -
-
-Chapter = http://mmif.clams.ai/vocabulary/Chapter/v6[source]
-
- -
-
-Interval = http://mmif.clams.ai/vocabulary/Interval/v5[source]
-
- -
-
-NamedEntity = http://mmif.clams.ai/vocabulary/NamedEntity/v1[source]
-
- -
-
-NounChunk = http://mmif.clams.ai/vocabulary/NounChunk/v1[source]
-
- -
-
-Paragraph = http://mmif.clams.ai/vocabulary/Paragraph/v1[source]
-
- -
-
-Polygon = http://mmif.clams.ai/vocabulary/Polygon/v5[source]
-
- -
-
-Region = http://mmif.clams.ai/vocabulary/Region/v5[source]
-
- -
-
-Relation = http://mmif.clams.ai/vocabulary/Relation/v5[source]
-
- -
-
-Sentence = http://mmif.clams.ai/vocabulary/Sentence/v1[source]
-
- -
-
-Span = http://mmif.clams.ai/vocabulary/Span/v5[source]
-
- -
-
-TimeFrame = http://mmif.clams.ai/vocabulary/TimeFrame/v6[source]
-
- -
-
-TimePoint = http://mmif.clams.ai/vocabulary/TimePoint/v5[source]
-
- -
-
-Token = http://mmif.clams.ai/vocabulary/Token/v1[source]
-
- -
-
-VerbChunk = http://mmif.clams.ai/vocabulary/VerbChunk/v1[source]
-
- -
-
-VideoObject = http://mmif.clams.ai/vocabulary/VideoObject/v5[source]
-
- -
-
-typevers = {'Alignment': 'v1', 'Annotation': 'v6', 'BoundingBox': 'v5', 'Chapter': 'v6', 'Interval': 'v5', 'NamedEntity': 'v1', 'NounChunk': 'v1', 'Paragraph': 'v1', 'Polygon': 'v5', 'Region': 'v5', 'Relation': 'v5', 'Sentence': 'v1', 'Span': 'v5', 'TimeFrame': 'v6', 'TimePoint': 'v5', 'Token': 'v1', 'VerbChunk': 'v1', 'VideoObject': 'v5'}[source]
-
- -
- -
-
-

mmif.vocabulary.document_types module

-
-
-class mmif.vocabulary.document_types.DocumentTypes(type_uri, fuzzymode=True)[source]
-

Bases: DocumentTypesBase

-

This class contains the CLAMS document types -defined in the spec version 1.1.0 as class variables.

-
-
-AudioDocument = http://mmif.clams.ai/vocabulary/AudioDocument/v1[source]
-
- -
-
-Document = http://mmif.clams.ai/vocabulary/Document/v1[source]
-
- -
-
-ImageDocument = http://mmif.clams.ai/vocabulary/ImageDocument/v1[source]
-
- -
-
-TextDocument = http://mmif.clams.ai/vocabulary/TextDocument/v1[source]
-
- -
-
-VideoDocument = http://mmif.clams.ai/vocabulary/VideoDocument/v1[source]
-
- -
-
-typevers = {'AudioDocument': 'v1', 'Document': 'v1', 'ImageDocument': 'v1', 'TextDocument': 'v1', 'VideoDocument': 'v1'}[source]
-
- -
- -
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 1.0.0 - - -
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0.3.0
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0.3.1
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0.3.2
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0.3.3
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0.3.4
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- - - \ No newline at end of file diff --git a/docs/1.0.0/consumer-tutorial.html b/docs/1.0.0/consumer-tutorial.html deleted file mode 100644 index 333053c2..00000000 --- a/docs/1.0.0/consumer-tutorial.html +++ /dev/null @@ -1,170 +0,0 @@ - - - - - - - - - MMIF consumer — mmif-python documentation - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • MMIF consumer
    • -
  • -
    • -
-
-
-
-
- -
-

MMIF consumer

-

A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the appliance documentation to learn more about the appliance.

-

MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance.

-
    -

  1. The code must be hosted on a public git repository (e.g. Github, Gitlab, …)

    2. -

  2. Must listen to 5000 port.

    3. -

  3. Must expose /display route .

    4. -

  4. /display router should response to GET requests.

    5. -

  5. In the GET request, a public URL of the input MMIF file is passed via file URL parameter.

    6. -

  6. On the codebase root, there must be a Dockerfile that can build a docker image that runs the web app.

    7. -
-

We provide an example consumer at https://github.com/clamsproject/mmif-visualizer.

-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 1.0.0 - - -
-
- -
0.3.0
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0.3.2
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0.3.3
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- - -
- -
-
-
-
    -
    • -
  • Index
    • -
  • -
    • -
-
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-
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- - -

Index

- -
- A - | B - | C - | D - | E - | G - | I - | K - | L - | M - | N - | P - | R - | S - | T - | U - | V - -
-

A

- - - -
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B

- - -
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C

- - - -
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D

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V

- - - -
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- - -
- -
-
-
-
    -
    • -
  • Welcome to mmif-python’s documentation!
    • -
  • -
    • -
-
-
-
-
- -
-

Welcome to mmif-python’s documentation!

-
-

MultiMedia Interchange Format

-

MMIF is a JSON(-LD)-based data format designed for transferring annotation data between computational analysis applications in CLAMS project.

-
-

Contents

- -
-
-

API documentation:

- -
-
-
-
-

Indices and tables

- -
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 1.0.0 - - -
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- - - \ No newline at end of file diff --git a/docs/1.0.0/introduction.html b/docs/1.0.0/introduction.html deleted file mode 100644 index ba9d4806..00000000 --- a/docs/1.0.0/introduction.html +++ /dev/null @@ -1,243 +0,0 @@ - - - - - - - - - Getting Started — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
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    -
    • -
  • Getting Started
    • -
  • -
    • -
-
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-
- -
-

Getting Started

-
-

Overview

-

MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for reproducibility, transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF website. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects.

-
-
-

Prerequisites

-
    -

  • Python: the latest mmif-python requires Python 3.8 or newer. We have no plan to support Python 2.7.

    • -
-
-
-

Installation

-

Package mmif-python is distributed via the official PyPI. Users are supposed to pip-install to get latest release.

-
pip install mmif-python
-
-
-

This will install a package mmif to local python.

-

The MMIF format and specification is evolving over time, and mmif-python package will be updated along with the changes in MMIF format.

-
-

Note

-

MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and mmif-python versions, please take time to read our decision on the subject here. If you need to know which python SDK supports which specification version, see Target MMIF Versions page.

-
-
-
-

MMIF Serialization

-

mmif.serialize.mmif.Mmif represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of mmif.serialize.model.MmifObject, including the mmif.serialize.mmif.Mmif. To start with an existing MMIF str, simple initiate a new Mmif object with the file.

-
import mmif
-from mmif import Mmif
-
-mmif_str = """{
-"metadata": {
-  "mmif": "http://mmif.clams.ai/1.0.0"
-},
-"documents": [
-  {
-    "@type": "http://mmif.clams.ai/vocabulary/VideoDocument/v1",
-    "properties": {
-      "id": "m1",
-      "mime": "video/mp4",
-      "location": "file:///var/archive/video-0012.mp4"
-    }
-  },
-  {
-    "@type": "http://mmif.clams.ai/vocabulary/TextDocument/v1",
-    "properties": {
-      "id": "m2",
-      "mime": "text/plain",
-      "location": "file:///var/archive/video-0012-transcript.txt"
-    }
-  }
-],
-"views": []}"""
-mmif_obj = Mmif(mmif_str)
-
-
-

Few notes;

-
    -

  1. MMIF does not carry the primary source files in it.

    2. -

  2. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version mmif-python implementation of the MMIF might not be able to load an unsupported version of MMIF string.

    3. -
-

When serializing back to str, call mmif.serialize.model.MmifObject.serialize() on the object.

-

To get subcomponents, you can use various getters implemented in subclasses. For example;

-
from mmif.vocabulary.document_types import DocumentTypes
-
-for video in mmif_obj.Mmif.get_documents_by_type(DocumentTypes.VideoDocument):
-  with open(video.location_path(), 'b') as in_video:
-    # do something with the video file
-
-
-

For a full list of available helper methods, please refer to the API documentation.

-
-
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-
- -
-
-
-
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- - Other Versions - v: 1.0.0 - - -
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0.3.0
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0.3.2
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0.3.3
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0.3.4
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[0, 4], "specif": 6, "start": 4, "tabl": 3, "target": 6, "version": 6, "view": 0, "vocabulari": 1, "welcom": 3}}) \ No newline at end of file diff --git a/docs/1.0.0/target-versions.html b/docs/1.0.0/target-versions.html deleted file mode 100644 index c4191dc2..00000000 --- a/docs/1.0.0/target-versions.html +++ /dev/null @@ -1,241 +0,0 @@ - - - - - - - - - Target MMIF Versions — mmif-python documentation - - - - - - - - - - - - - - - - - -
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  • Target MMIF Versions
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Target MMIF Versions

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This article provides targeting MMIF specification versions of different versions of mmif-python SDK.

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Target Specification Versions

mmif-python version

Target MMIF Specification

1.0.0

1.1.0

0.5.2

0.5.0

0.5.1

0.5.0

0.5.0

0.5.0

0.4.8

0.4.2

0.4.7

0.4.1

0.4.6

0.4.0

0.4.5

0.4.0

0.4.4

0.4.0

0.4.3

0.4.0

0.4.2

0.4.0

0.4.1

0.4.0

0.4.0

0.4.0

0.3.5

0.3.1

0.3.4

0.3.1

0.3.3

0.3.1

0.3.2

0.3.1

0.3.1

0.3.0

0.3.0

0.3.0

0.2.2

0.2.1

0.2.1

0.2.1

0.2.0

0.2.1

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0.3.0
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0.3.1
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0.3.2
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0.3.3
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0.3.4
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0.3.5
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0.4.0
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0.4.1
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0.4.2
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0.4.3
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0.4.4
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0.4.5
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0.4.6
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0.4.7
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0.4.8
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0.5.0
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0.5.1
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0.5.2
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1.0.0
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1.0.1
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1.0.10
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1.0.11
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1.0.12
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1.0.13
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1.0.14
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1.0.15
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1.0.16
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1.0.17
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1.0.18
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1.0.19
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1.0.2
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1.0.3
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1.0.4
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1.0.5
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1.0.6
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1.0.7
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1.0.8
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1.0.9
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1.1.0
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The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the `appliance documentation `_ to learn more about the appliance. - -MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance. - -#. The code must be hosted on a public git repository (e.g. Github, Gitlab, ...) -#. Must listen to ``5000`` port. -#. Must expose ``/display`` route . -#. ``/display`` router should response to ``GET`` requests. -#. In the ``GET`` request, a public URL of the input MMIF file is passed via ``file`` URL parameter. -#. On the codebase root, there must be a ``Dockerfile`` that can build a `docker `_ image that runs the web app. - -We provide an example consumer at https://github.com/clamsproject/mmif-visualizer. diff --git a/docs/1.0.1/_sources/index.rst.txt b/docs/1.0.1/_sources/index.rst.txt deleted file mode 100644 index 1f6c350c..00000000 --- a/docs/1.0.1/_sources/index.rst.txt +++ /dev/null @@ -1,25 +0,0 @@ -Welcome to mmif-python's documentation! -======================================= - -.. mdinclude:: ../README.md - -.. toctree:: - :maxdepth: 2 - :caption: Contents - - introduction - target-versions - -.. toctree:: - :maxdepth: 2 - :caption: API documentation: - - modules - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/docs/1.0.1/_sources/introduction.rst.txt b/docs/1.0.1/_sources/introduction.rst.txt deleted file mode 100644 index b1070185..00000000 --- a/docs/1.0.1/_sources/introduction.rst.txt +++ /dev/null @@ -1,89 +0,0 @@ -.. _instroduction: - -Getting Started -=============== - - -Overview ---------- - -MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for reproducibility, transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF website `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects. - -Prerequisites -------------- - -* `Python `_: the latest ``mmif-python`` requires Python 3.8 or newer. We have no plan to support `Python 2.7 `_. - -Installation ---------------- - -Package ``mmif-python`` is distributed via the official PyPI. Users are supposed to pip-install to get latest release. - -.. code-block:: bash - - pip install mmif-python - -This will install a package `mmif` to local python. - -The MMIF format and specification is evolving over time, and ``mmif-python`` package will be updated along with the changes in MMIF format. - -.. note:: MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and ``mmif-python`` versions, please take time to read our decision on the subject `here `_. If you need to know which python SDK supports which specification version, see :ref:`target-versions` page. - -MMIF Serialization ---------------------------- - -:class:`mmif.serialize.mmif.Mmif` represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of :class:`mmif.serialize.model.MmifObject`, including the :class:`mmif.serialize.mmif.Mmif`. To start with an existing MMIF :class:`str`, simple initiate a new ``Mmif`` object with the file. - -.. code-block:: python - - import mmif - from mmif import Mmif - - mmif_str = """{ - "metadata": { - "mmif": "http://mmif.clams.ai/1.0.0" - }, - "documents": [ - { - "@type": "http://mmif.clams.ai/vocabulary/VideoDocument/v1", - "properties": { - "id": "m1", - "mime": "video/mp4", - "location": "file:///var/archive/video-0012.mp4" - } - }, - { - "@type": "http://mmif.clams.ai/vocabulary/TextDocument/v1", - "properties": { - "id": "m2", - "mime": "text/plain", - "location": "file:///var/archive/video-0012-transcript.txt" - } - } - ], - "views": []}""" - mmif_obj = Mmif(mmif_str) - - -Few notes; - -#. MMIF does not carry the primary source files in it. -#. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version ``mmif-python`` implementation of the MMIF might not be able to load an unsupported version of MMIF string. - -When serializing back to :class:`str`, call :meth:`mmif.serialize.model.MmifObject.serialize` on the object. - -To get subcomponents, you can use various getters implemented in subclasses. For example; - -.. code-block:: python - - from mmif.vocabulary.document_types import DocumentTypes - - for video in mmif_obj.Mmif.get_documents_by_type(DocumentTypes.VideoDocument): - with open(video.location_path(), 'b') as in_video: - # do something with the video file - - -For a full list of available helper methods, please refer to :ref:`the API documentation `. - diff --git a/docs/1.0.1/_sources/modules.rst.txt b/docs/1.0.1/_sources/modules.rst.txt deleted file mode 100644 index e4269c6d..00000000 --- a/docs/1.0.1/_sources/modules.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _apidoc: - -mmif package -============ - -.. toctree:: - :maxdepth: 4 - - autodoc/mmif.serialize - autodoc/mmif.vocabulary diff --git a/docs/1.0.1/_sources/target-versions.rst.txt b/docs/1.0.1/_sources/target-versions.rst.txt deleted file mode 100644 index 34216d3e..00000000 --- a/docs/1.0.1/_sources/target-versions.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _target-versions: - -Target MMIF Versions -==================== - -This article provides targeting MMIF specification versions of different versions of ``mmif-python`` SDK. - -.. csv-table:: Target Specification Versions - :file: target-versions.csv - :header-rows: 1 diff --git a/docs/1.0.1/_static/_sphinx_javascript_frameworks_compat.js b/docs/1.0.1/_static/_sphinx_javascript_frameworks_compat.js deleted file mode 100644 index 81415803..00000000 --- a/docs/1.0.1/_static/_sphinx_javascript_frameworks_compat.js +++ /dev/null @@ -1,123 +0,0 @@ -/* Compatability shim for jQuery and underscores.js. - * - * Copyright Sphinx contributors - * Released under the two clause BSD licence - */ - -/** - * small helper function to urldecode strings - * - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL - */ -jQuery.urldecode = function(x) { - if (!x) { - return x - } - return decodeURIComponent(x.replace(/\+/g, ' ')); -}; - -/** - * small helper function to urlencode strings - */ -jQuery.urlencode = encodeURIComponent; - -/** - * This function returns the parsed url parameters of the - * current request. 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- -/** - * Simple result scoring code. - */ -if (typeof Scorer === "undefined") { - var Scorer = { - // Implement the following function to further tweak the score for each result - // The function takes a result array [docname, title, anchor, descr, score, filename] - // and returns the new score. - /* - score: result => { - const [docname, title, anchor, descr, score, filename, kind] = result - return score - }, - */ - - // query matches the full name of an object - objNameMatch: 11, - // or matches in the last dotted part of the object name - objPartialMatch: 6, - // Additive scores depending on the priority of the object - objPrio: { - 0: 15, // used to be importantResults - 1: 5, // used to be objectResults - 2: -5, // used to be unimportantResults - }, - // Used when the priority is not in the mapping. - objPrioDefault: 0, - - // query found in title - title: 15, - partialTitle: 7, - // query found in terms - term: 5, - partialTerm: 2, - }; -} - -// Global search result kind enum, used by themes to style search results. -class SearchResultKind { - static get index() { return "index"; } - static get object() { return "object"; } - static get text() { return "text"; } - static get title() { return "title"; } -} - -const _removeChildren = (element) => { - while (element && element.lastChild) element.removeChild(element.lastChild); -}; - -/** - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping - */ -const _escapeRegExp = (string) => - string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string - -const _displayItem = (item, searchTerms, highlightTerms) => { - const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; - const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; - const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; - const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; - const contentRoot = document.documentElement.dataset.content_root; - - const [docName, title, anchor, descr, score, _filename, kind] = item; - - let listItem = document.createElement("li"); - // Add a class representing the item's type: - // can be used by a theme's CSS selector for styling - // See SearchResultKind for the class names. - listItem.classList.add(`kind-${kind}`); - let requestUrl; - let linkUrl; - if (docBuilder === "dirhtml") { - // dirhtml builder - let dirname = docName + "/"; - if (dirname.match(/\/index\/$/)) - dirname = dirname.substring(0, dirname.length - 6); - else if (dirname === "index/") dirname = ""; - requestUrl = contentRoot + dirname; - linkUrl = requestUrl; - } else { - // normal html builders - requestUrl = contentRoot + docName + docFileSuffix; - linkUrl = docName + docLinkSuffix; - } - let linkEl = listItem.appendChild(document.createElement("a")); - linkEl.href = linkUrl + anchor; - linkEl.dataset.score = score; - linkEl.innerHTML = title; - if (descr) { - listItem.appendChild(document.createElement("span")).innerHTML = - " (" + descr + ")"; - // highlight search terms in the description - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - } - else if (showSearchSummary) - fetch(requestUrl) - .then((responseData) => responseData.text()) - .then((data) => { - if (data) - listItem.appendChild( - Search.makeSearchSummary(data, searchTerms, anchor) - ); - // highlight search terms in the summary - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - }); - Search.output.appendChild(listItem); -}; -const _finishSearch = (resultCount) => { - Search.stopPulse(); - Search.title.innerText = _("Search Results"); - if (!resultCount) - Search.status.innerText = Documentation.gettext( - "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." - ); - else - Search.status.innerText = Documentation.ngettext( - "Search finished, found one page matching the search query.", - "Search finished, found ${resultCount} pages matching the search query.", - resultCount, - ).replace('${resultCount}', resultCount); -}; -const _displayNextItem = ( - results, - resultCount, - searchTerms, - highlightTerms, -) => { - // results left, load the summary and display it - // this is intended to be dynamic (don't sub resultsCount) - if (results.length) { - _displayItem(results.pop(), searchTerms, highlightTerms); - setTimeout( - () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), - 5 - ); - } - // search finished, update title and status message - else _finishSearch(resultCount); -}; -// Helper function used by query() to order search results. -// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. -// Order the results by score (in opposite order of appearance, since the -// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. -const _orderResultsByScoreThenName = (a, b) => { - const leftScore = a[4]; - const rightScore = b[4]; - if (leftScore === rightScore) { - // same score: sort alphabetically - const leftTitle = a[1].toLowerCase(); - const rightTitle = b[1].toLowerCase(); - if (leftTitle === rightTitle) return 0; - return leftTitle > rightTitle ? -1 : 1; // inverted is intentional - } - return leftScore > rightScore ? 1 : -1; -}; - -/** - * Default splitQuery function. Can be overridden in ``sphinx.search`` with a - * custom function per language. - * - * The regular expression works by splitting the string on consecutive characters - * that are not Unicode letters, numbers, underscores, or emoji characters. - * This is the same as ``\W+`` in Python, preserving the surrogate pair area. - */ -if (typeof splitQuery === "undefined") { - var splitQuery = (query) => query - .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) - .filter(term => term) // remove remaining empty strings -} - -/** - * Search Module - */ -const Search = { - _index: null, - _queued_query: null, - _pulse_status: -1, - - htmlToText: (htmlString, anchor) => { - const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - for (const removalQuery of [".headerlink", "script", "style"]) { - htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); - } - if (anchor) { - const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); - if (anchorContent) return anchorContent.textContent; - - console.warn( - `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` - ); - } - - // if anchor not specified or not found, fall back to main content - const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent) return docContent.textContent; - - console.warn( - "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." - ); - return ""; - }, - - init: () => { - const query = new URLSearchParams(window.location.search).get("q"); - document - .querySelectorAll('input[name="q"]') - .forEach((el) => (el.value = query)); - if (query) Search.performSearch(query); - }, - - loadIndex: (url) => - (document.body.appendChild(document.createElement("script")).src = url), - - setIndex: (index) => { - Search._index = index; - if (Search._queued_query !== null) { - const query = Search._queued_query; - Search._queued_query = null; - Search.query(query); - } - }, - - hasIndex: () => Search._index !== null, - - deferQuery: (query) => (Search._queued_query = query), - - stopPulse: () => (Search._pulse_status = -1), - - startPulse: () => { - if (Search._pulse_status >= 0) return; - - const pulse = () => { - Search._pulse_status = (Search._pulse_status + 1) % 4; - Search.dots.innerText = ".".repeat(Search._pulse_status); - if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); - }; - pulse(); - }, - - /** - * perform a search for something (or wait until index is loaded) - */ - performSearch: (query) => { - // create the required interface elements - const searchText = document.createElement("h2"); - searchText.textContent = _("Searching"); - const searchSummary = document.createElement("p"); - searchSummary.classList.add("search-summary"); - searchSummary.innerText = ""; - const searchList = document.createElement("ul"); - searchList.setAttribute("role", "list"); - searchList.classList.add("search"); - - const out = document.getElementById("search-results"); - Search.title = out.appendChild(searchText); - Search.dots = Search.title.appendChild(document.createElement("span")); - Search.status = out.appendChild(searchSummary); - Search.output = out.appendChild(searchList); - - const searchProgress = document.getElementById("search-progress"); - // Some themes don't use the search progress node - if (searchProgress) { - searchProgress.innerText = _("Preparing search..."); - } - Search.startPulse(); - - // index already loaded, the browser was quick! - if (Search.hasIndex()) Search.query(query); - else Search.deferQuery(query); - }, - - _parseQuery: (query) => { - // stem the search terms and add them to the correct list - const stemmer = new Stemmer(); - const searchTerms = new Set(); - const excludedTerms = new Set(); - const highlightTerms = new Set(); - const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); - splitQuery(query.trim()).forEach((queryTerm) => { - const queryTermLower = queryTerm.toLowerCase(); - - // maybe skip this "word" - // stopwords array is from language_data.js - if ( - stopwords.indexOf(queryTermLower) !== -1 || - queryTerm.match(/^\d+$/) - ) - return; - - // stem the word - let word = stemmer.stemWord(queryTermLower); - // select the correct list - if (word[0] === "-") excludedTerms.add(word.substr(1)); - else { - searchTerms.add(word); - highlightTerms.add(queryTermLower); - } - }); - - if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js - localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) - } - - // console.debug("SEARCH: searching for:"); - // console.info("required: ", [...searchTerms]); - // console.info("excluded: ", [...excludedTerms]); - - return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; - }, - - /** - * execute search (requires search index to be loaded) - */ - _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - - // Collect multiple result groups to be sorted separately and then ordered. - // Each is an array of [docname, title, anchor, descr, score, filename, kind]. - const normalResults = []; - const nonMainIndexResults = []; - - _removeChildren(document.getElementById("search-progress")); - - const queryLower = query.toLowerCase().trim(); - for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { - for (const [file, id] of foundTitles) { - const score = Math.round(Scorer.title * queryLower.length / title.length); - const boost = titles[file] === title ? 1 : 0; // add a boost for document titles - normalResults.push([ - docNames[file], - titles[file] !== title ? `${titles[file]} > ${title}` : title, - id !== null ? "#" + id : "", - null, - score + boost, - filenames[file], - SearchResultKind.title, - ]); - } - } - } - - // search for explicit entries in index directives - for (const [entry, foundEntries] of Object.entries(indexEntries)) { - if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id, isMain] of foundEntries) { - const score = Math.round(100 * queryLower.length / entry.length); - const result = [ - docNames[file], - titles[file], - id ? "#" + id : "", - null, - score, - filenames[file], - SearchResultKind.index, - ]; - if (isMain) { - normalResults.push(result); - } else { - nonMainIndexResults.push(result); - } - } - } - } - - // lookup as object - objectTerms.forEach((term) => - normalResults.push(...Search.performObjectSearch(term, objectTerms)) - ); - - // lookup as search terms in fulltext - normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); - - // let the scorer override scores with a custom scoring function - if (Scorer.score) { - normalResults.forEach((item) => (item[4] = Scorer.score(item))); - nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); - } - - // Sort each group of results by score and then alphabetically by name. - normalResults.sort(_orderResultsByScoreThenName); - nonMainIndexResults.sort(_orderResultsByScoreThenName); - - // Combine the result groups in (reverse) order. - // Non-main index entries are typically arbitrary cross-references, - // so display them after other results. - let results = [...nonMainIndexResults, ...normalResults]; - - // remove duplicate search results - // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept - let seen = new Set(); - results = results.reverse().reduce((acc, result) => { - let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); - if (!seen.has(resultStr)) { - acc.push(result); - seen.add(resultStr); - } - return acc; - }, []); - - return results.reverse(); - }, - - query: (query) => { - const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); - const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); - - // for debugging - //Search.lastresults = results.slice(); // a copy - // console.info("search results:", Search.lastresults); - - // print the results - _displayNextItem(results, results.length, searchTerms, highlightTerms); - }, - - /** - * search for object names - */ - performObjectSearch: (object, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const objects = Search._index.objects; - const objNames = Search._index.objnames; - const titles = Search._index.titles; - - const results = []; - - const objectSearchCallback = (prefix, match) => { - const name = match[4] - const fullname = (prefix ? prefix + "." : "") + name; - const fullnameLower = fullname.toLowerCase(); - if (fullnameLower.indexOf(object) < 0) return; - - let score = 0; - const parts = fullnameLower.split("."); - - // check for different match types: exact matches of full name or - // "last name" (i.e. last dotted part) - if (fullnameLower === object || parts.slice(-1)[0] === object) - score += Scorer.objNameMatch; - else if (parts.slice(-1)[0].indexOf(object) > -1) - score += Scorer.objPartialMatch; // matches in last name - - const objName = objNames[match[1]][2]; - const title = titles[match[0]]; - - // If more than one term searched for, we require other words to be - // found in the name/title/description - const otherTerms = new Set(objectTerms); - otherTerms.delete(object); - if (otherTerms.size > 0) { - const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); - if ( - [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) - ) - return; - } - - let anchor = match[3]; - if (anchor === "") anchor = fullname; - else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; - - const descr = objName + _(", in ") + title; - - // add custom score for some objects according to scorer - if (Scorer.objPrio.hasOwnProperty(match[2])) - score += Scorer.objPrio[match[2]]; - else score += Scorer.objPrioDefault; - - results.push([ - docNames[match[0]], - fullname, - "#" + anchor, - descr, - score, - filenames[match[0]], - SearchResultKind.object, - ]); - }; - Object.keys(objects).forEach((prefix) => - objects[prefix].forEach((array) => - objectSearchCallback(prefix, array) - ) - ); - return results; - }, - - /** - * search for full-text terms in the index - */ - performTermsSearch: (searchTerms, excludedTerms) => { - // prepare search - const terms = Search._index.terms; - const titleTerms = Search._index.titleterms; - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - - const scoreMap = new Map(); - const fileMap = new Map(); - - // perform the search on the required terms - searchTerms.forEach((word) => { - const files = []; - const arr = [ - { files: terms[word], score: Scorer.term }, - { files: titleTerms[word], score: Scorer.title }, - ]; - // add support for partial matches - if (word.length > 2) { - const escapedWord = _escapeRegExp(word); - if (!terms.hasOwnProperty(word)) { - Object.keys(terms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: terms[term], score: Scorer.partialTerm }); - }); - } - if (!titleTerms.hasOwnProperty(word)) { - Object.keys(titleTerms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); - }); - } - } - - // no match but word was a required one - if (arr.every((record) => record.files === undefined)) return; - - // found search word in contents - arr.forEach((record) => { - if (record.files === undefined) return; - - let recordFiles = record.files; - if (recordFiles.length === undefined) recordFiles = [recordFiles]; - files.push(...recordFiles); - - // set score for the word in each file - recordFiles.forEach((file) => { - if (!scoreMap.has(file)) scoreMap.set(file, {}); - scoreMap.get(file)[word] = record.score; - }); - }); - - // create the mapping - files.forEach((file) => { - if (!fileMap.has(file)) fileMap.set(file, [word]); - else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); - }); - }); - - // now check if the files don't contain excluded terms - const results = []; - for (const [file, wordList] of fileMap) { - // check if all requirements are matched - - // as search terms with length < 3 are discarded - const filteredTermCount = [...searchTerms].filter( - (term) => term.length > 2 - ).length; - if ( - wordList.length !== searchTerms.size && - wordList.length !== filteredTermCount - ) - continue; - - // ensure that none of the excluded terms is in the search result - if ( - [...excludedTerms].some( - (term) => - terms[term] === file || - titleTerms[term] === file || - (terms[term] || []).includes(file) || - (titleTerms[term] || []).includes(file) - ) - ) - break; - - // select one (max) score for the file. - const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); - // add result to the result list - results.push([ - docNames[file], - titles[file], - "", - null, - score, - filenames[file], - SearchResultKind.text, - ]); - } - return results; - }, - - /** - * helper function to return a node containing the - * search summary for a given text. keywords is a list - * of stemmed words. - */ - makeSearchSummary: (htmlText, keywords, anchor) => { - const text = Search.htmlToText(htmlText, anchor); - if (text === "") return null; - - const textLower = text.toLowerCase(); - const actualStartPosition = [...keywords] - .map((k) => textLower.indexOf(k.toLowerCase())) - .filter((i) => i > -1) - .slice(-1)[0]; - const startWithContext = Math.max(actualStartPosition - 120, 0); - - const top = startWithContext === 0 ? "" : "..."; - const tail = startWithContext + 240 < text.length ? "..." : ""; - - let summary = document.createElement("p"); - summary.classList.add("context"); - summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; - - return summary; - }, -}; - -_ready(Search.init); diff --git a/docs/1.0.1/_static/sphinx_highlight.js b/docs/1.0.1/_static/sphinx_highlight.js deleted file mode 100644 index 8a96c69a..00000000 --- a/docs/1.0.1/_static/sphinx_highlight.js +++ /dev/null @@ -1,154 +0,0 @@ -/* Highlighting utilities for Sphinx HTML documentation. */ -"use strict"; - -const SPHINX_HIGHLIGHT_ENABLED = true - -/** - * highlight a given string on a node by wrapping it in - * span elements with the given class name. - */ -const _highlight = (node, addItems, text, className) => { - if (node.nodeType === Node.TEXT_NODE) { - const val = node.nodeValue; - const parent = node.parentNode; - const pos = val.toLowerCase().indexOf(text); - if ( - pos >= 0 && - !parent.classList.contains(className) && - !parent.classList.contains("nohighlight") - ) { - let span; - - const closestNode = parent.closest("body, svg, foreignObject"); - const isInSVG = closestNode && closestNode.matches("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.classList.add(className); - } - - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - const rest = document.createTextNode(val.substr(pos + text.length)); - parent.insertBefore( - span, - parent.insertBefore( - rest, - node.nextSibling - ) - ); - node.nodeValue = val.substr(0, pos); - /* There may be more occurrences of search term in this node. So call this - * function recursively on the remaining fragment. - */ - _highlight(rest, addItems, text, className); - - if (isInSVG) { - const rect = document.createElementNS( - "http://www.w3.org/2000/svg", - "rect" - ); - const bbox = parent.getBBox(); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute("class", className); - addItems.push({ parent: parent, target: rect }); - } - } - } else if (node.matches && !node.matches("button, select, textarea")) { - node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); - } -}; -const _highlightText = (thisNode, text, className) => { - let addItems = []; - _highlight(thisNode, addItems, text, className); - addItems.forEach((obj) => - obj.parent.insertAdjacentElement("beforebegin", obj.target) - ); -}; - -/** - * Small JavaScript module for the documentation. - */ -const SphinxHighlight = { - - /** - * highlight the search words provided in localstorage in the text - */ - highlightSearchWords: () => { - if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight - - // get and clear terms from localstorage - const url = new URL(window.location); - const highlight = - localStorage.getItem("sphinx_highlight_terms") - || url.searchParams.get("highlight") - || ""; - localStorage.removeItem("sphinx_highlight_terms") - url.searchParams.delete("highlight"); - window.history.replaceState({}, "", url); - - // get individual terms from highlight string - const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); - if (terms.length === 0) return; // nothing to do - - // There should never be more than one element matching "div.body" - const divBody = document.querySelectorAll("div.body"); - const body = divBody.length ? divBody[0] : document.querySelector("body"); - window.setTimeout(() => { - terms.forEach((term) => _highlightText(body, term, "highlighted")); - }, 10); - - const searchBox = document.getElementById("searchbox"); - if (searchBox === null) return; - searchBox.appendChild( - document - .createRange() - .createContextualFragment( - '

' + - '' + - _("Hide Search Matches") + - "

" - ) - ); - }, - - /** - * helper function to hide the search marks again - */ - hideSearchWords: () => { - document - .querySelectorAll("#searchbox .highlight-link") - .forEach((el) => el.remove()); - document - .querySelectorAll("span.highlighted") - .forEach((el) => el.classList.remove("highlighted")); - localStorage.removeItem("sphinx_highlight_terms") - }, - - initEscapeListener: () => { - // only install a listener if it is really needed - if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; - - document.addEventListener("keydown", (event) => { - // bail for input elements - if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; - // bail with special keys - if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; - if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { - SphinxHighlight.hideSearchWords(); - event.preventDefault(); - } - }); - }, -}; - -_ready(() => { - /* Do not call highlightSearchWords() when we are on the search page. - * It will highlight words from the *previous* search query. - */ - if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); - SphinxHighlight.initEscapeListener(); -}); diff --git a/docs/1.0.1/autodoc/mmif.serialize.html b/docs/1.0.1/autodoc/mmif.serialize.html deleted file mode 100644 index c644745d..00000000 --- a/docs/1.0.1/autodoc/mmif.serialize.html +++ /dev/null @@ -1,1175 +0,0 @@ - - - - - - - - - mmif.serialize module — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.serialize module

-
-

mmif.serialize.model module

-

The model module contains the classes used to represent an -abstract MMIF object as a live Python object.

-

The MmifObject class or one of its derivatives is subclassed by -all other classes defined in this SDK, except for MmifObjectEncoder.

-

These objects are generally instantiated from JSON, either as a string -or as an already-loaded Python dictionary. This base class provides the -core functionality for deserializing MMIF JSON data into live objects -and serializing live objects into MMIF JSON data. Specialized behavior -for the different components of MMIF is added in the subclasses.

-
-
-class mmif.serialize.model.DataDict(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject, Generic[T, S]

-
-
-empty()[source]
-
- -
-
-get(key: T, default=None) → S | None[source]
-
- -
-
-items()[source]
-
- -
-
-keys()[source]
-
- -
-
-update(other, overwrite)[source]
-
- -
-
-values()[source]
-
- -
- -
-
-class mmif.serialize.model.DataList(mmif_obj: bytes | str | list | None = None)[source]
-

Bases: MmifObject, Generic[T]

-

The DataList class is an abstraction that represents the -various lists found in a MMIF file, such as documents, subdocuments, -views, and annotations.

-
-
Parameters:
-

mmif_obj (Union[str, list]) – the data that the list contains

-
-
-
-
-append(value, overwrite)[source]
-
- -
-
-deserialize(mmif_json: str | list) → None[source]
-

Passes the input data into the internal deserializer.

-
- -
-
-empty()[source]
-
- -
-
-get(key: str) → T | None[source]
-

Standard dictionary-style get() method, albeit with no default -parameter. Relies on the implementation of __getitem__.

-

Will return None if the key is not found.

-
-
Parameters:
-

key – the key to search for

-
-
Returns:
-

the value matching that key

-
-
-
- -
- -
-
-class mmif.serialize.model.MmifObject(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: object

-

Abstract superclass for MMIF related key-value pair objects.

-

Any MMIF object can be initialized as an empty placeholder or -an actual representation with a JSON formatted string or equivalent -dict object argument.

-

This superclass has four specially designed instance variables, and these -variable names cannot be used as attribute names for MMIF objects.

-
    -

  1. _unnamed_attributes: -Only can be either None or an empty dictionary. If it’s set to None, -it means the class won’t take any Additional Attributes in the JSON -schema sense. If it’s a dict, users can throw any k-v pairs to the -class, EXCEPT for the reserved two key names.

    2. -

  2. _attribute_classes: -This is a dict from a key name to a specific python class to use for -deserialize the value. Note that a key name in this dict does NOT -have to be a named attribute, but is recommended to be one.

    3. -

  3. _required_attributes: -This is a simple list of names of attributes that are required in the object. -When serialize, an object will skip its empty (e.g. zero-length, or None) -attributes unless they are in this list. Otherwise, the serialized JSON -string would have empty representations (e.g. "", []).

    4. -

  4. _exclude_from_diff: -This is a simple list of names of attributes that should be excluded from -the diff calculation in __eq__.

    5. -
-

# TODO (krim @ 8/17/20): this dict is however, a duplicate with the type hints in the class definition. -Maybe there is a better way to utilize type hints (e.g. getting them as a programmatically), but for now -developers should be careful to add types to hints as well as to this dict.

-

Also note that those special attributes MUST be set in the __init__() -before calling super method, otherwise deserialization will not work.

-

And also, a subclass that has one or more named attributes, it must -set those attributes in the __init__() before calling super method. When -serializing a MmifObject, all empty attributes will be ignored, so for -optional named attributes, you must leave the values empty (len == 0), but -NOT None. Any None-valued named attributes will cause issues with current -implementation.

-
-
Parameters:
-

mmif_obj – JSON string or dict to initialize an object. -If not given, an empty object will be initialized, sometimes with -an ID value automatically generated, based on its parent object.

-
-
-
-
-deserialize(mmif_json: str | dict) → None[source]
-

Takes a JSON-formatted string or a simple dict that’s json-loaded from -such a string as an input and populates object’s fields with the values -specified in the input.

-
-
Parameters:
-

mmif_json – JSON-formatted string or dict from such a string -that represents a MMIF object

-
-
-
- -
-
-disallow_additional_properties() → None[source]
-

Call this method in __init__() to prevent the insertion -of unnamed attributes after initialization.

-
- -
-
-static is_empty(obj) → bool[source]
-

return True if the obj is None or “emtpy”. The emptiness first defined as -having zero length. But for objects that lack __len__ method, we need -additional check.

-
- -
-
-reserved_names: Set[str] = {'_attribute_classes', '_exclude_from_diff', '_required_attributes', '_unnamed_attributes', 'reserved_names'}[source]
-
- -
-
-serialize(pretty: bool = False) → str[source]
-

Generates JSON representation of an object.

-
-
Parameters:
-

pretty – If True, returns string representation with indentation.

-
-
Returns:
-

JSON string of the object.

-
-
-
- -
-
-set_additional_property(key: str, value: Any) → None[source]
-

Method to set values in _unnamed_attributes.

-
-
Parameters:
-
    -

  • key – the attribute name

    • -

  • value – the desired value

    • -
-
-
Returns:
-

None

-
-
Raise:
-

AttributeError if additional properties are disallowed by disallow_additional_properties()

-
-
-
- -
- -
-
-class mmif.serialize.model.MmifObjectEncoder(*, skipkeys=False, ensure_ascii=True, check_circular=True, allow_nan=True, sort_keys=False, indent=None, separators=None, default=None)[source]
-

Bases: JSONEncoder

-

Encoder class to define behaviors of de-/serialization

-
-
-default(obj: MmifObject)[source]
-

Overrides default encoding behavior to prioritize MmifObject.serialize().

-
- -
- -
-
-

mmif.serialize.mmif module

-

The mmif module contains the classes used to represent a full MMIF -file as a live Python object.

-

See the specification docs and the JSON Schema file for more information.

-
-
-class mmif.serialize.mmif.Mmif(mmif_obj: bytes | str | dict | None = None, *, validate: bool = True)[source]
-

Bases: MmifObject

-

MmifObject that represents a full MMIF file.

-
-
Parameters:
-
    -

  • mmif_obj – the JSON data

    • -

  • validate – whether to validate the data against the MMIF JSON schema.

    • -
-
-
-
-
-add_document(document: Document, overwrite=False) → None[source]
-

Appends a Document object to the documents list.

-

Fails if there is already a document with the same ID in the MMIF object.

-
-
Parameters:
-
    -

  • document – the Document object to add

    • -

  • overwrite – if set to True, will overwrite -an existing view with the same ID

    • -
-
-
Returns:
-

None

-
-
-
- -
-
-add_view(view: View, overwrite=False) → None[source]
-

Appends a View object to the views list.

-

Fails if there is already a view with the same ID in the MMIF object.

-
-
Parameters:
-
    -

  • view – the Document object to add

    • -

  • overwrite – if set to True, will overwrite -an existing view with the same ID

    • -
-
-
Returns:
-

None

-
-
-
- -
-
-get_alignments(at_type1: str | TypesBase, at_type2: str | TypesBase) → Dict[str, List[Annotation]][source]
-

Finds views where alignments between two given annotation types occurred.

-
-
Returns:
-

a dict that keyed by view IDs (str) and has lists of alignment Annotation objects as values.

-
-
-
- -
-
-get_all_views_contain(at_types: TypesBase | str | List[str | TypesBase]) → List[View][source]
-

Returns the list of all views in the MMIF if given types -are present in that view’s ‘contains’ metadata.

-
-
Parameters:
-

at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

-
-
Returns:
-

the list of views that contain the type

-
-
-
- -
-
-get_document_by_id(doc_id: str) → Document[source]
-

Finds a Document object with the given ID.

-
-
Parameters:
-

doc_id – the ID to search for

-
-
Returns:
-

a reference to the corresponding document, if it exists

-
-
Raises:
-

Exception – if there is no corresponding document

-
-
-
- -
-
-get_document_location(m_type: DocumentTypes | str, path_only=False) → str | None[source]
-

Method to get the location of first document of given type.

-
-
Parameters:
-

m_type – the type to search for

-
-
Returns:
-

the value of the location field in the corresponding document

-
-
-
- -
-
-get_documents_by_app(app_id: str) → List[Document][source]
-

Method to get all documents object queries by its originated app name.

-
-
Parameters:
-

app_id – the app name to search for

-
-
Returns:
-

a list of documents matching the requested app name, or an empty list if the app not found

-
-
-
- -
-
-get_documents_by_property(prop_key: str, prop_value: str) → List[Document][source]
-

Method to retrieve documents by an arbitrary key-value pair in the document properties objects.

-
-
Parameters:
-
    -

  • prop_key – the metadata key to search for

    • -

  • prop_value – the metadata value to match

    • -
-
-
Returns:
-

a list of documents matching the requested metadata key-value pair

-
-
-
- -
-
-get_documents_by_type(doc_type: str | DocumentTypes) → List[Document][source]
-

Method to get all documents where the type matches a particular document type, which should be one of the CLAMS document types.

-
-
Parameters:
-

doc_type – the type of documents to search for, must be one of Document type defined in the CLAMS vocabulary.

-
-
Returns:
-

a list of documents matching the requested type, or an empty list if none found.

-
-
-
- -
-
-get_documents_in_view(vid: str | None = None) → List[Document][source]
-

Method to get all documents object queries by a view id.

-
-
Parameters:
-

vid – the source view ID to search for

-
-
Returns:
-

a list of documents matching the requested source view ID, or an empty list if the view not found

-
-
-
- -
-
-get_documents_locations(m_type: DocumentTypes | str, path_only=False) → List[str | None][source]
-

This method returns the file paths of documents of given type. -Only top-level documents have locations, so we only check them.

-
-
Parameters:
-

m_type – the type to search for

-
-
Returns:
-

a list of the values of the location fields in the corresponding documents

-
-
-
- -
-
-get_view_by_id(req_view_id: str) → View[source]
-

Finds a View object with the given ID.

-
-
Parameters:
-

req_view_id – the ID to search for

-
-
Returns:
-

a reference to the corresponding view, if it exists

-
-
Raises:
-

Exception – if there is no corresponding view

-
-
-
- -
-
-get_view_contains(at_types: TypesBase | str | List[str | TypesBase]) → View | None[source]
-

Returns the last view appended that contains the given -types in its ‘contains’ metadata.

-
-
Parameters:
-

at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

-
-
Returns:
-

the view, or None if the type is not found

-
-
-
- -
-
-get_views_contain(at_types: TypesBase | str | List[str | TypesBase]) → List[View][source]
-

An alias to get_all_views_contain method.

-
- -
-
-get_views_for_document(doc_id: str)[source]
-

Returns the list of all views that have annotations anchored on a particular document. -Note that when the document is insids a view (generated during the pipeline’s running), -doc_id must be prefixed with the view_id.

-
- -
-
-id_delimiter: ClassVar[str] = ':'[source]
-
- -
-
-new_view() → View[source]
-

Creates an empty view with a new ID and appends it to the views list.

-
-
Returns:
-

a reference to the new View object

-
-
-
- -
-
-new_view_id() → str[source]
-

Fetches an ID for a new view.

-
-
Returns:
-

the ID

-
-
-
- -
-
-sanitize()[source]
-

Sanitizes a Mmif object by running some safeguards. -Concretely, it performs the following before returning the JSON string.

-
    -

  1. validating output using built-in MMIF jsonschema

    2. -

  2. remove non-existing annotation types from contains metadata

    3. -
-
- -
-
-serialize(pretty: bool = False, sanitize: bool = False) → str[source]
-

Generates JSON representation of an object.

-
-
Parameters:
-

pretty – If True, returns string representation with indentation.

-
-
Returns:
-

JSON string of the object.

-
-
-
- -
-
-static validate(json_str: bytes | str | dict) → None[source]
-

Validates a MMIF JSON object against the MMIF Schema. -Note that this method operates before processing by MmifObject._load_str, -so it expects @ and not _ for the JSON-LD @-keys.

-
-
Raises:
-

jsonschema.exceptions.ValidationError – if the input fails validation

-
-
Parameters:
-

json_str – a MMIF JSON dict or string

-
-
Returns:
-

None

-
-
-
- -
-
-view_prefix: ClassVar[str] = 'v_'[source]
-
- -
- -
-
-

mmif.serialize.view module

-

The view module contains the classes used to represent a MMIF view -as a live Python object.

-

In MMIF, views are created by apps in a pipeline that are annotating -data that was previously present in the MMIF file.

-
-
-class mmif.serialize.view.Contain(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-

Contain object that represents the metadata of a single -annotation type in the contains metadata of a MMIF view.

-
- -
-
-class mmif.serialize.view.View(view_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-

View object that represents a single view in a MMIF file.

-

A view is identified by an ID, and contains certain metadata, -a list of annotations, and potentially a JSON-LD @context -IRI.

-

If view_obj is not provided, an empty View will be generated.

-
-
Parameters:
-

view_obj – the JSON data that defines the view

-
-
-
-
-add_annotation(annotation: Annotation, overwrite=False) → Annotation[source]
-

Adds an annotation to the current view.

-

Fails if there is already an annotation with the same ID -in the view, unless overwrite is set to True.

-
-
Parameters:
-
-
-
Raises:
-

KeyError – if overwrite is set to False and -an annotation with the same ID exists -in the view

-
-
Returns:
-

the same Annotation object passed in as annotation

-
-
-
- -
-
-add_document(document: Document, overwrite=False) → Annotation[source]
-

Appends a Document object to the annotations list.

-

Fails if there is already a document with the same ID in the annotations list.

-
-
Parameters:
-
    -

  • document – the Document object to add

    • -

  • overwrite – if set to True, will overwrite -an existing view with the same ID

    • -
-
-
Returns:
-

None

-
-
-
- -
-
-get_annotation_by_id(ann_id)[source]
-
- -
-
-get_annotations(at_type: str | TypesBase | None = None, **properties) → Generator[Annotation, None, None][source]
-

Look for certain annotations in this view, specified by parameters

-
-
Parameters:
-
    -

  • at_type – @type of the annotations to look for. When this is None, any @type will match.

    • -

  • properties – properties of the annotations to look for. When given more than one property, all properties must match. Note that annotation type metadata are specified in the contains view metadata, not in individual annotation objects.

    • -
-
-
-
- -
-
-get_document_by_id(doc_id) → Document[source]
-
- -
-
-get_documents() → List[Document][source]
-
- -
-
-new_annotation(at_type: str | TypesBase, aid: str | None = None, overwrite=False, **properties) → Annotation[source]
-

Generates a new mmif.serialize.annotation.Annotation -object and adds it to the current view.

-

Fails if there is already an annotation with the same ID -in the view, unless overwrite is set to True.

-
-
Parameters:
-
    -

  • at_type – the desired @type of the annotation.

    • -

  • aid – the desired ID of the annotation, when not given, -the mmif SDK tries to automatically generate an ID based on -Annotation type and existing annotations in the view.

    • -

  • overwrite – if set to True, will overwrite an -existing annotation with the same ID.

    • -
-
-
Raises:
-

KeyError – if overwrite is set to False and -an annotation with the same ID exists -in the view.

-
-
Returns:
-

the generated mmif.serialize.annotation.Annotation

-
-
-
- -
-
-new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
-

Adds a new element to the contains metadata.

-
-
Parameters:
-
    -

  • at_type – the @type of the annotation type being added

    • -

  • contains_metadata – any metadata associated with the annotation type

    • -
-
-
Returns:
-

the generated Contain object

-
-
-
- -
-
-new_textdocument(text: str, lang: str = 'en', did: str | None = None, overwrite=False, **properties) → Document[source]
-

Generates a new mmif.serialize.annotation.Document -object, particularly typed as TextDocument and adds it to the current view.

-

Fails if there is already a text document with the same ID -in the view, unless overwrite is set to True.

-
-
Parameters:
-
    -

  • text – text content of the new document

    • -

  • lang – ISO 639-1 code of the language used in the new document

    • -

  • did – the desired ID of the document, when not given, -the mmif SDK tries to automatically generate an ID based on -Annotation type and existing documents in the view.

    • -

  • overwrite – if set to True, will overwrite an -existing document with the same ID

    • -
-
-
Raises:
-

KeyError – if overwrite is set to False and -an document with the same ID exists -in the view

-
-
Returns:
-

the generated mmif.serialize.annotation.Document

-
-
-
- -
-
-set_error(err_message: str, err_trace: str) → None[source]
-
- -
- -
-
-class mmif.serialize.view.ViewMetadata(viewmetadata_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-

ViewMetadata object that represents the metadata object within a MMIF view.

-
-
Parameters:
-

viewmetadata_obj – the JSON data that defines the metadata

-
-
-
-
-add_parameter(param_key, param_value)[source]
-
- -
-
-add_parameters(**runtime_params)[source]
-
- -
-
-add_warnings(*warnings: Warning)[source]
-
- -
-
-emtpy_warnings()[source]
-
- -
-
-get_parameter(param_key)[source]
-
- -
-
-new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
-

Adds a new element to the contains dictionary.

-
-
Parameters:
-
    -

  • at_type – the @type of the annotation type being added

    • -

  • contains_metadata – any metadata associated with the annotation type

    • -
-
-
Returns:
-

the generated Contain object

-
-
-
- -
-
-set_error(message: str, stack_trace: str)[source]
-
- -
- -
-
-

mmif.serialize.annotation module

-

The annotation module contains the classes used to represent a -MMIF annotation as a live Python object.

-

In MMIF, annotations are created by apps in a pipeline as a part -of a view. For documentation on how views are represented, see -mmif.serialize.view.

-
-
-class mmif.serialize.annotation.Annotation(anno_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-

MmifObject that represents an annotation in a MMIF view.

-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]]) → None[source]
-

Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

-
- -
-
-property at_type: TypesBase[source]
-
- -
-
-property id: str[source]
-
- -
-
-is_document()[source]
-
- -
-
-is_type(at_type: str | TypesBase) → bool[source]
-

Check if the @type of this object matches.

-
- -
- -
-
-class mmif.serialize.annotation.AnnotationProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject, MutableMapping[str, T]

-

AnnotationProperties object that represents the -properties object within a MMIF annotation.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
- -
-
-class mmif.serialize.annotation.Document(doc_obj: bytes | str | dict | None = None)[source]
-

Bases: Annotation

-

Document object that represents a single document in a MMIF file.

-

A document is identified by an ID, and contains certain attributes -and potentially contains the contents of the document itself, -metadata about how the document was created, and/or a list of -subdocuments grouped together logically.

-

If document_obj is not provided, an empty Document will be generated.

-
-
Parameters:
-

document_obj – the JSON data that defines the document

-
-
-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None]) → None[source]
-

Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

-
- -
-
-property location: str | None[source]
-

location property must be a legitimate URI. That is, should the document be a local file -then the file:// scheme must be used. -Returns None when no location is set.

-
- -
-
-location_address() → str | None[source]
-

Retrieves the full address from the document location URI. -Returns None when no location is set.

-
- -
-
-location_path() → str | None[source]
-

Retrieves only path name of the document location (hostname is ignored). -Useful to get a path of a local file. -Returns None when no location is set.

-
- -
-
-location_scheme() → str | None[source]
-

Retrieves URI scheme of the document location. -Returns None when no location is set.

-
- -
-
-property parent: str[source]
-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.DocumentProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: AnnotationProperties

-

DocumentProperties object that represents the -properties object within a MMIF document.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
-
-property location: str | None[source]
-

location property must be a legitimate URI. That is, should the document be a local file -then the file:// scheme must be used. -Returns None when no location is set.

-
- -
-
-location_address() → str | None[source]
-

Retrieves the full address from the document location URI. -Returns None when no location is set.

-
- -
-
-location_path() → str | None[source]
-

Retrieves only path name of the document location (hostname is ignored). -Useful to get a path of a local file. -Returns None when no location is set.

-
- -
-
-location_scheme() → str | None[source]
-

Retrieves URI scheme of the document location. -Returns None when no location is set.

-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.Text(text_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-
-
-property lang: str[source]
-
- -
-
-property value: str[source]
-
- -
- -
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- - - \ No newline at end of file diff --git a/docs/1.0.1/autodoc/mmif.vocabulary.html b/docs/1.0.1/autodoc/mmif.vocabulary.html deleted file mode 100644 index 958b827b..00000000 --- a/docs/1.0.1/autodoc/mmif.vocabulary.html +++ /dev/null @@ -1,324 +0,0 @@ - - - - - - - - - mmif.vocabulary module — mmif-python documentation - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.vocabulary module

-
-

mmif.vocabulary.annotation_types module

-
-
-class mmif.vocabulary.annotation_types.AnnotationTypes(type_uri, fuzzymode=True)[source]
-

Bases: AnnotationTypesBase

-

This class contains the CLAMS annotation types -defined in the spec version 1.1.0 as class variables.

-
-
-Alignment = http://mmif.clams.ai/vocabulary/Alignment/v1[source]
-
- -
-
-Annotation = http://mmif.clams.ai/vocabulary/Annotation/v6[source]
-
- -
-
-BoundingBox = http://mmif.clams.ai/vocabulary/BoundingBox/v5[source]
-
- -
-
-Chapter = http://mmif.clams.ai/vocabulary/Chapter/v6[source]
-
- -
-
-Interval = http://mmif.clams.ai/vocabulary/Interval/v5[source]
-
- -
-
-NamedEntity = http://mmif.clams.ai/vocabulary/NamedEntity/v1[source]
-
- -
-
-NounChunk = http://mmif.clams.ai/vocabulary/NounChunk/v1[source]
-
- -
-
-Paragraph = http://mmif.clams.ai/vocabulary/Paragraph/v1[source]
-
- -
-
-Polygon = http://mmif.clams.ai/vocabulary/Polygon/v5[source]
-
- -
-
-Region = http://mmif.clams.ai/vocabulary/Region/v5[source]
-
- -
-
-Relation = http://mmif.clams.ai/vocabulary/Relation/v5[source]
-
- -
-
-Sentence = http://mmif.clams.ai/vocabulary/Sentence/v1[source]
-
- -
-
-Span = http://mmif.clams.ai/vocabulary/Span/v5[source]
-
- -
-
-TimeFrame = http://mmif.clams.ai/vocabulary/TimeFrame/v6[source]
-
- -
-
-TimePoint = http://mmif.clams.ai/vocabulary/TimePoint/v5[source]
-
- -
-
-Token = http://mmif.clams.ai/vocabulary/Token/v1[source]
-
- -
-
-VerbChunk = http://mmif.clams.ai/vocabulary/VerbChunk/v1[source]
-
- -
-
-VideoObject = http://mmif.clams.ai/vocabulary/VideoObject/v5[source]
-
- -
-
-typevers = {'Alignment': 'v1', 'Annotation': 'v6', 'BoundingBox': 'v5', 'Chapter': 'v6', 'Interval': 'v5', 'NamedEntity': 'v1', 'NounChunk': 'v1', 'Paragraph': 'v1', 'Polygon': 'v5', 'Region': 'v5', 'Relation': 'v5', 'Sentence': 'v1', 'Span': 'v5', 'TimeFrame': 'v6', 'TimePoint': 'v5', 'Token': 'v1', 'VerbChunk': 'v1', 'VideoObject': 'v5'}[source]
-
- -
- -
-
-

mmif.vocabulary.document_types module

-
-
-class mmif.vocabulary.document_types.DocumentTypes(type_uri, fuzzymode=True)[source]
-

Bases: DocumentTypesBase

-

This class contains the CLAMS document types -defined in the spec version 1.1.0 as class variables.

-
-
-AudioDocument = http://mmif.clams.ai/vocabulary/AudioDocument/v1[source]
-
- -
-
-Document = http://mmif.clams.ai/vocabulary/Document/v1[source]
-
- -
-
-ImageDocument = http://mmif.clams.ai/vocabulary/ImageDocument/v1[source]
-
- -
-
-TextDocument = http://mmif.clams.ai/vocabulary/TextDocument/v1[source]
-
- -
-
-VideoDocument = http://mmif.clams.ai/vocabulary/VideoDocument/v1[source]
-
- -
-
-typevers = {'AudioDocument': 'v1', 'Document': 'v1', 'ImageDocument': 'v1', 'TextDocument': 'v1', 'VideoDocument': 'v1'}[source]
-
- -
- -
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 1.0.1 - - -
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0.3.0
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0.3.2
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0.3.3
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0.3.4
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- - - \ No newline at end of file diff --git a/docs/1.0.1/consumer-tutorial.html b/docs/1.0.1/consumer-tutorial.html deleted file mode 100644 index ac7aac58..00000000 --- a/docs/1.0.1/consumer-tutorial.html +++ /dev/null @@ -1,170 +0,0 @@ - - - - - - - - - MMIF consumer — mmif-python documentation - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • MMIF consumer
    • -
  • -
    • -
-
-
-
-
- -
-

MMIF consumer

-

A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the appliance documentation to learn more about the appliance.

-

MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance.

-
    -

  1. The code must be hosted on a public git repository (e.g. Github, Gitlab, …)

    2. -

  2. Must listen to 5000 port.

    3. -

  3. Must expose /display route .

    4. -

  4. /display router should response to GET requests.

    5. -

  5. In the GET request, a public URL of the input MMIF file is passed via file URL parameter.

    6. -

  6. On the codebase root, there must be a Dockerfile that can build a docker image that runs the web app.

    7. -
-

We provide an example consumer at https://github.com/clamsproject/mmif-visualizer.

-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 1.0.1 - - -
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0.3.0
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0.3.2
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- - -
- -
-
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-
    -
    • -
  • Index
    • -
  • -
    • -
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-
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- - -

Index

- -
- A - | B - | C - | D - | E - | G - | I - | K - | L - | M - | N - | P - | R - | S - | T - | U - | V - -
-

A

- - - -
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B

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- - - -
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V

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- - -
- -
-
-
-
    -
    • -
  • Welcome to mmif-python’s documentation!
    • -
  • -
    • -
-
-
-
-
- -
-

Welcome to mmif-python’s documentation!

-
-

MultiMedia Interchange Format

-

MMIF is a JSON(-LD)-based data format designed for transferring annotation data between computational analysis applications in CLAMS project.

-
-

Contents

- -
-
-

API documentation:

- -
-
-
-
-

Indices and tables

- -
- - -
-
- -
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-
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- - Other Versions - v: 1.0.1 - - -
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- - - \ No newline at end of file diff --git a/docs/1.0.1/introduction.html b/docs/1.0.1/introduction.html deleted file mode 100644 index 1e1df090..00000000 --- a/docs/1.0.1/introduction.html +++ /dev/null @@ -1,243 +0,0 @@ - - - - - - - - - Getting Started — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
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  • Getting Started
    • -
  • -
    • -
-
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- -
-

Getting Started

-
-

Overview

-

MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for reproducibility, transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF website. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects.

-
-
-

Prerequisites

-
    -

  • Python: the latest mmif-python requires Python 3.8 or newer. We have no plan to support Python 2.7.

    • -
-
-
-

Installation

-

Package mmif-python is distributed via the official PyPI. Users are supposed to pip-install to get latest release.

-
pip install mmif-python
-
-
-

This will install a package mmif to local python.

-

The MMIF format and specification is evolving over time, and mmif-python package will be updated along with the changes in MMIF format.

-
-

Note

-

MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and mmif-python versions, please take time to read our decision on the subject here. If you need to know which python SDK supports which specification version, see Target MMIF Versions page.

-
-
-
-

MMIF Serialization

-

mmif.serialize.mmif.Mmif represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of mmif.serialize.model.MmifObject, including the mmif.serialize.mmif.Mmif. To start with an existing MMIF str, simple initiate a new Mmif object with the file.

-
import mmif
-from mmif import Mmif
-
-mmif_str = """{
-"metadata": {
-  "mmif": "http://mmif.clams.ai/1.0.0"
-},
-"documents": [
-  {
-    "@type": "http://mmif.clams.ai/vocabulary/VideoDocument/v1",
-    "properties": {
-      "id": "m1",
-      "mime": "video/mp4",
-      "location": "file:///var/archive/video-0012.mp4"
-    }
-  },
-  {
-    "@type": "http://mmif.clams.ai/vocabulary/TextDocument/v1",
-    "properties": {
-      "id": "m2",
-      "mime": "text/plain",
-      "location": "file:///var/archive/video-0012-transcript.txt"
-    }
-  }
-],
-"views": []}"""
-mmif_obj = Mmif(mmif_str)
-
-
-

Few notes;

-
    -

  1. MMIF does not carry the primary source files in it.

    2. -

  2. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version mmif-python implementation of the MMIF might not be able to load an unsupported version of MMIF string.

    3. -
-

When serializing back to str, call mmif.serialize.model.MmifObject.serialize() on the object.

-

To get subcomponents, you can use various getters implemented in subclasses. For example;

-
from mmif.vocabulary.document_types import DocumentTypes
-
-for video in mmif_obj.Mmif.get_documents_by_type(DocumentTypes.VideoDocument):
-  with open(video.location_path(), 'b') as in_video:
-    # do something with the video file
-
-
-

For a full list of available helper methods, please refer to the API documentation.

-
-
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-
- -
-
-
-
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- - Other Versions - v: 1.0.1 - - -
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0.3.0
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0.3.2
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0.3.3
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[0, 4], "specif": 6, "start": 4, "tabl": 3, "target": 6, "version": 6, "view": 0, "vocabulari": 1, "welcom": 3}}) \ No newline at end of file diff --git a/docs/1.0.1/target-versions.html b/docs/1.0.1/target-versions.html deleted file mode 100644 index fa7c127f..00000000 --- a/docs/1.0.1/target-versions.html +++ /dev/null @@ -1,244 +0,0 @@ - - - - - - - - - Target MMIF Versions — mmif-python documentation - - - - - - - - - - - - - - - - - -
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  • Target MMIF Versions
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Target MMIF Versions

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This article provides targeting MMIF specification versions of different versions of mmif-python SDK.

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Target Specification Versions

mmif-python version

Target MMIF Specification

1.0.1

1.1.0

1.0.0

0.5.0

0.5.2

0.5.0

0.5.1

0.5.0

0.5.0

0.5.0

0.4.8

0.4.2

0.4.7

0.4.1

0.4.6

0.4.0

0.4.5

0.4.0

0.4.4

0.4.0

0.4.3

0.4.0

0.4.2

0.4.0

0.4.1

0.4.0

0.4.0

0.4.0

0.3.5

0.3.1

0.3.4

0.3.1

0.3.3

0.3.1

0.3.2

0.3.1

0.3.1

0.3.0

0.3.0

0.3.0

0.2.2

0.2.1

0.2.1

0.2.1

0.2.0

0.2.1

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0.3.0
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0.3.1
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0.3.2
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0.3.3
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0.3.4
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0.3.5
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0.4.0
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0.4.1
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0.4.2
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0.4.3
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0.4.4
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0.4.5
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0.4.6
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0.4.7
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0.4.8
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0.5.0
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0.5.1
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0.5.2
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1.0.0
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1.0.1
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1.0.10
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1.0.11
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1.0.12
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1.0.13
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1.0.14
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1.0.15
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1.0.16
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1.0.17
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1.0.18
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1.0.19
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1.0.2
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1.0.3
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1.0.4
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1.0.5
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1.0.6
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1.0.7
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1.0.8
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1.0.9
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1.1.0
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-mmif.serialize.model module ---------------------------- - -.. automodule:: mmif.serialize.model - :members: - :undoc-members: - :show-inheritance: - -mmif.serialize.mmif module --------------------------- - -.. automodule:: mmif.serialize.mmif - :members: - :undoc-members: - :show-inheritance: - -mmif.serialize.view module --------------------------- - -.. automodule:: mmif.serialize.view - :members: - :undoc-members: - :show-inheritance: - -mmif.serialize.annotation module --------------------------------- - -.. automodule:: mmif.serialize.annotation - :members: - :undoc-members: - :show-inheritance: - diff --git a/docs/1.0.10/_sources/autodoc/mmif.utils.rst.txt b/docs/1.0.10/_sources/autodoc/mmif.utils.rst.txt deleted file mode 100644 index 64195e45..00000000 --- a/docs/1.0.10/_sources/autodoc/mmif.utils.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -mmif.utils module -================= - -mmif.utils.video_document_helper module ----------------------------------------- - -.. automodule:: mmif.utils.video_document_helper - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/1.0.10/_sources/autodoc/mmif.vocabulary.rst.txt b/docs/1.0.10/_sources/autodoc/mmif.vocabulary.rst.txt deleted file mode 100644 index d250c6a3..00000000 --- a/docs/1.0.10/_sources/autodoc/mmif.vocabulary.rst.txt +++ /dev/null @@ -1,18 +0,0 @@ -mmif.vocabulary module -====================== - -mmif.vocabulary.annotation\_types module ----------------------------------------- - -.. automodule:: mmif.vocabulary.annotation_types - :members: - :undoc-members: - :show-inheritance: - -mmif.vocabulary.document\_types module --------------------------------------- - -.. automodule:: mmif.vocabulary.document_types - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/1.0.10/_sources/autodoc/mmif_docloc_http.rst.txt b/docs/1.0.10/_sources/autodoc/mmif_docloc_http.rst.txt deleted file mode 100644 index b76c8df5..00000000 --- a/docs/1.0.10/_sources/autodoc/mmif_docloc_http.rst.txt +++ /dev/null @@ -1,11 +0,0 @@ -mmif_docloc_http package -======================== - -MMIF document location helper module for `http` and `https` schemes. -If you want to write your own docloc scheme handler, please use the source code of this module as a reference. -See this :ref:`plug-in section ` for more information. - -.. automodule:: mmif_docloc_http - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/1.0.10/_sources/consumer-tutorial.rst.txt b/docs/1.0.10/_sources/consumer-tutorial.rst.txt deleted file mode 100644 index c54634e2..00000000 --- a/docs/1.0.10/_sources/consumer-tutorial.rst.txt +++ /dev/null @@ -1,17 +0,0 @@ -.. _consumer-tutorial: - -MMIF consumer -================================= - -A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the `appliance documentation `_ to learn more about the appliance. - -MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance. - -#. The code must be hosted on a public git repository (e.g. Github, Gitlab, ...) -#. Must listen to ``5000`` port. -#. Must expose ``/display`` route . -#. ``/display`` router should response to ``GET`` requests. -#. In the ``GET`` request, a public URL of the input MMIF file is passed via ``file`` URL parameter. -#. On the codebase root, there must be a ``Dockerfile`` that can build a `docker `_ image that runs the web app. - -We provide an example consumer at https://github.com/clamsproject/mmif-visualizer. diff --git a/docs/1.0.10/_sources/index.rst.txt b/docs/1.0.10/_sources/index.rst.txt deleted file mode 100644 index beb56aae..00000000 --- a/docs/1.0.10/_sources/index.rst.txt +++ /dev/null @@ -1,26 +0,0 @@ -Welcome to mmif-python's documentation! -======================================= - -.. mdinclude:: ../README.md - -.. toctree:: - :maxdepth: 2 - :caption: Contents - - introduction - plugins - target-versions - -.. toctree:: - :maxdepth: 2 - :caption: API documentation: - - modules - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/docs/1.0.10/_sources/introduction.rst.txt b/docs/1.0.10/_sources/introduction.rst.txt deleted file mode 100644 index cfd9eaf7..00000000 --- a/docs/1.0.10/_sources/introduction.rst.txt +++ /dev/null @@ -1,89 +0,0 @@ -.. _introduction: - -Getting Started -=============== - - -Overview ---------- - -MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for reproducibility, transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF website `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects. - -Prerequisites -------------- - -* `Python `_: the latest ``mmif-python`` requires Python 3.8 or newer. We have no plan to support `Python 2.7 `_. - -Installation ---------------- - -Package ``mmif-python`` is distributed via the official PyPI. Users are supposed to pip-install to get latest release. - -.. code-block:: bash - - pip install mmif-python - -This will install a package `mmif` to local python. - -The MMIF format and specification is evolving over time, and ``mmif-python`` package will be updated along with the changes in MMIF format. - -.. note:: MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and ``mmif-python`` versions, please take time to read our decision on the subject `here `_. If you need to know which python SDK supports which specification version, see :ref:`target-versions` page. - -MMIF Serialization ---------------------------- - -:class:`mmif.serialize.mmif.Mmif` represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of :class:`mmif.serialize.model.MmifObject`, including the :class:`mmif.serialize.mmif.Mmif`. To start with an existing MMIF :class:`str`, simple initiate a new ``Mmif`` object with the file. - -.. code-block:: python - - import mmif - from mmif import Mmif - - mmif_str = """{ - "metadata": { - "mmif": "http://mmif.clams.ai/1.0.0" - }, - "documents": [ - { - "@type": "http://mmif.clams.ai/vocabulary/VideoDocument/v1", - "properties": { - "id": "m1", - "mime": "video/mp4", - "location": "file:///var/archive/video-0012.mp4" - } - }, - { - "@type": "http://mmif.clams.ai/vocabulary/TextDocument/v1", - "properties": { - "id": "m2", - "mime": "text/plain", - "location": "file:///var/archive/video-0012-transcript.txt" - } - } - ], - "views": []}""" - mmif_obj = Mmif(mmif_str) - - -Few notes; - -#. MMIF does not carry the primary source files in it. -#. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version ``mmif-python`` implementation of the MMIF might not be able to load an unsupported version of MMIF string. - -When serializing back to :class:`str`, call :meth:`mmif.serialize.model.MmifObject.serialize` on the object. - -To get subcomponents, you can use various getters implemented in subclasses. For example; - -.. code-block:: python - - from mmif.vocabulary.document_types import DocumentTypes - - for video in mmif_obj.Mmif.get_documents_by_type(DocumentTypes.VideoDocument): - with open(video.location_path(), 'b') as in_video: - # do something with the video file - - -For a full list of available helper methods, please refer to :ref:`the API documentation `. - diff --git a/docs/1.0.10/_sources/modules.rst.txt b/docs/1.0.10/_sources/modules.rst.txt deleted file mode 100644 index 4bb9307d..00000000 --- a/docs/1.0.10/_sources/modules.rst.txt +++ /dev/null @@ -1,20 +0,0 @@ -.. _apidoc: - -mmif package -============ - -.. toctree:: - :maxdepth: 4 - - autodoc/mmif.serialize - autodoc/mmif.vocabulary - autodoc/mmif.utils - -mmif_docloc_http package -======================== - -.. toctree:: - :maxdepth: 2 - - autodoc/mmif_docloc_http - diff --git a/docs/1.0.10/_sources/plugins.rst.txt b/docs/1.0.10/_sources/plugins.rst.txt deleted file mode 100644 index 9907c495..00000000 --- a/docs/1.0.10/_sources/plugins.rst.txt +++ /dev/null @@ -1,83 +0,0 @@ -.. _plugins: - -Developing plugins for MMIF Python SDK -====================================== - - -Overview --------- - -As MMIF JSON files can carry information about media document files without actually carrying file contents, file accessing modules in ``mmif`` Python package (distributed as ``mmif-python`` on PyPI) are designed to be lightweight and flexible so that it can work with additional "plugin" Python packages that can handle concrete file access. - - -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF website `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects. - -Developer can write simple plugins that can provide additional functionalities to ``mmif-python``. For example, ``mmif-python`` does not provide any file access functionality beyond a local file system (with ``file`` scheme), but it can be extended with a plugin that can handle file access over different protocols (e.g. ``http``, ``s3``, ``ftp``, etc). - -This document contains information about how to write plugins for ``mmif-python``. - -.. _docloc_plugin: - -Document Location Scheme Plugins -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -:class:`mmif.serialize.annotation.Document` class has various methods to access parts of ``location`` property of the document. The location is in `URI/IRI format `_ (``SCHEME://HOSTNAME/PATH``, in a nutshell) and it has to be resolved to a local file for CLAMS Apps to process the local file to analyze and extract information about the media and its contents. The core ``mmif-python`` distribution only provides a default implementation that can handle ``file`` scheme URIs. - -To add a document location handler plugin, you need to implement a Python `"package" `_ (do not confuse with PYPI distribution), that meets these requirements; - -#. the package must be named ``mmif_docloc_``. For example, to implement a handler for ``s3`` scheme, the package name must be ``mmif_docloc_s3``. The prefix is important as it's used in the plugin discovery process from the core ``mmif-python`` modules. -#. the top module of the package must have a function named ``resolve``. The function must take a single argument, which is a :class:`str` of the document location URI. The function must return a :class:`str` of the local file path. For example, if the document location is ``s3://mybucket/myfile.mp4``, a Python user should be able to to something like this; - -.. code-block:: python - - import mmif_docloc_s3 - resolved = mmif_docloc_s3.resolve('s3://mybucket/myfile.mp4') - # then resolved must be a local file path that can be used to open the file - - -Here's a minimal example codebase that you refer to when you develop a ``docloc`` plugin. - -(However, before you start writing your own plugin for a specific URI scheme, checking `if there's already a PyPI distribution `_ for the scheme might be a good idea.) - -.. code-block:: sh - - $ tree . - . - ├── mmif_docloc_dummy - │ └── __init__.py - ├── pyproject.toml - └── setup.cfg - - $ cat pyproject.toml - [build-system] - requires = ["setuptools"] - build-backend = "setuptools.build_meta" - - $ cat setup.cfg - [metadata] - name = mmif_docloc_dummy # this name is IMPORTANT - version = 0.0.1 - description = a plugin to mmif-pyhon to handle `dummy` location scheme - - -And the plugin code. - -.. code-block:: python - - # mmif_docloc_dummy/__init__.py - doc_types = {'video': 'mp4'} - - def resolve(docloc): - scheme = 'dummy' - if docloc.startswith(f'{scheme}://'): - doc_id, doc_type = docloc.split('.') - return f'/path/to/{doc_id}.{doc_types[doc_type]}' - else: - raise ValueError(f'cannot handle document location scheme: {docloc}') - -Bulit-in Document Location Scheme Plugins -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -At the moment, ``mmif-python`` PyPI distribution ships a built-in *docloc* plugin that support both ``http`` and ``https`` schemes. -Take a look at :mod:`mmif_docloc_http` module for details. diff --git a/docs/1.0.10/_sources/target-versions.rst.txt b/docs/1.0.10/_sources/target-versions.rst.txt deleted file mode 100644 index 34216d3e..00000000 --- a/docs/1.0.10/_sources/target-versions.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _target-versions: - -Target MMIF Versions -==================== - -This article provides targeting MMIF specification versions of different versions of ``mmif-python`` SDK. - -.. csv-table:: Target Specification Versions - :file: target-versions.csv - :header-rows: 1 diff --git a/docs/1.0.10/_static/_sphinx_javascript_frameworks_compat.js b/docs/1.0.10/_static/_sphinx_javascript_frameworks_compat.js deleted file mode 100644 index 81415803..00000000 --- a/docs/1.0.10/_static/_sphinx_javascript_frameworks_compat.js +++ /dev/null @@ -1,123 +0,0 @@ -/* Compatability shim for jQuery and underscores.js. - * - * Copyright Sphinx contributors - * Released under the two clause BSD licence - */ - -/** - * small helper function to urldecode strings - * - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL - */ -jQuery.urldecode = function(x) { - if (!x) { - return x - } - return decodeURIComponent(x.replace(/\+/g, ' ')); -}; - -/** - * small helper function to urlencode strings - */ -jQuery.urlencode = encodeURIComponent; - -/** - * This function returns the parsed url parameters of the - * current request. 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- document.dispatchEvent(event); - }); -}); \ No newline at end of file diff --git a/docs/1.0.10/_static/language_data.js b/docs/1.0.10/_static/language_data.js deleted file mode 100644 index c7fe6c6f..00000000 --- a/docs/1.0.10/_static/language_data.js +++ /dev/null @@ -1,192 +0,0 @@ -/* - * This script contains the language-specific data used by searchtools.js, - * namely the list of stopwords, stemmer, scorer and splitter. - */ - -var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"]; - - -/* Non-minified version is copied as a separate JS file, if available */ - -/** - * Porter Stemmer - */ -var Stemmer = function() { - - var step2list = { - ational: 'ate', - tional: 'tion', - enci: 'ence', - anci: 'ance', - izer: 'ize', - bli: 'ble', - alli: 'al', - entli: 'ent', - eli: 'e', - ousli: 'ous', - ization: 'ize', - ation: 'ate', - ator: 'ate', - alism: 'al', - iveness: 'ive', - fulness: 'ful', - ousness: 'ous', - aliti: 'al', - iviti: 'ive', - biliti: 'ble', - logi: 'log' - }; 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} - static get object() { return "object"; } - static get text() { return "text"; } - static get title() { return "title"; } -} - -const _removeChildren = (element) => { - while (element && element.lastChild) element.removeChild(element.lastChild); -}; - -/** - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping - */ -const _escapeRegExp = (string) => - string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string - -const _displayItem = (item, searchTerms, highlightTerms) => { - const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; - const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; - const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; - const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; - const contentRoot = document.documentElement.dataset.content_root; - - const [docName, title, anchor, descr, score, _filename, kind] = item; - - let listItem = document.createElement("li"); - // Add a class representing the item's type: - // can be used by a theme's CSS selector for styling - // See SearchResultKind for the class names. - listItem.classList.add(`kind-${kind}`); - let requestUrl; - let linkUrl; - if (docBuilder === "dirhtml") { - // dirhtml builder - let dirname = docName + "/"; - if (dirname.match(/\/index\/$/)) - dirname = dirname.substring(0, dirname.length - 6); - else if (dirname === "index/") dirname = ""; - requestUrl = contentRoot + dirname; - linkUrl = requestUrl; - } else { - // normal html builders - requestUrl = contentRoot + docName + docFileSuffix; - linkUrl = docName + docLinkSuffix; - } - let linkEl = listItem.appendChild(document.createElement("a")); - linkEl.href = linkUrl + anchor; - linkEl.dataset.score = score; - linkEl.innerHTML = title; - if (descr) { - listItem.appendChild(document.createElement("span")).innerHTML = - " (" + descr + ")"; - // highlight search terms in the description - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - } - else if (showSearchSummary) - fetch(requestUrl) - .then((responseData) => responseData.text()) - .then((data) => { - if (data) - listItem.appendChild( - Search.makeSearchSummary(data, searchTerms, anchor) - ); 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Please make sure that all words are spelled correctly and that you've selected enough categories." - ); - else - Search.status.innerText = Documentation.ngettext( - "Search finished, found one page matching the search query.", - "Search finished, found ${resultCount} pages matching the search query.", - resultCount, - ).replace('${resultCount}', resultCount); -}; -const _displayNextItem = ( - results, - resultCount, - searchTerms, - highlightTerms, -) => { - // results left, load the summary and display it - // this is intended to be dynamic (don't sub resultsCount) - if (results.length) { - _displayItem(results.pop(), searchTerms, highlightTerms); - setTimeout( - () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), - 5 - ); - } - // search finished, update title and status message - else _finishSearch(resultCount); -}; -// Helper function used by query() to order search results. -// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. -// Order the results by score (in opposite order of appearance, since the -// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. -const _orderResultsByScoreThenName = (a, b) => { - const leftScore = a[4]; - const rightScore = b[4]; - if (leftScore === rightScore) { - // same score: sort alphabetically - const leftTitle = a[1].toLowerCase(); - const rightTitle = b[1].toLowerCase(); - if (leftTitle === rightTitle) return 0; - return leftTitle > rightTitle ? -1 : 1; // inverted is intentional - } - return leftScore > rightScore ? 1 : -1; -}; - -/** - * Default splitQuery function. Can be overridden in ``sphinx.search`` with a - * custom function per language. - * - * The regular expression works by splitting the string on consecutive characters - * that are not Unicode letters, numbers, underscores, or emoji characters. - * This is the same as ``\W+`` in Python, preserving the surrogate pair area. - */ -if (typeof splitQuery === "undefined") { - var splitQuery = (query) => query - .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) - .filter(term => term) // remove remaining empty strings -} - -/** - * Search Module - */ -const Search = { - _index: null, - _queued_query: null, - _pulse_status: -1, - - htmlToText: (htmlString, anchor) => { - const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - for (const removalQuery of [".headerlink", "script", "style"]) { - htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); - } - if (anchor) { - const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); - if (anchorContent) return anchorContent.textContent; - - console.warn( - `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` - ); - } - - // if anchor not specified or not found, fall back to main content - const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent) return docContent.textContent; - - console.warn( - "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." - ); - return ""; - }, - - init: () => { - const query = new URLSearchParams(window.location.search).get("q"); - document - .querySelectorAll('input[name="q"]') - .forEach((el) => (el.value = query)); - if (query) Search.performSearch(query); - }, - - loadIndex: (url) => - (document.body.appendChild(document.createElement("script")).src = url), - - setIndex: (index) => { - Search._index = index; - if (Search._queued_query !== null) { - const query = Search._queued_query; - Search._queued_query = null; - Search.query(query); - } - }, - - hasIndex: () => Search._index !== null, - - deferQuery: (query) => (Search._queued_query = query), - - stopPulse: () => (Search._pulse_status = -1), - - startPulse: () => { - if (Search._pulse_status >= 0) return; - - const pulse = () => { - Search._pulse_status = (Search._pulse_status + 1) % 4; - Search.dots.innerText = ".".repeat(Search._pulse_status); - if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); - }; - pulse(); - }, - - /** - * perform a search for something (or wait until index is loaded) - */ - performSearch: (query) => { - // create the required interface elements - const searchText = document.createElement("h2"); - searchText.textContent = _("Searching"); - const searchSummary = document.createElement("p"); - searchSummary.classList.add("search-summary"); - searchSummary.innerText = ""; - const searchList = document.createElement("ul"); - searchList.setAttribute("role", "list"); - searchList.classList.add("search"); - - const out = document.getElementById("search-results"); - Search.title = out.appendChild(searchText); - Search.dots = Search.title.appendChild(document.createElement("span")); - Search.status = out.appendChild(searchSummary); - Search.output = out.appendChild(searchList); - - const searchProgress = document.getElementById("search-progress"); - // Some themes don't use the search progress node - if (searchProgress) { - searchProgress.innerText = _("Preparing search..."); - } - Search.startPulse(); - - // index already loaded, the browser was quick! - if (Search.hasIndex()) Search.query(query); - else Search.deferQuery(query); - }, - - _parseQuery: (query) => { - // stem the search terms and add them to the correct list - const stemmer = new Stemmer(); - const searchTerms = new Set(); - const excludedTerms = new Set(); - const highlightTerms = new Set(); - const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); - splitQuery(query.trim()).forEach((queryTerm) => { - const queryTermLower = queryTerm.toLowerCase(); - - // maybe skip this "word" - // stopwords array is from language_data.js - if ( - stopwords.indexOf(queryTermLower) !== -1 || - queryTerm.match(/^\d+$/) - ) - return; - - // stem the word - let word = stemmer.stemWord(queryTermLower); - // select the correct list - if (word[0] === "-") excludedTerms.add(word.substr(1)); - else { - searchTerms.add(word); - highlightTerms.add(queryTermLower); - } - }); - - if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js - localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) - } - - // console.debug("SEARCH: searching for:"); - // console.info("required: ", [...searchTerms]); - // console.info("excluded: ", [...excludedTerms]); - - return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; - }, - - /** - * execute search (requires search index to be loaded) - */ - _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - - // Collect multiple result groups to be sorted separately and then ordered. - // Each is an array of [docname, title, anchor, descr, score, filename, kind]. - const normalResults = []; - const nonMainIndexResults = []; - - _removeChildren(document.getElementById("search-progress")); - - const queryLower = query.toLowerCase().trim(); - for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { - for (const [file, id] of foundTitles) { - const score = Math.round(Scorer.title * queryLower.length / title.length); - const boost = titles[file] === title ? 1 : 0; // add a boost for document titles - normalResults.push([ - docNames[file], - titles[file] !== title ? `${titles[file]} > ${title}` : title, - id !== null ? "#" + id : "", - null, - score + boost, - filenames[file], - SearchResultKind.title, - ]); - } - } - } - - // search for explicit entries in index directives - for (const [entry, foundEntries] of Object.entries(indexEntries)) { - if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id, isMain] of foundEntries) { - const score = Math.round(100 * queryLower.length / entry.length); - const result = [ - docNames[file], - titles[file], - id ? "#" + id : "", - null, - score, - filenames[file], - SearchResultKind.index, - ]; - if (isMain) { - normalResults.push(result); - } else { - nonMainIndexResults.push(result); - } - } - } - } - - // lookup as object - objectTerms.forEach((term) => - normalResults.push(...Search.performObjectSearch(term, objectTerms)) - ); - - // lookup as search terms in fulltext - normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); - - // let the scorer override scores with a custom scoring function - if (Scorer.score) { - normalResults.forEach((item) => (item[4] = Scorer.score(item))); - nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); - } - - // Sort each group of results by score and then alphabetically by name. - normalResults.sort(_orderResultsByScoreThenName); - nonMainIndexResults.sort(_orderResultsByScoreThenName); - - // Combine the result groups in (reverse) order. - // Non-main index entries are typically arbitrary cross-references, - // so display them after other results. - let results = [...nonMainIndexResults, ...normalResults]; - - // remove duplicate search results - // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept - let seen = new Set(); - results = results.reverse().reduce((acc, result) => { - let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); - if (!seen.has(resultStr)) { - acc.push(result); - seen.add(resultStr); - } - return acc; - }, []); - - return results.reverse(); - }, - - query: (query) => { - const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); - const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); - - // for debugging - //Search.lastresults = results.slice(); // a copy - // console.info("search results:", Search.lastresults); - - // print the results - _displayNextItem(results, results.length, searchTerms, highlightTerms); - }, - - /** - * search for object names - */ - performObjectSearch: (object, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const objects = Search._index.objects; - const objNames = Search._index.objnames; - const titles = Search._index.titles; - - const results = []; - - const objectSearchCallback = (prefix, match) => { - const name = match[4] - const fullname = (prefix ? prefix + "." : "") + name; - const fullnameLower = fullname.toLowerCase(); - if (fullnameLower.indexOf(object) < 0) return; - - let score = 0; - const parts = fullnameLower.split("."); - - // check for different match types: exact matches of full name or - // "last name" (i.e. last dotted part) - if (fullnameLower === object || parts.slice(-1)[0] === object) - score += Scorer.objNameMatch; - else if (parts.slice(-1)[0].indexOf(object) > -1) - score += Scorer.objPartialMatch; // matches in last name - - const objName = objNames[match[1]][2]; - const title = titles[match[0]]; - - // If more than one term searched for, we require other words to be - // found in the name/title/description - const otherTerms = new Set(objectTerms); - otherTerms.delete(object); - if (otherTerms.size > 0) { - const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); - if ( - [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) - ) - return; - } - - let anchor = match[3]; - if (anchor === "") anchor = fullname; - else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; - - const descr = objName + _(", in ") + title; - - // add custom score for some objects according to scorer - if (Scorer.objPrio.hasOwnProperty(match[2])) - score += Scorer.objPrio[match[2]]; - else score += Scorer.objPrioDefault; - - results.push([ - docNames[match[0]], - fullname, - "#" + anchor, - descr, - score, - filenames[match[0]], - SearchResultKind.object, - ]); - }; - Object.keys(objects).forEach((prefix) => - objects[prefix].forEach((array) => - objectSearchCallback(prefix, array) - ) - ); - return results; - }, - - /** - * search for full-text terms in the index - */ - performTermsSearch: (searchTerms, excludedTerms) => { - // prepare search - const terms = Search._index.terms; - const titleTerms = Search._index.titleterms; - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - - const scoreMap = new Map(); - const fileMap = new Map(); - - // perform the search on the required terms - searchTerms.forEach((word) => { - const files = []; - const arr = [ - { files: terms[word], score: Scorer.term }, - { files: titleTerms[word], score: Scorer.title }, - ]; - // add support for partial matches - if (word.length > 2) { - const escapedWord = _escapeRegExp(word); - if (!terms.hasOwnProperty(word)) { - Object.keys(terms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: terms[term], score: Scorer.partialTerm }); - }); - } - if (!titleTerms.hasOwnProperty(word)) { - Object.keys(titleTerms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); - }); - } - } - - // no match but word was a required one - if (arr.every((record) => record.files === undefined)) return; - - // found search word in contents - arr.forEach((record) => { - if (record.files === undefined) return; - - let recordFiles = record.files; - if (recordFiles.length === undefined) recordFiles = [recordFiles]; - files.push(...recordFiles); - - // set score for the word in each file - recordFiles.forEach((file) => { - if (!scoreMap.has(file)) scoreMap.set(file, {}); - scoreMap.get(file)[word] = record.score; - }); - }); - - // create the mapping - files.forEach((file) => { - if (!fileMap.has(file)) fileMap.set(file, [word]); - else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); - }); - }); - - // now check if the files don't contain excluded terms - const results = []; - for (const [file, wordList] of fileMap) { - // check if all requirements are matched - - // as search terms with length < 3 are discarded - const filteredTermCount = [...searchTerms].filter( - (term) => term.length > 2 - ).length; - if ( - wordList.length !== searchTerms.size && - wordList.length !== filteredTermCount - ) - continue; - - // ensure that none of the excluded terms is in the search result - if ( - [...excludedTerms].some( - (term) => - terms[term] === file || - titleTerms[term] === file || - (terms[term] || []).includes(file) || - (titleTerms[term] || []).includes(file) - ) - ) - break; - - // select one (max) score for the file. - const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); - // add result to the result list - results.push([ - docNames[file], - titles[file], - "", - null, - score, - filenames[file], - SearchResultKind.text, - ]); - } - return results; - }, - - /** - * helper function to return a node containing the - * search summary for a given text. keywords is a list - * of stemmed words. - */ - makeSearchSummary: (htmlText, keywords, anchor) => { - const text = Search.htmlToText(htmlText, anchor); - if (text === "") return null; - - const textLower = text.toLowerCase(); - const actualStartPosition = [...keywords] - .map((k) => textLower.indexOf(k.toLowerCase())) - .filter((i) => i > -1) - .slice(-1)[0]; - const startWithContext = Math.max(actualStartPosition - 120, 0); - - const top = startWithContext === 0 ? "" : "..."; - const tail = startWithContext + 240 < text.length ? "..." : ""; - - let summary = document.createElement("p"); - summary.classList.add("context"); - summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; - - return summary; - }, -}; - -_ready(Search.init); diff --git a/docs/1.0.10/_static/sphinx_highlight.js b/docs/1.0.10/_static/sphinx_highlight.js deleted file mode 100644 index 8a96c69a..00000000 --- a/docs/1.0.10/_static/sphinx_highlight.js +++ /dev/null @@ -1,154 +0,0 @@ -/* Highlighting utilities for Sphinx HTML documentation. */ -"use strict"; - -const SPHINX_HIGHLIGHT_ENABLED = true - -/** - * highlight a given string on a node by wrapping it in - * span elements with the given class name. - */ -const _highlight = (node, addItems, text, className) => { - if (node.nodeType === Node.TEXT_NODE) { - const val = node.nodeValue; - const parent = node.parentNode; - const pos = val.toLowerCase().indexOf(text); - if ( - pos >= 0 && - !parent.classList.contains(className) && - !parent.classList.contains("nohighlight") - ) { - let span; - - const closestNode = parent.closest("body, svg, foreignObject"); - const isInSVG = closestNode && closestNode.matches("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.classList.add(className); - } - - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - const rest = document.createTextNode(val.substr(pos + text.length)); - parent.insertBefore( - span, - parent.insertBefore( - rest, - node.nextSibling - ) - ); - node.nodeValue = val.substr(0, pos); - /* There may be more occurrences of search term in this node. So call this - * function recursively on the remaining fragment. - */ - _highlight(rest, addItems, text, className); - - if (isInSVG) { - const rect = document.createElementNS( - "http://www.w3.org/2000/svg", - "rect" - ); - const bbox = parent.getBBox(); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute("class", className); - addItems.push({ parent: parent, target: rect }); - } - } - } else if (node.matches && !node.matches("button, select, textarea")) { - node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); - } -}; -const _highlightText = (thisNode, text, className) => { - let addItems = []; - _highlight(thisNode, addItems, text, className); - addItems.forEach((obj) => - obj.parent.insertAdjacentElement("beforebegin", obj.target) - ); -}; - -/** - * Small JavaScript module for the documentation. - */ -const SphinxHighlight = { - - /** - * highlight the search words provided in localstorage in the text - */ - highlightSearchWords: () => { - if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight - - // get and clear terms from localstorage - const url = new URL(window.location); - const highlight = - localStorage.getItem("sphinx_highlight_terms") - || url.searchParams.get("highlight") - || ""; - localStorage.removeItem("sphinx_highlight_terms") - url.searchParams.delete("highlight"); - window.history.replaceState({}, "", url); - - // get individual terms from highlight string - const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); - if (terms.length === 0) return; // nothing to do - - // There should never be more than one element matching "div.body" - const divBody = document.querySelectorAll("div.body"); - const body = divBody.length ? divBody[0] : document.querySelector("body"); - window.setTimeout(() => { - terms.forEach((term) => _highlightText(body, term, "highlighted")); - }, 10); - - const searchBox = document.getElementById("searchbox"); - if (searchBox === null) return; - searchBox.appendChild( - document - .createRange() - .createContextualFragment( - '

' + - '' + - _("Hide Search Matches") + - "

" - ) - ); - }, - - /** - * helper function to hide the search marks again - */ - hideSearchWords: () => { - document - .querySelectorAll("#searchbox .highlight-link") - .forEach((el) => el.remove()); - document - .querySelectorAll("span.highlighted") - .forEach((el) => el.classList.remove("highlighted")); - localStorage.removeItem("sphinx_highlight_terms") - }, - - initEscapeListener: () => { - // only install a listener if it is really needed - if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; - - document.addEventListener("keydown", (event) => { - // bail for input elements - if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; - // bail with special keys - if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; - if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { - SphinxHighlight.hideSearchWords(); - event.preventDefault(); - } - }); - }, -}; - -_ready(() => { - /* Do not call highlightSearchWords() when we are on the search page. - * It will highlight words from the *previous* search query. - */ - if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); - SphinxHighlight.initEscapeListener(); -}); diff --git a/docs/1.0.10/autodoc/mmif.serialize.html b/docs/1.0.10/autodoc/mmif.serialize.html deleted file mode 100644 index 62c298ef..00000000 --- a/docs/1.0.10/autodoc/mmif.serialize.html +++ /dev/null @@ -1,1302 +0,0 @@ - - - - - - - - - mmif.serialize module — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.serialize module

-
-

mmif.serialize.model module

-

The model module contains the classes used to represent an -abstract MMIF object as a live Python object.

-

The MmifObject class or one of its derivatives is subclassed by -all other classes defined in this SDK, except for MmifObjectEncoder.

-

These objects are generally instantiated from JSON, either as a string -or as an already-loaded Python dictionary. This base class provides the -core functionality for deserializing MMIF JSON data into live objects -and serializing live objects into MMIF JSON data. Specialized behavior -for the different components of MMIF is added in the subclasses.

-
-
-class mmif.serialize.model.DataDict(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject, Generic[T, S]

-
-
-empty()[source]
-
- -
-
-get(key: T, default=None) → S | None[source]
-
- -
-
-items()[source]
-
- -
-
-keys()[source]
-
- -
-
-update(other, overwrite)[source]
-
- -
-
-values()[source]
-
- -
- -
-
-class mmif.serialize.model.DataList(mmif_obj: bytes | str | list | None = None)[source]
-

Bases: MmifObject, Generic[T]

-

The DataList class is an abstraction that represents the -various lists found in a MMIF file, such as documents, subdocuments, -views, and annotations.

-
-
Parameters:
-

mmif_obj (Union[str, list]) – the data that the list contains

-
-
-
-
-append(value, overwrite)[source]
-
- -
-
-deserialize(mmif_json: str | list) → None[source]
-

Passes the input data into the internal deserializer.

-
- -
-
-empty()[source]
-
- -
-
-get(key: str) → T | None[source]
-

Standard dictionary-style get() method, albeit with no default -parameter. Relies on the implementation of __getitem__.

-

Will return None if the key is not found.

-
-
Parameters:
-

key – the key to search for

-
-
Returns:
-

the value matching that key

-
-
-
- -
- -
-
-class mmif.serialize.model.MmifObject(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: object

-

Abstract superclass for MMIF related key-value pair objects.

-

Any MMIF object can be initialized as an empty placeholder or -an actual representation with a JSON formatted string or equivalent -dict object argument.

-

This superclass has four specially designed instance variables, and these -variable names cannot be used as attribute names for MMIF objects.

-
    -

  1. _unnamed_attributes: -Only can be either None or an empty dictionary. If it’s set to None, -it means the class won’t take any Additional Attributes in the JSON -schema sense. If it’s a dict, users can throw any k-v pairs to the -class, EXCEPT for the reserved two key names.

    2. -

  2. _attribute_classes: -This is a dict from a key name to a specific python class to use for -deserialize the value. Note that a key name in this dict does NOT -have to be a named attribute, but is recommended to be one.

    3. -

  3. _required_attributes: -This is a simple list of names of attributes that are required in the object. -When serialize, an object will skip its empty (e.g. zero-length, or None) -attributes unless they are in this list. Otherwise, the serialized JSON -string would have empty representations (e.g. "", []).

    4. -

  4. _exclude_from_diff: -This is a simple list of names of attributes that should be excluded from -the diff calculation in __eq__.

    5. -
-

# TODO (krim @ 8/17/20): this dict is however, a duplicate with the type hints in the class definition. -Maybe there is a better way to utilize type hints (e.g. getting them as a programmatically), but for now -developers should be careful to add types to hints as well as to this dict.

-

Also note that those special attributes MUST be set in the __init__() -before calling super method, otherwise deserialization will not work.

-

And also, a subclass that has one or more named attributes, it must -set those attributes in the __init__() before calling super method. When -serializing a MmifObject, all empty attributes will be ignored, so for -optional named attributes, you must leave the values empty (len == 0), but -NOT None. Any None-valued named attributes will cause issues with current -implementation.

-
-
Parameters:
-

mmif_obj – JSON string or dict to initialize an object. -If not given, an empty object will be initialized, sometimes with -an ID value automatically generated, based on its parent object.

-
-
-
-
-deserialize(mmif_json: str | dict) → None[source]
-

Takes a JSON-formatted string or a simple dict that’s json-loaded from -such a string as an input and populates object’s fields with the values -specified in the input.

-
-
Parameters:
-

mmif_json – JSON-formatted string or dict from such a string -that represents a MMIF object

-
-
-
- -
-
-disallow_additional_properties() → None[source]
-

Call this method in __init__() to prevent the insertion -of unnamed attributes after initialization.

-
- -
-
-static is_empty(obj) → bool[source]
-

return True if the obj is None or “emtpy”. The emptiness first defined as -having zero length. But for objects that lack __len__ method, we need -additional check.

-
- -
-
-reserved_names: Set[str] = {'_attribute_classes', '_exclude_from_diff', '_required_attributes', '_unnamed_attributes', 'reserved_names'}[source]
-
- -
-
-serialize(pretty: bool = False) → str[source]
-

Generates JSON representation of an object.

-
-
Parameters:
-

pretty – If True, returns string representation with indentation.

-
-
Returns:
-

JSON string of the object.

-
-
-
- -
-
-set_additional_property(key: str, value: Any) → None[source]
-

Method to set values in _unnamed_attributes.

-
-
Parameters:
-
    -

  • key – the attribute name

    • -

  • value – the desired value

    • -
-
-
Returns:
-

None

-
-
Raise:
-

AttributeError if additional properties are disallowed by disallow_additional_properties()

-
-
-
- -
- -
-
-class mmif.serialize.model.MmifObjectEncoder(*, skipkeys=False, ensure_ascii=True, check_circular=True, allow_nan=True, sort_keys=False, indent=None, separators=None, default=None)[source]
-

Bases: JSONEncoder

-

Encoder class to define behaviors of de-/serialization

-
-
-default(obj: MmifObject)[source]
-

Overrides default encoding behavior to prioritize MmifObject.serialize().

-
- -
- -
-
-

mmif.serialize.mmif module

-

The mmif module contains the classes used to represent a full MMIF -file as a live Python object.

-

See the specification docs and the JSON Schema file for more information.

-
-
-class mmif.serialize.mmif.Mmif(mmif_obj: bytes | str | dict | None = None, *, validate: bool = True)[source]
-

Bases: MmifObject

-

MmifObject that represents a full MMIF file.

-
-
Parameters:
-
    -

  • mmif_obj – the JSON data

    • -

  • validate – whether to validate the data against the MMIF JSON schema.

    • -
-
-
-
-
-add_document(document: Document, overwrite=False) → None[source]
-

Appends a Document object to the documents list.

-

Fails if there is already a document with the same ID in the MMIF object.

-
-
Parameters:
-
    -

  • document – the Document object to add

    • -

  • overwrite – if set to True, will overwrite -an existing view with the same ID

    • -
-
-
Returns:
-

None

-
-
-
- -
-
-add_view(view: View, overwrite=False) → None[source]
-

Appends a View object to the views list.

-

Fails if there is already a view with the same ID in the MMIF object.

-
-
Parameters:
-
    -

  • view – the Document object to add

    • -

  • overwrite – if set to True, will overwrite -an existing view with the same ID

    • -
-
-
Returns:
-

None

-
-
-
- -
-
-generate_capital_annotations()[source]
-

Automatically convert any “pending” temporary properties from -Document objects to Annotation objects . The generated Annotation -objects are then added to the last View in the views lists.

-

See https://github.com/clamsproject/mmif-python/issues/226 for rationale -behind this behavior and discussion.

-
- -
-
-get_alignments(at_type1: str | TypesBase, at_type2: str | TypesBase) → Dict[str, List[Annotation]][source]
-

Finds views where alignments between two given annotation types occurred.

-
-
Returns:
-

a dict that keyed by view IDs (str) and has lists of alignment Annotation objects as values.

-
-
-
- -
-
-get_all_views_contain(at_types: TypesBase | str | List[str | TypesBase]) → List[View][source]
-

Returns the list of all views in the MMIF if given types -are present in that view’s ‘contains’ metadata.

-
-
Parameters:
-

at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

-
-
Returns:
-

the list of views that contain the type

-
-
-
- -
-
-get_document_by_id(doc_id: str) → Document[source]
-

Finds a Document object with the given ID.

-
-
Parameters:
-

doc_id – the ID to search for

-
-
Returns:
-

a reference to the corresponding document, if it exists

-
-
Raises:
-

KeyError – if there is no corresponding document

-
-
-
- -
-
-get_document_location(m_type: DocumentTypes | str, path_only=False) → str | None[source]
-

Method to get the location of first document of given type.

-
-
Parameters:
-

m_type – the type to search for

-
-
Returns:
-

the value of the location field in the corresponding document

-
-
-
- -
-
-get_documents_by_app(app_id: str) → List[Document][source]
-

Method to get all documents object queries by its originated app name.

-
-
Parameters:
-

app_id – the app name to search for

-
-
Returns:
-

a list of documents matching the requested app name, or an empty list if the app not found

-
-
-
- -
-
-get_documents_by_property(prop_key: str, prop_value: str) → List[Document][source]
-

Method to retrieve documents by an arbitrary key-value pair in the document properties objects.

-
-
Parameters:
-
    -

  • prop_key – the metadata key to search for

    • -

  • prop_value – the metadata value to match

    • -
-
-
Returns:
-

a list of documents matching the requested metadata key-value pair

-
-
-
- -
-
-get_documents_by_type(doc_type: str | DocumentTypes) → List[Document][source]
-

Method to get all documents where the type matches a particular document type, which should be one of the CLAMS document types.

-
-
Parameters:
-

doc_type – the type of documents to search for, must be one of Document type defined in the CLAMS vocabulary.

-
-
Returns:
-

a list of documents matching the requested type, or an empty list if none found.

-
-
-
- -
-
-get_documents_in_view(vid: str | None = None) → List[Document][source]
-

Method to get all documents object queries by a view id.

-
-
Parameters:
-

vid – the source view ID to search for

-
-
Returns:
-

a list of documents matching the requested source view ID, or an empty list if the view not found

-
-
-
- -
-
-get_documents_locations(m_type: DocumentTypes | str, path_only=False) → List[str | None][source]
-

This method returns the file paths of documents of given type. -Only top-level documents have locations, so we only check them.

-
-
Parameters:
-

m_type – the type to search for

-
-
Returns:
-

a list of the values of the location fields in the corresponding documents

-
-
-
- -
-
-get_end(annotation: Annotation) → int | float[source]
-

An alias to get_anchor_point method with start=False.

-
- -
-
-get_start(annotation: Annotation) → int | float[source]
-

An alias to get_anchor_point method with start=True.

-
- -
-
-get_view_by_id(req_view_id: str) → View[source]
-

Finds a View object with the given ID.

-
-
Parameters:
-

req_view_id – the ID to search for

-
-
Returns:
-

a reference to the corresponding view, if it exists

-
-
Raises:
-

Exception – if there is no corresponding view

-
-
-
- -
-
-get_view_contains(at_types: TypesBase | str | List[str | TypesBase]) → View | None[source]
-

Returns the last view appended that contains the given -types in its ‘contains’ metadata.

-
-
Parameters:
-

at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

-
-
Returns:
-

the view, or None if the type is not found

-
-
-
- -
-
-get_views_contain(at_types: TypesBase | str | List[str | TypesBase]) → List[View][source]
-

An alias to get_all_views_contain method.

-
- -
-
-get_views_for_document(doc_id: str) → List[View][source]
-

Returns the list of all views that have annotations anchored on a particular document. -Note that when the document is inside a view (generated during the pipeline’s running), -doc_id must be prefixed with the view_id.

-
- -
-
-id_delimiter: ClassVar[str] = ':'[source]
-
- -
-
-new_view() → View[source]
-

Creates an empty view with a new ID and appends it to the views list.

-
-
Returns:
-

a reference to the new View object

-
-
-
- -
-
-new_view_id() → str[source]
-

Fetches an ID for a new view.

-
-
Returns:
-

the ID

-
-
-
- -
-
-sanitize()[source]
-

Sanitizes a Mmif object by running some safeguards. -Concretely, it performs the following before returning the JSON string.

-
    -

  1. validating output using built-in MMIF jsonschema

    2. -

  2. remove non-existing annotation types from contains metadata

    3. -
-
- -
-
-serialize(pretty: bool = False, sanitize: bool = False, autogenerate_capital_annotations=True) → str[source]
-

Serializes the MMIF object to a JSON string.

-
-
Parameters:
-
    -

  • sanitize – If True, performs some sanitization of before returning -the JSON string. See sanitize() for details.

    • -

  • autogenerate_capital_annotations – If True, automatically convert -any “pending” temporary properties from Document objects to -Annotation objects. See generate_capital_annotations() for -details.

    • -

  • pretty – If True, returns string representation with indentation.

    • -
-
-
Returns:
-

JSON string of the MMIF object.

-
-
-
- -
-
-static validate(json_str: bytes | str | dict) → None[source]
-

Validates a MMIF JSON object against the MMIF Schema. -Note that this method operates before processing by MmifObject._load_str, -so it expects @ and not _ for the JSON-LD @-keys.

-
-
Raises:
-

jsonschema.exceptions.ValidationError – if the input fails validation

-
-
Parameters:
-

json_str – a MMIF JSON dict or string

-
-
Returns:
-

None

-
-
-
- -
-
-view_prefix: ClassVar[str] = 'v_'[source]
-
- -
- -
-
-

mmif.serialize.view module

-

The view module contains the classes used to represent a MMIF view -as a live Python object.

-

In MMIF, views are created by apps in a pipeline that are annotating -data that was previously present in the MMIF file.

-
-
-class mmif.serialize.view.Contain(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: DataDict[str, str]

-

Contain object that represents the metadata of a single -annotation type in the contains metadata of a MMIF view.

-
- -
-
-class mmif.serialize.view.View(view_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-

View object that represents a single view in a MMIF file.

-

A view is identified by an ID, and contains certain metadata, -a list of annotations, and potentially a JSON-LD @context -IRI.

-

If view_obj is not provided, an empty View will be generated.

-
-
Parameters:
-

view_obj – the JSON data that defines the view

-
-
-
-
-add_annotation(annotation: Annotation, overwrite=False) → Annotation[source]
-

Adds an annotation to the current view.

-

Fails if there is already an annotation with the same ID -in the view, unless overwrite is set to True.

-
-
Parameters:
-
-
-
Raises:
-

KeyError – if overwrite is set to False and -an annotation with the same ID exists -in the view

-
-
Returns:
-

the same Annotation object passed in as annotation

-
-
-
- -
-
-add_document(document: Document, overwrite=False) → Annotation[source]
-

Appends a Document object to the annotations list.

-

Fails if there is already a document with the same ID in the annotations list.

-
-
Parameters:
-
    -

  • document – the Document object to add

    • -

  • overwrite – if set to True, will overwrite -an existing view with the same ID

    • -
-
-
Returns:
-

None

-
-
-
- -
-
-get_annotation_by_id(ann_id) → Annotation[source]
-
- -
-
-get_annotations(at_type: str | TypesBase | None = None, **properties) → Generator[Annotation, None, None][source]
-

Look for certain annotations in this view, specified by parameters

-
-
Parameters:
-
    -

  • at_type – @type of the annotations to look for. When this is None, any @type will match.

    • -

  • properties – properties of the annotations to look for. When given more than one property, all properties must match. Note that annotation type metadata are specified in the contains view metadata, not in individual annotation objects.

    • -
-
-
-
- -
-
-get_document_by_id(doc_id) → Document[source]
-
- -
-
-get_documents() → List[Document][source]
-
- -
-
-new_annotation(at_type: str | TypesBase, aid: str | None = None, overwrite=False, **properties) → Annotation[source]
-

Generates a new mmif.serialize.annotation.Annotation -object and adds it to the current view.

-

Fails if there is already an annotation with the same ID -in the view, unless overwrite is set to True.

-
-
Parameters:
-
    -

  • at_type – the desired @type of the annotation.

    • -

  • aid – the desired ID of the annotation, when not given, -the mmif SDK tries to automatically generate an ID based on -Annotation type and existing annotations in the view.

    • -

  • overwrite – if set to True, will overwrite an -existing annotation with the same ID.

    • -
-
-
Raises:
-

KeyError – if overwrite is set to False and -an annotation with the same ID exists -in the view.

-
-
Returns:
-

the generated mmif.serialize.annotation.Annotation

-
-
-
- -
-
-new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
-

Adds a new element to the contains metadata.

-
-
Parameters:
-
    -

  • at_type – the @type of the annotation type being added

    • -

  • contains_metadata – any metadata associated with the annotation type

    • -
-
-
Returns:
-

the generated Contain object

-
-
-
- -
-
-new_textdocument(text: str, lang: str = 'en', did: str | None = None, overwrite=False, **properties) → Document[source]
-

Generates a new mmif.serialize.annotation.Document -object, particularly typed as TextDocument and adds it to the current view.

-

Fails if there is already a text document with the same ID -in the view, unless overwrite is set to True.

-
-
Parameters:
-
    -

  • text – text content of the new document

    • -

  • lang – ISO 639-1 code of the language used in the new document

    • -

  • did – the desired ID of the document, when not given, -the mmif SDK tries to automatically generate an ID based on -Annotation type and existing documents in the view.

    • -

  • overwrite – if set to True, will overwrite an -existing document with the same ID

    • -
-
-
Raises:
-

KeyError – if overwrite is set to False and -an document with the same ID exists -in the view

-
-
Returns:
-

the generated mmif.serialize.annotation.Document

-
-
-
- -
-
-set_error(err_message: str, err_trace: str) → None[source]
-
- -
- -
-
-class mmif.serialize.view.ViewMetadata(viewmetadata_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-

ViewMetadata object that represents the metadata object within a MMIF view.

-
-
Parameters:
-

viewmetadata_obj – the JSON data that defines the metadata

-
-
-
-
-add_contain(contain: Contain, at_type: str | TypesBase)[source]
-
- -
-
-add_parameter(param_key, param_value)[source]
-
- -
-
-add_parameters(**runtime_params)[source]
-
- -
-
-add_warnings(*warnings: Warning)[source]
-
- -
-
-emtpy_warnings()[source]
-
- -
-
-get_parameter(param_key)[source]
-
- -
-
-new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
-

Adds a new element to the contains dictionary.

-
-
Parameters:
-
    -

  • at_type – the @type of the annotation type being added

    • -

  • contains_metadata – any metadata associated with the annotation type

    • -
-
-
Returns:
-

the generated Contain object

-
-
-
- -
-
-set_error(message: str, stack_trace: str)[source]
-
- -
- -
-
-

mmif.serialize.annotation module

-

The annotation module contains the classes used to represent a -MMIF annotation as a live Python object.

-

In MMIF, annotations are created by apps in a pipeline as a part -of a view. For documentation on how views are represented, see -mmif.serialize.view.

-
-
-class mmif.serialize.annotation.Annotation(anno_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-

MmifObject that represents an annotation in a MMIF view.

-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]]) → None[source]
-

Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

-
- -
-
-property at_type: TypesBase[source]
-
- -
-
-static check_prop_value_is_simple_enough(value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]]) → bool[source]
-
- -
-
-get(prop_name: str) → AnnotationProperties | str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]][source]
-

A special getter for Annotation properties. This is to allow for -directly accessing properties without having to go through the -properties object, or view-level annotation properties encoded in the -view.metadata.contains dict. Note that the regular props will take -the priority over the ephemeral props when there are conflicts.

-
- -
-
-get_property(prop_name: str) → AnnotationProperties | str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]][source]
-

A special getter for Annotation properties. This is to allow for -directly accessing properties without having to go through the -properties object, or view-level annotation properties encoded in the -view.metadata.contains dict. Note that the regular props will take -the priority over the ephemeral props when there are conflicts.

-
- -
-
-property id: str[source]
-
- -
-
-is_document()[source]
-
- -
-
-is_type(at_type: str | TypesBase) → bool[source]
-

Check if the @type of this object matches.

-
- -
-
-property parent: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.AnnotationProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject, MutableMapping[str, T]

-

AnnotationProperties object that represents the -properties object within a MMIF annotation.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
- -
-
-class mmif.serialize.annotation.Document(doc_obj: bytes | str | dict | None = None)[source]
-

Bases: Annotation

-

Document object that represents a single document in a MMIF file.

-

A document is identified by an ID, and contains certain attributes -and potentially contains the contents of the document itself, -metadata about how the document was created, and/or a list of -subdocuments grouped together logically.

-

If document_obj is not provided, an empty Document will be generated.

-
-
Parameters:
-

document_obj – the JSON data that defines the document

-
-
-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None]) → None[source]
-

Adds a property to the document’s properties.

-

Unlike the parent Annotation class, added properties of a -Document object can be lost during serialization unless it belongs -to somewhere in a Mmif object. This is because we want to keep -Document object as “read-only” as possible. Thus, if you want to add -a property to a Document object,

-
    -

  • add the document to a Mmif object (either in the documents list or -in a view from the views list), or

    • -

  • directly write to Document.properties instead of using this method -(which is not recommended).

    • -
-

With the former method, the SDK will record the added property as a -Annotation annotation object, separate from the original Document -object. See Mmif.generate_capital_annotations() for more.

-

A few notes to keep in mind:

-
    -

  1. You can’t overwrite an existing property of a Document object.

    2. -

  2. A MMIF can have multiple Annotation objects with the same -property name but different values. When this happens, the SDK will -only keep the latest value (in order of appearances in views list) of -the property, effectively overwriting the previous values.

    3. -
-
- -
-
-get(prop_name)[source]
-

A special getter for Document properties. The major difference from -the super class’s Annotation.get() method is that Document -class has one more set of “pending” properties, that are added after -the Document object is created and will be serialized as a separate -Annotation object of which @type = Annotation. The -pending properties will take the priority over the regular properties -when there are conflicts.

-
- -
-
-get_property(prop_name)[source]
-

A special getter for Document properties. The major difference from -the super class’s Annotation.get() method is that Document -class has one more set of “pending” properties, that are added after -the Document object is created and will be serialized as a separate -Annotation object of which @type = Annotation. The -pending properties will take the priority over the regular properties -when there are conflicts.

-
- -
-
-property location: str | None[source]
-

location property must be a legitimate URI. That is, should the document be a local file -then the file:// scheme must be used. -Returns None when no location is set.

-
- -
-
-location_address() → str | None[source]
-

Retrieves the full address from the document location URI. -Returns None when no location is set.

-
- -
-
-location_path(nonexist_ok=True) → str | None[source]
-

Retrieves a path that’s resolved to a pathname in the local file system. -To obtain the original value of the “path” part in the location string -(before resolving), use properties.location_path_literal method. -Returns None when no location is set.

-
-
Parameters:
-

nonexist_ok – if False, raise FileNotFoundError when the resolved path doesn’t exist

-
-
-
- -
-
-location_scheme() → str | None[source]
-

Retrieves URI scheme of the document location. -Returns None when no location is set.

-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.DocumentProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: AnnotationProperties

-

DocumentProperties object that represents the -properties object within a MMIF document.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
-
-property location: str | None[source]
-

location property must be a legitimate URI. That is, should the document be a local file -then the file:// scheme must be used. -Returns None when no location is set.

-
- -
-
-location_address() → str | None[source]
-

Retrieves the full address from the document location URI. -Returns None when no location is set.

-
- -
-
-location_path() → str | None[source]
-
- -
-
-location_path_literal() → str | None[source]
-

Retrieves only path name of the document location (hostname is ignored). -Returns None when no location is set.

-
- -
-
-location_path_resolved(nonexist_ok=True) → str | None[source]
-

Retrieves only path name of the document location (hostname is ignored), -and then try to resolve the path name in the local file system. -This method should be used when the document scheme is file or empty. -For other schemes, users should install mmif-locdoc-<scheme> plugin.

-

Returns None when no location is set. -Raise ValueError when no code found to resolve the given location scheme.

-
- -
-
-location_scheme() → str | None[source]
-

Retrieves URI scheme of the document location. -Returns None when no location is set.

-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.Text(text_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-
-
-property lang: str[source]
-
- -
-
-property value: str[source]
-
- -
- -
-
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-
- -
-
-
-
- -
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- - - \ No newline at end of file diff --git a/docs/1.0.10/autodoc/mmif.utils.html b/docs/1.0.10/autodoc/mmif.utils.html deleted file mode 100644 index b2d2c66e..00000000 --- a/docs/1.0.10/autodoc/mmif.utils.html +++ /dev/null @@ -1,362 +0,0 @@ - - - - - - - - - mmif.utils module — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.utils module

-
-

mmif.utils.video_document_helper module

-
-
-mmif.utils.video_document_helper.capture(video_document: Document)[source]
-

Captures a video file using OpenCV and adds fps, frame count, and duration as properties to the document.

-
-
Parameters:
-

video_document – Document instance that holds a video document ("@type": ".../VideoDocument/...")

-
-
Returns:
-

OpenCV VideoCapture object

-
-
-
- -
-
-mmif.utils.video_document_helper.convert_timeframe(mmif: Mmif, time_frame: Annotation, out_unit: str) → Tuple[int | float | str, int | float | str][source]
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Converts start and end points in a TimeFrame annotation a different time unit.

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  • time_frame – Annotation instance that holds a time interval annotation ("@type": ".../TimeFrame/...")

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  • out_unit – time unit to which the point is converted

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tuple of frame numbers (integer) or seconds/milliseconds (float) of input start and end

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-mmif.utils.video_document_helper.convert_timepoint(mmif: Mmif, timepoint: Annotation, out_unit: str) → int | float | str[source]
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Converts a time point included in an annotation to a different time unit. -The input annotation must have timePoint property.

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-
Parameters:
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  • mmif – input MMIF to obtain fps and input timeunit

    • -

  • timepoint – Annotation instance with timePoint property

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  • out_unit – time unit to which the point is converted (frames, seconds, milliseconds)

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frame number (integer) or second/millisecond (float) of input timepoint

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-mmif.utils.video_document_helper.extract_frames_as_images(video_document: Document, framenums: List[int], as_PIL: bool = False)[source]
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Extracts frames from a video document as a list of numpy.ndarray. -Use with sample_frames() function to get the list of frame numbers first.

-
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Parameters:
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  • video_document – Document instance that holds a video document ("@type": ".../VideoDocument/...")

    • -

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frames as a list of ndarray or Image

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-mmif.utils.video_document_helper.extract_mid_frame(mmif: Mmif, time_frame: Annotation, as_PIL: bool = False)[source]
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Extracts the middle frame of a time interval annotation as a numpy ndarray.

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frame as a numpy.ndarray or PIL.Image.Image

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-mmif.utils.video_document_helper.framenum_to_millisecond(video_doc: Document, frame: int)[source]
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Converts a frame number to a millisecond value.

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Converts a frame number to a second value.

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-mmif.utils.video_document_helper.get_annotation_property(mmif, annotation, prop_name)[source]
-
-

Deprecated since version 1.0.8: Use mmif.serialize.annotation.Annotation.get_property() method instead.

-
-

Get a property value from an annotation. If the property is not found in the annotation, it will look up the metadata of the annotation’s parent view and return the value from there. -xisting

-
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-mmif.utils.video_document_helper.get_framerate(video_document: Document) → float[source]
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Gets the frame rate of a video document. First by checking the fps property of the document, then by capturing the video.

-
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Parameters:
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video_document – Document instance that holds a video document ("@type": ".../VideoDocument/...")

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Returns:
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frames per second as a float, rounded to 2 decimal places

-
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-mmif.utils.video_document_helper.get_mid_framenum(mmif: Mmif, time_frame: Annotation)[source]
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Calculates the middle frame number of a time interval annotation.

-
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Parameters:
-
    -

  • mmif – Mmif instance

    • -

  • time_frame – Annotation instance that holds a time interval annotation ("@type": ".../TimeFrame/...")

    • -
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-

middle frame number as an integer

-
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- -
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-mmif.utils.video_document_helper.millisecond_to_framenum(video_doc: Document, millisecond: float) → int[source]
-

Converts a millisecond value to a frame number.

-
- -
-
-mmif.utils.video_document_helper.sample_frames(start_frame: int, end_frame: int, sample_ratio: int = 1) → List[int][source]
-

Helper function to sample frames from a time interval. -Can also be used as a “cutoff” function when used with start_frame==0 and sample_ratio==1.

-
-
Parameters:
-
    -

  • start_frame – start frame of the interval

    • -

  • end_frame – end frame of the interval

    • -

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    • -
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Converts a second value to a frame number.

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mmif.vocabulary module

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mmif.vocabulary.annotation_types module

-
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-class mmif.vocabulary.annotation_types.AnnotationTypes(type_uri, fuzzymode=True)[source]
-

Bases: AnnotationTypesBase

-

This class contains the CLAMS annotation types -defined in the spec version 1.1.0 as class variables.

-
-
-Alignment = http://mmif.clams.ai/vocabulary/Alignment/v1[source]
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-Annotation = http://mmif.clams.ai/vocabulary/Annotation/v6[source]
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-BoundingBox = http://mmif.clams.ai/vocabulary/BoundingBox/v5[source]
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-Chapter = http://mmif.clams.ai/vocabulary/Chapter/v6[source]
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-Interval = http://mmif.clams.ai/vocabulary/Interval/v5[source]
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-NamedEntity = http://mmif.clams.ai/vocabulary/NamedEntity/v1[source]
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-NounChunk = http://mmif.clams.ai/vocabulary/NounChunk/v1[source]
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-Paragraph = http://mmif.clams.ai/vocabulary/Paragraph/v1[source]
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-Polygon = http://mmif.clams.ai/vocabulary/Polygon/v5[source]
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-Region = http://mmif.clams.ai/vocabulary/Region/v5[source]
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-Relation = http://mmif.clams.ai/vocabulary/Relation/v5[source]
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-Sentence = http://mmif.clams.ai/vocabulary/Sentence/v1[source]
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-Span = http://mmif.clams.ai/vocabulary/Span/v5[source]
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-TimeFrame = http://mmif.clams.ai/vocabulary/TimeFrame/v6[source]
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-TimePoint = http://mmif.clams.ai/vocabulary/TimePoint/v5[source]
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-Token = http://mmif.clams.ai/vocabulary/Token/v1[source]
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-VerbChunk = http://mmif.clams.ai/vocabulary/VerbChunk/v1[source]
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-VideoObject = http://mmif.clams.ai/vocabulary/VideoObject/v5[source]
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-prop_aliases = {'BoundingBox': {'label': {'boxType', 'label'}}, 'TimeFrame': {'label': {'frameType', 'label'}}}[source]
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- -
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-typevers = {'Alignment': 'v1', 'Annotation': 'v6', 'BoundingBox': 'v5', 'Chapter': 'v6', 'Interval': 'v5', 'NamedEntity': 'v1', 'NounChunk': 'v1', 'Paragraph': 'v1', 'Polygon': 'v5', 'Region': 'v5', 'Relation': 'v5', 'Sentence': 'v1', 'Span': 'v5', 'TimeFrame': 'v6', 'TimePoint': 'v5', 'Token': 'v1', 'VerbChunk': 'v1', 'VideoObject': 'v5'}[source]
-
- -
- -
-
-

mmif.vocabulary.document_types module

-
-
-class mmif.vocabulary.document_types.DocumentTypes(type_uri, fuzzymode=True)[source]
-

Bases: DocumentTypesBase

-

This class contains the CLAMS document types -defined in the spec version 1.1.0 as class variables.

-
-
-AudioDocument = http://mmif.clams.ai/vocabulary/AudioDocument/v1[source]
-
- -
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-Document = http://mmif.clams.ai/vocabulary/Document/v1[source]
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- -
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-ImageDocument = http://mmif.clams.ai/vocabulary/ImageDocument/v1[source]
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- -
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-TextDocument = http://mmif.clams.ai/vocabulary/TextDocument/v1[source]
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-VideoDocument = http://mmif.clams.ai/vocabulary/VideoDocument/v1[source]
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-typevers = {'AudioDocument': 'v1', 'Document': 'v1', 'ImageDocument': 'v1', 'TextDocument': 'v1', 'VideoDocument': 'v1'}[source]
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- - - \ No newline at end of file diff --git a/docs/1.0.10/autodoc/mmif_docloc_http.html b/docs/1.0.10/autodoc/mmif_docloc_http.html deleted file mode 100644 index 15db10c5..00000000 --- a/docs/1.0.10/autodoc/mmif_docloc_http.html +++ /dev/null @@ -1,179 +0,0 @@ - - - - - - - - - mmif_docloc_http package — mmif-python documentation - - - - - - - - - - - - - - - - -
- - -
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mmif_docloc_http package

-

MMIF document location helper module for http and https schemes. -If you want to write your own docloc scheme handler, please use the source code of this module as a reference. -See this plug-in section for more information.

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-mmif_docloc_http.resolve(docloc)[source]
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  • MMIF consumer
    • -
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MMIF consumer

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A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the appliance documentation to learn more about the appliance.

-

MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance.

-
    -

  1. The code must be hosted on a public git repository (e.g. Github, Gitlab, …)

    2. -

  2. Must listen to 5000 port.

    3. -

  3. Must expose /display route .

    4. -

  4. /display router should response to GET requests.

    5. -

  5. In the GET request, a public URL of the input MMIF file is passed via file URL parameter.

    6. -

  6. On the codebase root, there must be a Dockerfile that can build a docker image that runs the web app.

    7. -
-

We provide an example consumer at https://github.com/clamsproject/mmif-visualizer.

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  • Index
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Index

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  • Welcome to mmif-python’s documentation!
    • -
  • -
    • -
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Welcome to mmif-python’s documentation!

-
-

MultiMedia Interchange Format

-

MMIF is a JSON(-LD)-based data format designed for transferring annotation data between computational analysis applications in CLAMS project.

-
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Contents

- -
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API documentation:

- -
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Indices and tables

- -
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  • Getting Started
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  • -
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Getting Started

-
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Overview

-

MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for reproducibility, transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF website. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects.

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Prerequisites

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    -

  • Python: the latest mmif-python requires Python 3.8 or newer. We have no plan to support Python 2.7.

    • -
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Installation

-

Package mmif-python is distributed via the official PyPI. Users are supposed to pip-install to get latest release.

-
pip install mmif-python
-
-
-

This will install a package mmif to local python.

-

The MMIF format and specification is evolving over time, and mmif-python package will be updated along with the changes in MMIF format.

-
-

Note

-

MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and mmif-python versions, please take time to read our decision on the subject here. If you need to know which python SDK supports which specification version, see Target MMIF Versions page.

-
-
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MMIF Serialization

-

mmif.serialize.mmif.Mmif represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of mmif.serialize.model.MmifObject, including the mmif.serialize.mmif.Mmif. To start with an existing MMIF str, simple initiate a new Mmif object with the file.

-
import mmif
-from mmif import Mmif
-
-mmif_str = """{
-"metadata": {
-  "mmif": "http://mmif.clams.ai/1.0.0"
-},
-"documents": [
-  {
-    "@type": "http://mmif.clams.ai/vocabulary/VideoDocument/v1",
-    "properties": {
-      "id": "m1",
-      "mime": "video/mp4",
-      "location": "file:///var/archive/video-0012.mp4"
-    }
-  },
-  {
-    "@type": "http://mmif.clams.ai/vocabulary/TextDocument/v1",
-    "properties": {
-      "id": "m2",
-      "mime": "text/plain",
-      "location": "file:///var/archive/video-0012-transcript.txt"
-    }
-  }
-],
-"views": []}"""
-mmif_obj = Mmif(mmif_str)
-
-
-

Few notes;

-
    -

  1. MMIF does not carry the primary source files in it.

    2. -

  2. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version mmif-python implementation of the MMIF might not be able to load an unsupported version of MMIF string.

    3. -
-

When serializing back to str, call mmif.serialize.model.MmifObject.serialize() on the object.

-

To get subcomponents, you can use various getters implemented in subclasses. For example;

-
from mmif.vocabulary.document_types import DocumentTypes
-
-for video in mmif_obj.Mmif.get_documents_by_type(DocumentTypes.VideoDocument):
-  with open(video.location_path(), 'b') as in_video:
-    # do something with the video file
-
-
-

For a full list of available helper methods, please refer to the API documentation.

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mmif package

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mmif_docloc_http package

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Developing plugins for MMIF Python SDK

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Overview

-

As MMIF JSON files can carry information about media document files without actually carrying file contents, file accessing modules in mmif Python package (distributed as mmif-python on PyPI) are designed to be lightweight and flexible so that it can work with additional “plugin” Python packages that can handle concrete file access.

-

This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF website. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects.

-

Developer can write simple plugins that can provide additional functionalities to mmif-python. For example, mmif-python does not provide any file access functionality beyond a local file system (with file scheme), but it can be extended with a plugin that can handle file access over different protocols (e.g. http, s3, ftp, etc).

-

This document contains information about how to write plugins for mmif-python.

-
-

Document Location Scheme Plugins

-

mmif.serialize.annotation.Document class has various methods to access parts of location property of the document. The location is in URI/IRI format (SCHEME://HOSTNAME/PATH, in a nutshell) and it has to be resolved to a local file for CLAMS Apps to process the local file to analyze and extract information about the media and its contents. The core mmif-python distribution only provides a default implementation that can handle file scheme URIs.

-

To add a document location handler plugin, you need to implement a Python “package” (do not confuse with PYPI distribution), that meets these requirements;

-
    -

  1. the package must be named mmif_docloc_<SCHEME>. For example, to implement a handler for s3 scheme, the package name must be mmif_docloc_s3. The prefix is important as it’s used in the plugin discovery process from the core mmif-python modules.

    2. -

  2. the top module of the package must have a function named resolve. The function must take a single argument, which is a str of the document location URI. The function must return a str of the local file path. For example, if the document location is s3://mybucket/myfile.mp4, a Python user should be able to to something like this;

    3. -
-
import mmif_docloc_s3
-resolved = mmif_docloc_s3.resolve('s3://mybucket/myfile.mp4')
-# then resolved must be a local file path that can be used to open the file
-
-
-

Here’s a minimal example codebase that you refer to when you develop a docloc plugin.

-

(However, before you start writing your own plugin for a specific URI scheme, checking if there’s already a PyPI distribution for the scheme might be a good idea.)

-
$ tree .
-.
-├── mmif_docloc_dummy
-│   └── __init__.py
-├── pyproject.toml
-└── setup.cfg
-
- $ cat pyproject.toml
-[build-system]
-requires = ["setuptools"]
-build-backend = "setuptools.build_meta"
-
-$ cat setup.cfg
-[metadata]
-name = mmif_docloc_dummy  # this name is IMPORTANT
-version = 0.0.1
-description = a plugin to mmif-pyhon to handle `dummy` location scheme
-
-
-

And the plugin code.

-
# mmif_docloc_dummy/__init__.py
-doc_types = {'video': 'mp4'}
-
-def resolve(docloc):
-    scheme = 'dummy'
-    if docloc.startswith(f'{scheme}://'):
-        doc_id, doc_type = docloc.split('.')
-        return f'/path/to/{doc_id}.{doc_types[doc_type]}'
-    else:
-        raise ValueError(f'cannot handle document location scheme: {docloc}')
-
-
-
-
-

Bulit-in Document Location Scheme Plugins

-

At the moment, mmif-python PyPI distribution ships a built-in docloc plugin that support both http and https schemes. -Take a look at mmif_docloc_http module for details.

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"mmif.serialize.annotation.Annotation", false]], "annotation (mmif.vocabulary.annotation_types.annotationtypes attribute)": [[2, "mmif.vocabulary.annotation_types.AnnotationTypes.Annotation", false]], "annotationproperties (class in mmif.serialize.annotation)": [[0, "mmif.serialize.annotation.AnnotationProperties", false]], "annotationtypes (class in mmif.vocabulary.annotation_types)": [[2, "mmif.vocabulary.annotation_types.AnnotationTypes", false]], "append() (mmif.serialize.model.datalist method)": [[0, "mmif.serialize.model.DataList.append", false]], "at_type (mmif.serialize.annotation.annotation property)": [[0, "mmif.serialize.annotation.Annotation.at_type", false]], "audiodocument (mmif.vocabulary.document_types.documenttypes attribute)": [[2, "mmif.vocabulary.document_types.DocumentTypes.AudioDocument", false]], "boundingbox (mmif.vocabulary.annotation_types.annotationtypes attribute)": [[2, "mmif.vocabulary.annotation_types.AnnotationTypes.BoundingBox", false]], "capture() (in module mmif.utils.video_document_helper)": [[1, "mmif.utils.video_document_helper.capture", false]], "chapter (mmif.vocabulary.annotation_types.annotationtypes attribute)": [[2, "mmif.vocabulary.annotation_types.AnnotationTypes.Chapter", false]], "check_prop_value_is_simple_enough() (mmif.serialize.annotation.annotation static method)": [[0, "mmif.serialize.annotation.Annotation.check_prop_value_is_simple_enough", false]], "contain (class in mmif.serialize.view)": [[0, "mmif.serialize.view.Contain", false]], "convert_timeframe() (in module mmif.utils.video_document_helper)": [[1, "mmif.utils.video_document_helper.convert_timeframe", false]], "convert_timepoint() (in module mmif.utils.video_document_helper)": [[1, "mmif.utils.video_document_helper.convert_timepoint", false]], "datadict (class in mmif.serialize.model)": [[0, "mmif.serialize.model.DataDict", false]], "datalist (class in mmif.serialize.model)": [[0, "mmif.serialize.model.DataList", false]], "default() 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"develop": 8, "document": [5, 8], "document_typ": 2, "format": 5, "get": 6, "indic": 5, "instal": 6, "interchang": 5, "locat": 8, "mmif": [0, 1, 2, 4, 5, 6, 7, 8, 9], "mmif_docloc_http": [3, 7], "model": 0, "modul": [0, 1, 2], "multimedia": 5, "overview": [6, 8], "packag": [3, 7], "plugin": 8, "prerequisit": 6, "python": [5, 8], "scheme": 8, "sdk": 8, "serial": [0, 6], "specif": 9, "start": 6, "tabl": 5, "target": 9, "util": 1, "version": 9, "video_document_help": 1, "view": 0, "vocabulari": 2, "welcom": 5}}) \ No newline at end of file diff --git a/docs/1.0.10/target-versions.html b/docs/1.0.10/target-versions.html deleted file mode 100644 index fb22877d..00000000 --- a/docs/1.0.10/target-versions.html +++ /dev/null @@ -1,273 +0,0 @@ - - - - - - - - - Target MMIF Versions — mmif-python documentation - - - - - - - - - - - - - - - - - -
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  • Target MMIF Versions
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Target MMIF Versions

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This article provides targeting MMIF specification versions of different versions of mmif-python SDK.

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Target Specification Versions

mmif-python version

Target MMIF Specification

1.0.10

1.1.0

1.0.9

1.1.0

1.0.8

1.0.0

1.0.7

1.0.0

1.0.6

1.0.0

1.0.5

1.0.0

1.0.4

1.0.0

1.0.3

1.0.0

1.0.2

1.0.0

1.0.1

1.0.0

1.0.0

0.5.0

0.5.2

0.5.0

0.5.1

0.5.0

0.5.0

0.5.0

0.4.8

0.4.2

0.4.7

0.4.1

0.4.6

0.4.0

0.4.5

0.4.0

0.4.4

0.4.0

0.4.3

0.4.0

0.4.2

0.4.0

0.4.1

0.4.0

0.4.0

0.4.0

0.3.5

0.3.1

0.3.4

0.3.1

0.3.3

0.3.1

0.3.2

0.3.1

0.3.1

0.3.0

0.3.0

0.3.0

0.2.2

0.2.1

0.2.1

0.2.1

0.2.0

0.2.1

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- - Other Versions - v: 1.0.10 - - -
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0.3.0
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0.3.1
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0.3.2
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0.3.3
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0.3.4
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0.3.5
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0.4.0
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0.4.1
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0.4.2
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0.4.3
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0.4.4
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0.4.5
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0.4.6
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0.4.7
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0.4.8
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0.5.0
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0.5.1
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0.5.2
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1.0.0
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1.0.1
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1.0.10
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1.0.11
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1.0.12
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1.0.13
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1.0.14
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1.0.15
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1.0.16
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1.0.17
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1.0.18
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1.0.19
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1.0.2
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1.0.3
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1.0.4
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1.0.5
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1.0.6
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1.0.7
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1.0.8
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1.0.9
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1.1.0
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-mmif.serialize.model module ---------------------------- - -.. automodule:: mmif.serialize.model - :members: - :undoc-members: - :show-inheritance: - -mmif.serialize.mmif module --------------------------- - -.. automodule:: mmif.serialize.mmif - :members: - :undoc-members: - :show-inheritance: - -mmif.serialize.view module --------------------------- - -.. automodule:: mmif.serialize.view - :members: - :undoc-members: - :show-inheritance: - -mmif.serialize.annotation module --------------------------------- - -.. automodule:: mmif.serialize.annotation - :members: - :undoc-members: - :show-inheritance: - diff --git a/docs/1.0.11/_sources/autodoc/mmif.utils.rst.txt b/docs/1.0.11/_sources/autodoc/mmif.utils.rst.txt deleted file mode 100644 index 9a6ecc44..00000000 --- a/docs/1.0.11/_sources/autodoc/mmif.utils.rst.txt +++ /dev/null @@ -1,18 +0,0 @@ -mmif.utils module -================= - -mmif.utils.video_document_helper module ----------------------------------------- - -.. automodule:: mmif.utils.video_document_helper - :members: - :undoc-members: - :show-inheritance: - -mmif.utils.sequence_helper module ---------------------------------- - -.. automodule:: mmif.utils.sequence_helper - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/1.0.11/_sources/autodoc/mmif.vocabulary.rst.txt b/docs/1.0.11/_sources/autodoc/mmif.vocabulary.rst.txt deleted file mode 100644 index d250c6a3..00000000 --- a/docs/1.0.11/_sources/autodoc/mmif.vocabulary.rst.txt +++ /dev/null @@ -1,18 +0,0 @@ -mmif.vocabulary module -====================== - -mmif.vocabulary.annotation\_types module ----------------------------------------- - -.. automodule:: mmif.vocabulary.annotation_types - :members: - :undoc-members: - :show-inheritance: - -mmif.vocabulary.document\_types module --------------------------------------- - -.. automodule:: mmif.vocabulary.document_types - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/1.0.11/_sources/autodoc/mmif_docloc_http.rst.txt b/docs/1.0.11/_sources/autodoc/mmif_docloc_http.rst.txt deleted file mode 100644 index b76c8df5..00000000 --- a/docs/1.0.11/_sources/autodoc/mmif_docloc_http.rst.txt +++ /dev/null @@ -1,11 +0,0 @@ -mmif_docloc_http package -======================== - -MMIF document location helper module for `http` and `https` schemes. -If you want to write your own docloc scheme handler, please use the source code of this module as a reference. -See this :ref:`plug-in section ` for more information. - -.. automodule:: mmif_docloc_http - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/1.0.11/_sources/consumer-tutorial.rst.txt b/docs/1.0.11/_sources/consumer-tutorial.rst.txt deleted file mode 100644 index c54634e2..00000000 --- a/docs/1.0.11/_sources/consumer-tutorial.rst.txt +++ /dev/null @@ -1,17 +0,0 @@ -.. _consumer-tutorial: - -MMIF consumer -================================= - -A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the `appliance documentation `_ to learn more about the appliance. - -MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance. - -#. The code must be hosted on a public git repository (e.g. Github, Gitlab, ...) -#. Must listen to ``5000`` port. -#. Must expose ``/display`` route . -#. ``/display`` router should response to ``GET`` requests. -#. In the ``GET`` request, a public URL of the input MMIF file is passed via ``file`` URL parameter. -#. On the codebase root, there must be a ``Dockerfile`` that can build a `docker `_ image that runs the web app. - -We provide an example consumer at https://github.com/clamsproject/mmif-visualizer. diff --git a/docs/1.0.11/_sources/index.rst.txt b/docs/1.0.11/_sources/index.rst.txt deleted file mode 100644 index beb56aae..00000000 --- a/docs/1.0.11/_sources/index.rst.txt +++ /dev/null @@ -1,26 +0,0 @@ -Welcome to mmif-python's documentation! -======================================= - -.. mdinclude:: ../README.md - -.. toctree:: - :maxdepth: 2 - :caption: Contents - - introduction - plugins - target-versions - -.. toctree:: - :maxdepth: 2 - :caption: API documentation: - - modules - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/docs/1.0.11/_sources/introduction.rst.txt b/docs/1.0.11/_sources/introduction.rst.txt deleted file mode 100644 index cfd9eaf7..00000000 --- a/docs/1.0.11/_sources/introduction.rst.txt +++ /dev/null @@ -1,89 +0,0 @@ -.. _introduction: - -Getting Started -=============== - - -Overview ---------- - -MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for reproducibility, transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF website `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects. - -Prerequisites -------------- - -* `Python `_: the latest ``mmif-python`` requires Python 3.8 or newer. We have no plan to support `Python 2.7 `_. - -Installation ---------------- - -Package ``mmif-python`` is distributed via the official PyPI. Users are supposed to pip-install to get latest release. - -.. code-block:: bash - - pip install mmif-python - -This will install a package `mmif` to local python. - -The MMIF format and specification is evolving over time, and ``mmif-python`` package will be updated along with the changes in MMIF format. - -.. note:: MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and ``mmif-python`` versions, please take time to read our decision on the subject `here `_. If you need to know which python SDK supports which specification version, see :ref:`target-versions` page. - -MMIF Serialization ---------------------------- - -:class:`mmif.serialize.mmif.Mmif` represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of :class:`mmif.serialize.model.MmifObject`, including the :class:`mmif.serialize.mmif.Mmif`. To start with an existing MMIF :class:`str`, simple initiate a new ``Mmif`` object with the file. - -.. code-block:: python - - import mmif - from mmif import Mmif - - mmif_str = """{ - "metadata": { - "mmif": "http://mmif.clams.ai/1.0.0" - }, - "documents": [ - { - "@type": "http://mmif.clams.ai/vocabulary/VideoDocument/v1", - "properties": { - "id": "m1", - "mime": "video/mp4", - "location": "file:///var/archive/video-0012.mp4" - } - }, - { - "@type": "http://mmif.clams.ai/vocabulary/TextDocument/v1", - "properties": { - "id": "m2", - "mime": "text/plain", - "location": "file:///var/archive/video-0012-transcript.txt" - } - } - ], - "views": []}""" - mmif_obj = Mmif(mmif_str) - - -Few notes; - -#. MMIF does not carry the primary source files in it. -#. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version ``mmif-python`` implementation of the MMIF might not be able to load an unsupported version of MMIF string. - -When serializing back to :class:`str`, call :meth:`mmif.serialize.model.MmifObject.serialize` on the object. - -To get subcomponents, you can use various getters implemented in subclasses. For example; - -.. code-block:: python - - from mmif.vocabulary.document_types import DocumentTypes - - for video in mmif_obj.Mmif.get_documents_by_type(DocumentTypes.VideoDocument): - with open(video.location_path(), 'b') as in_video: - # do something with the video file - - -For a full list of available helper methods, please refer to :ref:`the API documentation `. - diff --git a/docs/1.0.11/_sources/modules.rst.txt b/docs/1.0.11/_sources/modules.rst.txt deleted file mode 100644 index 4bb9307d..00000000 --- a/docs/1.0.11/_sources/modules.rst.txt +++ /dev/null @@ -1,20 +0,0 @@ -.. _apidoc: - -mmif package -============ - -.. toctree:: - :maxdepth: 4 - - autodoc/mmif.serialize - autodoc/mmif.vocabulary - autodoc/mmif.utils - -mmif_docloc_http package -======================== - -.. toctree:: - :maxdepth: 2 - - autodoc/mmif_docloc_http - diff --git a/docs/1.0.11/_sources/plugins.rst.txt b/docs/1.0.11/_sources/plugins.rst.txt deleted file mode 100644 index 9907c495..00000000 --- a/docs/1.0.11/_sources/plugins.rst.txt +++ /dev/null @@ -1,83 +0,0 @@ -.. _plugins: - -Developing plugins for MMIF Python SDK -====================================== - - -Overview --------- - -As MMIF JSON files can carry information about media document files without actually carrying file contents, file accessing modules in ``mmif`` Python package (distributed as ``mmif-python`` on PyPI) are designed to be lightweight and flexible so that it can work with additional "plugin" Python packages that can handle concrete file access. - - -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF website `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects. - -Developer can write simple plugins that can provide additional functionalities to ``mmif-python``. For example, ``mmif-python`` does not provide any file access functionality beyond a local file system (with ``file`` scheme), but it can be extended with a plugin that can handle file access over different protocols (e.g. ``http``, ``s3``, ``ftp``, etc). - -This document contains information about how to write plugins for ``mmif-python``. - -.. _docloc_plugin: - -Document Location Scheme Plugins -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -:class:`mmif.serialize.annotation.Document` class has various methods to access parts of ``location`` property of the document. The location is in `URI/IRI format `_ (``SCHEME://HOSTNAME/PATH``, in a nutshell) and it has to be resolved to a local file for CLAMS Apps to process the local file to analyze and extract information about the media and its contents. The core ``mmif-python`` distribution only provides a default implementation that can handle ``file`` scheme URIs. - -To add a document location handler plugin, you need to implement a Python `"package" `_ (do not confuse with PYPI distribution), that meets these requirements; - -#. the package must be named ``mmif_docloc_``. For example, to implement a handler for ``s3`` scheme, the package name must be ``mmif_docloc_s3``. The prefix is important as it's used in the plugin discovery process from the core ``mmif-python`` modules. -#. the top module of the package must have a function named ``resolve``. The function must take a single argument, which is a :class:`str` of the document location URI. The function must return a :class:`str` of the local file path. For example, if the document location is ``s3://mybucket/myfile.mp4``, a Python user should be able to to something like this; - -.. code-block:: python - - import mmif_docloc_s3 - resolved = mmif_docloc_s3.resolve('s3://mybucket/myfile.mp4') - # then resolved must be a local file path that can be used to open the file - - -Here's a minimal example codebase that you refer to when you develop a ``docloc`` plugin. - -(However, before you start writing your own plugin for a specific URI scheme, checking `if there's already a PyPI distribution `_ for the scheme might be a good idea.) - -.. code-block:: sh - - $ tree . - . - ├── mmif_docloc_dummy - │ └── __init__.py - ├── pyproject.toml - └── setup.cfg - - $ cat pyproject.toml - [build-system] - requires = ["setuptools"] - build-backend = "setuptools.build_meta" - - $ cat setup.cfg - [metadata] - name = mmif_docloc_dummy # this name is IMPORTANT - version = 0.0.1 - description = a plugin to mmif-pyhon to handle `dummy` location scheme - - -And the plugin code. - -.. code-block:: python - - # mmif_docloc_dummy/__init__.py - doc_types = {'video': 'mp4'} - - def resolve(docloc): - scheme = 'dummy' - if docloc.startswith(f'{scheme}://'): - doc_id, doc_type = docloc.split('.') - return f'/path/to/{doc_id}.{doc_types[doc_type]}' - else: - raise ValueError(f'cannot handle document location scheme: {docloc}') - -Bulit-in Document Location Scheme Plugins -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -At the moment, ``mmif-python`` PyPI distribution ships a built-in *docloc* plugin that support both ``http`` and ``https`` schemes. -Take a look at :mod:`mmif_docloc_http` module for details. diff --git a/docs/1.0.11/_sources/target-versions.rst.txt b/docs/1.0.11/_sources/target-versions.rst.txt deleted file mode 100644 index 34216d3e..00000000 --- a/docs/1.0.11/_sources/target-versions.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _target-versions: - -Target MMIF Versions -==================== - -This article provides targeting MMIF specification versions of different versions of ``mmif-python`` SDK. - -.. csv-table:: Target Specification Versions - :file: target-versions.csv - :header-rows: 1 diff --git a/docs/1.0.11/_static/_sphinx_javascript_frameworks_compat.js b/docs/1.0.11/_static/_sphinx_javascript_frameworks_compat.js deleted file mode 100644 index 81415803..00000000 --- a/docs/1.0.11/_static/_sphinx_javascript_frameworks_compat.js +++ /dev/null @@ -1,123 +0,0 @@ -/* Compatability shim for jQuery and underscores.js. - * - * Copyright Sphinx contributors - * Released under the two clause BSD licence - */ - -/** - * small helper function to urldecode strings - * - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL - */ -jQuery.urldecode = function(x) { - if (!x) { - return x - } - return decodeURIComponent(x.replace(/\+/g, ' ')); -}; - -/** - * small helper function to urlencode strings - */ -jQuery.urlencode = encodeURIComponent; - -/** - * This function returns the parsed url parameters of the - * current request. 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- document.dispatchEvent(event); - }); -}); \ No newline at end of file diff --git a/docs/1.0.11/_static/language_data.js b/docs/1.0.11/_static/language_data.js deleted file mode 100644 index c7fe6c6f..00000000 --- a/docs/1.0.11/_static/language_data.js +++ /dev/null @@ -1,192 +0,0 @@ -/* - * This script contains the language-specific data used by searchtools.js, - * namely the list of stopwords, stemmer, scorer and splitter. - */ - -var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"]; - - -/* Non-minified version is copied as a separate JS file, if available */ - -/** - * Porter Stemmer - */ -var Stemmer = function() { - - var step2list = { - ational: 'ate', - tional: 'tion', - enci: 'ence', - anci: 'ance', - izer: 'ize', - bli: 'ble', - alli: 'al', - entli: 'ent', - eli: 'e', - ousli: 'ous', - ization: 'ize', - ation: 'ate', - ator: 'ate', - alism: 'al', - iveness: 'ive', - fulness: 'ful', - ousness: 'ous', - aliti: 'al', - iviti: 'ive', - biliti: 'ble', - logi: 'log' - }; 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} - static get object() { return "object"; } - static get text() { return "text"; } - static get title() { return "title"; } -} - -const _removeChildren = (element) => { - while (element && element.lastChild) element.removeChild(element.lastChild); -}; - -/** - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping - */ -const _escapeRegExp = (string) => - string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string - -const _displayItem = (item, searchTerms, highlightTerms) => { - const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; - const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; - const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; - const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; - const contentRoot = document.documentElement.dataset.content_root; - - const [docName, title, anchor, descr, score, _filename, kind] = item; - - let listItem = document.createElement("li"); - // Add a class representing the item's type: - // can be used by a theme's CSS selector for styling - // See SearchResultKind for the class names. - listItem.classList.add(`kind-${kind}`); - let requestUrl; - let linkUrl; - if (docBuilder === "dirhtml") { - // dirhtml builder - let dirname = docName + "/"; - if (dirname.match(/\/index\/$/)) - dirname = dirname.substring(0, dirname.length - 6); - else if (dirname === "index/") dirname = ""; - requestUrl = contentRoot + dirname; - linkUrl = requestUrl; - } else { - // normal html builders - requestUrl = contentRoot + docName + docFileSuffix; - linkUrl = docName + docLinkSuffix; - } - let linkEl = listItem.appendChild(document.createElement("a")); - linkEl.href = linkUrl + anchor; - linkEl.dataset.score = score; - linkEl.innerHTML = title; - if (descr) { - listItem.appendChild(document.createElement("span")).innerHTML = - " (" + descr + ")"; - // highlight search terms in the description - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - } - else if (showSearchSummary) - fetch(requestUrl) - .then((responseData) => responseData.text()) - .then((data) => { - if (data) - listItem.appendChild( - Search.makeSearchSummary(data, searchTerms, anchor) - ); 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Please make sure that all words are spelled correctly and that you've selected enough categories." - ); - else - Search.status.innerText = Documentation.ngettext( - "Search finished, found one page matching the search query.", - "Search finished, found ${resultCount} pages matching the search query.", - resultCount, - ).replace('${resultCount}', resultCount); -}; -const _displayNextItem = ( - results, - resultCount, - searchTerms, - highlightTerms, -) => { - // results left, load the summary and display it - // this is intended to be dynamic (don't sub resultsCount) - if (results.length) { - _displayItem(results.pop(), searchTerms, highlightTerms); - setTimeout( - () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), - 5 - ); - } - // search finished, update title and status message - else _finishSearch(resultCount); -}; -// Helper function used by query() to order search results. -// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. -// Order the results by score (in opposite order of appearance, since the -// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. -const _orderResultsByScoreThenName = (a, b) => { - const leftScore = a[4]; - const rightScore = b[4]; - if (leftScore === rightScore) { - // same score: sort alphabetically - const leftTitle = a[1].toLowerCase(); - const rightTitle = b[1].toLowerCase(); - if (leftTitle === rightTitle) return 0; - return leftTitle > rightTitle ? -1 : 1; // inverted is intentional - } - return leftScore > rightScore ? 1 : -1; -}; - -/** - * Default splitQuery function. Can be overridden in ``sphinx.search`` with a - * custom function per language. - * - * The regular expression works by splitting the string on consecutive characters - * that are not Unicode letters, numbers, underscores, or emoji characters. - * This is the same as ``\W+`` in Python, preserving the surrogate pair area. - */ -if (typeof splitQuery === "undefined") { - var splitQuery = (query) => query - .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) - .filter(term => term) // remove remaining empty strings -} - -/** - * Search Module - */ -const Search = { - _index: null, - _queued_query: null, - _pulse_status: -1, - - htmlToText: (htmlString, anchor) => { - const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - for (const removalQuery of [".headerlink", "script", "style"]) { - htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); - } - if (anchor) { - const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); - if (anchorContent) return anchorContent.textContent; - - console.warn( - `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` - ); - } - - // if anchor not specified or not found, fall back to main content - const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent) return docContent.textContent; - - console.warn( - "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." - ); - return ""; - }, - - init: () => { - const query = new URLSearchParams(window.location.search).get("q"); - document - .querySelectorAll('input[name="q"]') - .forEach((el) => (el.value = query)); - if (query) Search.performSearch(query); - }, - - loadIndex: (url) => - (document.body.appendChild(document.createElement("script")).src = url), - - setIndex: (index) => { - Search._index = index; - if (Search._queued_query !== null) { - const query = Search._queued_query; - Search._queued_query = null; - Search.query(query); - } - }, - - hasIndex: () => Search._index !== null, - - deferQuery: (query) => (Search._queued_query = query), - - stopPulse: () => (Search._pulse_status = -1), - - startPulse: () => { - if (Search._pulse_status >= 0) return; - - const pulse = () => { - Search._pulse_status = (Search._pulse_status + 1) % 4; - Search.dots.innerText = ".".repeat(Search._pulse_status); - if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); - }; - pulse(); - }, - - /** - * perform a search for something (or wait until index is loaded) - */ - performSearch: (query) => { - // create the required interface elements - const searchText = document.createElement("h2"); - searchText.textContent = _("Searching"); - const searchSummary = document.createElement("p"); - searchSummary.classList.add("search-summary"); - searchSummary.innerText = ""; - const searchList = document.createElement("ul"); - searchList.setAttribute("role", "list"); - searchList.classList.add("search"); - - const out = document.getElementById("search-results"); - Search.title = out.appendChild(searchText); - Search.dots = Search.title.appendChild(document.createElement("span")); - Search.status = out.appendChild(searchSummary); - Search.output = out.appendChild(searchList); - - const searchProgress = document.getElementById("search-progress"); - // Some themes don't use the search progress node - if (searchProgress) { - searchProgress.innerText = _("Preparing search..."); - } - Search.startPulse(); - - // index already loaded, the browser was quick! - if (Search.hasIndex()) Search.query(query); - else Search.deferQuery(query); - }, - - _parseQuery: (query) => { - // stem the search terms and add them to the correct list - const stemmer = new Stemmer(); - const searchTerms = new Set(); - const excludedTerms = new Set(); - const highlightTerms = new Set(); - const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); - splitQuery(query.trim()).forEach((queryTerm) => { - const queryTermLower = queryTerm.toLowerCase(); - - // maybe skip this "word" - // stopwords array is from language_data.js - if ( - stopwords.indexOf(queryTermLower) !== -1 || - queryTerm.match(/^\d+$/) - ) - return; - - // stem the word - let word = stemmer.stemWord(queryTermLower); - // select the correct list - if (word[0] === "-") excludedTerms.add(word.substr(1)); - else { - searchTerms.add(word); - highlightTerms.add(queryTermLower); - } - }); - - if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js - localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) - } - - // console.debug("SEARCH: searching for:"); - // console.info("required: ", [...searchTerms]); - // console.info("excluded: ", [...excludedTerms]); - - return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; - }, - - /** - * execute search (requires search index to be loaded) - */ - _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - - // Collect multiple result groups to be sorted separately and then ordered. - // Each is an array of [docname, title, anchor, descr, score, filename, kind]. - const normalResults = []; - const nonMainIndexResults = []; - - _removeChildren(document.getElementById("search-progress")); - - const queryLower = query.toLowerCase().trim(); - for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { - for (const [file, id] of foundTitles) { - const score = Math.round(Scorer.title * queryLower.length / title.length); - const boost = titles[file] === title ? 1 : 0; // add a boost for document titles - normalResults.push([ - docNames[file], - titles[file] !== title ? `${titles[file]} > ${title}` : title, - id !== null ? "#" + id : "", - null, - score + boost, - filenames[file], - SearchResultKind.title, - ]); - } - } - } - - // search for explicit entries in index directives - for (const [entry, foundEntries] of Object.entries(indexEntries)) { - if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id, isMain] of foundEntries) { - const score = Math.round(100 * queryLower.length / entry.length); - const result = [ - docNames[file], - titles[file], - id ? "#" + id : "", - null, - score, - filenames[file], - SearchResultKind.index, - ]; - if (isMain) { - normalResults.push(result); - } else { - nonMainIndexResults.push(result); - } - } - } - } - - // lookup as object - objectTerms.forEach((term) => - normalResults.push(...Search.performObjectSearch(term, objectTerms)) - ); - - // lookup as search terms in fulltext - normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); - - // let the scorer override scores with a custom scoring function - if (Scorer.score) { - normalResults.forEach((item) => (item[4] = Scorer.score(item))); - nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); - } - - // Sort each group of results by score and then alphabetically by name. - normalResults.sort(_orderResultsByScoreThenName); - nonMainIndexResults.sort(_orderResultsByScoreThenName); - - // Combine the result groups in (reverse) order. - // Non-main index entries are typically arbitrary cross-references, - // so display them after other results. - let results = [...nonMainIndexResults, ...normalResults]; - - // remove duplicate search results - // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept - let seen = new Set(); - results = results.reverse().reduce((acc, result) => { - let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); - if (!seen.has(resultStr)) { - acc.push(result); - seen.add(resultStr); - } - return acc; - }, []); - - return results.reverse(); - }, - - query: (query) => { - const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); - const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); - - // for debugging - //Search.lastresults = results.slice(); // a copy - // console.info("search results:", Search.lastresults); - - // print the results - _displayNextItem(results, results.length, searchTerms, highlightTerms); - }, - - /** - * search for object names - */ - performObjectSearch: (object, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const objects = Search._index.objects; - const objNames = Search._index.objnames; - const titles = Search._index.titles; - - const results = []; - - const objectSearchCallback = (prefix, match) => { - const name = match[4] - const fullname = (prefix ? prefix + "." : "") + name; - const fullnameLower = fullname.toLowerCase(); - if (fullnameLower.indexOf(object) < 0) return; - - let score = 0; - const parts = fullnameLower.split("."); - - // check for different match types: exact matches of full name or - // "last name" (i.e. last dotted part) - if (fullnameLower === object || parts.slice(-1)[0] === object) - score += Scorer.objNameMatch; - else if (parts.slice(-1)[0].indexOf(object) > -1) - score += Scorer.objPartialMatch; // matches in last name - - const objName = objNames[match[1]][2]; - const title = titles[match[0]]; - - // If more than one term searched for, we require other words to be - // found in the name/title/description - const otherTerms = new Set(objectTerms); - otherTerms.delete(object); - if (otherTerms.size > 0) { - const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); - if ( - [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) - ) - return; - } - - let anchor = match[3]; - if (anchor === "") anchor = fullname; - else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; - - const descr = objName + _(", in ") + title; - - // add custom score for some objects according to scorer - if (Scorer.objPrio.hasOwnProperty(match[2])) - score += Scorer.objPrio[match[2]]; - else score += Scorer.objPrioDefault; - - results.push([ - docNames[match[0]], - fullname, - "#" + anchor, - descr, - score, - filenames[match[0]], - SearchResultKind.object, - ]); - }; - Object.keys(objects).forEach((prefix) => - objects[prefix].forEach((array) => - objectSearchCallback(prefix, array) - ) - ); - return results; - }, - - /** - * search for full-text terms in the index - */ - performTermsSearch: (searchTerms, excludedTerms) => { - // prepare search - const terms = Search._index.terms; - const titleTerms = Search._index.titleterms; - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - - const scoreMap = new Map(); - const fileMap = new Map(); - - // perform the search on the required terms - searchTerms.forEach((word) => { - const files = []; - const arr = [ - { files: terms[word], score: Scorer.term }, - { files: titleTerms[word], score: Scorer.title }, - ]; - // add support for partial matches - if (word.length > 2) { - const escapedWord = _escapeRegExp(word); - if (!terms.hasOwnProperty(word)) { - Object.keys(terms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: terms[term], score: Scorer.partialTerm }); - }); - } - if (!titleTerms.hasOwnProperty(word)) { - Object.keys(titleTerms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); - }); - } - } - - // no match but word was a required one - if (arr.every((record) => record.files === undefined)) return; - - // found search word in contents - arr.forEach((record) => { - if (record.files === undefined) return; - - let recordFiles = record.files; - if (recordFiles.length === undefined) recordFiles = [recordFiles]; - files.push(...recordFiles); - - // set score for the word in each file - recordFiles.forEach((file) => { - if (!scoreMap.has(file)) scoreMap.set(file, {}); - scoreMap.get(file)[word] = record.score; - }); - }); - - // create the mapping - files.forEach((file) => { - if (!fileMap.has(file)) fileMap.set(file, [word]); - else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); - }); - }); - - // now check if the files don't contain excluded terms - const results = []; - for (const [file, wordList] of fileMap) { - // check if all requirements are matched - - // as search terms with length < 3 are discarded - const filteredTermCount = [...searchTerms].filter( - (term) => term.length > 2 - ).length; - if ( - wordList.length !== searchTerms.size && - wordList.length !== filteredTermCount - ) - continue; - - // ensure that none of the excluded terms is in the search result - if ( - [...excludedTerms].some( - (term) => - terms[term] === file || - titleTerms[term] === file || - (terms[term] || []).includes(file) || - (titleTerms[term] || []).includes(file) - ) - ) - break; - - // select one (max) score for the file. - const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); - // add result to the result list - results.push([ - docNames[file], - titles[file], - "", - null, - score, - filenames[file], - SearchResultKind.text, - ]); - } - return results; - }, - - /** - * helper function to return a node containing the - * search summary for a given text. keywords is a list - * of stemmed words. - */ - makeSearchSummary: (htmlText, keywords, anchor) => { - const text = Search.htmlToText(htmlText, anchor); - if (text === "") return null; - - const textLower = text.toLowerCase(); - const actualStartPosition = [...keywords] - .map((k) => textLower.indexOf(k.toLowerCase())) - .filter((i) => i > -1) - .slice(-1)[0]; - const startWithContext = Math.max(actualStartPosition - 120, 0); - - const top = startWithContext === 0 ? "" : "..."; - const tail = startWithContext + 240 < text.length ? "..." : ""; - - let summary = document.createElement("p"); - summary.classList.add("context"); - summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; - - return summary; - }, -}; - -_ready(Search.init); diff --git a/docs/1.0.11/_static/sphinx_highlight.js b/docs/1.0.11/_static/sphinx_highlight.js deleted file mode 100644 index 8a96c69a..00000000 --- a/docs/1.0.11/_static/sphinx_highlight.js +++ /dev/null @@ -1,154 +0,0 @@ -/* Highlighting utilities for Sphinx HTML documentation. */ -"use strict"; - -const SPHINX_HIGHLIGHT_ENABLED = true - -/** - * highlight a given string on a node by wrapping it in - * span elements with the given class name. - */ -const _highlight = (node, addItems, text, className) => { - if (node.nodeType === Node.TEXT_NODE) { - const val = node.nodeValue; - const parent = node.parentNode; - const pos = val.toLowerCase().indexOf(text); - if ( - pos >= 0 && - !parent.classList.contains(className) && - !parent.classList.contains("nohighlight") - ) { - let span; - - const closestNode = parent.closest("body, svg, foreignObject"); - const isInSVG = closestNode && closestNode.matches("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.classList.add(className); - } - - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - const rest = document.createTextNode(val.substr(pos + text.length)); - parent.insertBefore( - span, - parent.insertBefore( - rest, - node.nextSibling - ) - ); - node.nodeValue = val.substr(0, pos); - /* There may be more occurrences of search term in this node. So call this - * function recursively on the remaining fragment. - */ - _highlight(rest, addItems, text, className); - - if (isInSVG) { - const rect = document.createElementNS( - "http://www.w3.org/2000/svg", - "rect" - ); - const bbox = parent.getBBox(); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute("class", className); - addItems.push({ parent: parent, target: rect }); - } - } - } else if (node.matches && !node.matches("button, select, textarea")) { - node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); - } -}; -const _highlightText = (thisNode, text, className) => { - let addItems = []; - _highlight(thisNode, addItems, text, className); - addItems.forEach((obj) => - obj.parent.insertAdjacentElement("beforebegin", obj.target) - ); -}; - -/** - * Small JavaScript module for the documentation. - */ -const SphinxHighlight = { - - /** - * highlight the search words provided in localstorage in the text - */ - highlightSearchWords: () => { - if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight - - // get and clear terms from localstorage - const url = new URL(window.location); - const highlight = - localStorage.getItem("sphinx_highlight_terms") - || url.searchParams.get("highlight") - || ""; - localStorage.removeItem("sphinx_highlight_terms") - url.searchParams.delete("highlight"); - window.history.replaceState({}, "", url); - - // get individual terms from highlight string - const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); - if (terms.length === 0) return; // nothing to do - - // There should never be more than one element matching "div.body" - const divBody = document.querySelectorAll("div.body"); - const body = divBody.length ? divBody[0] : document.querySelector("body"); - window.setTimeout(() => { - terms.forEach((term) => _highlightText(body, term, "highlighted")); - }, 10); - - const searchBox = document.getElementById("searchbox"); - if (searchBox === null) return; - searchBox.appendChild( - document - .createRange() - .createContextualFragment( - '

' + - '' + - _("Hide Search Matches") + - "

" - ) - ); - }, - - /** - * helper function to hide the search marks again - */ - hideSearchWords: () => { - document - .querySelectorAll("#searchbox .highlight-link") - .forEach((el) => el.remove()); - document - .querySelectorAll("span.highlighted") - .forEach((el) => el.classList.remove("highlighted")); - localStorage.removeItem("sphinx_highlight_terms") - }, - - initEscapeListener: () => { - // only install a listener if it is really needed - if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; - - document.addEventListener("keydown", (event) => { - // bail for input elements - if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; - // bail with special keys - if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; - if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { - SphinxHighlight.hideSearchWords(); - event.preventDefault(); - } - }); - }, -}; - -_ready(() => { - /* Do not call highlightSearchWords() when we are on the search page. - * It will highlight words from the *previous* search query. - */ - if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); - SphinxHighlight.initEscapeListener(); -}); diff --git a/docs/1.0.11/autodoc/mmif.serialize.html b/docs/1.0.11/autodoc/mmif.serialize.html deleted file mode 100644 index b4a9efae..00000000 --- a/docs/1.0.11/autodoc/mmif.serialize.html +++ /dev/null @@ -1,1317 +0,0 @@ - - - - - - - - - mmif.serialize module — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.serialize module

-
-

mmif.serialize.model module

-

The model module contains the classes used to represent an -abstract MMIF object as a live Python object.

-

The MmifObject class or one of its derivatives is subclassed by -all other classes defined in this SDK, except for MmifObjectEncoder.

-

These objects are generally instantiated from JSON, either as a string -or as an already-loaded Python dictionary. This base class provides the -core functionality for deserializing MMIF JSON data into live objects -and serializing live objects into MMIF JSON data. Specialized behavior -for the different components of MMIF is added in the subclasses.

-
-
-class mmif.serialize.model.DataDict(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject, Generic[T, S]

-
-
-empty()[source]
-
- -
-
-get(key: T, default=None) → S | None[source]
-
- -
-
-items()[source]
-
- -
-
-keys()[source]
-
- -
-
-update(other, overwrite)[source]
-
- -
-
-values()[source]
-
- -
- -
-
-class mmif.serialize.model.DataList(mmif_obj: bytes | str | list | None = None)[source]
-

Bases: MmifObject, Generic[T]

-

The DataList class is an abstraction that represents the -various lists found in a MMIF file, such as documents, subdocuments, -views, and annotations.

-
-
Parameters:
-

mmif_obj (Union[str, list]) – the data that the list contains

-
-
-
-
-append(value, overwrite)[source]
-
- -
-
-deserialize(mmif_json: str | list) → None[source]
-

Passes the input data into the internal deserializer.

-
- -
-
-empty()[source]
-
- -
-
-get(key: str) → T | None[source]
-

Standard dictionary-style get() method, albeit with no default -parameter. Relies on the implementation of __getitem__.

-

Will return None if the key is not found.

-
-
Parameters:
-

key – the key to search for

-
-
Returns:
-

the value matching that key

-
-
-
- -
- -
-
-class mmif.serialize.model.MmifObject(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: object

-

Abstract superclass for MMIF related key-value pair objects.

-

Any MMIF object can be initialized as an empty placeholder or -an actual representation with a JSON formatted string or equivalent -dict object argument.

-

This superclass has four specially designed instance variables, and these -variable names cannot be used as attribute names for MMIF objects.

-
    -

  1. _unnamed_attributes: -Only can be either None or an empty dictionary. If it’s set to None, -it means the class won’t take any Additional Attributes in the JSON -schema sense. If it’s a dict, users can throw any k-v pairs to the -class, EXCEPT for the reserved two key names.

    2. -

  2. _attribute_classes: -This is a dict from a key name to a specific python class to use for -deserialize the value. Note that a key name in this dict does NOT -have to be a named attribute, but is recommended to be one.

    3. -

  3. _required_attributes: -This is a simple list of names of attributes that are required in the object. -When serialize, an object will skip its empty (e.g. zero-length, or None) -attributes unless they are in this list. Otherwise, the serialized JSON -string would have empty representations (e.g. "", []).

    4. -

  4. _exclude_from_diff: -This is a simple list of names of attributes that should be excluded from -the diff calculation in __eq__.

    5. -
-

# TODO (krim @ 8/17/20): this dict is however, a duplicate with the type hints in the class definition. -Maybe there is a better way to utilize type hints (e.g. getting them as a programmatically), but for now -developers should be careful to add types to hints as well as to this dict.

-

Also note that those special attributes MUST be set in the __init__() -before calling super method, otherwise deserialization will not work.

-

And also, a subclass that has one or more named attributes, it must -set those attributes in the __init__() before calling super method. When -serializing a MmifObject, all empty attributes will be ignored, so for -optional named attributes, you must leave the values empty (len == 0), but -NOT None. Any None-valued named attributes will cause issues with current -implementation.

-
-
Parameters:
-

mmif_obj – JSON string or dict to initialize an object. -If not given, an empty object will be initialized, sometimes with -an ID value automatically generated, based on its parent object.

-
-
-
-
-deserialize(mmif_json: str | dict) → None[source]
-

Takes a JSON-formatted string or a simple dict that’s json-loaded from -such a string as an input and populates object’s fields with the values -specified in the input.

-
-
Parameters:
-

mmif_json – JSON-formatted string or dict from such a string -that represents a MMIF object

-
-
-
- -
-
-disallow_additional_properties() → None[source]
-

Call this method in __init__() to prevent the insertion -of unnamed attributes after initialization.

-
- -
-
-static is_empty(obj) → bool[source]
-

return True if the obj is None or “emtpy”. The emptiness first defined as -having zero length. But for objects that lack __len__ method, we need -additional check.

-
- -
-
-reserved_names: Set[str] = {'_attribute_classes', '_exclude_from_diff', '_required_attributes', '_unnamed_attributes', 'reserved_names'}[source]
-
- -
-
-serialize(pretty: bool = False) → str[source]
-

Generates JSON representation of an object.

-
-
Parameters:
-

pretty – If True, returns string representation with indentation.

-
-
Returns:
-

JSON string of the object.

-
-
-
- -
-
-set_additional_property(key: str, value: Any) → None[source]
-

Method to set values in _unnamed_attributes.

-
-
Parameters:
-
    -

  • key – the attribute name

    • -

  • value – the desired value

    • -
-
-
Returns:
-

None

-
-
Raise:
-

AttributeError if additional properties are disallowed by disallow_additional_properties()

-
-
-
- -
- -
-
-class mmif.serialize.model.MmifObjectEncoder(*, skipkeys=False, ensure_ascii=True, check_circular=True, allow_nan=True, sort_keys=False, indent=None, separators=None, default=None)[source]
-

Bases: JSONEncoder

-

Encoder class to define behaviors of de-/serialization

-
-
-default(obj: MmifObject)[source]
-

Overrides default encoding behavior to prioritize MmifObject.serialize().

-
- -
- -
-
-

mmif.serialize.mmif module

-

The mmif module contains the classes used to represent a full MMIF -file as a live Python object.

-

See the specification docs and the JSON Schema file for more information.

-
-
-class mmif.serialize.mmif.Mmif(mmif_obj: bytes | str | dict | None = None, *, validate: bool = True)[source]
-

Bases: MmifObject

-

MmifObject that represents a full MMIF file.

-
-
Parameters:
-
    -

  • mmif_obj – the JSON data

    • -

  • validate – whether to validate the data against the MMIF JSON schema.

    • -
-
-
-
-
-add_document(document: Document, overwrite=False) → None[source]
-

Appends a Document object to the documents list.

-

Fails if there is already a document with the same ID in the MMIF object.

-
-
Parameters:
-
    -

  • document – the Document object to add

    • -

  • overwrite – if set to True, will overwrite -an existing view with the same ID

    • -
-
-
Returns:
-

None

-
-
-
- -
-
-add_view(view: View, overwrite=False) → None[source]
-

Appends a View object to the views list.

-

Fails if there is already a view with the same ID in the MMIF object.

-
-
Parameters:
-
    -

  • view – the Document object to add

    • -

  • overwrite – if set to True, will overwrite -an existing view with the same ID

    • -
-
-
Returns:
-

None

-
-
-
- -
-
-generate_capital_annotations()[source]
-

Automatically convert any “pending” temporary properties from -Document objects to Annotation objects . The generated Annotation -objects are then added to the last View in the views lists.

-

See https://github.com/clamsproject/mmif-python/issues/226 for rationale -behind this behavior and discussion.

-
- -
-
-get_alignments(at_type1: str | TypesBase, at_type2: str | TypesBase) → Dict[str, List[Annotation]][source]
-

Finds views where alignments between two given annotation types occurred.

-
-
Returns:
-

a dict that keyed by view IDs (str) and has lists of alignment Annotation objects as values.

-
-
-
- -
-
-get_all_views_contain(at_types: TypesBase | str | List[str | TypesBase]) → List[View][source]
-

Returns the list of all views in the MMIF if given types -are present in that view’s ‘contains’ metadata.

-
-
Parameters:
-

at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

-
-
Returns:
-

the list of views that contain the type

-
-
-
- -
-
-get_document_by_id(doc_id: str) → Document[source]
-

Finds a Document object with the given ID.

-
-
Parameters:
-

doc_id – the ID to search for

-
-
Returns:
-

a reference to the corresponding document, if it exists

-
-
Raises:
-

KeyError – if there is no corresponding document

-
-
-
- -
-
-get_document_location(m_type: DocumentTypes | str, path_only=False) → str | None[source]
-

Method to get the location of first document of given type.

-
-
Parameters:
-

m_type – the type to search for

-
-
Returns:
-

the value of the location field in the corresponding document

-
-
-
- -
-
-get_documents_by_app(app_id: str) → List[Document][source]
-

Method to get all documents object queries by its originated app name.

-
-
Parameters:
-

app_id – the app name to search for

-
-
Returns:
-

a list of documents matching the requested app name, or an empty list if the app not found

-
-
-
- -
-
-get_documents_by_property(prop_key: str, prop_value: str) → List[Document][source]
-

Method to retrieve documents by an arbitrary key-value pair in the document properties objects.

-
-
Parameters:
-
    -

  • prop_key – the metadata key to search for

    • -

  • prop_value – the metadata value to match

    • -
-
-
Returns:
-

a list of documents matching the requested metadata key-value pair

-
-
-
- -
-
-get_documents_by_type(doc_type: str | DocumentTypes) → List[Document][source]
-

Method to get all documents where the type matches a particular document type, which should be one of the CLAMS document types.

-
-
Parameters:
-

doc_type – the type of documents to search for, must be one of Document type defined in the CLAMS vocabulary.

-
-
Returns:
-

a list of documents matching the requested type, or an empty list if none found.

-
-
-
- -
-
-get_documents_in_view(vid: str | None = None) → List[Document][source]
-

Method to get all documents object queries by a view id.

-
-
Parameters:
-

vid – the source view ID to search for

-
-
Returns:
-

a list of documents matching the requested source view ID, or an empty list if the view not found

-
-
-
- -
-
-get_documents_locations(m_type: DocumentTypes | str, path_only=False) → List[str | None][source]
-

This method returns the file paths of documents of given type. -Only top-level documents have locations, so we only check them.

-
-
Parameters:
-

m_type – the type to search for

-
-
Returns:
-

a list of the values of the location fields in the corresponding documents

-
-
-
- -
-
-get_end(annotation: Annotation) → int | float[source]
-

An alias to get_anchor_point method with start=False.

-
- -
-
-get_start(annotation: Annotation) → int | float[source]
-

An alias to get_anchor_point method with start=True.

-
- -
-
-get_view_by_id(req_view_id: str) → View[source]
-

Finds a View object with the given ID.

-
-
Parameters:
-

req_view_id – the ID to search for

-
-
Returns:
-

a reference to the corresponding view, if it exists

-
-
Raises:
-

Exception – if there is no corresponding view

-
-
-
- -
-
-get_view_contains(at_types: TypesBase | str | List[str | TypesBase]) → View | None[source]
-

Returns the last view appended that contains the given -types in its ‘contains’ metadata.

-
-
Parameters:
-

at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

-
-
Returns:
-

the view, or None if the type is not found

-
-
-
- -
-
-get_views_contain(at_types: TypesBase | str | List[str | TypesBase]) → List[View][source]
-

An alias to get_all_views_contain method.

-
- -
-
-get_views_for_document(doc_id: str) → List[View][source]
-

Returns the list of all views that have annotations anchored on a particular document. -Note that when the document is inside a view (generated during the pipeline’s running), -doc_id must be prefixed with the view_id.

-
- -
-
-id_delimiter: ClassVar[str] = ':'[source]
-
- -
-
-new_view() → View[source]
-

Creates an empty view with a new ID and appends it to the views list.

-
-
Returns:
-

a reference to the new View object

-
-
-
- -
-
-new_view_id() → str[source]
-

Fetches an ID for a new view.

-
-
Returns:
-

the ID

-
-
-
- -
-
-sanitize()[source]
-

Sanitizes a Mmif object by running some safeguards. -Concretely, it performs the following before returning the JSON string.

-
    -

  1. validating output using built-in MMIF jsonschema

    2. -

  2. remove non-existing annotation types from contains metadata

    3. -
-
- -
-
-serialize(pretty: bool = False, sanitize: bool = False, autogenerate_capital_annotations=True) → str[source]
-

Serializes the MMIF object to a JSON string.

-
-
Parameters:
-
    -

  • sanitize – If True, performs some sanitization of before returning -the JSON string. See sanitize() for details.

    • -

  • autogenerate_capital_annotations – If True, automatically convert -any “pending” temporary properties from Document objects to -Annotation objects. See generate_capital_annotations() for -details.

    • -

  • pretty – If True, returns string representation with indentation.

    • -
-
-
Returns:
-

JSON string of the MMIF object.

-
-
-
- -
-
-static validate(json_str: bytes | str | dict) → None[source]
-

Validates a MMIF JSON object against the MMIF Schema. -Note that this method operates before processing by MmifObject._load_str, -so it expects @ and not _ for the JSON-LD @-keys.

-
-
Raises:
-

jsonschema.exceptions.ValidationError – if the input fails validation

-
-
Parameters:
-

json_str – a MMIF JSON dict or string

-
-
Returns:
-

None

-
-
-
- -
-
-view_prefix: ClassVar[str] = 'v_'[source]
-
- -
- -
-
-

mmif.serialize.view module

-

The view module contains the classes used to represent a MMIF view -as a live Python object.

-

In MMIF, views are created by apps in a pipeline that are annotating -data that was previously present in the MMIF file.

-
-
-class mmif.serialize.view.Contain(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: DataDict[str, str]

-

Contain object that represents the metadata of a single -annotation type in the contains metadata of a MMIF view.

-
- -
-
-class mmif.serialize.view.View(view_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-

View object that represents a single view in a MMIF file.

-

A view is identified by an ID, and contains certain metadata, -a list of annotations, and potentially a JSON-LD @context -IRI.

-

If view_obj is not provided, an empty View will be generated.

-
-
Parameters:
-

view_obj – the JSON data that defines the view

-
-
-
-
-add_annotation(annotation: Annotation, overwrite=False) → Annotation[source]
-

Adds an annotation to the current view.

-

Fails if there is already an annotation with the same ID -in the view, unless overwrite is set to True.

-
-
Parameters:
-
-
-
Raises:
-

KeyError – if overwrite is set to False and -an annotation with the same ID exists -in the view

-
-
Returns:
-

the same Annotation object passed in as annotation

-
-
-
- -
-
-add_document(document: Document, overwrite=False) → Annotation[source]
-

Appends a Document object to the annotations list.

-

Fails if there is already a document with the same ID in the annotations list.

-
-
Parameters:
-
    -

  • document – the Document object to add

    • -

  • overwrite – if set to True, will overwrite -an existing view with the same ID

    • -
-
-
Returns:
-

None

-
-
-
- -
-
-get_annotation_by_id(ann_id) → Annotation[source]
-
- -
-
-get_annotations(at_type: str | TypesBase | None = None, **properties) → Generator[Annotation, None, None][source]
-

Look for certain annotations in this view, specified by parameters

-
-
Parameters:
-
    -

  • at_type – @type of the annotations to look for. When this is None, any @type will match.

    • -

  • properties – properties of the annotations to look for. When given more than one property, all properties must match. Note that annotation type metadata are specified in the contains view metadata, not in individual annotation objects.

    • -
-
-
-
- -
-
-get_document_by_id(doc_id) → Document[source]
-
- -
-
-get_documents() → List[Document][source]
-
- -
-
-new_annotation(at_type: str | TypesBase, aid: str | None = None, overwrite=False, **properties) → Annotation[source]
-

Generates a new mmif.serialize.annotation.Annotation -object and adds it to the current view.

-

Fails if there is already an annotation with the same ID -in the view, unless overwrite is set to True.

-
-
Parameters:
-
    -

  • at_type – the desired @type of the annotation.

    • -

  • aid – the desired ID of the annotation, when not given, -the mmif SDK tries to automatically generate an ID based on -Annotation type and existing annotations in the view.

    • -

  • overwrite – if set to True, will overwrite an -existing annotation with the same ID.

    • -
-
-
Raises:
-

KeyError – if overwrite is set to False and -an annotation with the same ID exists -in the view.

-
-
Returns:
-

the generated mmif.serialize.annotation.Annotation

-
-
-
- -
-
-new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
-

Adds a new element to the contains metadata.

-
-
Parameters:
-
    -

  • at_type – the @type of the annotation type being added

    • -

  • contains_metadata – any metadata associated with the annotation type

    • -
-
-
Returns:
-

the generated Contain object

-
-
-
- -
-
-new_textdocument(text: str, lang: str = 'en', did: str | None = None, overwrite=False, **properties) → Document[source]
-

Generates a new mmif.serialize.annotation.Document -object, particularly typed as TextDocument and adds it to the current view.

-

Fails if there is already a text document with the same ID -in the view, unless overwrite is set to True.

-
-
Parameters:
-
    -

  • text – text content of the new document

    • -

  • lang – ISO 639-1 code of the language used in the new document

    • -

  • did – the desired ID of the document, when not given, -the mmif SDK tries to automatically generate an ID based on -Annotation type and existing documents in the view.

    • -

  • overwrite – if set to True, will overwrite an -existing document with the same ID

    • -
-
-
Raises:
-

KeyError – if overwrite is set to False and -an document with the same ID exists -in the view

-
-
Returns:
-

the generated mmif.serialize.annotation.Document

-
-
-
- -
-
-set_error(err_message: str, err_trace: str) → None[source]
-
- -
- -
-
-class mmif.serialize.view.ViewMetadata(viewmetadata_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-

ViewMetadata object that represents the metadata object within a MMIF view.

-
-
Parameters:
-

viewmetadata_obj – the JSON data that defines the metadata

-
-
-
-
-add_app_configuration(config_key: str, config_value: str | int | float | bool | None | List[str | int | float | bool | None]) → None[source]
-

Add a configuration key-value pair to the app_configuration dictionary.

-
- -
-
-add_contain(contain: Contain, at_type: str | TypesBase) → None[source]
-
- -
-
-add_parameter(param_key: str, param_value: str)[source]
-

Add a single runtime parameter to the view metadata. Note that parameter value must be a string.

-
- -
-
-add_parameters(**runtime_params: str)[source]
-

Add runtime parameters as a batch (dict) to the view metadata. Note that parameter values must be strings.

-
- -
-
-add_warnings(*warnings: Warning)[source]
-
- -
-
-emtpy_warnings()[source]
-
- -
-
-get_app_configuration(config_key: str) → str | int | float | bool | None | List[str | int | float | bool | None][source]
-

Get a configuration value from the app_configuration dictionary.

-
- -
-
-get_parameter(param_key: str) → str[source]
-

Get a runtime parameter from the view metadata.

-
- -
-
-new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
-

Adds a new element to the contains dictionary.

-
-
Parameters:
-
    -

  • at_type – the @type of the annotation type being added

    • -

  • contains_metadata – any metadata associated with the annotation type

    • -
-
-
Returns:
-

the generated Contain object

-
-
-
- -
-
-set_error(message: str, stack_trace: str)[source]
-
- -
- -
-
-

mmif.serialize.annotation module

-

The annotation module contains the classes used to represent a -MMIF annotation as a live Python object.

-

In MMIF, annotations are created by apps in a pipeline as a part -of a view. For documentation on how views are represented, see -mmif.serialize.view.

-
-
-class mmif.serialize.annotation.Annotation(anno_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-

MmifObject that represents an annotation in a MMIF view.

-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]]) → None[source]
-

Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

-
- -
-
-property at_type: TypesBase[source]
-
- -
-
-static check_prop_value_is_simple_enough(value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]]) → bool[source]
-
- -
-
-get(prop_name: str) → AnnotationProperties | str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]][source]
-

A special getter for Annotation properties. This is to allow for -directly accessing properties without having to go through the -properties object, or view-level annotation properties encoded in the -view.metadata.contains dict. Note that the regular props will take -the priority over the ephemeral props when there are conflicts.

-
- -
-
-get_property(prop_name: str) → AnnotationProperties | str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]][source]
-

A special getter for Annotation properties. This is to allow for -directly accessing properties without having to go through the -properties object, or view-level annotation properties encoded in the -view.metadata.contains dict. Note that the regular props will take -the priority over the ephemeral props when there are conflicts.

-
- -
-
-property id: str[source]
-
- -
-
-is_document()[source]
-
- -
-
-is_type(at_type: str | TypesBase) → bool[source]
-

Check if the @type of this object matches.

-
- -
-
-property parent: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.AnnotationProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject, MutableMapping[str, T]

-

AnnotationProperties object that represents the -properties object within a MMIF annotation.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
- -
-
-class mmif.serialize.annotation.Document(doc_obj: bytes | str | dict | None = None)[source]
-

Bases: Annotation

-

Document object that represents a single document in a MMIF file.

-

A document is identified by an ID, and contains certain attributes -and potentially contains the contents of the document itself, -metadata about how the document was created, and/or a list of -subdocuments grouped together logically.

-

If document_obj is not provided, an empty Document will be generated.

-
-
Parameters:
-

document_obj – the JSON data that defines the document

-
-
-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None]) → None[source]
-

Adds a property to the document’s properties.

-

Unlike the parent Annotation class, added properties of a -Document object can be lost during serialization unless it belongs -to somewhere in a Mmif object. This is because we want to keep -Document object as “read-only” as possible. Thus, if you want to add -a property to a Document object,

-
    -

  • add the document to a Mmif object (either in the documents list or -in a view from the views list), or

    • -

  • directly write to Document.properties instead of using this method -(which is not recommended).

    • -
-

With the former method, the SDK will record the added property as a -Annotation annotation object, separate from the original Document -object. See Mmif.generate_capital_annotations() for more.

-

A few notes to keep in mind:

-
    -

  1. You can’t overwrite an existing property of a Document object.

    2. -

  2. A MMIF can have multiple Annotation objects with the same -property name but different values. When this happens, the SDK will -only keep the latest value (in order of appearances in views list) of -the property, effectively overwriting the previous values.

    3. -
-
- -
-
-get(prop_name)[source]
-

A special getter for Document properties. The major difference from -the super class’s Annotation.get() method is that Document -class has one more set of “pending” properties, that are added after -the Document object is created and will be serialized as a separate -Annotation object of which @type = Annotation. The -pending properties will take the priority over the regular properties -when there are conflicts.

-
- -
-
-get_property(prop_name)[source]
-

A special getter for Document properties. The major difference from -the super class’s Annotation.get() method is that Document -class has one more set of “pending” properties, that are added after -the Document object is created and will be serialized as a separate -Annotation object of which @type = Annotation. The -pending properties will take the priority over the regular properties -when there are conflicts.

-
- -
-
-property location: str | None[source]
-

location property must be a legitimate URI. That is, should the document be a local file -then the file:// scheme must be used. -Returns None when no location is set.

-
- -
-
-location_address() → str | None[source]
-

Retrieves the full address from the document location URI. -Returns None when no location is set.

-
- -
-
-location_path(nonexist_ok=True) → str | None[source]
-

Retrieves a path that’s resolved to a pathname in the local file system. -To obtain the original value of the “path” part in the location string -(before resolving), use properties.location_path_literal method. -Returns None when no location is set.

-
-
Parameters:
-

nonexist_ok – if False, raise FileNotFoundError when the resolved path doesn’t exist

-
-
-
- -
-
-location_scheme() → str | None[source]
-

Retrieves URI scheme of the document location. -Returns None when no location is set.

-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.DocumentProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: AnnotationProperties

-

DocumentProperties object that represents the -properties object within a MMIF document.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
-
-property location: str | None[source]
-

location property must be a legitimate URI. That is, should the document be a local file -then the file:// scheme must be used. -Returns None when no location is set.

-
- -
-
-location_address() → str | None[source]
-

Retrieves the full address from the document location URI. -Returns None when no location is set.

-
- -
-
-location_path() → str | None[source]
-
- -
-
-location_path_literal() → str | None[source]
-

Retrieves only path name of the document location (hostname is ignored). -Returns None when no location is set.

-
- -
-
-location_path_resolved(nonexist_ok=True) → str | None[source]
-

Retrieves only path name of the document location (hostname is ignored), -and then try to resolve the path name in the local file system. -This method should be used when the document scheme is file or empty. -For other schemes, users should install mmif-locdoc-<scheme> plugin.

-

Returns None when no location is set. -Raise ValueError when no code found to resolve the given location scheme.

-
- -
-
-location_scheme() → str | None[source]
-

Retrieves URI scheme of the document location. -Returns None when no location is set.

-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.Text(text_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-
-
-property lang: str[source]
-
- -
-
-property value: str[source]
-
- -
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- - - \ No newline at end of file diff --git a/docs/1.0.11/autodoc/mmif.utils.html b/docs/1.0.11/autodoc/mmif.utils.html deleted file mode 100644 index 764318c3..00000000 --- a/docs/1.0.11/autodoc/mmif.utils.html +++ /dev/null @@ -1,578 +0,0 @@ - - - - - - - - - mmif.utils module — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
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mmif.utils module

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mmif.utils.video_document_helper module

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-mmif.utils.video_document_helper.capture(video_document: Document)[source]
-

Captures a video file using OpenCV and adds fps, frame count, and duration as properties to the document.

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Parameters:
-

video_document – Document instance that holds a video document ("@type": ".../VideoDocument/...")

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Returns:
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OpenCV VideoCapture object

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-mmif.utils.video_document_helper.convert_timeframe(mmif: Mmif, time_frame: Annotation, out_unit: str) → Tuple[int | float | str, int | float | str][source]
-

Converts start and end points in a TimeFrame annotation a different time unit.

-
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Parameters:
-
    -

  • mmif – Mmif instance

    • -

  • time_frame – Annotation instance that holds a time interval annotation ("@type": ".../TimeFrame/...")

    • -

  • out_unit – time unit to which the point is converted

    • -
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Returns:
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tuple of frame numbers (integer) or seconds/milliseconds (float) of input start and end

-
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- -
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-mmif.utils.video_document_helper.convert_timepoint(mmif: Mmif, timepoint: Annotation, out_unit: str) → int | float | str[source]
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Converts a time point included in an annotation to a different time unit. -The input annotation must have timePoint property.

-
-
Parameters:
-
    -

  • mmif – input MMIF to obtain fps and input timeunit

    • -

  • timepoint – Annotation instance with timePoint property

    • -

  • out_unit – time unit to which the point is converted (frames, seconds, milliseconds)

    • -
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Returns:
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frame number (integer) or second/millisecond (float) of input timepoint

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- -
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-mmif.utils.video_document_helper.extract_frames_as_images(video_document: Document, framenums: List[int], as_PIL: bool = False)[source]
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Extracts frames from a video document as a list of numpy.ndarray. -Use with sample_frames() function to get the list of frame numbers first.

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Parameters:
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    -

  • video_document – Document instance that holds a video document ("@type": ".../VideoDocument/...")

    • -

  • framenums – integers representing the frame numbers to extract

    • -

  • as_PIL – return PIL.Image.Image instead of ndarray

    • -
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Returns:
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frames as a list of ndarray or Image

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-mmif.utils.video_document_helper.extract_mid_frame(mmif: Mmif, time_frame: Annotation, as_PIL: bool = False)[source]
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Extracts the middle frame of a time interval annotation as a numpy ndarray.

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Parameters:
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    -

  • mmif – Mmif instance

    • -

  • time_frame – Annotation instance that holds a time interval annotation ("@type": ".../TimeFrame/...")

    • -

  • as_PIL – return Image instead of ndarray

    • -
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Returns:
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frame as a numpy.ndarray or PIL.Image.Image

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-mmif.utils.video_document_helper.framenum_to_millisecond(video_doc: Document, frame: int)[source]
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Converts a frame number to a millisecond value.

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-mmif.utils.video_document_helper.framenum_to_second(video_doc: Document, frame: int)[source]
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Converts a frame number to a second value.

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-mmif.utils.video_document_helper.get_annotation_property(mmif, annotation, prop_name)[source]
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-

Deprecated since version 1.0.8: Use mmif.serialize.annotation.Annotation.get_property() method instead.

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Get a property value from an annotation. If the property is not found in the annotation, it will look up the metadata of the annotation’s parent view and return the value from there. -xisting

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-mmif.utils.video_document_helper.get_framerate(video_document: Document) → float[source]
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Gets the frame rate of a video document. First by checking the fps property of the document, then by capturing the video.

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Parameters:
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video_document – Document instance that holds a video document ("@type": ".../VideoDocument/...")

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Returns:
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frames per second as a float, rounded to 2 decimal places

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-mmif.utils.video_document_helper.get_mid_framenum(mmif: Mmif, time_frame: Annotation)[source]
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Calculates the middle frame number of a time interval annotation.

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Parameters:
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    -

  • mmif – Mmif instance

    • -

  • time_frame – Annotation instance that holds a time interval annotation ("@type": ".../TimeFrame/...")

    • -
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Returns:
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middle frame number as an integer

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-mmif.utils.video_document_helper.millisecond_to_framenum(video_doc: Document, millisecond: float) → int[source]
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Converts a millisecond value to a frame number.

-
- -
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-mmif.utils.video_document_helper.sample_frames(start_frame: int, end_frame: int, sample_ratio: int = 1) → List[int][source]
-

Helper function to sample frames from a time interval. -Can also be used as a “cutoff” function when used with start_frame==0 and sample_ratio==1.

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-
Parameters:
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    -

  • start_frame – start frame of the interval

    • -

  • end_frame – end frame of the interval

    • -

  • sample_ratio – sample ratio (or step) to configure how often to take a frame, default is 1, meaning all consecutive frames are sampled

    • -
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-mmif.utils.video_document_helper.second_to_framenum(video_doc: Document, second) → int[source]
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Converts a second value to a frame number.

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- -
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-

mmif.utils.sequence_helper module

-

This module provides helpers for handling sequence labeling. Specifically, it provides

-
    -

  • a generalized label re-mapper for “post-binning” of labels

    • -

  • conversion from a list of CLAMS annotations (with classification props) into a list of reals (scores by labels), can be combined with the label re-mapper mentioned above

    • -

  • mmif.utils.sequence_helper.smooth_outlying_short_intervals(): a simple smoothing algorithm by trimming “short” outlier sequences

    • -
-

However, it DOES NOT provide

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    -

  • direct conversion between CLAMS annotations. For example, it does not directly handle stitching of TimePoint into TimeFrames.

    • -

  • support for multi-class scenario, such as handling of _competing_ subsequence or overlapping labels.

    • -
-

Some functions can use optional external libraries (e.g., numpy) for better performance. -Hence, if you see a warning about missing optional packages, you might want to install them by running pip install mmif-python[seq].

-
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-mmif.utils.sequence_helper.build_label_remapper(src_labels: List[str], dst_labels: Dict[str, str | int | float | bool | None]) → Dict[str, str | int | float | bool | None][source]
-

Build a label remapper dictionary from source and destination labels.

-
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Parameters:
-
    -

  • src_labels – a list of all labels on the source side

    • -

  • dst_labels – a dict from source labels to destination labels. -Source labels not in this dict will be remapped to a negative label (-).

    • -
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Returns:
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a dict that exhaustively maps source labels to destination labels

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-mmif.utils.sequence_helper.build_score_lists(classifications: ~typing.List[~typing.Dict], label_remapper: ~typing.Dict, score_remap_op: ~typing.Callable[[...], float] = <built-in function max>) → Tuple[Dict[str, int], numpy.ndarray][source]
-

Build lists of scores indexed by the label names.

-
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Parameters:
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    -

  • classifications – list of dictionaries of classification results, taken from input annotation objects

    • -

  • label_remapper – a dictionary that maps source label names to destination label names (formerly “postbin”)

    • -

  • score_remap_op – a function to remap the scores from multiple source labels binned to a destination label -common choices are max, min, or sum

    • -
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Returns:
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    -

  1. a dictionary that maps label names to their index in the score list

    2. -

  2. 2-d numpy array of scores, of which rows are indexed by label map dict (first return value)

    3. -
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-mmif.utils.sequence_helper.smooth_outlying_short_intervals(scores: List[float], min_spseq_size: int, min_snseq_size: int, min_score: float = 0.5)[source]
-

Given a list of scores, a score threshold, and smoothing parameters, -identify the intervals of “positive” scores by “trimming” the short -positive sequences (“spseq”) and short negative sequences (“snseq”). To -decide the positivity, first step is binarization of the scores by the -min_score threshold. Given Sr as “raw” input real-number scores -list, and min_score=0.5,

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-
Sr: [0.3, 0.6, 0.2, 0.8, 0.2, 0.9, 0.8, 0.5, 0.1, 0.5, 0.8, 0.3, 1.0, 0.7, 0.5, 0.5, 0.5, 0.8, 0.3, 0.6]
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the binarization is done by simply comparing each score to the -threshold to get S list of binary scores

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1.0 :                                     |                      
-0.9 :                |                    |                      
-0.8 :          |     |  |           |     |              |       
-0.7 :          |     |  |           |     |  |           |       
-0.6 :    |     |     |  |           |     |  |           |     | 
-0.5 :----+-----+-----+--+--+-----+--+-----+--+--+--+--+--+-----+-
-0.4 :    |     |     |  |  |     |  |     |  |  |  |  |  |     | 
-0.3 : |  |     |     |  |  |     |  |  |  |  |  |  |  |  |  |  | 
-0.2 : |  |  |  |  |  |  |  |     |  |  |  |  |  |  |  |  |  |  | 
-0.1 : |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | 
-0.0 +------------------------------------------------------------
-raw :.3 .6 .2 .8 .2 .9 .8 .5 .1 .5 .8 .3 1. .7 .5 .5 .5 .8 .3 .6
- S  : 0  1  0  1  0  1  1  0  0  0  1  0  1  1  0  1  1  1  0  1 
-
-
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Note that the size of a positive or negative sequence can be as small -as 1.

-

Then, here are examples of smoothing a list of binary scores into -intervals, by trimming “very short” (under thresholds) sequences of -positive or negative:

-
-

Note

-

legends:

-
    -

  • t is unit index (e.g. time index)

    • -

  • S is the list of binary scores (zeros and ones)

    • -

  • I is the list of intervals after smoothing

    • -
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    -

  1. with params min_spseq_size==1, min_snseq_size==4

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    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1]
-I: [0, 1--1--1--1--1--1--1--1--1--1--1--1, 0--0--0--0--0--0, 1]
-
    -
    -

    Explanation: min_snseq_size is used to smooth short sequences -of negative predictions. In this, zeros from t[7:10] are smoothed -into “one” I, while zeros from t[13:19] are kept as “zero” I. Note -that the “short” snseqs at the either ends (t[0:1]) are never -smoothed.

    -
    -
    2. -

  2. with params min_spseq_size==4, min_snseq_size==2

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1]
-I: [0, 1--1--1--1--1--1, 0--0--0--0--0--0--0--0--0--0--0--0--0]
-
    -
    -

    Explanation: min_spseq_size is used to smooth short sequences -of positive predictions. In this example, the spseqs of ones from -both t[10:13] and t[19:20] are smoothed. Note that the “short” -spseqs at the either ends (t[19:20]) are always smoothed.

    -
    -
    3. -

  3. with params min_spseq_size==4, min_snseq_size==4

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1]
-I: [0, 1--1--1--1--1--1--1--1--1--1--1--1--0--0--0--0--0--0--0]
-
    -
    -

    Explanation: When two threshold parameters are working together, -the algorithm will prioritize the smoothing of the snseqs over the -smoothing of the spseqs. Thus, in this example, the snseq t[7:10] -gets first smoothed “up” before the spseq t[10:13] is smoothed -“down”, resulting in a long final I.

    -
    -
    4. -

  4. with params min_spseq_size==4, min_snseq_size==4

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [1, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 1, 1]
-I: [1--1--1--1--1--1--1, 0--0--0--0, 1--1--1--1--1--1--1--1--1]
-
    -
    -

    Explanation: Since smoothing of snseqs is prioritized, short spseqs -at the beginning or the end can be kept.

    -
    -
    5. -

  5. with params min_spseq_size==1, min_snseq_size==1

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 1, 1]
-I: [0--0--0, 1--1--1--1, 0--0--0--0, 1--1--1--1, 0--0--0, 1--1]
-
    -
    -

    Explanation: When both width thresholds are set to 1, the algorithm -works essentially in the “stitching” only mode.

    -
    -
    6. -
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Parameters:
-
    -

  • scores – SORTED list of scores to be smoothed. The score list -is assumed to be “exhaust” the entire time or space of -the underlying document segment. -(Sorted by the start, and then by the end of anchors)

    • -

  • min_score – minimum threshold to use to discard -low-scored units (strictly less than)

    • -

  • min_spseq_size – minimum size of a positive sequence not to be -smoothed (greater or equal to)

    • -

  • min_snseq_size – minimum size of a negative sequence not to be -smoothed (greater or equal to)

    • -
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Returns:
-

list of tuples of start(inclusive)/end(exclusive) indices -of the “positive” sequences. Negative sequences (regardless of -their size) are not included in the output.

-
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- -
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-mmif.utils.sequence_helper.validate_labelset(annotations: Iterable[Annotation]) → List[str][source]
-

Simple check for a list of annotations to see if they have the same label set.

-
-
Raise:
-

AttributeError if an element in the input list doesn’t have the labelset property

-
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Raise:
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ValueError if different labelset values are found

-
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Returns:
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a list of the common labelset value (list of label names)

-
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- - - \ No newline at end of file diff --git a/docs/1.0.11/autodoc/mmif.vocabulary.html b/docs/1.0.11/autodoc/mmif.vocabulary.html deleted file mode 100644 index e9fd9c60..00000000 --- a/docs/1.0.11/autodoc/mmif.vocabulary.html +++ /dev/null @@ -1,319 +0,0 @@ - - - - - - - - - mmif.vocabulary module — mmif-python documentation - - - - - - - - - - - - - - - - - -
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mmif.vocabulary module

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mmif.vocabulary.annotation_types module

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-class mmif.vocabulary.annotation_types.AnnotationTypes(type_uri, fuzzymode=True)[source]
-

Bases: AnnotationTypesBase

-

This class contains the CLAMS annotation types -defined in the spec version 1.1.0 as class variables.

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-Alignment = http://mmif.clams.ai/vocabulary/Alignment/v1[source]
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-Annotation = http://mmif.clams.ai/vocabulary/Annotation/v6[source]
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-BoundingBox = http://mmif.clams.ai/vocabulary/BoundingBox/v5[source]
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-Chapter = http://mmif.clams.ai/vocabulary/Chapter/v6[source]
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-Interval = http://mmif.clams.ai/vocabulary/Interval/v5[source]
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-NamedEntity = http://mmif.clams.ai/vocabulary/NamedEntity/v1[source]
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-NounChunk = http://mmif.clams.ai/vocabulary/NounChunk/v1[source]
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-Paragraph = http://mmif.clams.ai/vocabulary/Paragraph/v1[source]
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-Polygon = http://mmif.clams.ai/vocabulary/Polygon/v5[source]
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-Region = http://mmif.clams.ai/vocabulary/Region/v5[source]
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-Relation = http://mmif.clams.ai/vocabulary/Relation/v5[source]
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-Sentence = http://mmif.clams.ai/vocabulary/Sentence/v1[source]
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-Span = http://mmif.clams.ai/vocabulary/Span/v5[source]
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-TimeFrame = http://mmif.clams.ai/vocabulary/TimeFrame/v6[source]
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-TimePoint = http://mmif.clams.ai/vocabulary/TimePoint/v5[source]
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-Token = http://mmif.clams.ai/vocabulary/Token/v1[source]
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-VerbChunk = http://mmif.clams.ai/vocabulary/VerbChunk/v1[source]
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-VideoObject = http://mmif.clams.ai/vocabulary/VideoObject/v5[source]
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mmif.vocabulary.document_types module

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-class mmif.vocabulary.document_types.DocumentTypes(type_uri, fuzzymode=True)[source]
-

Bases: DocumentTypesBase

-

This class contains the CLAMS document types -defined in the spec version 1.1.0 as class variables.

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-AudioDocument = http://mmif.clams.ai/vocabulary/AudioDocument/v1[source]
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-Document = http://mmif.clams.ai/vocabulary/Document/v1[source]
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-ImageDocument = http://mmif.clams.ai/vocabulary/ImageDocument/v1[source]
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-TextDocument = http://mmif.clams.ai/vocabulary/TextDocument/v1[source]
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-VideoDocument = http://mmif.clams.ai/vocabulary/VideoDocument/v1[source]
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- - - \ No newline at end of file diff --git a/docs/1.0.11/autodoc/mmif_docloc_http.html b/docs/1.0.11/autodoc/mmif_docloc_http.html deleted file mode 100644 index 14adf769..00000000 --- a/docs/1.0.11/autodoc/mmif_docloc_http.html +++ /dev/null @@ -1,179 +0,0 @@ - - - - - - - - - mmif_docloc_http package — mmif-python documentation - - - - - - - - - - - - - - - - -
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- -
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mmif_docloc_http package

-

MMIF document location helper module for http and https schemes. -If you want to write your own docloc scheme handler, please use the source code of this module as a reference. -See this plug-in section for more information.

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-mmif_docloc_http.resolve(docloc)[source]
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MMIF consumer

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A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the appliance documentation to learn more about the appliance.

-

MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance.

-
    -

  1. The code must be hosted on a public git repository (e.g. Github, Gitlab, …)

    2. -

  2. Must listen to 5000 port.

    3. -

  3. Must expose /display route .

    4. -

  4. /display router should response to GET requests.

    5. -

  5. In the GET request, a public URL of the input MMIF file is passed via file URL parameter.

    6. -

  6. On the codebase root, there must be a Dockerfile that can build a docker image that runs the web app.

    7. -
-

We provide an example consumer at https://github.com/clamsproject/mmif-visualizer.

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  • Welcome to mmif-python’s documentation!
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Welcome to mmif-python’s documentation!

-
-

MultiMedia Interchange Format

-

MMIF is a JSON(-LD)-based data format designed for transferring annotation data between computational analysis applications in CLAMS project.

-
-
-

mmif-python

-

mmif-python is a Python implementation of the MMIF data format. -mmif-python provides various helper classes and functions to handle MMIF JSON in Python, -including ;

-
    -

  1. de-/serialization of MMIF internal data structures to/from JSON

    2. -

  2. validation of MMIF JSON

    3. -

  3. handling of CLAMS vocabulary types

    4. -

  4. navigation of MMIF object via various “search” methods (e.g. mmif.get_all_views_contain(vocab_type)))

    5. -
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For more …

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Contents

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API documentation:

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Indices and tables

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  • Getting Started
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Getting Started

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Overview

-

MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for reproducibility, transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF website. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects.

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Prerequisites

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    -

  • Python: the latest mmif-python requires Python 3.8 or newer. We have no plan to support Python 2.7.

    • -
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Installation

-

Package mmif-python is distributed via the official PyPI. Users are supposed to pip-install to get latest release.

-
pip install mmif-python
-
-
-

This will install a package mmif to local python.

-

The MMIF format and specification is evolving over time, and mmif-python package will be updated along with the changes in MMIF format.

-
-

Note

-

MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and mmif-python versions, please take time to read our decision on the subject here. If you need to know which python SDK supports which specification version, see Target MMIF Versions page.

-
-
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MMIF Serialization

-

mmif.serialize.mmif.Mmif represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of mmif.serialize.model.MmifObject, including the mmif.serialize.mmif.Mmif. To start with an existing MMIF str, simple initiate a new Mmif object with the file.

-
import mmif
-from mmif import Mmif
-
-mmif_str = """{
-"metadata": {
-  "mmif": "http://mmif.clams.ai/1.0.0"
-},
-"documents": [
-  {
-    "@type": "http://mmif.clams.ai/vocabulary/VideoDocument/v1",
-    "properties": {
-      "id": "m1",
-      "mime": "video/mp4",
-      "location": "file:///var/archive/video-0012.mp4"
-    }
-  },
-  {
-    "@type": "http://mmif.clams.ai/vocabulary/TextDocument/v1",
-    "properties": {
-      "id": "m2",
-      "mime": "text/plain",
-      "location": "file:///var/archive/video-0012-transcript.txt"
-    }
-  }
-],
-"views": []}"""
-mmif_obj = Mmif(mmif_str)
-
-
-

Few notes;

-
    -

  1. MMIF does not carry the primary source files in it.

    2. -

  2. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version mmif-python implementation of the MMIF might not be able to load an unsupported version of MMIF string.

    3. -
-

When serializing back to str, call mmif.serialize.model.MmifObject.serialize() on the object.

-

To get subcomponents, you can use various getters implemented in subclasses. For example;

-
from mmif.vocabulary.document_types import DocumentTypes
-
-for video in mmif_obj.Mmif.get_documents_by_type(DocumentTypes.VideoDocument):
-  with open(video.location_path(), 'b') as in_video:
-    # do something with the video file
-
-
-

For a full list of available helper methods, please refer to the API documentation.

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mmif package

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mmif_docloc_http package

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- - - \ No newline at end of file diff --git a/docs/1.0.11/objects.inv b/docs/1.0.11/objects.inv deleted file mode 100644 index da81aaef..00000000 Binary files a/docs/1.0.11/objects.inv and /dev/null differ diff --git a/docs/1.0.11/plugins.html b/docs/1.0.11/plugins.html deleted file mode 100644 index 9fbcd97e..00000000 --- a/docs/1.0.11/plugins.html +++ /dev/null @@ -1,234 +0,0 @@ - - - - - - - - - Developing plugins for MMIF Python SDK — mmif-python documentation - - - - - - - - - - - - - - - - - -
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Developing plugins for MMIF Python SDK

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Overview

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As MMIF JSON files can carry information about media document files without actually carrying file contents, file accessing modules in mmif Python package (distributed as mmif-python on PyPI) are designed to be lightweight and flexible so that it can work with additional “plugin” Python packages that can handle concrete file access.

-

This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF website. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects.

-

Developer can write simple plugins that can provide additional functionalities to mmif-python. For example, mmif-python does not provide any file access functionality beyond a local file system (with file scheme), but it can be extended with a plugin that can handle file access over different protocols (e.g. http, s3, ftp, etc).

-

This document contains information about how to write plugins for mmif-python.

-
-

Document Location Scheme Plugins

-

mmif.serialize.annotation.Document class has various methods to access parts of location property of the document. The location is in URI/IRI format (SCHEME://HOSTNAME/PATH, in a nutshell) and it has to be resolved to a local file for CLAMS Apps to process the local file to analyze and extract information about the media and its contents. The core mmif-python distribution only provides a default implementation that can handle file scheme URIs.

-

To add a document location handler plugin, you need to implement a Python “package” (do not confuse with PYPI distribution), that meets these requirements;

-
    -

  1. the package must be named mmif_docloc_<SCHEME>. For example, to implement a handler for s3 scheme, the package name must be mmif_docloc_s3. The prefix is important as it’s used in the plugin discovery process from the core mmif-python modules.

    2. -

  2. the top module of the package must have a function named resolve. The function must take a single argument, which is a str of the document location URI. The function must return a str of the local file path. For example, if the document location is s3://mybucket/myfile.mp4, a Python user should be able to to something like this;

    3. -
-
import mmif_docloc_s3
-resolved = mmif_docloc_s3.resolve('s3://mybucket/myfile.mp4')
-# then resolved must be a local file path that can be used to open the file
-
-
-

Here’s a minimal example codebase that you refer to when you develop a docloc plugin.

-

(However, before you start writing your own plugin for a specific URI scheme, checking if there’s already a PyPI distribution for the scheme might be a good idea.)

-
$ tree .
-.
-├── mmif_docloc_dummy
-│   └── __init__.py
-├── pyproject.toml
-└── setup.cfg
-
- $ cat pyproject.toml
-[build-system]
-requires = ["setuptools"]
-build-backend = "setuptools.build_meta"
-
-$ cat setup.cfg
-[metadata]
-name = mmif_docloc_dummy  # this name is IMPORTANT
-version = 0.0.1
-description = a plugin to mmif-pyhon to handle `dummy` location scheme
-
-
-

And the plugin code.

-
# mmif_docloc_dummy/__init__.py
-doc_types = {'video': 'mp4'}
-
-def resolve(docloc):
-    scheme = 'dummy'
-    if docloc.startswith(f'{scheme}://'):
-        doc_id, doc_type = docloc.split('.')
-        return f'/path/to/{doc_id}.{doc_types[doc_type]}'
-    else:
-        raise ValueError(f'cannot handle document location scheme: {docloc}')
-
-
-
-
-

Bulit-in Document Location Scheme Plugins

-

At the moment, mmif-python PyPI distribution ships a built-in docloc plugin that support both http and https schemes. -Take a look at mmif_docloc_http module for details.

-
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- - Other Versions - v: 1.0.11 - - -
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Python Module Index

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- m
- mmif -
    - mmif.serialize.annotation -
    - mmif.serialize.mmif -
    - mmif.serialize.model -
    - mmif.serialize.view -
    - mmif.utils.sequence_helper -
    - mmif.utils.video_document_helper -
    - mmif.vocabulary.annotation_types -
    - mmif.vocabulary.document_types -
- mmif_docloc_http -
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0.3.3
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0.4.0
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0.4.1
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0.4.3
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0.4.4
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0.4.6
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0.4.7
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0.4.8
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0.5.0
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0.5.1
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0.5.2
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1.0.0
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1.0.1
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1.0.10
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1.0.11
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1.0.12
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1.0.13
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1.0.14
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1.0.15
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1.0.16
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1.0.17
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1.0.18
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1.0.19
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1.0.2
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1.0.3
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1.0.4
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1.0.5
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1.0.6
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1.1.0
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1, "retriev": 0, "return": [0, 1, 8], "root": 4, "round": 1, "rout": 4, "router": 4, "row": 1, "run": [0, 1, 4], "runtim": 0, "runtime_param": 0, "s3": 8, "safeguard": 0, "same": [0, 1], "sampl": 1, "sample_fram": [1, 7], "sample_ratio": 1, "sanit": [0, 7], "scenario": 1, "schema": [0, 5], "scheme": [0, 3], "score": 1, "score_remap_op": 1, "sdk": [0, 5, 6, 9], "search": [0, 5], "second": 1, "second_to_framenum": [1, 7], "section": 3, "see": [0, 1, 3, 6], "segment": 1, "sens": 0, "sentenc": [2, 7], "separ": 0, "seq": 1, "sequenc": 1, "sequence_help": 7, "serial": [1, 5, 7, 8], "set": [0, 1], "set_additional_properti": [0, 7], "set_error": [0, 7], "setup": 8, "setuptool": 8, "ship": 8, "short": 1, "should": [0, 4, 8], "side": 1, "simpl": [0, 1, 6, 8], "simpli": 1, "sinc": 1, "singl": [0, 8], "size": 1, "skip": 0, "skipkei": 0, "small": 1, "smooth": 1, "smooth_outlying_short_interv": [1, 7], "snseq": 1, "so": [0, 8], "some": [0, 1], "someth": [6, 8], "sometim": 0, "somewher": 0, "sort": 1, "sort_kei": 0, "sourc": [0, 1, 2, 3, 6, 8], "space": 1, "span": [2, 7], "spec": 2, "special": 0, "specif": [0, 1, 5, 6, 8], "specifi": 0, "split": 8, "spseq": 1, "sr": 1, "src_label": 1, "stack_trac": 0, "standard": 0, "start": [0, 1, 5, 8], "start_fram": 1, "startswith": 8, "static": 0, "step": 1, "stitch": 1, "str": [0, 1, 6, 8], "strictli": 1, "string": [0, 6], "structur": 5, "style": 0, "subclass": [0, 6], "subcompon": 6, "subdocu": 0, "subject": 6, "subsequ": 1, "sum": 1, "super": 0, "superclass": 0, "support": [1, 6, 8], "suppos": 6, "system": [0, 8], "t": [0, 1], "take": [0, 1, 6, 8], "taken": 1, "target": [5, 6], "temporari": 0, "text": [0, 6, 7], "text_languag": [0, 7], "text_obj": 0, "text_valu": [0, 7], "textdocu": [0, 2, 6, 7], "than": [0, 1], "thei": [0, 1], "them": [0, 1], "thi": [0, 1, 2, 3, 4, 6, 8, 9], "those": 0, "threshold": 1, "through": 0, "throw": 0, "thu": [0, 1], "time": [1, 6], "time_fram": 1, "timefram": [1, 2, 7], "timepoint": [1, 2, 7], "timeunit": 1, "todo": 0, "togeth": [0, 1], "token": [2, 7], "toml": 8, "top": [0, 6, 8], "transcript": 6, "transfer": 5, "transpar": 6, "tree": 8, "tri": 0, "trim": 1, "true": [0, 2], "try": 0, "tupl": 1, "turn": 4, "two": [0, 1], "txt": 6, "type": [0, 1, 2, 5, 6], "type_uri": 2, "typesbas": 0, "under": 1, "underli": 1, "union": 0, "unit": 1, "unless": 0, "unlik": 0, "unnam": 0, "unsupport": 6, "up": 1, "updat": [0, 6, 7], "uri": [0, 8], "url": 4, "us": [0, 1, 3, 6, 8], "user": [0, 6, 8], "util": [0, 5, 7], "v": 0, "v1": [2, 6], "v5": 2, "v6": 2, "v_": 0, "valid": [0, 5, 7], "validate_labelset": [1, 7], "validationerror": 0, "valu": [0, 1, 7], "valueerror": [0, 1, 8], "var": 6, "variabl": [0, 2], "variou": [0, 5, 6, 8], "verbchunk": [2, 7], "veri": 1, "version": [1, 2, 5, 6, 8], "via": [4, 5, 6], "vid": 0, "video": [1, 6, 8], "video_doc": 1, "video_docu": 1, "video_document_help": 7, "videocaptur": 1, "videodocu": [1, 2, 6, 7], "videoobject": [2, 7], "view": [1, 6, 7], "view_id": 0, "view_obj": 0, "view_prefix": [0, 7], "viewmetadata": [0, 7], "viewmetadata_obj": 0, "visit": [6, 8], "visual": 4, "vocab_typ": 5, "vocabulari": [0, 5, 6, 7], "wa": 0, "wai": 0, "want": [0, 1, 3], "warn": [0, 1], "we": [0, 4, 6], "web": 4, "websit": [6, 8], "well": [0, 6, 8], "when": [0, 1, 6, 8], "where": 0, "whether": 0, "which": [0, 1, 6, 8], "while": 1, "width": 1, "within": 0, "without": [0, 8], "won": 0, "work": [0, 1, 8], "workflow": 6, "would": 0, "write": [0, 3, 8], "xist": 1, "you": [0, 1, 3, 6, 8], "your": [3, 8], "zero": [0, 1]}, "titles": ["mmif.serialize module", "mmif.utils module", "mmif.vocabulary module", "mmif_docloc_http package", "MMIF consumer", "Welcome to mmif-python\u2019s documentation!", "Getting Started", "mmif package", "Developing plugins for MMIF Python SDK", "Target MMIF Versions"], "titleterms": {"": 5, "For": 5, "annot": 0, "annotation_typ": 2, "api": 5, "bulit": 8, "consum": 4, "content": 5, "develop": 8, "document": [5, 8], "document_typ": 2, "format": 5, "get": 6, "indic": 5, "instal": 6, "interchang": 5, "locat": 8, "mmif": [0, 1, 2, 4, 5, 6, 7, 8, 9], "mmif_docloc_http": [3, 7], "model": 0, "modul": [0, 1, 2], "more": 5, "multimedia": 5, "overview": [6, 8], "packag": [3, 7], "plugin": 8, "prerequisit": 6, "python": [5, 8], "scheme": 8, "sdk": 8, "sequence_help": 1, "serial": [0, 6], "specif": 9, "start": 6, "tabl": 5, "target": 9, "util": 1, "version": 9, "video_document_help": 1, "view": 0, "vocabulari": 2, "welcom": 5}}) \ No newline at end of file diff --git a/docs/1.0.11/target-versions.html b/docs/1.0.11/target-versions.html deleted file mode 100644 index 6e6b3c7f..00000000 --- a/docs/1.0.11/target-versions.html +++ /dev/null @@ -1,279 +0,0 @@ - - - - - - - - - Target MMIF Versions — mmif-python documentation - - - - - - - - - - - - - - - - - -
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Target MMIF Versions

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This article provides targeting MMIF specification versions of different versions of mmif-python SDK.

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Target Specification Versions

mmif-python version

Target MMIF Specification

1.0.11

1.1.0

1.0.10.dev1

1.0.3

1.0.10

1.0.2

1.0.9

1.1.0

1.0.8

1.0.0

1.0.7

1.0.0

1.0.6

1.0.0

1.0.5

1.0.0

1.0.4

1.0.0

1.0.3

1.0.0

1.0.2

1.0.0

1.0.1

1.0.0

1.0.0

0.5.0

0.5.2

0.5.0

0.5.1

0.5.0

0.5.0

0.5.0

0.4.8

0.4.2

0.4.7

0.4.1

0.4.6

0.4.0

0.4.5

0.4.0

0.4.4

0.4.0

0.4.3

0.4.0

0.4.2

0.4.0

0.4.1

0.4.0

0.4.0

0.4.0

0.3.5

0.3.1

0.3.4

0.3.1

0.3.3

0.3.1

0.3.2

0.3.1

0.3.1

0.3.0

0.3.0

0.3.0

0.2.2

0.2.1

0.2.1

0.2.1

0.2.0

0.2.1

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0.3.0
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0.3.1
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0.3.2
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0.3.3
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0.3.4
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0.3.5
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0.4.0
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0.4.1
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0.4.2
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0.4.3
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0.4.4
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0.4.5
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0.4.6
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0.4.7
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0.4.8
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0.5.0
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0.5.1
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0.5.2
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1.0.0
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1.0.1
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1.0.10
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1.0.11
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1.0.12
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1.0.13
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1.0.14
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1.0.15
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1.0.16
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1.0.17
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1.0.18
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1.0.19
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1.0.2
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1.0.3
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1.0.4
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1.0.5
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1.0.6
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1.0.7
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1.0.8
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1.0.9
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1.1.0
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-mmif.serialize.model module ---------------------------- - -.. automodule:: mmif.serialize.model - :members: - :undoc-members: - :show-inheritance: - -mmif.serialize.mmif module --------------------------- - -.. automodule:: mmif.serialize.mmif - :members: - :undoc-members: - :show-inheritance: - -mmif.serialize.view module --------------------------- - -.. automodule:: mmif.serialize.view - :members: - :undoc-members: - :show-inheritance: - -mmif.serialize.annotation module --------------------------------- - -.. automodule:: mmif.serialize.annotation - :members: - :undoc-members: - :show-inheritance: - diff --git a/docs/1.0.12/_sources/autodoc/mmif.utils.rst.txt b/docs/1.0.12/_sources/autodoc/mmif.utils.rst.txt deleted file mode 100644 index 9a6ecc44..00000000 --- a/docs/1.0.12/_sources/autodoc/mmif.utils.rst.txt +++ /dev/null @@ -1,18 +0,0 @@ -mmif.utils module -================= - -mmif.utils.video_document_helper module ----------------------------------------- - -.. automodule:: mmif.utils.video_document_helper - :members: - :undoc-members: - :show-inheritance: - -mmif.utils.sequence_helper module ---------------------------------- - -.. automodule:: mmif.utils.sequence_helper - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/1.0.12/_sources/autodoc/mmif.vocabulary.rst.txt b/docs/1.0.12/_sources/autodoc/mmif.vocabulary.rst.txt deleted file mode 100644 index d250c6a3..00000000 --- a/docs/1.0.12/_sources/autodoc/mmif.vocabulary.rst.txt +++ /dev/null @@ -1,18 +0,0 @@ -mmif.vocabulary module -====================== - -mmif.vocabulary.annotation\_types module ----------------------------------------- - -.. automodule:: mmif.vocabulary.annotation_types - :members: - :undoc-members: - :show-inheritance: - -mmif.vocabulary.document\_types module --------------------------------------- - -.. automodule:: mmif.vocabulary.document_types - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/1.0.12/_sources/autodoc/mmif_docloc_http.rst.txt b/docs/1.0.12/_sources/autodoc/mmif_docloc_http.rst.txt deleted file mode 100644 index b76c8df5..00000000 --- a/docs/1.0.12/_sources/autodoc/mmif_docloc_http.rst.txt +++ /dev/null @@ -1,11 +0,0 @@ -mmif_docloc_http package -======================== - -MMIF document location helper module for `http` and `https` schemes. -If you want to write your own docloc scheme handler, please use the source code of this module as a reference. -See this :ref:`plug-in section ` for more information. - -.. automodule:: mmif_docloc_http - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/1.0.12/_sources/consumer-tutorial.rst.txt b/docs/1.0.12/_sources/consumer-tutorial.rst.txt deleted file mode 100644 index c54634e2..00000000 --- a/docs/1.0.12/_sources/consumer-tutorial.rst.txt +++ /dev/null @@ -1,17 +0,0 @@ -.. _consumer-tutorial: - -MMIF consumer -================================= - -A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the `appliance documentation `_ to learn more about the appliance. - -MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance. - -#. The code must be hosted on a public git repository (e.g. Github, Gitlab, ...) -#. Must listen to ``5000`` port. -#. Must expose ``/display`` route . -#. ``/display`` router should response to ``GET`` requests. -#. In the ``GET`` request, a public URL of the input MMIF file is passed via ``file`` URL parameter. -#. On the codebase root, there must be a ``Dockerfile`` that can build a `docker `_ image that runs the web app. - -We provide an example consumer at https://github.com/clamsproject/mmif-visualizer. diff --git a/docs/1.0.12/_sources/index.rst.txt b/docs/1.0.12/_sources/index.rst.txt deleted file mode 100644 index beb56aae..00000000 --- a/docs/1.0.12/_sources/index.rst.txt +++ /dev/null @@ -1,26 +0,0 @@ -Welcome to mmif-python's documentation! -======================================= - -.. mdinclude:: ../README.md - -.. toctree:: - :maxdepth: 2 - :caption: Contents - - introduction - plugins - target-versions - -.. toctree:: - :maxdepth: 2 - :caption: API documentation: - - modules - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/docs/1.0.12/_sources/introduction.rst.txt b/docs/1.0.12/_sources/introduction.rst.txt deleted file mode 100644 index cfd9eaf7..00000000 --- a/docs/1.0.12/_sources/introduction.rst.txt +++ /dev/null @@ -1,89 +0,0 @@ -.. _introduction: - -Getting Started -=============== - - -Overview ---------- - -MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for reproducibility, transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF website `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects. - -Prerequisites -------------- - -* `Python `_: the latest ``mmif-python`` requires Python 3.8 or newer. We have no plan to support `Python 2.7 `_. - -Installation ---------------- - -Package ``mmif-python`` is distributed via the official PyPI. Users are supposed to pip-install to get latest release. - -.. code-block:: bash - - pip install mmif-python - -This will install a package `mmif` to local python. - -The MMIF format and specification is evolving over time, and ``mmif-python`` package will be updated along with the changes in MMIF format. - -.. note:: MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and ``mmif-python`` versions, please take time to read our decision on the subject `here `_. If you need to know which python SDK supports which specification version, see :ref:`target-versions` page. - -MMIF Serialization ---------------------------- - -:class:`mmif.serialize.mmif.Mmif` represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of :class:`mmif.serialize.model.MmifObject`, including the :class:`mmif.serialize.mmif.Mmif`. To start with an existing MMIF :class:`str`, simple initiate a new ``Mmif`` object with the file. - -.. code-block:: python - - import mmif - from mmif import Mmif - - mmif_str = """{ - "metadata": { - "mmif": "http://mmif.clams.ai/1.0.0" - }, - "documents": [ - { - "@type": "http://mmif.clams.ai/vocabulary/VideoDocument/v1", - "properties": { - "id": "m1", - "mime": "video/mp4", - "location": "file:///var/archive/video-0012.mp4" - } - }, - { - "@type": "http://mmif.clams.ai/vocabulary/TextDocument/v1", - "properties": { - "id": "m2", - "mime": "text/plain", - "location": "file:///var/archive/video-0012-transcript.txt" - } - } - ], - "views": []}""" - mmif_obj = Mmif(mmif_str) - - -Few notes; - -#. MMIF does not carry the primary source files in it. -#. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version ``mmif-python`` implementation of the MMIF might not be able to load an unsupported version of MMIF string. - -When serializing back to :class:`str`, call :meth:`mmif.serialize.model.MmifObject.serialize` on the object. - -To get subcomponents, you can use various getters implemented in subclasses. For example; - -.. code-block:: python - - from mmif.vocabulary.document_types import DocumentTypes - - for video in mmif_obj.Mmif.get_documents_by_type(DocumentTypes.VideoDocument): - with open(video.location_path(), 'b') as in_video: - # do something with the video file - - -For a full list of available helper methods, please refer to :ref:`the API documentation `. - diff --git a/docs/1.0.12/_sources/modules.rst.txt b/docs/1.0.12/_sources/modules.rst.txt deleted file mode 100644 index 4bb9307d..00000000 --- a/docs/1.0.12/_sources/modules.rst.txt +++ /dev/null @@ -1,20 +0,0 @@ -.. _apidoc: - -mmif package -============ - -.. toctree:: - :maxdepth: 4 - - autodoc/mmif.serialize - autodoc/mmif.vocabulary - autodoc/mmif.utils - -mmif_docloc_http package -======================== - -.. toctree:: - :maxdepth: 2 - - autodoc/mmif_docloc_http - diff --git a/docs/1.0.12/_sources/plugins.rst.txt b/docs/1.0.12/_sources/plugins.rst.txt deleted file mode 100644 index 9907c495..00000000 --- a/docs/1.0.12/_sources/plugins.rst.txt +++ /dev/null @@ -1,83 +0,0 @@ -.. _plugins: - -Developing plugins for MMIF Python SDK -====================================== - - -Overview --------- - -As MMIF JSON files can carry information about media document files without actually carrying file contents, file accessing modules in ``mmif`` Python package (distributed as ``mmif-python`` on PyPI) are designed to be lightweight and flexible so that it can work with additional "plugin" Python packages that can handle concrete file access. - - -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF website `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects. - -Developer can write simple plugins that can provide additional functionalities to ``mmif-python``. For example, ``mmif-python`` does not provide any file access functionality beyond a local file system (with ``file`` scheme), but it can be extended with a plugin that can handle file access over different protocols (e.g. ``http``, ``s3``, ``ftp``, etc). - -This document contains information about how to write plugins for ``mmif-python``. - -.. _docloc_plugin: - -Document Location Scheme Plugins -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -:class:`mmif.serialize.annotation.Document` class has various methods to access parts of ``location`` property of the document. The location is in `URI/IRI format `_ (``SCHEME://HOSTNAME/PATH``, in a nutshell) and it has to be resolved to a local file for CLAMS Apps to process the local file to analyze and extract information about the media and its contents. The core ``mmif-python`` distribution only provides a default implementation that can handle ``file`` scheme URIs. - -To add a document location handler plugin, you need to implement a Python `"package" `_ (do not confuse with PYPI distribution), that meets these requirements; - -#. the package must be named ``mmif_docloc_``. For example, to implement a handler for ``s3`` scheme, the package name must be ``mmif_docloc_s3``. The prefix is important as it's used in the plugin discovery process from the core ``mmif-python`` modules. -#. the top module of the package must have a function named ``resolve``. The function must take a single argument, which is a :class:`str` of the document location URI. The function must return a :class:`str` of the local file path. For example, if the document location is ``s3://mybucket/myfile.mp4``, a Python user should be able to to something like this; - -.. code-block:: python - - import mmif_docloc_s3 - resolved = mmif_docloc_s3.resolve('s3://mybucket/myfile.mp4') - # then resolved must be a local file path that can be used to open the file - - -Here's a minimal example codebase that you refer to when you develop a ``docloc`` plugin. - -(However, before you start writing your own plugin for a specific URI scheme, checking `if there's already a PyPI distribution `_ for the scheme might be a good idea.) - -.. code-block:: sh - - $ tree . - . - ├── mmif_docloc_dummy - │ └── __init__.py - ├── pyproject.toml - └── setup.cfg - - $ cat pyproject.toml - [build-system] - requires = ["setuptools"] - build-backend = "setuptools.build_meta" - - $ cat setup.cfg - [metadata] - name = mmif_docloc_dummy # this name is IMPORTANT - version = 0.0.1 - description = a plugin to mmif-pyhon to handle `dummy` location scheme - - -And the plugin code. - -.. code-block:: python - - # mmif_docloc_dummy/__init__.py - doc_types = {'video': 'mp4'} - - def resolve(docloc): - scheme = 'dummy' - if docloc.startswith(f'{scheme}://'): - doc_id, doc_type = docloc.split('.') - return f'/path/to/{doc_id}.{doc_types[doc_type]}' - else: - raise ValueError(f'cannot handle document location scheme: {docloc}') - -Bulit-in Document Location Scheme Plugins -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -At the moment, ``mmif-python`` PyPI distribution ships a built-in *docloc* plugin that support both ``http`` and ``https`` schemes. -Take a look at :mod:`mmif_docloc_http` module for details. diff --git a/docs/1.0.12/_sources/target-versions.rst.txt b/docs/1.0.12/_sources/target-versions.rst.txt deleted file mode 100644 index 34216d3e..00000000 --- a/docs/1.0.12/_sources/target-versions.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _target-versions: - -Target MMIF Versions -==================== - -This article provides targeting MMIF specification versions of different versions of ``mmif-python`` SDK. - -.. csv-table:: Target Specification Versions - :file: target-versions.csv - :header-rows: 1 diff --git a/docs/1.0.12/_static/_sphinx_javascript_frameworks_compat.js b/docs/1.0.12/_static/_sphinx_javascript_frameworks_compat.js deleted file mode 100644 index 81415803..00000000 --- a/docs/1.0.12/_static/_sphinx_javascript_frameworks_compat.js +++ /dev/null @@ -1,123 +0,0 @@ -/* Compatability shim for jQuery and underscores.js. - * - * Copyright Sphinx contributors - * Released under the two clause BSD licence - */ - -/** - * small helper function to urldecode strings - * - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL - */ -jQuery.urldecode = function(x) { - if (!x) { - return x - } - return decodeURIComponent(x.replace(/\+/g, ' ')); -}; - -/** - * small helper function to urlencode strings - */ -jQuery.urlencode = encodeURIComponent; - -/** - * This function returns the parsed url parameters of the - * current request. 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- -/** - * Simple result scoring code. - */ -if (typeof Scorer === "undefined") { - var Scorer = { - // Implement the following function to further tweak the score for each result - // The function takes a result array [docname, title, anchor, descr, score, filename] - // and returns the new score. - /* - score: result => { - const [docname, title, anchor, descr, score, filename, kind] = result - return score - }, - */ - - // query matches the full name of an object - objNameMatch: 11, - // or matches in the last dotted part of the object name - objPartialMatch: 6, - // Additive scores depending on the priority of the object - objPrio: { - 0: 15, // used to be importantResults - 1: 5, // used to be objectResults - 2: -5, // used to be unimportantResults - }, - // Used when the priority is not in the mapping. - objPrioDefault: 0, - - // query found in title - title: 15, - partialTitle: 7, - // query found in terms - term: 5, - partialTerm: 2, - }; -} - -// Global search result kind enum, used by themes to style search results. -class SearchResultKind { - static get index() { return "index"; } - static get object() { return "object"; } - static get text() { return "text"; } - static get title() { return "title"; } -} - -const _removeChildren = (element) => { - while (element && element.lastChild) element.removeChild(element.lastChild); -}; - -/** - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping - */ -const _escapeRegExp = (string) => - string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string - -const _displayItem = (item, searchTerms, highlightTerms) => { - const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; - const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; - const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; - const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; - const contentRoot = document.documentElement.dataset.content_root; - - const [docName, title, anchor, descr, score, _filename, kind] = item; - - let listItem = document.createElement("li"); - // Add a class representing the item's type: - // can be used by a theme's CSS selector for styling - // See SearchResultKind for the class names. - listItem.classList.add(`kind-${kind}`); - let requestUrl; - let linkUrl; - if (docBuilder === "dirhtml") { - // dirhtml builder - let dirname = docName + "/"; - if (dirname.match(/\/index\/$/)) - dirname = dirname.substring(0, dirname.length - 6); - else if (dirname === "index/") dirname = ""; - requestUrl = contentRoot + dirname; - linkUrl = requestUrl; - } else { - // normal html builders - requestUrl = contentRoot + docName + docFileSuffix; - linkUrl = docName + docLinkSuffix; - } - let linkEl = listItem.appendChild(document.createElement("a")); - linkEl.href = linkUrl + anchor; - linkEl.dataset.score = score; - linkEl.innerHTML = title; - if (descr) { - listItem.appendChild(document.createElement("span")).innerHTML = - " (" + descr + ")"; - // highlight search terms in the description - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - } - else if (showSearchSummary) - fetch(requestUrl) - .then((responseData) => responseData.text()) - .then((data) => { - if (data) - listItem.appendChild( - Search.makeSearchSummary(data, searchTerms, anchor) - ); - // highlight search terms in the summary - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - }); - Search.output.appendChild(listItem); -}; -const _finishSearch = (resultCount) => { - Search.stopPulse(); - Search.title.innerText = _("Search Results"); - if (!resultCount) - Search.status.innerText = Documentation.gettext( - "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." - ); - else - Search.status.innerText = Documentation.ngettext( - "Search finished, found one page matching the search query.", - "Search finished, found ${resultCount} pages matching the search query.", - resultCount, - ).replace('${resultCount}', resultCount); -}; -const _displayNextItem = ( - results, - resultCount, - searchTerms, - highlightTerms, -) => { - // results left, load the summary and display it - // this is intended to be dynamic (don't sub resultsCount) - if (results.length) { - _displayItem(results.pop(), searchTerms, highlightTerms); - setTimeout( - () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), - 5 - ); - } - // search finished, update title and status message - else _finishSearch(resultCount); -}; -// Helper function used by query() to order search results. -// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. -// Order the results by score (in opposite order of appearance, since the -// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. -const _orderResultsByScoreThenName = (a, b) => { - const leftScore = a[4]; - const rightScore = b[4]; - if (leftScore === rightScore) { - // same score: sort alphabetically - const leftTitle = a[1].toLowerCase(); - const rightTitle = b[1].toLowerCase(); - if (leftTitle === rightTitle) return 0; - return leftTitle > rightTitle ? -1 : 1; // inverted is intentional - } - return leftScore > rightScore ? 1 : -1; -}; - -/** - * Default splitQuery function. Can be overridden in ``sphinx.search`` with a - * custom function per language. - * - * The regular expression works by splitting the string on consecutive characters - * that are not Unicode letters, numbers, underscores, or emoji characters. - * This is the same as ``\W+`` in Python, preserving the surrogate pair area. - */ -if (typeof splitQuery === "undefined") { - var splitQuery = (query) => query - .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) - .filter(term => term) // remove remaining empty strings -} - -/** - * Search Module - */ -const Search = { - _index: null, - _queued_query: null, - _pulse_status: -1, - - htmlToText: (htmlString, anchor) => { - const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - for (const removalQuery of [".headerlink", "script", "style"]) { - htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); - } - if (anchor) { - const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); - if (anchorContent) return anchorContent.textContent; - - console.warn( - `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` - ); - } - - // if anchor not specified or not found, fall back to main content - const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent) return docContent.textContent; - - console.warn( - "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." - ); - return ""; - }, - - init: () => { - const query = new URLSearchParams(window.location.search).get("q"); - document - .querySelectorAll('input[name="q"]') - .forEach((el) => (el.value = query)); - if (query) Search.performSearch(query); - }, - - loadIndex: (url) => - (document.body.appendChild(document.createElement("script")).src = url), - - setIndex: (index) => { - Search._index = index; - if (Search._queued_query !== null) { - const query = Search._queued_query; - Search._queued_query = null; - Search.query(query); - } - }, - - hasIndex: () => Search._index !== null, - - deferQuery: (query) => (Search._queued_query = query), - - stopPulse: () => (Search._pulse_status = -1), - - startPulse: () => { - if (Search._pulse_status >= 0) return; - - const pulse = () => { - Search._pulse_status = (Search._pulse_status + 1) % 4; - Search.dots.innerText = ".".repeat(Search._pulse_status); - if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); - }; - pulse(); - }, - - /** - * perform a search for something (or wait until index is loaded) - */ - performSearch: (query) => { - // create the required interface elements - const searchText = document.createElement("h2"); - searchText.textContent = _("Searching"); - const searchSummary = document.createElement("p"); - searchSummary.classList.add("search-summary"); - searchSummary.innerText = ""; - const searchList = document.createElement("ul"); - searchList.setAttribute("role", "list"); - searchList.classList.add("search"); - - const out = document.getElementById("search-results"); - Search.title = out.appendChild(searchText); - Search.dots = Search.title.appendChild(document.createElement("span")); - Search.status = out.appendChild(searchSummary); - Search.output = out.appendChild(searchList); - - const searchProgress = document.getElementById("search-progress"); - // Some themes don't use the search progress node - if (searchProgress) { - searchProgress.innerText = _("Preparing search..."); - } - Search.startPulse(); - - // index already loaded, the browser was quick! - if (Search.hasIndex()) Search.query(query); - else Search.deferQuery(query); - }, - - _parseQuery: (query) => { - // stem the search terms and add them to the correct list - const stemmer = new Stemmer(); - const searchTerms = new Set(); - const excludedTerms = new Set(); - const highlightTerms = new Set(); - const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); - splitQuery(query.trim()).forEach((queryTerm) => { - const queryTermLower = queryTerm.toLowerCase(); - - // maybe skip this "word" - // stopwords array is from language_data.js - if ( - stopwords.indexOf(queryTermLower) !== -1 || - queryTerm.match(/^\d+$/) - ) - return; - - // stem the word - let word = stemmer.stemWord(queryTermLower); - // select the correct list - if (word[0] === "-") excludedTerms.add(word.substr(1)); - else { - searchTerms.add(word); - highlightTerms.add(queryTermLower); - } - }); - - if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js - localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) - } - - // console.debug("SEARCH: searching for:"); - // console.info("required: ", [...searchTerms]); - // console.info("excluded: ", [...excludedTerms]); - - return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; - }, - - /** - * execute search (requires search index to be loaded) - */ - _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - - // Collect multiple result groups to be sorted separately and then ordered. - // Each is an array of [docname, title, anchor, descr, score, filename, kind]. - const normalResults = []; - const nonMainIndexResults = []; - - _removeChildren(document.getElementById("search-progress")); - - const queryLower = query.toLowerCase().trim(); - for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { - for (const [file, id] of foundTitles) { - const score = Math.round(Scorer.title * queryLower.length / title.length); - const boost = titles[file] === title ? 1 : 0; // add a boost for document titles - normalResults.push([ - docNames[file], - titles[file] !== title ? `${titles[file]} > ${title}` : title, - id !== null ? "#" + id : "", - null, - score + boost, - filenames[file], - SearchResultKind.title, - ]); - } - } - } - - // search for explicit entries in index directives - for (const [entry, foundEntries] of Object.entries(indexEntries)) { - if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id, isMain] of foundEntries) { - const score = Math.round(100 * queryLower.length / entry.length); - const result = [ - docNames[file], - titles[file], - id ? "#" + id : "", - null, - score, - filenames[file], - SearchResultKind.index, - ]; - if (isMain) { - normalResults.push(result); - } else { - nonMainIndexResults.push(result); - } - } - } - } - - // lookup as object - objectTerms.forEach((term) => - normalResults.push(...Search.performObjectSearch(term, objectTerms)) - ); - - // lookup as search terms in fulltext - normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); - - // let the scorer override scores with a custom scoring function - if (Scorer.score) { - normalResults.forEach((item) => (item[4] = Scorer.score(item))); - nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); - } - - // Sort each group of results by score and then alphabetically by name. - normalResults.sort(_orderResultsByScoreThenName); - nonMainIndexResults.sort(_orderResultsByScoreThenName); - - // Combine the result groups in (reverse) order. - // Non-main index entries are typically arbitrary cross-references, - // so display them after other results. - let results = [...nonMainIndexResults, ...normalResults]; - - // remove duplicate search results - // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept - let seen = new Set(); - results = results.reverse().reduce((acc, result) => { - let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); - if (!seen.has(resultStr)) { - acc.push(result); - seen.add(resultStr); - } - return acc; - }, []); - - return results.reverse(); - }, - - query: (query) => { - const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); - const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); - - // for debugging - //Search.lastresults = results.slice(); // a copy - // console.info("search results:", Search.lastresults); - - // print the results - _displayNextItem(results, results.length, searchTerms, highlightTerms); - }, - - /** - * search for object names - */ - performObjectSearch: (object, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const objects = Search._index.objects; - const objNames = Search._index.objnames; - const titles = Search._index.titles; - - const results = []; - - const objectSearchCallback = (prefix, match) => { - const name = match[4] - const fullname = (prefix ? prefix + "." : "") + name; - const fullnameLower = fullname.toLowerCase(); - if (fullnameLower.indexOf(object) < 0) return; - - let score = 0; - const parts = fullnameLower.split("."); - - // check for different match types: exact matches of full name or - // "last name" (i.e. last dotted part) - if (fullnameLower === object || parts.slice(-1)[0] === object) - score += Scorer.objNameMatch; - else if (parts.slice(-1)[0].indexOf(object) > -1) - score += Scorer.objPartialMatch; // matches in last name - - const objName = objNames[match[1]][2]; - const title = titles[match[0]]; - - // If more than one term searched for, we require other words to be - // found in the name/title/description - const otherTerms = new Set(objectTerms); - otherTerms.delete(object); - if (otherTerms.size > 0) { - const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); - if ( - [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) - ) - return; - } - - let anchor = match[3]; - if (anchor === "") anchor = fullname; - else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; - - const descr = objName + _(", in ") + title; - - // add custom score for some objects according to scorer - if (Scorer.objPrio.hasOwnProperty(match[2])) - score += Scorer.objPrio[match[2]]; - else score += Scorer.objPrioDefault; - - results.push([ - docNames[match[0]], - fullname, - "#" + anchor, - descr, - score, - filenames[match[0]], - SearchResultKind.object, - ]); - }; - Object.keys(objects).forEach((prefix) => - objects[prefix].forEach((array) => - objectSearchCallback(prefix, array) - ) - ); - return results; - }, - - /** - * search for full-text terms in the index - */ - performTermsSearch: (searchTerms, excludedTerms) => { - // prepare search - const terms = Search._index.terms; - const titleTerms = Search._index.titleterms; - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - - const scoreMap = new Map(); - const fileMap = new Map(); - - // perform the search on the required terms - searchTerms.forEach((word) => { - const files = []; - const arr = [ - { files: terms[word], score: Scorer.term }, - { files: titleTerms[word], score: Scorer.title }, - ]; - // add support for partial matches - if (word.length > 2) { - const escapedWord = _escapeRegExp(word); - if (!terms.hasOwnProperty(word)) { - Object.keys(terms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: terms[term], score: Scorer.partialTerm }); - }); - } - if (!titleTerms.hasOwnProperty(word)) { - Object.keys(titleTerms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); - }); - } - } - - // no match but word was a required one - if (arr.every((record) => record.files === undefined)) return; - - // found search word in contents - arr.forEach((record) => { - if (record.files === undefined) return; - - let recordFiles = record.files; - if (recordFiles.length === undefined) recordFiles = [recordFiles]; - files.push(...recordFiles); - - // set score for the word in each file - recordFiles.forEach((file) => { - if (!scoreMap.has(file)) scoreMap.set(file, {}); - scoreMap.get(file)[word] = record.score; - }); - }); - - // create the mapping - files.forEach((file) => { - if (!fileMap.has(file)) fileMap.set(file, [word]); - else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); - }); - }); - - // now check if the files don't contain excluded terms - const results = []; - for (const [file, wordList] of fileMap) { - // check if all requirements are matched - - // as search terms with length < 3 are discarded - const filteredTermCount = [...searchTerms].filter( - (term) => term.length > 2 - ).length; - if ( - wordList.length !== searchTerms.size && - wordList.length !== filteredTermCount - ) - continue; - - // ensure that none of the excluded terms is in the search result - if ( - [...excludedTerms].some( - (term) => - terms[term] === file || - titleTerms[term] === file || - (terms[term] || []).includes(file) || - (titleTerms[term] || []).includes(file) - ) - ) - break; - - // select one (max) score for the file. - const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); - // add result to the result list - results.push([ - docNames[file], - titles[file], - "", - null, - score, - filenames[file], - SearchResultKind.text, - ]); - } - return results; - }, - - /** - * helper function to return a node containing the - * search summary for a given text. keywords is a list - * of stemmed words. - */ - makeSearchSummary: (htmlText, keywords, anchor) => { - const text = Search.htmlToText(htmlText, anchor); - if (text === "") return null; - - const textLower = text.toLowerCase(); - const actualStartPosition = [...keywords] - .map((k) => textLower.indexOf(k.toLowerCase())) - .filter((i) => i > -1) - .slice(-1)[0]; - const startWithContext = Math.max(actualStartPosition - 120, 0); - - const top = startWithContext === 0 ? "" : "..."; - const tail = startWithContext + 240 < text.length ? "..." : ""; - - let summary = document.createElement("p"); - summary.classList.add("context"); - summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; - - return summary; - }, -}; - -_ready(Search.init); diff --git a/docs/1.0.12/_static/sphinx_highlight.js b/docs/1.0.12/_static/sphinx_highlight.js deleted file mode 100644 index 8a96c69a..00000000 --- a/docs/1.0.12/_static/sphinx_highlight.js +++ /dev/null @@ -1,154 +0,0 @@ -/* Highlighting utilities for Sphinx HTML documentation. */ -"use strict"; - -const SPHINX_HIGHLIGHT_ENABLED = true - -/** - * highlight a given string on a node by wrapping it in - * span elements with the given class name. - */ -const _highlight = (node, addItems, text, className) => { - if (node.nodeType === Node.TEXT_NODE) { - const val = node.nodeValue; - const parent = node.parentNode; - const pos = val.toLowerCase().indexOf(text); - if ( - pos >= 0 && - !parent.classList.contains(className) && - !parent.classList.contains("nohighlight") - ) { - let span; - - const closestNode = parent.closest("body, svg, foreignObject"); - const isInSVG = closestNode && closestNode.matches("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.classList.add(className); - } - - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - const rest = document.createTextNode(val.substr(pos + text.length)); - parent.insertBefore( - span, - parent.insertBefore( - rest, - node.nextSibling - ) - ); - node.nodeValue = val.substr(0, pos); - /* There may be more occurrences of search term in this node. So call this - * function recursively on the remaining fragment. - */ - _highlight(rest, addItems, text, className); - - if (isInSVG) { - const rect = document.createElementNS( - "http://www.w3.org/2000/svg", - "rect" - ); - const bbox = parent.getBBox(); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute("class", className); - addItems.push({ parent: parent, target: rect }); - } - } - } else if (node.matches && !node.matches("button, select, textarea")) { - node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); - } -}; -const _highlightText = (thisNode, text, className) => { - let addItems = []; - _highlight(thisNode, addItems, text, className); - addItems.forEach((obj) => - obj.parent.insertAdjacentElement("beforebegin", obj.target) - ); -}; - -/** - * Small JavaScript module for the documentation. - */ -const SphinxHighlight = { - - /** - * highlight the search words provided in localstorage in the text - */ - highlightSearchWords: () => { - if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight - - // get and clear terms from localstorage - const url = new URL(window.location); - const highlight = - localStorage.getItem("sphinx_highlight_terms") - || url.searchParams.get("highlight") - || ""; - localStorage.removeItem("sphinx_highlight_terms") - url.searchParams.delete("highlight"); - window.history.replaceState({}, "", url); - - // get individual terms from highlight string - const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); - if (terms.length === 0) return; // nothing to do - - // There should never be more than one element matching "div.body" - const divBody = document.querySelectorAll("div.body"); - const body = divBody.length ? divBody[0] : document.querySelector("body"); - window.setTimeout(() => { - terms.forEach((term) => _highlightText(body, term, "highlighted")); - }, 10); - - const searchBox = document.getElementById("searchbox"); - if (searchBox === null) return; - searchBox.appendChild( - document - .createRange() - .createContextualFragment( - '

' + - '' + - _("Hide Search Matches") + - "

" - ) - ); - }, - - /** - * helper function to hide the search marks again - */ - hideSearchWords: () => { - document - .querySelectorAll("#searchbox .highlight-link") - .forEach((el) => el.remove()); - document - .querySelectorAll("span.highlighted") - .forEach((el) => el.classList.remove("highlighted")); - localStorage.removeItem("sphinx_highlight_terms") - }, - - initEscapeListener: () => { - // only install a listener if it is really needed - if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; - - document.addEventListener("keydown", (event) => { - // bail for input elements - if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; - // bail with special keys - if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; - if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { - SphinxHighlight.hideSearchWords(); - event.preventDefault(); - } - }); - }, -}; - -_ready(() => { - /* Do not call highlightSearchWords() when we are on the search page. - * It will highlight words from the *previous* search query. - */ - if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); - SphinxHighlight.initEscapeListener(); -}); diff --git a/docs/1.0.12/autodoc/mmif.serialize.html b/docs/1.0.12/autodoc/mmif.serialize.html deleted file mode 100644 index 398e94c5..00000000 --- a/docs/1.0.12/autodoc/mmif.serialize.html +++ /dev/null @@ -1,1317 +0,0 @@ - - - - - - - - - mmif.serialize module — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
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mmif.serialize module

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mmif.serialize.model module

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The model module contains the classes used to represent an -abstract MMIF object as a live Python object.

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The MmifObject class or one of its derivatives is subclassed by -all other classes defined in this SDK, except for MmifObjectEncoder.

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These objects are generally instantiated from JSON, either as a string -or as an already-loaded Python dictionary. This base class provides the -core functionality for deserializing MMIF JSON data into live objects -and serializing live objects into MMIF JSON data. Specialized behavior -for the different components of MMIF is added in the subclasses.

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-class mmif.serialize.model.DataDict(mmif_obj: bytes | str | dict | None = None)[source]
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Bases: MmifObject, Generic[T, S]

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-empty()[source]
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-get(key: T, default=None) → S | None[source]
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-items()[source]
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-keys()[source]
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-update(other, overwrite)[source]
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-values()[source]
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-class mmif.serialize.model.DataList(mmif_obj: bytes | str | list | None = None)[source]
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Bases: MmifObject, Generic[T]

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The DataList class is an abstraction that represents the -various lists found in a MMIF file, such as documents, subdocuments, -views, and annotations.

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Parameters:
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mmif_obj (Union[str, list]) – the data that the list contains

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-append(value, overwrite)[source]
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-deserialize(mmif_json: str | list) → None[source]
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Passes the input data into the internal deserializer.

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-empty()[source]
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-get(key: str) → T | None[source]
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Standard dictionary-style get() method, albeit with no default -parameter. Relies on the implementation of __getitem__.

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Will return None if the key is not found.

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Parameters:
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key – the key to search for

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Returns:
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the value matching that key

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-class mmif.serialize.model.MmifObject(mmif_obj: bytes | str | dict | None = None)[source]
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Bases: object

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Abstract superclass for MMIF related key-value pair objects.

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Any MMIF object can be initialized as an empty placeholder or -an actual representation with a JSON formatted string or equivalent -dict object argument.

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This superclass has four specially designed instance variables, and these -variable names cannot be used as attribute names for MMIF objects.

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  1. _unnamed_attributes: -Only can be either None or an empty dictionary. If it’s set to None, -it means the class won’t take any Additional Attributes in the JSON -schema sense. If it’s a dict, users can throw any k-v pairs to the -class, EXCEPT for the reserved two key names.

    2. -

  2. _attribute_classes: -This is a dict from a key name to a specific python class to use for -deserialize the value. Note that a key name in this dict does NOT -have to be a named attribute, but is recommended to be one.

    3. -

  3. _required_attributes: -This is a simple list of names of attributes that are required in the object. -When serialize, an object will skip its empty (e.g. zero-length, or None) -attributes unless they are in this list. Otherwise, the serialized JSON -string would have empty representations (e.g. "", []).

    4. -

  4. _exclude_from_diff: -This is a simple list of names of attributes that should be excluded from -the diff calculation in __eq__.

    5. -
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# TODO (krim @ 8/17/20): this dict is however, a duplicate with the type hints in the class definition. -Maybe there is a better way to utilize type hints (e.g. getting them as a programmatically), but for now -developers should be careful to add types to hints as well as to this dict.

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Also note that those special attributes MUST be set in the __init__() -before calling super method, otherwise deserialization will not work.

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And also, a subclass that has one or more named attributes, it must -set those attributes in the __init__() before calling super method. When -serializing a MmifObject, all empty attributes will be ignored, so for -optional named attributes, you must leave the values empty (len == 0), but -NOT None. Any None-valued named attributes will cause issues with current -implementation.

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Parameters:
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mmif_obj – JSON string or dict to initialize an object. -If not given, an empty object will be initialized, sometimes with -an ID value automatically generated, based on its parent object.

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-deserialize(mmif_json: str | dict) → None[source]
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Takes a JSON-formatted string or a simple dict that’s json-loaded from -such a string as an input and populates object’s fields with the values -specified in the input.

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Parameters:
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mmif_json – JSON-formatted string or dict from such a string -that represents a MMIF object

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-disallow_additional_properties() → None[source]
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Call this method in __init__() to prevent the insertion -of unnamed attributes after initialization.

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-static is_empty(obj) → bool[source]
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return True if the obj is None or “emtpy”. The emptiness first defined as -having zero length. But for objects that lack __len__ method, we need -additional check.

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-reserved_names: Set[str] = {'_attribute_classes', '_exclude_from_diff', '_required_attributes', '_unnamed_attributes', 'reserved_names'}[source]
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-serialize(pretty: bool = False) → str[source]
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Generates JSON representation of an object.

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Parameters:
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pretty – If True, returns string representation with indentation.

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Returns:
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JSON string of the object.

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-set_additional_property(key: str, value: Any) → None[source]
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Method to set values in _unnamed_attributes.

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Parameters:
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  • key – the attribute name

    • -

  • value – the desired value

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Returns:
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None

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Raise:
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AttributeError if additional properties are disallowed by disallow_additional_properties()

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-class mmif.serialize.model.MmifObjectEncoder(*, skipkeys=False, ensure_ascii=True, check_circular=True, allow_nan=True, sort_keys=False, indent=None, separators=None, default=None)[source]
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Bases: JSONEncoder

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Encoder class to define behaviors of de-/serialization

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-default(obj: MmifObject)[source]
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Overrides default encoding behavior to prioritize MmifObject.serialize().

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mmif.serialize.mmif module

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The mmif module contains the classes used to represent a full MMIF -file as a live Python object.

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See the specification docs and the JSON Schema file for more information.

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-class mmif.serialize.mmif.Mmif(mmif_obj: bytes | str | dict | None = None, *, validate: bool = True)[source]
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Bases: MmifObject

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MmifObject that represents a full MMIF file.

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Parameters:
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  • mmif_obj – the JSON data

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  • validate – whether to validate the data against the MMIF JSON schema.

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-add_document(document: Document, overwrite=False) → None[source]
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Appends a Document object to the documents list.

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Fails if there is already a document with the same ID in the MMIF object.

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Parameters:
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  • document – the Document object to add

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  • overwrite – if set to True, will overwrite -an existing view with the same ID

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Returns:
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None

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-add_view(view: View, overwrite=False) → None[source]
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Appends a View object to the views list.

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Fails if there is already a view with the same ID in the MMIF object.

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Parameters:
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  • view – the Document object to add

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  • overwrite – if set to True, will overwrite -an existing view with the same ID

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Returns:
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None

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-generate_capital_annotations()[source]
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Automatically convert any “pending” temporary properties from -Document objects to Annotation objects . The generated Annotation -objects are then added to the last View in the views lists.

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See https://github.com/clamsproject/mmif-python/issues/226 for rationale -behind this behavior and discussion.

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-get_alignments(at_type1: str | TypesBase, at_type2: str | TypesBase) → Dict[str, List[Annotation]][source]
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Finds views where alignments between two given annotation types occurred.

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Returns:
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a dict that keyed by view IDs (str) and has lists of alignment Annotation objects as values.

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-get_all_views_contain(at_types: TypesBase | str | List[str | TypesBase]) → List[View][source]
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Returns the list of all views in the MMIF if given types -are present in that view’s ‘contains’ metadata.

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Parameters:
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at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

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Returns:
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the list of views that contain the type

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-get_document_by_id(doc_id: str) → Document[source]
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Finds a Document object with the given ID.

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Parameters:
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doc_id – the ID to search for

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Returns:
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a reference to the corresponding document, if it exists

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Raises:
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KeyError – if there is no corresponding document

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-get_document_location(m_type: DocumentTypes | str, path_only=False) → str | None[source]
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Method to get the location of first document of given type.

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Parameters:
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m_type – the type to search for

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Returns:
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the value of the location field in the corresponding document

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-get_documents_by_app(app_id: str) → List[Document][source]
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Method to get all documents object queries by its originated app name.

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Parameters:
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app_id – the app name to search for

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Returns:
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a list of documents matching the requested app name, or an empty list if the app not found

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-get_documents_by_property(prop_key: str, prop_value: str) → List[Document][source]
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Method to retrieve documents by an arbitrary key-value pair in the document properties objects.

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Parameters:
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  • prop_key – the metadata key to search for

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  • prop_value – the metadata value to match

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Returns:
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a list of documents matching the requested metadata key-value pair

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-get_documents_by_type(doc_type: str | DocumentTypes) → List[Document][source]
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Method to get all documents where the type matches a particular document type, which should be one of the CLAMS document types.

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Parameters:
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doc_type – the type of documents to search for, must be one of Document type defined in the CLAMS vocabulary.

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Returns:
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a list of documents matching the requested type, or an empty list if none found.

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-get_documents_in_view(vid: str | None = None) → List[Document][source]
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Method to get all documents object queries by a view id.

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Parameters:
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vid – the source view ID to search for

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Returns:
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a list of documents matching the requested source view ID, or an empty list if the view not found

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-get_documents_locations(m_type: DocumentTypes | str, path_only=False) → List[str | None][source]
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This method returns the file paths of documents of given type. -Only top-level documents have locations, so we only check them.

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Parameters:
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m_type – the type to search for

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Returns:
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a list of the values of the location fields in the corresponding documents

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-get_end(annotation: Annotation) → int | float[source]
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An alias to get_anchor_point method with start=False.

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-get_start(annotation: Annotation) → int | float[source]
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An alias to get_anchor_point method with start=True.

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-get_view_by_id(req_view_id: str) → View[source]
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Finds a View object with the given ID.

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Parameters:
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req_view_id – the ID to search for

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Returns:
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a reference to the corresponding view, if it exists

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Raises:
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Exception – if there is no corresponding view

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-get_view_contains(at_types: TypesBase | str | List[str | TypesBase]) → View | None[source]
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Returns the last view appended that contains the given -types in its ‘contains’ metadata.

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Parameters:
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at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

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Returns:
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the view, or None if the type is not found

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-get_views_contain(at_types: TypesBase | str | List[str | TypesBase]) → List[View][source]
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An alias to get_all_views_contain method.

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-get_views_for_document(doc_id: str) → List[View][source]
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Returns the list of all views that have annotations anchored on a particular document. -Note that when the document is inside a view (generated during the pipeline’s running), -doc_id must be prefixed with the view_id.

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-id_delimiter: ClassVar[str] = ':'[source]
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-new_view() → View[source]
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Creates an empty view with a new ID and appends it to the views list.

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Returns:
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a reference to the new View object

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-new_view_id() → str[source]
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Fetches an ID for a new view.

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Returns:
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the ID

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-sanitize()[source]
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Sanitizes a Mmif object by running some safeguards. -Concretely, it performs the following before returning the JSON string.

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  1. validating output using built-in MMIF jsonschema

    2. -

  2. remove non-existing annotation types from contains metadata

    3. -
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-serialize(pretty: bool = False, sanitize: bool = False, autogenerate_capital_annotations=True) → str[source]
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Serializes the MMIF object to a JSON string.

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Parameters:
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  • sanitize – If True, performs some sanitization of before returning -the JSON string. See sanitize() for details.

    • -

  • autogenerate_capital_annotations – If True, automatically convert -any “pending” temporary properties from Document objects to -Annotation objects. See generate_capital_annotations() for -details.

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  • pretty – If True, returns string representation with indentation.

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Returns:
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JSON string of the MMIF object.

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-static validate(json_str: bytes | str | dict) → None[source]
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Validates a MMIF JSON object against the MMIF Schema. -Note that this method operates before processing by MmifObject._load_str, -so it expects @ and not _ for the JSON-LD @-keys.

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Raises:
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jsonschema.exceptions.ValidationError – if the input fails validation

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Parameters:
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json_str – a MMIF JSON dict or string

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Returns:
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None

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-view_prefix: ClassVar[str] = 'v_'[source]
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mmif.serialize.view module

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The view module contains the classes used to represent a MMIF view -as a live Python object.

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In MMIF, views are created by apps in a pipeline that are annotating -data that was previously present in the MMIF file.

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-class mmif.serialize.view.Contain(mmif_obj: bytes | str | dict | None = None)[source]
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Bases: DataDict[str, str]

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Contain object that represents the metadata of a single -annotation type in the contains metadata of a MMIF view.

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-class mmif.serialize.view.View(view_obj: bytes | str | dict | None = None)[source]
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Bases: MmifObject

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View object that represents a single view in a MMIF file.

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A view is identified by an ID, and contains certain metadata, -a list of annotations, and potentially a JSON-LD @context -IRI.

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If view_obj is not provided, an empty View will be generated.

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Parameters:
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view_obj – the JSON data that defines the view

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-add_annotation(annotation: Annotation, overwrite=False) → Annotation[source]
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Adds an annotation to the current view.

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Fails if there is already an annotation with the same ID -in the view, unless overwrite is set to True.

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Parameters:
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Raises:
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KeyError – if overwrite is set to False and -an annotation with the same ID exists -in the view

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Returns:
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the same Annotation object passed in as annotation

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-add_document(document: Document, overwrite=False) → Annotation[source]
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Appends a Document object to the annotations list.

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Fails if there is already a document with the same ID in the annotations list.

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Parameters:
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  • document – the Document object to add

    • -

  • overwrite – if set to True, will overwrite -an existing view with the same ID

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Returns:
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None

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-get_annotation_by_id(ann_id) → Annotation[source]
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-get_annotations(at_type: str | TypesBase | None = None, **properties) → Generator[Annotation, None, None][source]
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Look for certain annotations in this view, specified by parameters

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Parameters:
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    -

  • at_type – @type of the annotations to look for. When this is None, any @type will match.

    • -

  • properties – properties of the annotations to look for. When given more than one property, all properties must match. Note that annotation type metadata are specified in the contains view metadata, not in individual annotation objects.

    • -
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-get_document_by_id(doc_id) → Document[source]
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-get_documents() → List[Document][source]
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-new_annotation(at_type: str | TypesBase, aid: str | None = None, overwrite=False, **properties) → Annotation[source]
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Generates a new mmif.serialize.annotation.Annotation -object and adds it to the current view.

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Fails if there is already an annotation with the same ID -in the view, unless overwrite is set to True.

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Parameters:
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  • at_type – the desired @type of the annotation.

    • -

  • aid – the desired ID of the annotation, when not given, -the mmif SDK tries to automatically generate an ID based on -Annotation type and existing annotations in the view.

    • -

  • overwrite – if set to True, will overwrite an -existing annotation with the same ID.

    • -
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Raises:
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KeyError – if overwrite is set to False and -an annotation with the same ID exists -in the view.

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Returns:
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the generated mmif.serialize.annotation.Annotation

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-new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
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Adds a new element to the contains metadata.

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Parameters:
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  • at_type – the @type of the annotation type being added

    • -

  • contains_metadata – any metadata associated with the annotation type

    • -
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Returns:
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the generated Contain object

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-new_textdocument(text: str, lang: str = 'en', did: str | None = None, overwrite=False, **properties) → Document[source]
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Generates a new mmif.serialize.annotation.Document -object, particularly typed as TextDocument and adds it to the current view.

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Fails if there is already a text document with the same ID -in the view, unless overwrite is set to True.

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Parameters:
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  • text – text content of the new document

    • -

  • lang – ISO 639-1 code of the language used in the new document

    • -

  • did – the desired ID of the document, when not given, -the mmif SDK tries to automatically generate an ID based on -Annotation type and existing documents in the view.

    • -

  • overwrite – if set to True, will overwrite an -existing document with the same ID

    • -
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Raises:
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KeyError – if overwrite is set to False and -an document with the same ID exists -in the view

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Returns:
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the generated mmif.serialize.annotation.Document

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-set_error(err_message: str, err_trace: str) → None[source]
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- -
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-class mmif.serialize.view.ViewMetadata(viewmetadata_obj: bytes | str | dict | None = None)[source]
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Bases: MmifObject

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ViewMetadata object that represents the metadata object within a MMIF view.

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Parameters:
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viewmetadata_obj – the JSON data that defines the metadata

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-add_app_configuration(config_key: str, config_value: str | int | float | bool | None | List[str | int | float | bool | None]) → None[source]
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Add a configuration key-value pair to the app_configuration dictionary.

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-add_contain(contain: Contain, at_type: str | TypesBase) → None[source]
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-add_parameter(param_key: str, param_value: str)[source]
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Add a single runtime parameter to the view metadata. Note that parameter value must be a string.

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-add_parameters(**runtime_params: str)[source]
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Add runtime parameters as a batch (dict) to the view metadata. Note that parameter values must be strings.

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-add_warnings(*warnings: Warning)[source]
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-emtpy_warnings()[source]
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-get_app_configuration(config_key: str) → str | int | float | bool | None | List[str | int | float | bool | None][source]
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Get a configuration value from the app_configuration dictionary.

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-get_parameter(param_key: str) → str[source]
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Get a runtime parameter from the view metadata.

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-new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
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Adds a new element to the contains dictionary.

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Parameters:
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    -

  • at_type – the @type of the annotation type being added

    • -

  • contains_metadata – any metadata associated with the annotation type

    • -
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Returns:
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the generated Contain object

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-set_error(message: str, stack_trace: str)[source]
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- -
- -
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mmif.serialize.annotation module

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The annotation module contains the classes used to represent a -MMIF annotation as a live Python object.

-

In MMIF, annotations are created by apps in a pipeline as a part -of a view. For documentation on how views are represented, see -mmif.serialize.view.

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-class mmif.serialize.annotation.Annotation(anno_obj: bytes | str | dict | None = None)[source]
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Bases: MmifObject

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MmifObject that represents an annotation in a MMIF view.

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-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]]) → None[source]
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Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

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- -
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-property at_type: TypesBase[source]
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- -
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-static check_prop_value_is_simple_enough(value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]]) → bool[source]
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- -
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-get(prop_name: str) → AnnotationProperties | str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]][source]
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A special getter for Annotation properties. This is to allow for -directly accessing properties without having to go through the -properties object, or view-level annotation properties encoded in the -view.metadata.contains dict. Note that the regular props will take -the priority over the ephemeral props when there are conflicts.

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- -
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-get_property(prop_name: str) → AnnotationProperties | str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]][source]
-

A special getter for Annotation properties. This is to allow for -directly accessing properties without having to go through the -properties object, or view-level annotation properties encoded in the -view.metadata.contains dict. Note that the regular props will take -the priority over the ephemeral props when there are conflicts.

-
- -
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-property id: str[source]
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- -
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-is_document()[source]
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- -
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-is_type(at_type: str | TypesBase) → bool[source]
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Check if the @type of this object matches.

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- -
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-property parent: str[source]
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- -
- -
-
-class mmif.serialize.annotation.AnnotationProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject, MutableMapping[str, T]

-

AnnotationProperties object that represents the -properties object within a MMIF annotation.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
- -
-
-class mmif.serialize.annotation.Document(doc_obj: bytes | str | dict | None = None)[source]
-

Bases: Annotation

-

Document object that represents a single document in a MMIF file.

-

A document is identified by an ID, and contains certain attributes -and potentially contains the contents of the document itself, -metadata about how the document was created, and/or a list of -subdocuments grouped together logically.

-

If document_obj is not provided, an empty Document will be generated.

-
-
Parameters:
-

document_obj – the JSON data that defines the document

-
-
-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None]) → None[source]
-

Adds a property to the document’s properties.

-

Unlike the parent Annotation class, added properties of a -Document object can be lost during serialization unless it belongs -to somewhere in a Mmif object. This is because we want to keep -Document object as “read-only” as possible. Thus, if you want to add -a property to a Document object,

-
    -

  • add the document to a Mmif object (either in the documents list or -in a view from the views list), or

    • -

  • directly write to Document.properties instead of using this method -(which is not recommended).

    • -
-

With the former method, the SDK will record the added property as a -Annotation annotation object, separate from the original Document -object. See Mmif.generate_capital_annotations() for more.

-

A few notes to keep in mind:

-
    -

  1. You can’t overwrite an existing property of a Document object.

    2. -

  2. A MMIF can have multiple Annotation objects with the same -property name but different values. When this happens, the SDK will -only keep the latest value (in order of appearances in views list) of -the property, effectively overwriting the previous values.

    3. -
-
- -
-
-get(prop_name)[source]
-

A special getter for Document properties. The major difference from -the super class’s Annotation.get() method is that Document -class has one more set of “pending” properties, that are added after -the Document object is created and will be serialized as a separate -Annotation object of which @type = Annotation. The -pending properties will take the priority over the regular properties -when there are conflicts.

-
- -
-
-get_property(prop_name)[source]
-

A special getter for Document properties. The major difference from -the super class’s Annotation.get() method is that Document -class has one more set of “pending” properties, that are added after -the Document object is created and will be serialized as a separate -Annotation object of which @type = Annotation. The -pending properties will take the priority over the regular properties -when there are conflicts.

-
- -
-
-property location: str | None[source]
-

location property must be a legitimate URI. That is, should the document be a local file -then the file:// scheme must be used. -Returns None when no location is set.

-
- -
-
-location_address() → str | None[source]
-

Retrieves the full address from the document location URI. -Returns None when no location is set.

-
- -
-
-location_path(nonexist_ok=True) → str | None[source]
-

Retrieves a path that’s resolved to a pathname in the local file system. -To obtain the original value of the “path” part in the location string -(before resolving), use properties.location_path_literal method. -Returns None when no location is set.

-
-
Parameters:
-

nonexist_ok – if False, raise FileNotFoundError when the resolved path doesn’t exist

-
-
-
- -
-
-location_scheme() → str | None[source]
-

Retrieves URI scheme of the document location. -Returns None when no location is set.

-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.DocumentProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: AnnotationProperties

-

DocumentProperties object that represents the -properties object within a MMIF document.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
-
-property location: str | None[source]
-

location property must be a legitimate URI. That is, should the document be a local file -then the file:// scheme must be used. -Returns None when no location is set.

-
- -
-
-location_address() → str | None[source]
-

Retrieves the full address from the document location URI. -Returns None when no location is set.

-
- -
-
-location_path() → str | None[source]
-
- -
-
-location_path_literal() → str | None[source]
-

Retrieves only path name of the document location (hostname is ignored). -Returns None when no location is set.

-
- -
-
-location_path_resolved(nonexist_ok=True) → str | None[source]
-

Retrieves only path name of the document location (hostname is ignored), -and then try to resolve the path name in the local file system. -This method should be used when the document scheme is file or empty. -For other schemes, users should install mmif-locdoc-<scheme> plugin.

-

Returns None when no location is set. -Raise ValueError when no code found to resolve the given location scheme.

-
- -
-
-location_scheme() → str | None[source]
-

Retrieves URI scheme of the document location. -Returns None when no location is set.

-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.Text(text_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-
-
-property lang: str[source]
-
- -
-
-property value: str[source]
-
- -
- -
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- - -
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- -
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- - - \ No newline at end of file diff --git a/docs/1.0.12/autodoc/mmif.utils.html b/docs/1.0.12/autodoc/mmif.utils.html deleted file mode 100644 index 5c6bf16d..00000000 --- a/docs/1.0.12/autodoc/mmif.utils.html +++ /dev/null @@ -1,578 +0,0 @@ - - - - - - - - - mmif.utils module — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.utils module

-
-

mmif.utils.video_document_helper module

-
-
-mmif.utils.video_document_helper.capture(video_document: Document)[source]
-

Captures a video file using OpenCV and adds fps, frame count, and duration as properties to the document.

-
-
Parameters:
-

video_document – Document instance that holds a video document ("@type": ".../VideoDocument/...")

-
-
Returns:
-

OpenCV VideoCapture object

-
-
-
- -
-
-mmif.utils.video_document_helper.convert_timeframe(mmif: Mmif, time_frame: Annotation, out_unit: str) → Tuple[int | float | str, int | float | str][source]
-

Converts start and end points in a TimeFrame annotation a different time unit.

-
-
Parameters:
-
    -

  • mmif – Mmif instance

    • -

  • time_frame – Annotation instance that holds a time interval annotation ("@type": ".../TimeFrame/...")

    • -

  • out_unit – time unit to which the point is converted

    • -
-
-
Returns:
-

tuple of frame numbers (integer) or seconds/milliseconds (float) of input start and end

-
-
-
- -
-
-mmif.utils.video_document_helper.convert_timepoint(mmif: Mmif, timepoint: Annotation, out_unit: str) → int | float | str[source]
-

Converts a time point included in an annotation to a different time unit. -The input annotation must have timePoint property.

-
-
Parameters:
-
    -

  • mmif – input MMIF to obtain fps and input timeunit

    • -

  • timepoint – Annotation instance with timePoint property

    • -

  • out_unit – time unit to which the point is converted (frames, seconds, milliseconds)

    • -
-
-
Returns:
-

frame number (integer) or second/millisecond (float) of input timepoint

-
-
-
- -
-
-mmif.utils.video_document_helper.extract_frames_as_images(video_document: Document, framenums: List[int], as_PIL: bool = False)[source]
-

Extracts frames from a video document as a list of numpy.ndarray. -Use with sample_frames() function to get the list of frame numbers first.

-
-
Parameters:
-
    -

  • video_document – Document instance that holds a video document ("@type": ".../VideoDocument/...")

    • -

  • framenums – integers representing the frame numbers to extract

    • -

  • as_PIL – return PIL.Image.Image instead of ndarray

    • -
-
-
Returns:
-

frames as a list of ndarray or Image

-
-
-
- -
-
-mmif.utils.video_document_helper.extract_mid_frame(mmif: Mmif, time_frame: Annotation, as_PIL: bool = False)[source]
-

Extracts the middle frame of a time interval annotation as a numpy ndarray.

-
-
Parameters:
-
    -

  • mmif – Mmif instance

    • -

  • time_frame – Annotation instance that holds a time interval annotation ("@type": ".../TimeFrame/...")

    • -

  • as_PIL – return Image instead of ndarray

    • -
-
-
Returns:
-

frame as a numpy.ndarray or PIL.Image.Image

-
-
-
- -
-
-mmif.utils.video_document_helper.framenum_to_millisecond(video_doc: Document, frame: int)[source]
-

Converts a frame number to a millisecond value.

-
- -
-
-mmif.utils.video_document_helper.framenum_to_second(video_doc: Document, frame: int)[source]
-

Converts a frame number to a second value.

-
- -
-
-mmif.utils.video_document_helper.get_annotation_property(mmif, annotation, prop_name)[source]
-
-

Deprecated since version 1.0.8: Use mmif.serialize.annotation.Annotation.get_property() method instead.

-
-

Get a property value from an annotation. If the property is not found in the annotation, it will look up the metadata of the annotation’s parent view and return the value from there. -xisting

-
- -
-
-mmif.utils.video_document_helper.get_framerate(video_document: Document) → float[source]
-

Gets the frame rate of a video document. First by checking the fps property of the document, then by capturing the video.

-
-
Parameters:
-

video_document – Document instance that holds a video document ("@type": ".../VideoDocument/...")

-
-
Returns:
-

frames per second as a float, rounded to 2 decimal places

-
-
-
- -
-
-mmif.utils.video_document_helper.get_mid_framenum(mmif: Mmif, time_frame: Annotation)[source]
-

Calculates the middle frame number of a time interval annotation.

-
-
Parameters:
-
    -

  • mmif – Mmif instance

    • -

  • time_frame – Annotation instance that holds a time interval annotation ("@type": ".../TimeFrame/...")

    • -
-
-
Returns:
-

middle frame number as an integer

-
-
-
- -
-
-mmif.utils.video_document_helper.millisecond_to_framenum(video_doc: Document, millisecond: float) → int[source]
-

Converts a millisecond value to a frame number.

-
- -
-
-mmif.utils.video_document_helper.sample_frames(start_frame: int, end_frame: int, sample_ratio: int = 1) → List[int][source]
-

Helper function to sample frames from a time interval. -Can also be used as a “cutoff” function when used with start_frame==0 and sample_ratio==1.

-
-
Parameters:
-
    -

  • start_frame – start frame of the interval

    • -

  • end_frame – end frame of the interval

    • -

  • sample_ratio – sample ratio (or step) to configure how often to take a frame, default is 1, meaning all consecutive frames are sampled

    • -
-
-
-
- -
-
-mmif.utils.video_document_helper.second_to_framenum(video_doc: Document, second) → int[source]
-

Converts a second value to a frame number.

-
- -
-
-

mmif.utils.sequence_helper module

-

This module provides helpers for handling sequence labeling. Specifically, it provides

-
    -

  • a generalized label re-mapper for “post-binning” of labels

    • -

  • conversion from a list of CLAMS annotations (with classification props) into a list of reals (scores by labels), can be combined with the label re-mapper mentioned above

    • -

  • mmif.utils.sequence_helper.smooth_outlying_short_intervals(): a simple smoothing algorithm by trimming “short” outlier sequences

    • -
-

However, it DOES NOT provide

-
    -

  • direct conversion between CLAMS annotations. For example, it does not directly handle stitching of TimePoint into TimeFrames.

    • -

  • support for multi-class scenario, such as handling of _competing_ subsequence or overlapping labels.

    • -
-

Some functions can use optional external libraries (e.g., numpy) for better performance. -Hence, if you see a warning about missing optional packages, you might want to install them by running pip install mmif-python[seq].

-
-
-mmif.utils.sequence_helper.build_label_remapper(src_labels: List[str], dst_labels: Dict[str, str | int | float | bool | None]) → Dict[str, str | int | float | bool | None][source]
-

Build a label remapper dictionary from source and destination labels.

-
-
Parameters:
-
    -

  • src_labels – a list of all labels on the source side

    • -

  • dst_labels – a dict from source labels to destination labels. -Source labels not in this dict will be remapped to a negative label (-).

    • -
-
-
Returns:
-

a dict that exhaustively maps source labels to destination labels

-
-
-
- -
-
-mmif.utils.sequence_helper.build_score_lists(classifications: ~typing.List[~typing.Dict], label_remapper: ~typing.Dict, score_remap_op: ~typing.Callable[[...], float] = <built-in function max>) → Tuple[Dict[str, int], numpy.ndarray][source]
-

Build lists of scores indexed by the label names.

-
-
Parameters:
-
    -

  • classifications – list of dictionaries of classification results, taken from input annotation objects

    • -

  • label_remapper – a dictionary that maps source label names to destination label names (formerly “postbin”)

    • -

  • score_remap_op – a function to remap the scores from multiple source labels binned to a destination label -common choices are max, min, or sum

    • -
-
-
Returns:
-

    -

  1. a dictionary that maps label names to their index in the score list

    2. -

  2. 2-d numpy array of scores, of which rows are indexed by label map dict (first return value)

    3. -
-

-
-
-
- -
-
-mmif.utils.sequence_helper.smooth_outlying_short_intervals(scores: List[float], min_spseq_size: int, min_snseq_size: int, min_score: float = 0.5)[source]
-

Given a list of scores, a score threshold, and smoothing parameters, -identify the intervals of “positive” scores by “trimming” the short -positive sequences (“spseq”) and short negative sequences (“snseq”). To -decide the positivity, first step is binarization of the scores by the -min_score threshold. Given Sr as “raw” input real-number scores -list, and min_score=0.5,

-
-
Sr: [0.3, 0.6, 0.2, 0.8, 0.2, 0.9, 0.8, 0.5, 0.1, 0.5, 0.8, 0.3, 1.0, 0.7, 0.5, 0.5, 0.5, 0.8, 0.3, 0.6]
-
-
-
-

the binarization is done by simply comparing each score to the -threshold to get S list of binary scores

-
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1.0 :                                     |                      
-0.9 :                |                    |                      
-0.8 :          |     |  |           |     |              |       
-0.7 :          |     |  |           |     |  |           |       
-0.6 :    |     |     |  |           |     |  |           |     | 
-0.5 :----+-----+-----+--+--+-----+--+-----+--+--+--+--+--+-----+-
-0.4 :    |     |     |  |  |     |  |     |  |  |  |  |  |     | 
-0.3 : |  |     |     |  |  |     |  |  |  |  |  |  |  |  |  |  | 
-0.2 : |  |  |  |  |  |  |  |     |  |  |  |  |  |  |  |  |  |  | 
-0.1 : |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | 
-0.0 +------------------------------------------------------------
-raw :.3 .6 .2 .8 .2 .9 .8 .5 .1 .5 .8 .3 1. .7 .5 .5 .5 .8 .3 .6
- S  : 0  1  0  1  0  1  1  0  0  0  1  0  1  1  0  1  1  1  0  1 
-
-
-
-

Note that the size of a positive or negative sequence can be as small -as 1.

-

Then, here are examples of smoothing a list of binary scores into -intervals, by trimming “very short” (under thresholds) sequences of -positive or negative:

-
-

Note

-

legends:

-
    -

  • t is unit index (e.g. time index)

    • -

  • S is the list of binary scores (zeros and ones)

    • -

  • I is the list of intervals after smoothing

    • -
-
-
    -

  1. with params min_spseq_size==1, min_snseq_size==4

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1]
-I: [0, 1--1--1--1--1--1--1--1--1--1--1--1, 0--0--0--0--0--0, 1]
-
    -
    -

    Explanation: min_snseq_size is used to smooth short sequences -of negative predictions. In this, zeros from t[7:10] are smoothed -into “one” I, while zeros from t[13:19] are kept as “zero” I. Note -that the “short” snseqs at the either ends (t[0:1]) are never -smoothed.

    -
    -
    2. -

  2. with params min_spseq_size==4, min_snseq_size==2

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1]
-I: [0, 1--1--1--1--1--1, 0--0--0--0--0--0--0--0--0--0--0--0--0]
-
    -
    -

    Explanation: min_spseq_size is used to smooth short sequences -of positive predictions. In this example, the spseqs of ones from -both t[10:13] and t[19:20] are smoothed. Note that the “short” -spseqs at the either ends (t[19:20]) are always smoothed.

    -
    -
    3. -

  3. with params min_spseq_size==4, min_snseq_size==4

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1]
-I: [0, 1--1--1--1--1--1--1--1--1--1--1--1--0--0--0--0--0--0--0]
-
    -
    -

    Explanation: When two threshold parameters are working together, -the algorithm will prioritize the smoothing of the snseqs over the -smoothing of the spseqs. Thus, in this example, the snseq t[7:10] -gets first smoothed “up” before the spseq t[10:13] is smoothed -“down”, resulting in a long final I.

    -
    -
    4. -

  4. with params min_spseq_size==4, min_snseq_size==4

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [1, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 1, 1]
-I: [1--1--1--1--1--1--1, 0--0--0--0, 1--1--1--1--1--1--1--1--1]
-
    -
    -

    Explanation: Since smoothing of snseqs is prioritized, short spseqs -at the beginning or the end can be kept.

    -
    -
    5. -

  5. with params min_spseq_size==1, min_snseq_size==1

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 1, 1]
-I: [0--0--0, 1--1--1--1, 0--0--0--0, 1--1--1--1, 0--0--0, 1--1]
-
    -
    -

    Explanation: When both width thresholds are set to 1, the algorithm -works essentially in the “stitching” only mode.

    -
    -
    6. -
-
-
Parameters:
-
    -

  • scores – SORTED list of scores to be smoothed. The score list -is assumed to be “exhaust” the entire time or space of -the underlying document segment. -(Sorted by the start, and then by the end of anchors)

    • -

  • min_score – minimum threshold to use to discard -low-scored units (strictly less than)

    • -

  • min_spseq_size – minimum size of a positive sequence not to be -smoothed (greater or equal to)

    • -

  • min_snseq_size – minimum size of a negative sequence not to be -smoothed (greater or equal to)

    • -
-
-
Returns:
-

list of tuples of start(inclusive)/end(exclusive) indices -of the “positive” sequences. Negative sequences (regardless of -their size) are not included in the output.

-
-
-
- -
-
-mmif.utils.sequence_helper.validate_labelset(annotations: Iterable[Annotation]) → List[str][source]
-

Simple check for a list of annotations to see if they have the same label set.

-
-
Raise:
-

AttributeError if an element in the input list doesn’t have the labelset property

-
-
Raise:
-

ValueError if different labelset values are found

-
-
Returns:
-

a list of the common labelset value (list of label names)

-
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- - Other Versions - v: 1.0.12 - - -
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mmif.vocabulary module

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mmif.vocabulary.annotation_types module

-
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-class mmif.vocabulary.annotation_types.AnnotationTypes(type_uri, fuzzymode=True)[source]
-

Bases: AnnotationTypesBase

-

This class contains the CLAMS annotation types -defined in the spec version 1.1.0 as class variables.

-
-
-Alignment = http://mmif.clams.ai/vocabulary/Alignment/v1[source]
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-Annotation = http://mmif.clams.ai/vocabulary/Annotation/v6[source]
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-BoundingBox = http://mmif.clams.ai/vocabulary/BoundingBox/v5[source]
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-Chapter = http://mmif.clams.ai/vocabulary/Chapter/v6[source]
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-Interval = http://mmif.clams.ai/vocabulary/Interval/v5[source]
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-NamedEntity = http://mmif.clams.ai/vocabulary/NamedEntity/v1[source]
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-NounChunk = http://mmif.clams.ai/vocabulary/NounChunk/v1[source]
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-Paragraph = http://mmif.clams.ai/vocabulary/Paragraph/v1[source]
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-Polygon = http://mmif.clams.ai/vocabulary/Polygon/v5[source]
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-Region = http://mmif.clams.ai/vocabulary/Region/v5[source]
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-Relation = http://mmif.clams.ai/vocabulary/Relation/v5[source]
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-Sentence = http://mmif.clams.ai/vocabulary/Sentence/v1[source]
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-Span = http://mmif.clams.ai/vocabulary/Span/v5[source]
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-TimeFrame = http://mmif.clams.ai/vocabulary/TimeFrame/v6[source]
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-TimePoint = http://mmif.clams.ai/vocabulary/TimePoint/v5[source]
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-Token = http://mmif.clams.ai/vocabulary/Token/v1[source]
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-VerbChunk = http://mmif.clams.ai/vocabulary/VerbChunk/v1[source]
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-VideoObject = http://mmif.clams.ai/vocabulary/VideoObject/v5[source]
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- -
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mmif.vocabulary.document_types module

-
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-class mmif.vocabulary.document_types.DocumentTypes(type_uri, fuzzymode=True)[source]
-

Bases: DocumentTypesBase

-

This class contains the CLAMS document types -defined in the spec version 1.1.0 as class variables.

-
-
-AudioDocument = http://mmif.clams.ai/vocabulary/AudioDocument/v1[source]
-
- -
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-Document = http://mmif.clams.ai/vocabulary/Document/v1[source]
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-ImageDocument = http://mmif.clams.ai/vocabulary/ImageDocument/v1[source]
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-TextDocument = http://mmif.clams.ai/vocabulary/TextDocument/v1[source]
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-VideoDocument = http://mmif.clams.ai/vocabulary/VideoDocument/v1[source]
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- - -
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- -
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- -
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mmif_docloc_http package

-

MMIF document location helper module for http and https schemes. -If you want to write your own docloc scheme handler, please use the source code of this module as a reference. -See this plug-in section for more information.

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-mmif_docloc_http.resolve(docloc)[source]
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  • MMIF consumer
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MMIF consumer

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A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the appliance documentation to learn more about the appliance.

-

MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance.

-
    -

  1. The code must be hosted on a public git repository (e.g. Github, Gitlab, …)

    2. -

  2. Must listen to 5000 port.

    3. -

  3. Must expose /display route .

    4. -

  4. /display router should response to GET requests.

    5. -

  5. In the GET request, a public URL of the input MMIF file is passed via file URL parameter.

    6. -

  6. On the codebase root, there must be a Dockerfile that can build a docker image that runs the web app.

    7. -
-

We provide an example consumer at https://github.com/clamsproject/mmif-visualizer.

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  • Welcome to mmif-python’s documentation!
    • -
  • -
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Welcome to mmif-python’s documentation!

-
-

MultiMedia Interchange Format

-

MMIF is a JSON(-LD)-based data format designed for transferring annotation data between computational analysis applications in CLAMS project.

-
-
-

mmif-python

-

mmif-python is a Python implementation of the MMIF data format. -mmif-python provides various helper classes and functions to handle MMIF JSON in Python, -including ;

-
    -

  1. de-/serialization of MMIF internal data structures to/from JSON

    2. -

  2. validation of MMIF JSON

    3. -

  3. handling of CLAMS vocabulary types

    4. -

  4. navigation of MMIF object via various “search” methods (e.g. mmif.get_all_views_contain(vocab_type)))

    5. -
-
-
-

For more …

- -
-

Contents

- -
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API documentation:

- -
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Indices and tables

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  • Getting Started
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Getting Started

-
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Overview

-

MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for reproducibility, transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF website. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects.

-
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Prerequisites

-
    -

  • Python: the latest mmif-python requires Python 3.8 or newer. We have no plan to support Python 2.7.

    • -
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-
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Installation

-

Package mmif-python is distributed via the official PyPI. Users are supposed to pip-install to get latest release.

-
pip install mmif-python
-
-
-

This will install a package mmif to local python.

-

The MMIF format and specification is evolving over time, and mmif-python package will be updated along with the changes in MMIF format.

-
-

Note

-

MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and mmif-python versions, please take time to read our decision on the subject here. If you need to know which python SDK supports which specification version, see Target MMIF Versions page.

-
-
-
-

MMIF Serialization

-

mmif.serialize.mmif.Mmif represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of mmif.serialize.model.MmifObject, including the mmif.serialize.mmif.Mmif. To start with an existing MMIF str, simple initiate a new Mmif object with the file.

-
import mmif
-from mmif import Mmif
-
-mmif_str = """{
-"metadata": {
-  "mmif": "http://mmif.clams.ai/1.0.0"
-},
-"documents": [
-  {
-    "@type": "http://mmif.clams.ai/vocabulary/VideoDocument/v1",
-    "properties": {
-      "id": "m1",
-      "mime": "video/mp4",
-      "location": "file:///var/archive/video-0012.mp4"
-    }
-  },
-  {
-    "@type": "http://mmif.clams.ai/vocabulary/TextDocument/v1",
-    "properties": {
-      "id": "m2",
-      "mime": "text/plain",
-      "location": "file:///var/archive/video-0012-transcript.txt"
-    }
-  }
-],
-"views": []}"""
-mmif_obj = Mmif(mmif_str)
-
-
-

Few notes;

-
    -

  1. MMIF does not carry the primary source files in it.

    2. -

  2. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version mmif-python implementation of the MMIF might not be able to load an unsupported version of MMIF string.

    3. -
-

When serializing back to str, call mmif.serialize.model.MmifObject.serialize() on the object.

-

To get subcomponents, you can use various getters implemented in subclasses. For example;

-
from mmif.vocabulary.document_types import DocumentTypes
-
-for video in mmif_obj.Mmif.get_documents_by_type(DocumentTypes.VideoDocument):
-  with open(video.location_path(), 'b') as in_video:
-    # do something with the video file
-
-
-

For a full list of available helper methods, please refer to the API documentation.

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mmif package

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mmif_docloc_http package

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- - - \ No newline at end of file diff --git a/docs/1.0.12/objects.inv b/docs/1.0.12/objects.inv deleted file mode 100644 index 86675ef6..00000000 Binary files a/docs/1.0.12/objects.inv and /dev/null differ diff --git a/docs/1.0.12/plugins.html b/docs/1.0.12/plugins.html deleted file mode 100644 index d2309c52..00000000 --- a/docs/1.0.12/plugins.html +++ /dev/null @@ -1,234 +0,0 @@ - - - - - - - - - Developing plugins for MMIF Python SDK — mmif-python documentation - - - - - - - - - - - - - - - - - -
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  • Developing plugins for MMIF Python SDK
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Developing plugins for MMIF Python SDK

-
-

Overview

-

As MMIF JSON files can carry information about media document files without actually carrying file contents, file accessing modules in mmif Python package (distributed as mmif-python on PyPI) are designed to be lightweight and flexible so that it can work with additional “plugin” Python packages that can handle concrete file access.

-

This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF website. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects.

-

Developer can write simple plugins that can provide additional functionalities to mmif-python. For example, mmif-python does not provide any file access functionality beyond a local file system (with file scheme), but it can be extended with a plugin that can handle file access over different protocols (e.g. http, s3, ftp, etc).

-

This document contains information about how to write plugins for mmif-python.

-
-

Document Location Scheme Plugins

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mmif.serialize.annotation.Document class has various methods to access parts of location property of the document. The location is in URI/IRI format (SCHEME://HOSTNAME/PATH, in a nutshell) and it has to be resolved to a local file for CLAMS Apps to process the local file to analyze and extract information about the media and its contents. The core mmif-python distribution only provides a default implementation that can handle file scheme URIs.

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To add a document location handler plugin, you need to implement a Python “package” (do not confuse with PYPI distribution), that meets these requirements;

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  1. the package must be named mmif_docloc_<SCHEME>. For example, to implement a handler for s3 scheme, the package name must be mmif_docloc_s3. The prefix is important as it’s used in the plugin discovery process from the core mmif-python modules.

    2. -

  2. the top module of the package must have a function named resolve. The function must take a single argument, which is a str of the document location URI. The function must return a str of the local file path. For example, if the document location is s3://mybucket/myfile.mp4, a Python user should be able to to something like this;

    3. -
-
import mmif_docloc_s3
-resolved = mmif_docloc_s3.resolve('s3://mybucket/myfile.mp4')
-# then resolved must be a local file path that can be used to open the file
-
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Here’s a minimal example codebase that you refer to when you develop a docloc plugin.

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(However, before you start writing your own plugin for a specific URI scheme, checking if there’s already a PyPI distribution for the scheme might be a good idea.)

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$ tree .
-.
-├── mmif_docloc_dummy
-│   └── __init__.py
-├── pyproject.toml
-└── setup.cfg
-
- $ cat pyproject.toml
-[build-system]
-requires = ["setuptools"]
-build-backend = "setuptools.build_meta"
-
-$ cat setup.cfg
-[metadata]
-name = mmif_docloc_dummy  # this name is IMPORTANT
-version = 0.0.1
-description = a plugin to mmif-pyhon to handle `dummy` location scheme
-
-
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And the plugin code.

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# mmif_docloc_dummy/__init__.py
-doc_types = {'video': 'mp4'}
-
-def resolve(docloc):
-    scheme = 'dummy'
-    if docloc.startswith(f'{scheme}://'):
-        doc_id, doc_type = docloc.split('.')
-        return f'/path/to/{doc_id}.{doc_types[doc_type]}'
-    else:
-        raise ValueError(f'cannot handle document location scheme: {docloc}')
-
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-
-

Bulit-in Document Location Scheme Plugins

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At the moment, mmif-python PyPI distribution ships a built-in docloc plugin that support both http and https schemes. -Take a look at mmif_docloc_http module for details.

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- - - - - - - - \ No newline at end of file diff --git a/docs/1.0.12/searchindex.js b/docs/1.0.12/searchindex.js deleted file mode 100644 index 6005e4a0..00000000 --- a/docs/1.0.12/searchindex.js +++ /dev/null @@ -1 +0,0 @@ -Search.setIndex({"alltitles": {"API documentation:": [[5, null]], "Bulit-in Document Location Scheme Plugins": [[8, "bulit-in-document-location-scheme-plugins"]], "Contents": [[5, null]], "Developing plugins for MMIF Python SDK": [[8, null]], "Document Location Scheme Plugins": [[8, "document-location-scheme-plugins"]], "For more \u2026": [[5, "for-more"]], "Getting Started": [[6, null]], "Indices and tables": [[5, "indices-and-tables"]], "Installation": [[6, "installation"]], "MMIF Serialization": [[6, "mmif-serialization"]], "MMIF consumer": [[4, null]], "MultiMedia Interchange Format": [[5, "multimedia-interchange-format"]], "Overview": [[6, "overview"], [8, "overview"]], "Prerequisites": [[6, "prerequisites"]], "Target MMIF Versions": [[9, null]], "Target Specification Versions": [[9, "id1"]], "Welcome to mmif-python\u2019s documentation!": [[5, null]], "mmif package": [[7, null]], "mmif-python": [[5, "mmif-python"]], "mmif.serialize module": [[0, null]], "mmif.serialize.annotation module": [[0, "module-mmif.serialize.annotation"]], "mmif.serialize.mmif module": [[0, "module-mmif.serialize.mmif"]], "mmif.serialize.model module": [[0, "module-mmif.serialize.model"]], "mmif.serialize.view module": [[0, "module-mmif.serialize.view"]], "mmif.utils module": [[1, null]], "mmif.utils.sequence_helper module": [[1, "module-mmif.utils.sequence_helper"]], "mmif.utils.video_document_helper module": [[1, "module-mmif.utils.video_document_helper"]], "mmif.vocabulary module": [[2, null]], "mmif.vocabulary.annotation_types module": [[2, "module-mmif.vocabulary.annotation_types"]], "mmif.vocabulary.document_types module": [[2, "module-mmif.vocabulary.document_types"]], "mmif_docloc_http package": [[3, null], [7, "mmif-docloc-http-package"]]}, 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"mmif.serialize.mmif.Mmif.add_view", false]], "add_warnings() (mmif.serialize.view.viewmetadata method)": [[0, "mmif.serialize.view.ViewMetadata.add_warnings", false]], "alignment (mmif.vocabulary.annotation_types.annotationtypes attribute)": [[2, "mmif.vocabulary.annotation_types.AnnotationTypes.Alignment", false]], "annotation (class in mmif.serialize.annotation)": [[0, "mmif.serialize.annotation.Annotation", false]], "annotation (mmif.vocabulary.annotation_types.annotationtypes attribute)": [[2, "mmif.vocabulary.annotation_types.AnnotationTypes.Annotation", false]], "annotationproperties (class in mmif.serialize.annotation)": [[0, "mmif.serialize.annotation.AnnotationProperties", false]], "annotationtypes (class in mmif.vocabulary.annotation_types)": [[2, "mmif.vocabulary.annotation_types.AnnotationTypes", false]], "append() (mmif.serialize.model.datalist method)": [[0, "mmif.serialize.model.DataList.append", false]], "at_type (mmif.serialize.annotation.annotation property)": [[0, "mmif.serialize.annotation.Annotation.at_type", false]], "audiodocument (mmif.vocabulary.document_types.documenttypes attribute)": [[2, "mmif.vocabulary.document_types.DocumentTypes.AudioDocument", false]], "boundingbox (mmif.vocabulary.annotation_types.annotationtypes attribute)": [[2, "mmif.vocabulary.annotation_types.AnnotationTypes.BoundingBox", false]], "build_label_remapper() (in module mmif.utils.sequence_helper)": [[1, "mmif.utils.sequence_helper.build_label_remapper", false]], "build_score_lists() (in module mmif.utils.sequence_helper)": [[1, "mmif.utils.sequence_helper.build_score_lists", false]], "capture() (in module mmif.utils.video_document_helper)": [[1, "mmif.utils.video_document_helper.capture", false]], "chapter (mmif.vocabulary.annotation_types.annotationtypes attribute)": [[2, "mmif.vocabulary.annotation_types.AnnotationTypes.Chapter", false]], "check_prop_value_is_simple_enough() (mmif.serialize.annotation.annotation static method)": [[0, "mmif.serialize.annotation.Annotation.check_prop_value_is_simple_enough", false]], "contain (class in mmif.serialize.view)": [[0, "mmif.serialize.view.Contain", false]], "convert_timeframe() (in module mmif.utils.video_document_helper)": [[1, "mmif.utils.video_document_helper.convert_timeframe", false]], "convert_timepoint() (in module mmif.utils.video_document_helper)": [[1, "mmif.utils.video_document_helper.convert_timepoint", false]], "datadict (class in mmif.serialize.model)": [[0, "mmif.serialize.model.DataDict", false]], "datalist (class in mmif.serialize.model)": [[0, "mmif.serialize.model.DataList", false]], "default() (mmif.serialize.model.mmifobjectencoder method)": [[0, "mmif.serialize.model.MmifObjectEncoder.default", false]], "deserialize() (mmif.serialize.model.datalist method)": [[0, "mmif.serialize.model.DataList.deserialize", false]], "deserialize() (mmif.serialize.model.mmifobject method)": [[0, "mmif.serialize.model.MmifObject.deserialize", false]], "disallow_additional_properties() (mmif.serialize.model.mmifobject method)": [[0, "mmif.serialize.model.MmifObject.disallow_additional_properties", false]], "document (class in mmif.serialize.annotation)": [[0, "mmif.serialize.annotation.Document", false]], "document (mmif.vocabulary.document_types.documenttypes attribute)": [[2, "mmif.vocabulary.document_types.DocumentTypes.Document", false]], "documentproperties (class in mmif.serialize.annotation)": [[0, "mmif.serialize.annotation.DocumentProperties", false]], "documenttypes (class in mmif.vocabulary.document_types)": [[2, "mmif.vocabulary.document_types.DocumentTypes", false]], "empty() (mmif.serialize.model.datadict method)": [[0, "mmif.serialize.model.DataDict.empty", false]], "empty() (mmif.serialize.model.datalist method)": [[0, "mmif.serialize.model.DataList.empty", false]], "emtpy_warnings() (mmif.serialize.view.viewmetadata method)": [[0, "mmif.serialize.view.ViewMetadata.emtpy_warnings", false]], "extract_frames_as_images() (in module mmif.utils.video_document_helper)": [[1, "mmif.utils.video_document_helper.extract_frames_as_images", false]], "extract_mid_frame() (in module mmif.utils.video_document_helper)": [[1, "mmif.utils.video_document_helper.extract_mid_frame", false]], "framenum_to_millisecond() (in module mmif.utils.video_document_helper)": [[1, "mmif.utils.video_document_helper.framenum_to_millisecond", false]], "framenum_to_second() (in module mmif.utils.video_document_helper)": [[1, "mmif.utils.video_document_helper.framenum_to_second", false]], "generate_capital_annotations() (mmif.serialize.mmif.mmif method)": [[0, "mmif.serialize.mmif.Mmif.generate_capital_annotations", false]], "get() (mmif.serialize.annotation.annotation method)": [[0, "mmif.serialize.annotation.Annotation.get", false]], "get() (mmif.serialize.annotation.document method)": [[0, "mmif.serialize.annotation.Document.get", false]], "get() (mmif.serialize.model.datadict method)": [[0, "mmif.serialize.model.DataDict.get", false]], "get() (mmif.serialize.model.datalist method)": [[0, "mmif.serialize.model.DataList.get", false]], "get_alignments() (mmif.serialize.mmif.mmif method)": [[0, "mmif.serialize.mmif.Mmif.get_alignments", false]], "get_all_views_contain() (mmif.serialize.mmif.mmif method)": [[0, "mmif.serialize.mmif.Mmif.get_all_views_contain", false]], "get_annotation_by_id() (mmif.serialize.view.view method)": [[0, "mmif.serialize.view.View.get_annotation_by_id", false]], "get_annotation_property() (in module mmif.utils.video_document_helper)": [[1, "mmif.utils.video_document_helper.get_annotation_property", false]], "get_annotations() (mmif.serialize.view.view method)": [[0, "mmif.serialize.view.View.get_annotations", false]], "get_app_configuration() (mmif.serialize.view.viewmetadata method)": [[0, "mmif.serialize.view.ViewMetadata.get_app_configuration", false]], "get_document_by_id() (mmif.serialize.mmif.mmif method)": [[0, "mmif.serialize.mmif.Mmif.get_document_by_id", false]], "get_document_by_id() (mmif.serialize.view.view method)": [[0, "mmif.serialize.view.View.get_document_by_id", false]], "get_document_location() (mmif.serialize.mmif.mmif method)": [[0, "mmif.serialize.mmif.Mmif.get_document_location", false]], "get_documents() (mmif.serialize.view.view method)": [[0, "mmif.serialize.view.View.get_documents", false]], "get_documents_by_app() (mmif.serialize.mmif.mmif method)": [[0, "mmif.serialize.mmif.Mmif.get_documents_by_app", false]], "get_documents_by_property() (mmif.serialize.mmif.mmif method)": [[0, "mmif.serialize.mmif.Mmif.get_documents_by_property", false]], "get_documents_by_type() (mmif.serialize.mmif.mmif method)": [[0, "mmif.serialize.mmif.Mmif.get_documents_by_type", false]], "get_documents_in_view() (mmif.serialize.mmif.mmif method)": [[0, "mmif.serialize.mmif.Mmif.get_documents_in_view", false]], "get_documents_locations() (mmif.serialize.mmif.mmif method)": [[0, "mmif.serialize.mmif.Mmif.get_documents_locations", false]], "get_end() (mmif.serialize.mmif.mmif method)": [[0, "mmif.serialize.mmif.Mmif.get_end", false]], "get_framerate() (in module mmif.utils.video_document_helper)": [[1, "mmif.utils.video_document_helper.get_framerate", false]], "get_mid_framenum() (in module mmif.utils.video_document_helper)": [[1, "mmif.utils.video_document_helper.get_mid_framenum", false]], "get_parameter() (mmif.serialize.view.viewmetadata method)": [[0, "mmif.serialize.view.ViewMetadata.get_parameter", false]], "get_property() (mmif.serialize.annotation.annotation method)": [[0, "mmif.serialize.annotation.Annotation.get_property", false]], "get_property() (mmif.serialize.annotation.document method)": [[0, "mmif.serialize.annotation.Document.get_property", false]], "get_start() (mmif.serialize.mmif.mmif method)": [[0, "mmif.serialize.mmif.Mmif.get_start", false]], "get_view_by_id() (mmif.serialize.mmif.mmif method)": [[0, "mmif.serialize.mmif.Mmif.get_view_by_id", false]], "get_view_contains() (mmif.serialize.mmif.mmif method)": [[0, "mmif.serialize.mmif.Mmif.get_view_contains", false]], "get_views_contain() (mmif.serialize.mmif.mmif method)": [[0, "mmif.serialize.mmif.Mmif.get_views_contain", false]], "get_views_for_document() (mmif.serialize.mmif.mmif method)": [[0, "mmif.serialize.mmif.Mmif.get_views_for_document", false]], "id (mmif.serialize.annotation.annotation property)": [[0, "mmif.serialize.annotation.Annotation.id", false]], "id_delimiter (mmif.serialize.mmif.mmif attribute)": [[0, "mmif.serialize.mmif.Mmif.id_delimiter", false]], "imagedocument (mmif.vocabulary.document_types.documenttypes attribute)": [[2, "mmif.vocabulary.document_types.DocumentTypes.ImageDocument", false]], "interval (mmif.vocabulary.annotation_types.annotationtypes attribute)": [[2, "mmif.vocabulary.annotation_types.AnnotationTypes.Interval", false]], "is_document() (mmif.serialize.annotation.annotation method)": [[0, "mmif.serialize.annotation.Annotation.is_document", false]], "is_empty() (mmif.serialize.model.mmifobject static method)": [[0, "mmif.serialize.model.MmifObject.is_empty", false]], "is_type() (mmif.serialize.annotation.annotation method)": [[0, "mmif.serialize.annotation.Annotation.is_type", false]], "items() (mmif.serialize.model.datadict method)": [[0, "mmif.serialize.model.DataDict.items", false]], "keys() (mmif.serialize.model.datadict method)": [[0, "mmif.serialize.model.DataDict.keys", false]], "lang (mmif.serialize.annotation.text property)": [[0, "mmif.serialize.annotation.Text.lang", false]], "location (mmif.serialize.annotation.document property)": [[0, "mmif.serialize.annotation.Document.location", false]], "location (mmif.serialize.annotation.documentproperties property)": [[0, "mmif.serialize.annotation.DocumentProperties.location", false]], "location_address() (mmif.serialize.annotation.document method)": [[0, "mmif.serialize.annotation.Document.location_address", false]], "location_address() (mmif.serialize.annotation.documentproperties method)": [[0, 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"format": 5, "get": 6, "indic": 5, "instal": 6, "interchang": 5, "locat": 8, "mmif": [0, 1, 2, 4, 5, 6, 7, 8, 9], "mmif_docloc_http": [3, 7], "model": 0, "modul": [0, 1, 2], "more": 5, "multimedia": 5, "overview": [6, 8], "packag": [3, 7], "plugin": 8, "prerequisit": 6, "python": [5, 8], "scheme": 8, "sdk": 8, "sequence_help": 1, "serial": [0, 6], "specif": 9, "start": 6, "tabl": 5, "target": 9, "util": 1, "version": 9, "video_document_help": 1, "view": 0, "vocabulari": 2, "welcom": 5}}) \ No newline at end of file diff --git a/docs/1.0.12/target-versions.html b/docs/1.0.12/target-versions.html deleted file mode 100644 index c30c723a..00000000 --- a/docs/1.0.12/target-versions.html +++ /dev/null @@ -1,282 +0,0 @@ - - - - - - - - - Target MMIF Versions — mmif-python documentation - - - - - - - - - - - - - - - - - -
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  • Target MMIF Versions
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Target MMIF Versions

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This article provides targeting MMIF specification versions of different versions of mmif-python SDK.

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Target Specification Versions

mmif-python version

Target MMIF Specification

1.0.12

1.1.0

1.0.11

1.0.4

1.0.10.dev1

1.0.3

1.0.10

1.0.2

1.0.9

1.1.0

1.0.8

1.0.0

1.0.7

1.0.0

1.0.6

1.0.0

1.0.5

1.0.0

1.0.4

1.0.0

1.0.3

1.0.0

1.0.2

1.0.0

1.0.1

1.0.0

1.0.0

0.5.0

0.5.2

0.5.0

0.5.1

0.5.0

0.5.0

0.5.0

0.4.8

0.4.2

0.4.7

0.4.1

0.4.6

0.4.0

0.4.5

0.4.0

0.4.4

0.4.0

0.4.3

0.4.0

0.4.2

0.4.0

0.4.1

0.4.0

0.4.0

0.4.0

0.3.5

0.3.1

0.3.4

0.3.1

0.3.3

0.3.1

0.3.2

0.3.1

0.3.1

0.3.0

0.3.0

0.3.0

0.2.2

0.2.1

0.2.1

0.2.1

0.2.0

0.2.1

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0.3.0
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0.3.1
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0.3.2
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0.3.3
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0.3.4
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0.3.5
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0.4.0
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0.4.1
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0.4.2
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0.4.3
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0.4.4
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0.4.5
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0.4.6
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0.4.7
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0.4.8
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0.5.0
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0.5.1
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0.5.2
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1.0.0
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1.0.1
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1.0.10
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1.0.11
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1.0.12
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1.0.13
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1.0.14
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1.0.15
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1.0.16
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1.0.17
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1.0.18
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1.0.19
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1.0.2
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1.0.3
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1.0.4
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1.0.5
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1.0.6
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1.0.7
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1.0.8
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1.0.9
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1.1.0
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-mmif.serialize.model module ---------------------------- - -.. automodule:: mmif.serialize.model - :members: - :undoc-members: - :show-inheritance: - -mmif.serialize.mmif module --------------------------- - -.. automodule:: mmif.serialize.mmif - :members: - :undoc-members: - :show-inheritance: - -mmif.serialize.view module --------------------------- - -.. automodule:: mmif.serialize.view - :members: - :undoc-members: - :show-inheritance: - -mmif.serialize.annotation module --------------------------------- - -.. automodule:: mmif.serialize.annotation - :members: - :undoc-members: - :show-inheritance: - diff --git a/docs/1.0.13/_sources/autodoc/mmif.utils.rst.txt b/docs/1.0.13/_sources/autodoc/mmif.utils.rst.txt deleted file mode 100644 index 9a6ecc44..00000000 --- a/docs/1.0.13/_sources/autodoc/mmif.utils.rst.txt +++ /dev/null @@ -1,18 +0,0 @@ -mmif.utils module -================= - -mmif.utils.video_document_helper module ----------------------------------------- - -.. automodule:: mmif.utils.video_document_helper - :members: - :undoc-members: - :show-inheritance: - -mmif.utils.sequence_helper module ---------------------------------- - -.. automodule:: mmif.utils.sequence_helper - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/1.0.13/_sources/autodoc/mmif.vocabulary.rst.txt b/docs/1.0.13/_sources/autodoc/mmif.vocabulary.rst.txt deleted file mode 100644 index d250c6a3..00000000 --- a/docs/1.0.13/_sources/autodoc/mmif.vocabulary.rst.txt +++ /dev/null @@ -1,18 +0,0 @@ -mmif.vocabulary module -====================== - -mmif.vocabulary.annotation\_types module ----------------------------------------- - -.. automodule:: mmif.vocabulary.annotation_types - :members: - :undoc-members: - :show-inheritance: - -mmif.vocabulary.document\_types module --------------------------------------- - -.. automodule:: mmif.vocabulary.document_types - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/1.0.13/_sources/autodoc/mmif_docloc_http.rst.txt b/docs/1.0.13/_sources/autodoc/mmif_docloc_http.rst.txt deleted file mode 100644 index b76c8df5..00000000 --- a/docs/1.0.13/_sources/autodoc/mmif_docloc_http.rst.txt +++ /dev/null @@ -1,11 +0,0 @@ -mmif_docloc_http package -======================== - -MMIF document location helper module for `http` and `https` schemes. -If you want to write your own docloc scheme handler, please use the source code of this module as a reference. -See this :ref:`plug-in section ` for more information. - -.. automodule:: mmif_docloc_http - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/1.0.13/_sources/consumer-tutorial.rst.txt b/docs/1.0.13/_sources/consumer-tutorial.rst.txt deleted file mode 100644 index c54634e2..00000000 --- a/docs/1.0.13/_sources/consumer-tutorial.rst.txt +++ /dev/null @@ -1,17 +0,0 @@ -.. _consumer-tutorial: - -MMIF consumer -================================= - -A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the `appliance documentation `_ to learn more about the appliance. - -MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance. - -#. The code must be hosted on a public git repository (e.g. Github, Gitlab, ...) -#. Must listen to ``5000`` port. -#. Must expose ``/display`` route . -#. ``/display`` router should response to ``GET`` requests. -#. In the ``GET`` request, a public URL of the input MMIF file is passed via ``file`` URL parameter. -#. On the codebase root, there must be a ``Dockerfile`` that can build a `docker `_ image that runs the web app. - -We provide an example consumer at https://github.com/clamsproject/mmif-visualizer. diff --git a/docs/1.0.13/_sources/index.rst.txt b/docs/1.0.13/_sources/index.rst.txt deleted file mode 100644 index beb56aae..00000000 --- a/docs/1.0.13/_sources/index.rst.txt +++ /dev/null @@ -1,26 +0,0 @@ -Welcome to mmif-python's documentation! -======================================= - -.. mdinclude:: ../README.md - -.. toctree:: - :maxdepth: 2 - :caption: Contents - - introduction - plugins - target-versions - -.. toctree:: - :maxdepth: 2 - :caption: API documentation: - - modules - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/docs/1.0.13/_sources/introduction.rst.txt b/docs/1.0.13/_sources/introduction.rst.txt deleted file mode 100644 index cfd9eaf7..00000000 --- a/docs/1.0.13/_sources/introduction.rst.txt +++ /dev/null @@ -1,89 +0,0 @@ -.. _introduction: - -Getting Started -=============== - - -Overview ---------- - -MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for reproducibility, transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF website `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects. - -Prerequisites -------------- - -* `Python `_: the latest ``mmif-python`` requires Python 3.8 or newer. We have no plan to support `Python 2.7 `_. - -Installation ---------------- - -Package ``mmif-python`` is distributed via the official PyPI. Users are supposed to pip-install to get latest release. - -.. code-block:: bash - - pip install mmif-python - -This will install a package `mmif` to local python. - -The MMIF format and specification is evolving over time, and ``mmif-python`` package will be updated along with the changes in MMIF format. - -.. note:: MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and ``mmif-python`` versions, please take time to read our decision on the subject `here `_. If you need to know which python SDK supports which specification version, see :ref:`target-versions` page. - -MMIF Serialization ---------------------------- - -:class:`mmif.serialize.mmif.Mmif` represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of :class:`mmif.serialize.model.MmifObject`, including the :class:`mmif.serialize.mmif.Mmif`. To start with an existing MMIF :class:`str`, simple initiate a new ``Mmif`` object with the file. - -.. code-block:: python - - import mmif - from mmif import Mmif - - mmif_str = """{ - "metadata": { - "mmif": "http://mmif.clams.ai/1.0.0" - }, - "documents": [ - { - "@type": "http://mmif.clams.ai/vocabulary/VideoDocument/v1", - "properties": { - "id": "m1", - "mime": "video/mp4", - "location": "file:///var/archive/video-0012.mp4" - } - }, - { - "@type": "http://mmif.clams.ai/vocabulary/TextDocument/v1", - "properties": { - "id": "m2", - "mime": "text/plain", - "location": "file:///var/archive/video-0012-transcript.txt" - } - } - ], - "views": []}""" - mmif_obj = Mmif(mmif_str) - - -Few notes; - -#. MMIF does not carry the primary source files in it. -#. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version ``mmif-python`` implementation of the MMIF might not be able to load an unsupported version of MMIF string. - -When serializing back to :class:`str`, call :meth:`mmif.serialize.model.MmifObject.serialize` on the object. - -To get subcomponents, you can use various getters implemented in subclasses. For example; - -.. code-block:: python - - from mmif.vocabulary.document_types import DocumentTypes - - for video in mmif_obj.Mmif.get_documents_by_type(DocumentTypes.VideoDocument): - with open(video.location_path(), 'b') as in_video: - # do something with the video file - - -For a full list of available helper methods, please refer to :ref:`the API documentation `. - diff --git a/docs/1.0.13/_sources/modules.rst.txt b/docs/1.0.13/_sources/modules.rst.txt deleted file mode 100644 index 4bb9307d..00000000 --- a/docs/1.0.13/_sources/modules.rst.txt +++ /dev/null @@ -1,20 +0,0 @@ -.. _apidoc: - -mmif package -============ - -.. toctree:: - :maxdepth: 4 - - autodoc/mmif.serialize - autodoc/mmif.vocabulary - autodoc/mmif.utils - -mmif_docloc_http package -======================== - -.. toctree:: - :maxdepth: 2 - - autodoc/mmif_docloc_http - diff --git a/docs/1.0.13/_sources/plugins.rst.txt b/docs/1.0.13/_sources/plugins.rst.txt deleted file mode 100644 index 9907c495..00000000 --- a/docs/1.0.13/_sources/plugins.rst.txt +++ /dev/null @@ -1,83 +0,0 @@ -.. _plugins: - -Developing plugins for MMIF Python SDK -====================================== - - -Overview --------- - -As MMIF JSON files can carry information about media document files without actually carrying file contents, file accessing modules in ``mmif`` Python package (distributed as ``mmif-python`` on PyPI) are designed to be lightweight and flexible so that it can work with additional "plugin" Python packages that can handle concrete file access. - - -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF website `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects. - -Developer can write simple plugins that can provide additional functionalities to ``mmif-python``. For example, ``mmif-python`` does not provide any file access functionality beyond a local file system (with ``file`` scheme), but it can be extended with a plugin that can handle file access over different protocols (e.g. ``http``, ``s3``, ``ftp``, etc). - -This document contains information about how to write plugins for ``mmif-python``. - -.. _docloc_plugin: - -Document Location Scheme Plugins -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -:class:`mmif.serialize.annotation.Document` class has various methods to access parts of ``location`` property of the document. The location is in `URI/IRI format `_ (``SCHEME://HOSTNAME/PATH``, in a nutshell) and it has to be resolved to a local file for CLAMS Apps to process the local file to analyze and extract information about the media and its contents. The core ``mmif-python`` distribution only provides a default implementation that can handle ``file`` scheme URIs. - -To add a document location handler plugin, you need to implement a Python `"package" `_ (do not confuse with PYPI distribution), that meets these requirements; - -#. the package must be named ``mmif_docloc_``. For example, to implement a handler for ``s3`` scheme, the package name must be ``mmif_docloc_s3``. The prefix is important as it's used in the plugin discovery process from the core ``mmif-python`` modules. -#. the top module of the package must have a function named ``resolve``. The function must take a single argument, which is a :class:`str` of the document location URI. The function must return a :class:`str` of the local file path. For example, if the document location is ``s3://mybucket/myfile.mp4``, a Python user should be able to to something like this; - -.. code-block:: python - - import mmif_docloc_s3 - resolved = mmif_docloc_s3.resolve('s3://mybucket/myfile.mp4') - # then resolved must be a local file path that can be used to open the file - - -Here's a minimal example codebase that you refer to when you develop a ``docloc`` plugin. - -(However, before you start writing your own plugin for a specific URI scheme, checking `if there's already a PyPI distribution `_ for the scheme might be a good idea.) - -.. code-block:: sh - - $ tree . - . - ├── mmif_docloc_dummy - │ └── __init__.py - ├── pyproject.toml - └── setup.cfg - - $ cat pyproject.toml - [build-system] - requires = ["setuptools"] - build-backend = "setuptools.build_meta" - - $ cat setup.cfg - [metadata] - name = mmif_docloc_dummy # this name is IMPORTANT - version = 0.0.1 - description = a plugin to mmif-pyhon to handle `dummy` location scheme - - -And the plugin code. - -.. code-block:: python - - # mmif_docloc_dummy/__init__.py - doc_types = {'video': 'mp4'} - - def resolve(docloc): - scheme = 'dummy' - if docloc.startswith(f'{scheme}://'): - doc_id, doc_type = docloc.split('.') - return f'/path/to/{doc_id}.{doc_types[doc_type]}' - else: - raise ValueError(f'cannot handle document location scheme: {docloc}') - -Bulit-in Document Location Scheme Plugins -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -At the moment, ``mmif-python`` PyPI distribution ships a built-in *docloc* plugin that support both ``http`` and ``https`` schemes. -Take a look at :mod:`mmif_docloc_http` module for details. diff --git a/docs/1.0.13/_sources/target-versions.rst.txt b/docs/1.0.13/_sources/target-versions.rst.txt deleted file mode 100644 index 34216d3e..00000000 --- a/docs/1.0.13/_sources/target-versions.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _target-versions: - -Target MMIF Versions -==================== - -This article provides targeting MMIF specification versions of different versions of ``mmif-python`` SDK. - -.. csv-table:: Target Specification Versions - :file: target-versions.csv - :header-rows: 1 diff --git a/docs/1.0.13/_static/_sphinx_javascript_frameworks_compat.js b/docs/1.0.13/_static/_sphinx_javascript_frameworks_compat.js deleted file mode 100644 index 81415803..00000000 --- a/docs/1.0.13/_static/_sphinx_javascript_frameworks_compat.js +++ /dev/null @@ -1,123 +0,0 @@ -/* Compatability shim for jQuery and underscores.js. - * - * Copyright Sphinx contributors - * Released under the two clause BSD licence - */ - -/** - * small helper function to urldecode strings - * - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL - */ -jQuery.urldecode = function(x) { - if (!x) { - return x - } - return decodeURIComponent(x.replace(/\+/g, ' ')); -}; - -/** - * small helper function to urlencode strings - */ -jQuery.urlencode = encodeURIComponent; - -/** - * This function returns the parsed url parameters of the - * current request. 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- document.dispatchEvent(event); - }); -}); \ No newline at end of file diff --git a/docs/1.0.13/_static/language_data.js b/docs/1.0.13/_static/language_data.js deleted file mode 100644 index c7fe6c6f..00000000 --- a/docs/1.0.13/_static/language_data.js +++ /dev/null @@ -1,192 +0,0 @@ -/* - * This script contains the language-specific data used by searchtools.js, - * namely the list of stopwords, stemmer, scorer and splitter. - */ - -var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"]; - - -/* Non-minified version is copied as a separate JS file, if available */ - -/** - * Porter Stemmer - */ -var Stemmer = function() { - - var step2list = { - ational: 'ate', - tional: 'tion', - enci: 'ence', - anci: 'ance', - izer: 'ize', - bli: 'ble', - alli: 'al', - entli: 'ent', - eli: 'e', - ousli: 'ous', - ization: 'ize', - ation: 'ate', - ator: 'ate', - alism: 'al', - iveness: 'ive', - fulness: 'ful', - ousness: 'ous', - aliti: 'al', - iviti: 'ive', - biliti: 'ble', - logi: 'log' - }; 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- -/** - * Simple result scoring code. - */ -if (typeof Scorer === "undefined") { - var Scorer = { - // Implement the following function to further tweak the score for each result - // The function takes a result array [docname, title, anchor, descr, score, filename] - // and returns the new score. - /* - score: result => { - const [docname, title, anchor, descr, score, filename, kind] = result - return score - }, - */ - - // query matches the full name of an object - objNameMatch: 11, - // or matches in the last dotted part of the object name - objPartialMatch: 6, - // Additive scores depending on the priority of the object - objPrio: { - 0: 15, // used to be importantResults - 1: 5, // used to be objectResults - 2: -5, // used to be unimportantResults - }, - // Used when the priority is not in the mapping. - objPrioDefault: 0, - - // query found in title - title: 15, - partialTitle: 7, - // query found in terms - term: 5, - partialTerm: 2, - }; -} - -// Global search result kind enum, used by themes to style search results. -class SearchResultKind { - static get index() { return "index"; } - static get object() { return "object"; } - static get text() { return "text"; } - static get title() { return "title"; } -} - -const _removeChildren = (element) => { - while (element && element.lastChild) element.removeChild(element.lastChild); -}; - -/** - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping - */ -const _escapeRegExp = (string) => - string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string - -const _displayItem = (item, searchTerms, highlightTerms) => { - const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; - const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; - const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; - const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; - const contentRoot = document.documentElement.dataset.content_root; - - const [docName, title, anchor, descr, score, _filename, kind] = item; - - let listItem = document.createElement("li"); - // Add a class representing the item's type: - // can be used by a theme's CSS selector for styling - // See SearchResultKind for the class names. - listItem.classList.add(`kind-${kind}`); - let requestUrl; - let linkUrl; - if (docBuilder === "dirhtml") { - // dirhtml builder - let dirname = docName + "/"; - if (dirname.match(/\/index\/$/)) - dirname = dirname.substring(0, dirname.length - 6); - else if (dirname === "index/") dirname = ""; - requestUrl = contentRoot + dirname; - linkUrl = requestUrl; - } else { - // normal html builders - requestUrl = contentRoot + docName + docFileSuffix; - linkUrl = docName + docLinkSuffix; - } - let linkEl = listItem.appendChild(document.createElement("a")); - linkEl.href = linkUrl + anchor; - linkEl.dataset.score = score; - linkEl.innerHTML = title; - if (descr) { - listItem.appendChild(document.createElement("span")).innerHTML = - " (" + descr + ")"; - // highlight search terms in the description - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - } - else if (showSearchSummary) - fetch(requestUrl) - .then((responseData) => responseData.text()) - .then((data) => { - if (data) - listItem.appendChild( - Search.makeSearchSummary(data, searchTerms, anchor) - ); 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Please make sure that all words are spelled correctly and that you've selected enough categories." - ); - else - Search.status.innerText = Documentation.ngettext( - "Search finished, found one page matching the search query.", - "Search finished, found ${resultCount} pages matching the search query.", - resultCount, - ).replace('${resultCount}', resultCount); -}; -const _displayNextItem = ( - results, - resultCount, - searchTerms, - highlightTerms, -) => { - // results left, load the summary and display it - // this is intended to be dynamic (don't sub resultsCount) - if (results.length) { - _displayItem(results.pop(), searchTerms, highlightTerms); - setTimeout( - () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), - 5 - ); - } - // search finished, update title and status message - else _finishSearch(resultCount); -}; -// Helper function used by query() to order search results. -// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. -// Order the results by score (in opposite order of appearance, since the -// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. -const _orderResultsByScoreThenName = (a, b) => { - const leftScore = a[4]; - const rightScore = b[4]; - if (leftScore === rightScore) { - // same score: sort alphabetically - const leftTitle = a[1].toLowerCase(); - const rightTitle = b[1].toLowerCase(); - if (leftTitle === rightTitle) return 0; - return leftTitle > rightTitle ? -1 : 1; // inverted is intentional - } - return leftScore > rightScore ? 1 : -1; -}; - -/** - * Default splitQuery function. Can be overridden in ``sphinx.search`` with a - * custom function per language. - * - * The regular expression works by splitting the string on consecutive characters - * that are not Unicode letters, numbers, underscores, or emoji characters. - * This is the same as ``\W+`` in Python, preserving the surrogate pair area. - */ -if (typeof splitQuery === "undefined") { - var splitQuery = (query) => query - .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) - .filter(term => term) // remove remaining empty strings -} - -/** - * Search Module - */ -const Search = { - _index: null, - _queued_query: null, - _pulse_status: -1, - - htmlToText: (htmlString, anchor) => { - const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - for (const removalQuery of [".headerlink", "script", "style"]) { - htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); - } - if (anchor) { - const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); - if (anchorContent) return anchorContent.textContent; - - console.warn( - `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` - ); - } - - // if anchor not specified or not found, fall back to main content - const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent) return docContent.textContent; - - console.warn( - "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." - ); - return ""; - }, - - init: () => { - const query = new URLSearchParams(window.location.search).get("q"); - document - .querySelectorAll('input[name="q"]') - .forEach((el) => (el.value = query)); - if (query) Search.performSearch(query); - }, - - loadIndex: (url) => - (document.body.appendChild(document.createElement("script")).src = url), - - setIndex: (index) => { - Search._index = index; - if (Search._queued_query !== null) { - const query = Search._queued_query; - Search._queued_query = null; - Search.query(query); - } - }, - - hasIndex: () => Search._index !== null, - - deferQuery: (query) => (Search._queued_query = query), - - stopPulse: () => (Search._pulse_status = -1), - - startPulse: () => { - if (Search._pulse_status >= 0) return; - - const pulse = () => { - Search._pulse_status = (Search._pulse_status + 1) % 4; - Search.dots.innerText = ".".repeat(Search._pulse_status); - if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); - }; - pulse(); - }, - - /** - * perform a search for something (or wait until index is loaded) - */ - performSearch: (query) => { - // create the required interface elements - const searchText = document.createElement("h2"); - searchText.textContent = _("Searching"); - const searchSummary = document.createElement("p"); - searchSummary.classList.add("search-summary"); - searchSummary.innerText = ""; - const searchList = document.createElement("ul"); - searchList.setAttribute("role", "list"); - searchList.classList.add("search"); - - const out = document.getElementById("search-results"); - Search.title = out.appendChild(searchText); - Search.dots = Search.title.appendChild(document.createElement("span")); - Search.status = out.appendChild(searchSummary); - Search.output = out.appendChild(searchList); - - const searchProgress = document.getElementById("search-progress"); - // Some themes don't use the search progress node - if (searchProgress) { - searchProgress.innerText = _("Preparing search..."); - } - Search.startPulse(); - - // index already loaded, the browser was quick! - if (Search.hasIndex()) Search.query(query); - else Search.deferQuery(query); - }, - - _parseQuery: (query) => { - // stem the search terms and add them to the correct list - const stemmer = new Stemmer(); - const searchTerms = new Set(); - const excludedTerms = new Set(); - const highlightTerms = new Set(); - const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); - splitQuery(query.trim()).forEach((queryTerm) => { - const queryTermLower = queryTerm.toLowerCase(); - - // maybe skip this "word" - // stopwords array is from language_data.js - if ( - stopwords.indexOf(queryTermLower) !== -1 || - queryTerm.match(/^\d+$/) - ) - return; - - // stem the word - let word = stemmer.stemWord(queryTermLower); - // select the correct list - if (word[0] === "-") excludedTerms.add(word.substr(1)); - else { - searchTerms.add(word); - highlightTerms.add(queryTermLower); - } - }); - - if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js - localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) - } - - // console.debug("SEARCH: searching for:"); - // console.info("required: ", [...searchTerms]); - // console.info("excluded: ", [...excludedTerms]); - - return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; - }, - - /** - * execute search (requires search index to be loaded) - */ - _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - - // Collect multiple result groups to be sorted separately and then ordered. - // Each is an array of [docname, title, anchor, descr, score, filename, kind]. - const normalResults = []; - const nonMainIndexResults = []; - - _removeChildren(document.getElementById("search-progress")); - - const queryLower = query.toLowerCase().trim(); - for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { - for (const [file, id] of foundTitles) { - const score = Math.round(Scorer.title * queryLower.length / title.length); - const boost = titles[file] === title ? 1 : 0; // add a boost for document titles - normalResults.push([ - docNames[file], - titles[file] !== title ? `${titles[file]} > ${title}` : title, - id !== null ? "#" + id : "", - null, - score + boost, - filenames[file], - SearchResultKind.title, - ]); - } - } - } - - // search for explicit entries in index directives - for (const [entry, foundEntries] of Object.entries(indexEntries)) { - if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id, isMain] of foundEntries) { - const score = Math.round(100 * queryLower.length / entry.length); - const result = [ - docNames[file], - titles[file], - id ? "#" + id : "", - null, - score, - filenames[file], - SearchResultKind.index, - ]; - if (isMain) { - normalResults.push(result); - } else { - nonMainIndexResults.push(result); - } - } - } - } - - // lookup as object - objectTerms.forEach((term) => - normalResults.push(...Search.performObjectSearch(term, objectTerms)) - ); - - // lookup as search terms in fulltext - normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); - - // let the scorer override scores with a custom scoring function - if (Scorer.score) { - normalResults.forEach((item) => (item[4] = Scorer.score(item))); - nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); - } - - // Sort each group of results by score and then alphabetically by name. - normalResults.sort(_orderResultsByScoreThenName); - nonMainIndexResults.sort(_orderResultsByScoreThenName); - - // Combine the result groups in (reverse) order. - // Non-main index entries are typically arbitrary cross-references, - // so display them after other results. - let results = [...nonMainIndexResults, ...normalResults]; - - // remove duplicate search results - // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept - let seen = new Set(); - results = results.reverse().reduce((acc, result) => { - let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); - if (!seen.has(resultStr)) { - acc.push(result); - seen.add(resultStr); - } - return acc; - }, []); - - return results.reverse(); - }, - - query: (query) => { - const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); - const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); - - // for debugging - //Search.lastresults = results.slice(); // a copy - // console.info("search results:", Search.lastresults); - - // print the results - _displayNextItem(results, results.length, searchTerms, highlightTerms); - }, - - /** - * search for object names - */ - performObjectSearch: (object, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const objects = Search._index.objects; - const objNames = Search._index.objnames; - const titles = Search._index.titles; - - const results = []; - - const objectSearchCallback = (prefix, match) => { - const name = match[4] - const fullname = (prefix ? prefix + "." : "") + name; - const fullnameLower = fullname.toLowerCase(); - if (fullnameLower.indexOf(object) < 0) return; - - let score = 0; - const parts = fullnameLower.split("."); - - // check for different match types: exact matches of full name or - // "last name" (i.e. last dotted part) - if (fullnameLower === object || parts.slice(-1)[0] === object) - score += Scorer.objNameMatch; - else if (parts.slice(-1)[0].indexOf(object) > -1) - score += Scorer.objPartialMatch; // matches in last name - - const objName = objNames[match[1]][2]; - const title = titles[match[0]]; - - // If more than one term searched for, we require other words to be - // found in the name/title/description - const otherTerms = new Set(objectTerms); - otherTerms.delete(object); - if (otherTerms.size > 0) { - const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); - if ( - [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) - ) - return; - } - - let anchor = match[3]; - if (anchor === "") anchor = fullname; - else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; - - const descr = objName + _(", in ") + title; - - // add custom score for some objects according to scorer - if (Scorer.objPrio.hasOwnProperty(match[2])) - score += Scorer.objPrio[match[2]]; - else score += Scorer.objPrioDefault; - - results.push([ - docNames[match[0]], - fullname, - "#" + anchor, - descr, - score, - filenames[match[0]], - SearchResultKind.object, - ]); - }; - Object.keys(objects).forEach((prefix) => - objects[prefix].forEach((array) => - objectSearchCallback(prefix, array) - ) - ); - return results; - }, - - /** - * search for full-text terms in the index - */ - performTermsSearch: (searchTerms, excludedTerms) => { - // prepare search - const terms = Search._index.terms; - const titleTerms = Search._index.titleterms; - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - - const scoreMap = new Map(); - const fileMap = new Map(); - - // perform the search on the required terms - searchTerms.forEach((word) => { - const files = []; - const arr = [ - { files: terms[word], score: Scorer.term }, - { files: titleTerms[word], score: Scorer.title }, - ]; - // add support for partial matches - if (word.length > 2) { - const escapedWord = _escapeRegExp(word); - if (!terms.hasOwnProperty(word)) { - Object.keys(terms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: terms[term], score: Scorer.partialTerm }); - }); - } - if (!titleTerms.hasOwnProperty(word)) { - Object.keys(titleTerms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); - }); - } - } - - // no match but word was a required one - if (arr.every((record) => record.files === undefined)) return; - - // found search word in contents - arr.forEach((record) => { - if (record.files === undefined) return; - - let recordFiles = record.files; - if (recordFiles.length === undefined) recordFiles = [recordFiles]; - files.push(...recordFiles); - - // set score for the word in each file - recordFiles.forEach((file) => { - if (!scoreMap.has(file)) scoreMap.set(file, {}); - scoreMap.get(file)[word] = record.score; - }); - }); - - // create the mapping - files.forEach((file) => { - if (!fileMap.has(file)) fileMap.set(file, [word]); - else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); - }); - }); - - // now check if the files don't contain excluded terms - const results = []; - for (const [file, wordList] of fileMap) { - // check if all requirements are matched - - // as search terms with length < 3 are discarded - const filteredTermCount = [...searchTerms].filter( - (term) => term.length > 2 - ).length; - if ( - wordList.length !== searchTerms.size && - wordList.length !== filteredTermCount - ) - continue; - - // ensure that none of the excluded terms is in the search result - if ( - [...excludedTerms].some( - (term) => - terms[term] === file || - titleTerms[term] === file || - (terms[term] || []).includes(file) || - (titleTerms[term] || []).includes(file) - ) - ) - break; - - // select one (max) score for the file. - const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); - // add result to the result list - results.push([ - docNames[file], - titles[file], - "", - null, - score, - filenames[file], - SearchResultKind.text, - ]); - } - return results; - }, - - /** - * helper function to return a node containing the - * search summary for a given text. keywords is a list - * of stemmed words. - */ - makeSearchSummary: (htmlText, keywords, anchor) => { - const text = Search.htmlToText(htmlText, anchor); - if (text === "") return null; - - const textLower = text.toLowerCase(); - const actualStartPosition = [...keywords] - .map((k) => textLower.indexOf(k.toLowerCase())) - .filter((i) => i > -1) - .slice(-1)[0]; - const startWithContext = Math.max(actualStartPosition - 120, 0); - - const top = startWithContext === 0 ? "" : "..."; - const tail = startWithContext + 240 < text.length ? "..." : ""; - - let summary = document.createElement("p"); - summary.classList.add("context"); - summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; - - return summary; - }, -}; - -_ready(Search.init); diff --git a/docs/1.0.13/_static/sphinx_highlight.js b/docs/1.0.13/_static/sphinx_highlight.js deleted file mode 100644 index 8a96c69a..00000000 --- a/docs/1.0.13/_static/sphinx_highlight.js +++ /dev/null @@ -1,154 +0,0 @@ -/* Highlighting utilities for Sphinx HTML documentation. */ -"use strict"; - -const SPHINX_HIGHLIGHT_ENABLED = true - -/** - * highlight a given string on a node by wrapping it in - * span elements with the given class name. - */ -const _highlight = (node, addItems, text, className) => { - if (node.nodeType === Node.TEXT_NODE) { - const val = node.nodeValue; - const parent = node.parentNode; - const pos = val.toLowerCase().indexOf(text); - if ( - pos >= 0 && - !parent.classList.contains(className) && - !parent.classList.contains("nohighlight") - ) { - let span; - - const closestNode = parent.closest("body, svg, foreignObject"); - const isInSVG = closestNode && closestNode.matches("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.classList.add(className); - } - - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - const rest = document.createTextNode(val.substr(pos + text.length)); - parent.insertBefore( - span, - parent.insertBefore( - rest, - node.nextSibling - ) - ); - node.nodeValue = val.substr(0, pos); - /* There may be more occurrences of search term in this node. So call this - * function recursively on the remaining fragment. - */ - _highlight(rest, addItems, text, className); - - if (isInSVG) { - const rect = document.createElementNS( - "http://www.w3.org/2000/svg", - "rect" - ); - const bbox = parent.getBBox(); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute("class", className); - addItems.push({ parent: parent, target: rect }); - } - } - } else if (node.matches && !node.matches("button, select, textarea")) { - node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); - } -}; -const _highlightText = (thisNode, text, className) => { - let addItems = []; - _highlight(thisNode, addItems, text, className); - addItems.forEach((obj) => - obj.parent.insertAdjacentElement("beforebegin", obj.target) - ); -}; - -/** - * Small JavaScript module for the documentation. - */ -const SphinxHighlight = { - - /** - * highlight the search words provided in localstorage in the text - */ - highlightSearchWords: () => { - if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight - - // get and clear terms from localstorage - const url = new URL(window.location); - const highlight = - localStorage.getItem("sphinx_highlight_terms") - || url.searchParams.get("highlight") - || ""; - localStorage.removeItem("sphinx_highlight_terms") - url.searchParams.delete("highlight"); - window.history.replaceState({}, "", url); - - // get individual terms from highlight string - const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); - if (terms.length === 0) return; // nothing to do - - // There should never be more than one element matching "div.body" - const divBody = document.querySelectorAll("div.body"); - const body = divBody.length ? divBody[0] : document.querySelector("body"); - window.setTimeout(() => { - terms.forEach((term) => _highlightText(body, term, "highlighted")); - }, 10); - - const searchBox = document.getElementById("searchbox"); - if (searchBox === null) return; - searchBox.appendChild( - document - .createRange() - .createContextualFragment( - '

' + - '' + - _("Hide Search Matches") + - "

" - ) - ); - }, - - /** - * helper function to hide the search marks again - */ - hideSearchWords: () => { - document - .querySelectorAll("#searchbox .highlight-link") - .forEach((el) => el.remove()); - document - .querySelectorAll("span.highlighted") - .forEach((el) => el.classList.remove("highlighted")); - localStorage.removeItem("sphinx_highlight_terms") - }, - - initEscapeListener: () => { - // only install a listener if it is really needed - if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; - - document.addEventListener("keydown", (event) => { - // bail for input elements - if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; - // bail with special keys - if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; - if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { - SphinxHighlight.hideSearchWords(); - event.preventDefault(); - } - }); - }, -}; - -_ready(() => { - /* Do not call highlightSearchWords() when we are on the search page. - * It will highlight words from the *previous* search query. - */ - if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); - SphinxHighlight.initEscapeListener(); -}); diff --git a/docs/1.0.13/autodoc/mmif.serialize.html b/docs/1.0.13/autodoc/mmif.serialize.html deleted file mode 100644 index 4e3bacbf..00000000 --- a/docs/1.0.13/autodoc/mmif.serialize.html +++ /dev/null @@ -1,1322 +0,0 @@ - - - - - - - - - mmif.serialize module — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.serialize module

-
-

mmif.serialize.model module

-

The model module contains the classes used to represent an -abstract MMIF object as a live Python object.

-

The MmifObject class or one of its derivatives is subclassed by -all other classes defined in this SDK, except for MmifObjectEncoder.

-

These objects are generally instantiated from JSON, either as a string -or as an already-loaded Python dictionary. This base class provides the -core functionality for deserializing MMIF JSON data into live objects -and serializing live objects into MMIF JSON data. Specialized behavior -for the different components of MMIF is added in the subclasses.

-
-
-class mmif.serialize.model.DataDict(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject, Generic[T, S]

-
-
-empty()[source]
-
- -
-
-get(key: T, default=None) → S | None[source]
-
- -
-
-items()[source]
-
- -
-
-keys()[source]
-
- -
-
-update(other, overwrite)[source]
-
- -
-
-values()[source]
-
- -
- -
-
-class mmif.serialize.model.DataList(mmif_obj: bytes | str | list | None = None)[source]
-

Bases: MmifObject, Generic[T]

-

The DataList class is an abstraction that represents the -various lists found in a MMIF file, such as documents, subdocuments, -views, and annotations.

-
-
Parameters:
-

mmif_obj (Union[str, list]) – the data that the list contains

-
-
-
-
-append(value, overwrite)[source]
-
- -
-
-deserialize(mmif_json: str | list) → None[source]
-

Passes the input data into the internal deserializer.

-
- -
-
-empty()[source]
-
- -
-
-get(key: str) → T | None[source]
-

Standard dictionary-style get() method, albeit with no default -parameter. Relies on the implementation of __getitem__.

-

Will return None if the key is not found.

-
-
Parameters:
-

key – the key to search for

-
-
Returns:
-

the value matching that key

-
-
-
- -
- -
-
-class mmif.serialize.model.MmifObject(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: object

-

Abstract superclass for MMIF related key-value pair objects.

-

Any MMIF object can be initialized as an empty placeholder or -an actual representation with a JSON formatted string or equivalent -dict object argument.

-

This superclass has four specially designed instance variables, and these -variable names cannot be used as attribute names for MMIF objects.

-
    -

  1. _unnamed_attributes: -Only can be either None or an empty dictionary. If it’s set to None, -it means the class won’t take any Additional Attributes in the JSON -schema sense. If it’s a dict, users can throw any k-v pairs to the -class, EXCEPT for the reserved two key names.

    2. -

  2. _attribute_classes: -This is a dict from a key name to a specific python class to use for -deserialize the value. Note that a key name in this dict does NOT -have to be a named attribute, but is recommended to be one.

    3. -

  3. _required_attributes: -This is a simple list of names of attributes that are required in the object. -When serialize, an object will skip its empty (e.g. zero-length, or None) -attributes unless they are in this list. Otherwise, the serialized JSON -string would have empty representations (e.g. "", []).

    4. -

  4. _exclude_from_diff: -This is a simple list of names of attributes that should be excluded from -the diff calculation in __eq__.

    5. -
-

# TODO (krim @ 8/17/20): this dict is however, a duplicate with the type hints in the class definition. -Maybe there is a better way to utilize type hints (e.g. getting them as a programmatically), but for now -developers should be careful to add types to hints as well as to this dict.

-

Also note that those special attributes MUST be set in the __init__() -before calling super method, otherwise deserialization will not work.

-

And also, a subclass that has one or more named attributes, it must -set those attributes in the __init__() before calling super method. When -serializing a MmifObject, all empty attributes will be ignored, so for -optional named attributes, you must leave the values empty (len == 0), but -NOT None. Any None-valued named attributes will cause issues with current -implementation.

-
-
Parameters:
-

mmif_obj – JSON string or dict to initialize an object. -If not given, an empty object will be initialized, sometimes with -an ID value automatically generated, based on its parent object.

-
-
-
-
-deserialize(mmif_json: str | dict) → None[source]
-

Takes a JSON-formatted string or a simple dict that’s json-loaded from -such a string as an input and populates object’s fields with the values -specified in the input.

-
-
Parameters:
-

mmif_json – JSON-formatted string or dict from such a string -that represents a MMIF object

-
-
-
- -
-
-disallow_additional_properties() → None[source]
-

Call this method in __init__() to prevent the insertion -of unnamed attributes after initialization.

-
- -
-
-id_delimiter: ClassVar[str] = ':'[source]
-
- -
-
-static is_empty(obj) → bool[source]
-

return True if the obj is None or “emtpy”. The emptiness first defined as -having zero length. But for objects that lack __len__ method, we need -additional check.

-
- -
-
-reserved_names: Set[str] = {'_attribute_classes', '_exclude_from_diff', '_required_attributes', '_unnamed_attributes', 'reserved_names'}[source]
-
- -
-
-serialize(pretty: bool = False) → str[source]
-

Generates JSON representation of an object.

-
-
Parameters:
-

pretty – If True, returns string representation with indentation.

-
-
Returns:
-

JSON string of the object.

-
-
-
- -
-
-set_additional_property(key: str, value: Any) → None[source]
-

Method to set values in _unnamed_attributes.

-
-
Parameters:
-
    -

  • key – the attribute name

    • -

  • value – the desired value

    • -
-
-
Returns:
-

None

-
-
Raise:
-

AttributeError if additional properties are disallowed by disallow_additional_properties()

-
-
-
- -
-
-view_prefix: ClassVar[str] = 'v_'[source]
-
- -
- -
-
-class mmif.serialize.model.MmifObjectEncoder(*, skipkeys=False, ensure_ascii=True, check_circular=True, allow_nan=True, sort_keys=False, indent=None, separators=None, default=None)[source]
-

Bases: JSONEncoder

-

Encoder class to define behaviors of de-/serialization

-
-
-default(obj: MmifObject)[source]
-

Overrides default encoding behavior to prioritize MmifObject.serialize().

-
- -
- -
-
-

mmif.serialize.mmif module

-

The mmif module contains the classes used to represent a full MMIF -file as a live Python object.

-

See the specification docs and the JSON Schema file for more information.

-
-
-class mmif.serialize.mmif.Mmif(mmif_obj: bytes | str | dict | None = None, *, validate: bool = True)[source]
-

Bases: MmifObject

-

MmifObject that represents a full MMIF file.

-
-
Parameters:
-
    -

  • mmif_obj – the JSON data

    • -

  • validate – whether to validate the data against the MMIF JSON schema.

    • -
-
-
-
-
-add_document(document: Document, overwrite=False) → None[source]
-

Appends a Document object to the documents list.

-

Fails if there is already a document with the same ID in the MMIF object.

-
-
Parameters:
-
    -

  • document – the Document object to add

    • -

  • overwrite – if set to True, will overwrite -an existing view with the same ID

    • -
-
-
Returns:
-

None

-
-
-
- -
-
-add_view(view: View, overwrite=False) → None[source]
-

Appends a View object to the views list.

-

Fails if there is already a view with the same ID in the MMIF object.

-
-
Parameters:
-
    -

  • view – the Document object to add

    • -

  • overwrite – if set to True, will overwrite -an existing view with the same ID

    • -
-
-
Returns:
-

None

-
-
-
- -
-
-generate_capital_annotations()[source]
-

Automatically convert any “pending” temporary properties from -Document objects to Annotation objects . The generated Annotation -objects are then added to the last View in the views lists.

-

See https://github.com/clamsproject/mmif-python/issues/226 for rationale -behind this behavior and discussion.

-
- -
-
-get_alignments(at_type1: str | TypesBase, at_type2: str | TypesBase) → Dict[str, List[Annotation]][source]
-

Finds views where alignments between two given annotation types occurred.

-
-
Returns:
-

a dict that keyed by view IDs (str) and has lists of alignment Annotation objects as values.

-
-
-
- -
-
-get_all_views_contain(at_types: TypesBase | str | List[str | TypesBase]) → List[View][source]
-

Returns the list of all views in the MMIF if given types -are present in that view’s ‘contains’ metadata.

-
-
Parameters:
-

at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

-
-
Returns:
-

the list of views that contain the type

-
-
-
- -
-
-get_document_by_id(doc_id: str) → Document[source]
-

Finds a Document object with the given ID.

-
-
Parameters:
-

doc_id – the ID to search for

-
-
Returns:
-

a reference to the corresponding document, if it exists

-
-
Raises:
-

KeyError – if there is no corresponding document

-
-
-
- -
-
-get_document_location(m_type: DocumentTypes | str, path_only=False) → str | None[source]
-

Method to get the location of first document of given type.

-
-
Parameters:
-

m_type – the type to search for

-
-
Returns:
-

the value of the location field in the corresponding document

-
-
-
- -
-
-get_documents_by_app(app_id: str) → List[Document][source]
-

Method to get all documents object queries by its originated app name.

-
-
Parameters:
-

app_id – the app name to search for

-
-
Returns:
-

a list of documents matching the requested app name, or an empty list if the app not found

-
-
-
- -
-
-get_documents_by_property(prop_key: str, prop_value: str) → List[Document][source]
-

Method to retrieve documents by an arbitrary key-value pair in the document properties objects.

-
-
Parameters:
-
    -

  • prop_key – the metadata key to search for

    • -

  • prop_value – the metadata value to match

    • -
-
-
Returns:
-

a list of documents matching the requested metadata key-value pair

-
-
-
- -
-
-get_documents_by_type(doc_type: str | DocumentTypes) → List[Document][source]
-

Method to get all documents where the type matches a particular document type, which should be one of the CLAMS document types.

-
-
Parameters:
-

doc_type – the type of documents to search for, must be one of Document type defined in the CLAMS vocabulary.

-
-
Returns:
-

a list of documents matching the requested type, or an empty list if none found.

-
-
-
- -
-
-get_documents_in_view(vid: str | None = None) → List[Document][source]
-

Method to get all documents object queries by a view id.

-
-
Parameters:
-

vid – the source view ID to search for

-
-
Returns:
-

a list of documents matching the requested source view ID, or an empty list if the view not found

-
-
-
- -
-
-get_documents_locations(m_type: DocumentTypes | str, path_only=False) → List[str | None][source]
-

This method returns the file paths of documents of given type. -Only top-level documents have locations, so we only check them.

-
-
Parameters:
-

m_type – the type to search for

-
-
Returns:
-

a list of the values of the location fields in the corresponding documents

-
-
-
- -
-
-get_end(annotation: Annotation) → int | float[source]
-

An alias to get_anchor_point method with start=False.

-
- -
-
-get_start(annotation: Annotation) → int | float[source]
-

An alias to get_anchor_point method with start=True.

-
- -
-
-get_view_by_id(req_view_id: str) → View[source]
-

Finds a View object with the given ID.

-
-
Parameters:
-

req_view_id – the ID to search for

-
-
Returns:
-

a reference to the corresponding view, if it exists

-
-
Raises:
-

Exception – if there is no corresponding view

-
-
-
- -
-
-get_view_contains(at_types: TypesBase | str | List[str | TypesBase]) → View | None[source]
-

Returns the last view appended that contains the given -types in its ‘contains’ metadata.

-
-
Parameters:
-

at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

-
-
Returns:
-

the view, or None if the type is not found

-
-
-
- -
-
-get_views_contain(at_types: TypesBase | str | List[str | TypesBase]) → List[View][source]
-

An alias to get_all_views_contain method.

-
- -
-
-get_views_for_document(doc_id: str) → List[View][source]
-

Returns the list of all views that have annotations anchored on a particular document. -Note that when the document is inside a view (generated during the pipeline’s running), -doc_id must be prefixed with the view_id.

-
- -
-
-new_view() → View[source]
-

Creates an empty view with a new ID and appends it to the views list.

-
-
Returns:
-

a reference to the new View object

-
-
-
- -
-
-new_view_id() → str[source]
-

Fetches an ID for a new view.

-
-
Returns:
-

the ID

-
-
-
- -
-
-sanitize()[source]
-

Sanitizes a Mmif object by running some safeguards. -Concretely, it performs the following before returning the JSON string.

-
    -

  1. validating output using built-in MMIF jsonschema

    2. -

  2. remove non-existing annotation types from contains metadata

    3. -
-
- -
-
-serialize(pretty: bool = False, sanitize: bool = False, autogenerate_capital_annotations=True) → str[source]
-

Serializes the MMIF object to a JSON string.

-
-
Parameters:
-
    -

  • sanitize – If True, performs some sanitization of before returning -the JSON string. See sanitize() for details.

    • -

  • autogenerate_capital_annotations – If True, automatically convert -any “pending” temporary properties from Document objects to -Annotation objects. See generate_capital_annotations() for -details.

    • -

  • pretty – If True, returns string representation with indentation.

    • -
-
-
Returns:
-

JSON string of the MMIF object.

-
-
-
- -
-
-static validate(json_str: bytes | str | dict) → None[source]
-

Validates a MMIF JSON object against the MMIF Schema. -Note that this method operates before processing by MmifObject._load_str, -so it expects @ and not _ for the JSON-LD @-keys.

-
-
Raises:
-

jsonschema.exceptions.ValidationError – if the input fails validation

-
-
Parameters:
-

json_str – a MMIF JSON dict or string

-
-
Returns:
-

None

-
-
-
- -
- -
-
-

mmif.serialize.view module

-

The view module contains the classes used to represent a MMIF view -as a live Python object.

-

In MMIF, views are created by apps in a pipeline that are annotating -data that was previously present in the MMIF file.

-
-
-class mmif.serialize.view.Contain(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: DataDict[str, str]

-

Contain object that represents the metadata of a single -annotation type in the contains metadata of a MMIF view.

-
- -
-
-class mmif.serialize.view.View(view_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-

View object that represents a single view in a MMIF file.

-

A view is identified by an ID, and contains certain metadata, -a list of annotations, and potentially a JSON-LD @context -IRI.

-

If view_obj is not provided, an empty View will be generated.

-
-
Parameters:
-

view_obj – the JSON data that defines the view

-
-
-
-
-add_annotation(annotation: Annotation, overwrite=False) → Annotation[source]
-

Adds an annotation to the current view.

-

Fails if there is already an annotation with the same ID -in the view, unless overwrite is set to True.

-
-
Parameters:
-
-
-
Raises:
-

KeyError – if overwrite is set to False and -an annotation with the same ID exists -in the view

-
-
Returns:
-

the same Annotation object passed in as annotation

-
-
-
- -
-
-add_document(document: Document, overwrite=False) → Annotation[source]
-

Appends a Document object to the annotations list.

-

Fails if there is already a document with the same ID in the annotations list.

-
-
Parameters:
-
    -

  • document – the Document object to add

    • -

  • overwrite – if set to True, will overwrite -an existing view with the same ID

    • -
-
-
Returns:
-

None

-
-
-
- -
-
-get_annotation_by_id(ann_id) → Annotation[source]
-
- -
-
-get_annotations(at_type: str | TypesBase | None = None, **properties) → Generator[Annotation, None, None][source]
-

Look for certain annotations in this view, specified by parameters

-
-
Parameters:
-
    -

  • at_type – @type of the annotations to look for. When this is None, any @type will match.

    • -

  • properties – properties of the annotations to look for. When given more than one property, all properties must match. Note that annotation type metadata are specified in the contains view metadata, not in individual annotation objects.

    • -
-
-
-
- -
-
-get_document_by_id(doc_id) → Document[source]
-
- -
-
-get_documents() → List[Document][source]
-
- -
-
-new_annotation(at_type: str | TypesBase, aid: str | None = None, overwrite=False, **properties) → Annotation[source]
-

Generates a new mmif.serialize.annotation.Annotation -object and adds it to the current view.

-

Fails if there is already an annotation with the same ID -in the view, unless overwrite is set to True.

-
-
Parameters:
-
    -

  • at_type – the desired @type of the annotation.

    • -

  • aid – the desired ID of the annotation, when not given, -the mmif SDK tries to automatically generate an ID based on -Annotation type and existing annotations in the view.

    • -

  • overwrite – if set to True, will overwrite an -existing annotation with the same ID.

    • -
-
-
Raises:
-

KeyError – if overwrite is set to False and -an annotation with the same ID exists -in the view.

-
-
Returns:
-

the generated mmif.serialize.annotation.Annotation

-
-
-
- -
-
-new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
-

Adds a new element to the contains metadata.

-
-
Parameters:
-
    -

  • at_type – the @type of the annotation type being added

    • -

  • contains_metadata – any metadata associated with the annotation type

    • -
-
-
Returns:
-

the generated Contain object

-
-
-
- -
-
-new_textdocument(text: str, lang: str = 'en', did: str | None = None, overwrite=False, **properties) → Document[source]
-

Generates a new mmif.serialize.annotation.Document -object, particularly typed as TextDocument and adds it to the current view.

-

Fails if there is already a text document with the same ID -in the view, unless overwrite is set to True.

-
-
Parameters:
-
    -

  • text – text content of the new document

    • -

  • lang – ISO 639-1 code of the language used in the new document

    • -

  • did – the desired ID of the document, when not given, -the mmif SDK tries to automatically generate an ID based on -Annotation type and existing documents in the view.

    • -

  • overwrite – if set to True, will overwrite an -existing document with the same ID

    • -
-
-
Raises:
-

KeyError – if overwrite is set to False and -an document with the same ID exists -in the view

-
-
Returns:
-

the generated mmif.serialize.annotation.Document

-
-
-
- -
-
-set_error(err_message: str, err_trace: str) → None[source]
-
- -
- -
-
-class mmif.serialize.view.ViewMetadata(viewmetadata_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-

ViewMetadata object that represents the metadata object within a MMIF view.

-
-
Parameters:
-

viewmetadata_obj – the JSON data that defines the metadata

-
-
-
-
-add_app_configuration(config_key: str, config_value: str | int | float | bool | None | List[str | int | float | bool | None]) → None[source]
-

Add a configuration key-value pair to the app_configuration dictionary.

-
- -
-
-add_contain(contain: Contain, at_type: str | TypesBase) → None[source]
-
- -
-
-add_parameter(param_key: str, param_value: str)[source]
-

Add a single runtime parameter to the view metadata. Note that parameter value must be a string.

-
- -
-
-add_parameters(**runtime_params: str)[source]
-

Add runtime parameters as a batch (dict) to the view metadata. Note that parameter values must be strings.

-
- -
-
-add_warnings(*warnings: Warning)[source]
-
- -
-
-emtpy_warnings()[source]
-
- -
-
-get_app_configuration(config_key: str) → str | int | float | bool | None | List[str | int | float | bool | None][source]
-

Get a configuration value from the app_configuration dictionary.

-
- -
-
-get_parameter(param_key: str) → str[source]
-

Get a runtime parameter from the view metadata.

-
- -
-
-new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
-

Adds a new element to the contains dictionary.

-
-
Parameters:
-
    -

  • at_type – the @type of the annotation type being added

    • -

  • contains_metadata – any metadata associated with the annotation type

    • -
-
-
Returns:
-

the generated Contain object

-
-
-
- -
-
-set_error(message: str, stack_trace: str)[source]
-
- -
- -
-
-

mmif.serialize.annotation module

-

The annotation module contains the classes used to represent a -MMIF annotation as a live Python object.

-

In MMIF, annotations are created by apps in a pipeline as a part -of a view. For documentation on how views are represented, see -mmif.serialize.view.

-
-
-class mmif.serialize.annotation.Annotation(anno_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-

MmifObject that represents an annotation in a MMIF view.

-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]]) → None[source]
-

Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

-
- -
-
-property at_type: TypesBase[source]
-
- -
-
-static check_prop_value_is_simple_enough(value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]]) → bool[source]
-
- -
-
-get(prop_name: str) → AnnotationProperties | str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]][source]
-

A special getter for Annotation properties. This is to allow for -directly accessing properties without having to go through the -properties object, or view-level annotation properties encoded in the -view.metadata.contains dict. Note that the regular props will take -the priority over the ephemeral props when there are conflicts.

-
- -
-
-get_property(prop_name: str) → AnnotationProperties | str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]][source]
-

A special getter for Annotation properties. This is to allow for -directly accessing properties without having to go through the -properties object, or view-level annotation properties encoded in the -view.metadata.contains dict. Note that the regular props will take -the priority over the ephemeral props when there are conflicts.

-
- -
-
-property id: str[source]
-
- -
-
-is_document()[source]
-
- -
-
-is_type(at_type: str | TypesBase) → bool[source]
-

Check if the @type of this object matches.

-
- -
-
-property long_id: str[source]
-
- -
-
-property parent: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.AnnotationProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject, MutableMapping[str, T]

-

AnnotationProperties object that represents the -properties object within a MMIF annotation.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
- -
-
-class mmif.serialize.annotation.Document(doc_obj: bytes | str | dict | None = None)[source]
-

Bases: Annotation

-

Document object that represents a single document in a MMIF file.

-

A document is identified by an ID, and contains certain attributes -and potentially contains the contents of the document itself, -metadata about how the document was created, and/or a list of -subdocuments grouped together logically.

-

If document_obj is not provided, an empty Document will be generated.

-
-
Parameters:
-

document_obj – the JSON data that defines the document

-
-
-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None]) → None[source]
-

Adds a property to the document’s properties.

-

Unlike the parent Annotation class, added properties of a -Document object can be lost during serialization unless it belongs -to somewhere in a Mmif object. This is because we want to keep -Document object as “read-only” as possible. Thus, if you want to add -a property to a Document object,

-
    -

  • add the document to a Mmif object (either in the documents list or -in a view from the views list), or

    • -

  • directly write to Document.properties instead of using this method -(which is not recommended).

    • -
-

With the former method, the SDK will record the added property as a -Annotation annotation object, separate from the original Document -object. See Mmif.generate_capital_annotations() for more.

-

A few notes to keep in mind:

-
    -

  1. You can’t overwrite an existing property of a Document object.

    2. -

  2. A MMIF can have multiple Annotation objects with the same -property name but different values. When this happens, the SDK will -only keep the latest value (in order of appearances in views list) of -the property, effectively overwriting the previous values.

    3. -
-
- -
-
-get(prop_name)[source]
-

A special getter for Document properties. The major difference from -the super class’s Annotation.get() method is that Document -class has one more set of “pending” properties, that are added after -the Document object is created and will be serialized as a separate -Annotation object of which @type = Annotation. The -pending properties will take the priority over the regular properties -when there are conflicts.

-
- -
-
-get_property(prop_name)[source]
-

A special getter for Document properties. The major difference from -the super class’s Annotation.get() method is that Document -class has one more set of “pending” properties, that are added after -the Document object is created and will be serialized as a separate -Annotation object of which @type = Annotation. The -pending properties will take the priority over the regular properties -when there are conflicts.

-
- -
-
-property location: str | None[source]
-

location property must be a legitimate URI. That is, should the document be a local file -then the file:// scheme must be used. -Returns None when no location is set.

-
- -
-
-location_address() → str | None[source]
-

Retrieves the full address from the document location URI. -Returns None when no location is set.

-
- -
-
-location_path(nonexist_ok=True) → str | None[source]
-

Retrieves a path that’s resolved to a pathname in the local file system. -To obtain the original value of the “path” part in the location string -(before resolving), use properties.location_path_literal method. -Returns None when no location is set.

-
-
Parameters:
-

nonexist_ok – if False, raise FileNotFoundError when the resolved path doesn’t exist

-
-
-
- -
-
-location_scheme() → str | None[source]
-

Retrieves URI scheme of the document location. -Returns None when no location is set.

-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.DocumentProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: AnnotationProperties

-

DocumentProperties object that represents the -properties object within a MMIF document.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
-
-property location: str | None[source]
-

location property must be a legitimate URI. That is, should the document be a local file -then the file:// scheme must be used. -Returns None when no location is set.

-
- -
-
-location_address() → str | None[source]
-

Retrieves the full address from the document location URI. -Returns None when no location is set.

-
- -
-
-location_path() → str | None[source]
-
- -
-
-location_path_literal() → str | None[source]
-

Retrieves only path name of the document location (hostname is ignored). -Returns None when no location is set.

-
- -
-
-location_path_resolved(nonexist_ok=True) → str | None[source]
-

Retrieves only path name of the document location (hostname is ignored), -and then try to resolve the path name in the local file system. -This method should be used when the document scheme is file or empty. -For other schemes, users should install mmif-locdoc-<scheme> plugin.

-

Returns None when no location is set. -Raise ValueError when no code found to resolve the given location scheme.

-
- -
-
-location_scheme() → str | None[source]
-

Retrieves URI scheme of the document location. -Returns None when no location is set.

-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.Text(text_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-
-
-property lang: str[source]
-
- -
-
-property value: str[source]
-
- -
- -
-
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-
- -
-
-
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- - - \ No newline at end of file diff --git a/docs/1.0.13/autodoc/mmif.utils.html b/docs/1.0.13/autodoc/mmif.utils.html deleted file mode 100644 index ad8f021c..00000000 --- a/docs/1.0.13/autodoc/mmif.utils.html +++ /dev/null @@ -1,578 +0,0 @@ - - - - - - - - - mmif.utils module — mmif-python documentation - - - - - - - - - - - - - - - - - -
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mmif.utils module

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mmif.utils.video_document_helper module

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-mmif.utils.video_document_helper.capture(video_document: Document)[source]
-

Captures a video file using OpenCV and adds fps, frame count, and duration as properties to the document.

-
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Parameters:
-

video_document – Document instance that holds a video document ("@type": ".../VideoDocument/...")

-
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Returns:
-

OpenCV VideoCapture object

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-mmif.utils.video_document_helper.convert_timeframe(mmif: Mmif, time_frame: Annotation, out_unit: str) → Tuple[int | float | str, int | float | str][source]
-

Converts start and end points in a TimeFrame annotation a different time unit.

-
-
Parameters:
-
    -

  • mmif – Mmif instance

    • -

  • time_frame – Annotation instance that holds a time interval annotation ("@type": ".../TimeFrame/...")

    • -

  • out_unit – time unit to which the point is converted

    • -
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Returns:
-

tuple of frame numbers (integer) or seconds/milliseconds (float) of input start and end

-
-
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- -
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-mmif.utils.video_document_helper.convert_timepoint(mmif: Mmif, timepoint: Annotation, out_unit: str) → int | float | str[source]
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Converts a time point included in an annotation to a different time unit. -The input annotation must have timePoint property.

-
-
Parameters:
-
    -

  • mmif – input MMIF to obtain fps and input timeunit

    • -

  • timepoint – Annotation instance with timePoint property

    • -

  • out_unit – time unit to which the point is converted (frames, seconds, milliseconds)

    • -
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Returns:
-

frame number (integer) or second/millisecond (float) of input timepoint

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-
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- -
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-mmif.utils.video_document_helper.extract_frames_as_images(video_document: Document, framenums: List[int], as_PIL: bool = False)[source]
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Extracts frames from a video document as a list of numpy.ndarray. -Use with sample_frames() function to get the list of frame numbers first.

-
-
Parameters:
-
    -

  • video_document – Document instance that holds a video document ("@type": ".../VideoDocument/...")

    • -

  • framenums – integers representing the frame numbers to extract

    • -

  • as_PIL – return PIL.Image.Image instead of ndarray

    • -
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Returns:
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frames as a list of ndarray or Image

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-mmif.utils.video_document_helper.extract_mid_frame(mmif: Mmif, time_frame: Annotation, as_PIL: bool = False)[source]
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Extracts the middle frame of a time interval annotation as a numpy ndarray.

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Parameters:
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    -

  • mmif – Mmif instance

    • -

  • time_frame – Annotation instance that holds a time interval annotation ("@type": ".../TimeFrame/...")

    • -

  • as_PIL – return Image instead of ndarray

    • -
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Returns:
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frame as a numpy.ndarray or PIL.Image.Image

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-mmif.utils.video_document_helper.framenum_to_millisecond(video_doc: Document, frame: int)[source]
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Converts a frame number to a millisecond value.

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-mmif.utils.video_document_helper.framenum_to_second(video_doc: Document, frame: int)[source]
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Converts a frame number to a second value.

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-mmif.utils.video_document_helper.get_annotation_property(mmif, annotation, prop_name)[source]
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-

Deprecated since version 1.0.8: Use mmif.serialize.annotation.Annotation.get_property() method instead.

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Get a property value from an annotation. If the property is not found in the annotation, it will look up the metadata of the annotation’s parent view and return the value from there. -xisting

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-mmif.utils.video_document_helper.get_framerate(video_document: Document) → float[source]
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Gets the frame rate of a video document. First by checking the fps property of the document, then by capturing the video.

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Parameters:
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video_document – Document instance that holds a video document ("@type": ".../VideoDocument/...")

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Returns:
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frames per second as a float, rounded to 2 decimal places

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-mmif.utils.video_document_helper.get_mid_framenum(mmif: Mmif, time_frame: Annotation)[source]
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Calculates the middle frame number of a time interval annotation.

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Parameters:
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    -

  • mmif – Mmif instance

    • -

  • time_frame – Annotation instance that holds a time interval annotation ("@type": ".../TimeFrame/...")

    • -
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Returns:
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middle frame number as an integer

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-mmif.utils.video_document_helper.millisecond_to_framenum(video_doc: Document, millisecond: float) → int[source]
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Converts a millisecond value to a frame number.

-
- -
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-mmif.utils.video_document_helper.sample_frames(start_frame: int, end_frame: int, sample_rate: float = 1) → List[int][source]
-

Helper function to sample frames from a time interval. -Can also be used as a “cutoff” function when used with start_frame==0 and sample_rate==1.

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-
Parameters:
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    -

  • start_frame – start frame of the interval

    • -

  • end_frame – end frame of the interval

    • -

  • sample_rate – sampling rate (or step) to configure how often to take a frame, default is 1, meaning all consecutive frames are sampled

    • -
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-mmif.utils.video_document_helper.second_to_framenum(video_doc: Document, second) → int[source]
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Converts a second value to a frame number.

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- -
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-

mmif.utils.sequence_helper module

-

This module provides helpers for handling sequence labeling. Specifically, it provides

-
    -

  • a generalized label re-mapper for “post-binning” of labels

    • -

  • conversion from a list of CLAMS annotations (with classification props) into a list of reals (scores by labels), can be combined with the label re-mapper mentioned above

    • -

  • mmif.utils.sequence_helper.smooth_outlying_short_intervals(): a simple smoothing algorithm by trimming “short” outlier sequences

    • -
-

However, it DOES NOT provide

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    -

  • direct conversion between CLAMS annotations. For example, it does not directly handle stitching of TimePoint into TimeFrames.

    • -

  • support for multi-class scenario, such as handling of _competing_ subsequence or overlapping labels.

    • -
-

Some functions can use optional external libraries (e.g., numpy) for better performance. -Hence, if you see a warning about missing optional packages, you might want to install them by running pip install mmif-python[seq].

-
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-mmif.utils.sequence_helper.build_label_remapper(src_labels: List[str], dst_labels: Dict[str, str | int | float | bool | None]) → Dict[str, str | int | float | bool | None][source]
-

Build a label remapper dictionary from source and destination labels.

-
-
Parameters:
-
    -

  • src_labels – a list of all labels on the source side

    • -

  • dst_labels – a dict from source labels to destination labels. -Source labels not in this dict will be remapped to a negative label (-).

    • -
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Returns:
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a dict that exhaustively maps source labels to destination labels

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- -
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-mmif.utils.sequence_helper.build_score_lists(classifications: ~typing.List[~typing.Dict], label_remapper: ~typing.Dict, score_remap_op: ~typing.Callable[[...], float] = <built-in function max>) → Tuple[Dict[str, int], numpy.ndarray][source]
-

Build lists of scores indexed by the label names.

-
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Parameters:
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    -

  • classifications – list of dictionaries of classification results, taken from input annotation objects

    • -

  • label_remapper – a dictionary that maps source label names to destination label names (formerly “postbin”)

    • -

  • score_remap_op – a function to remap the scores from multiple source labels binned to a destination label -common choices are max, min, or sum

    • -
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Returns:
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    -

  1. a dictionary that maps label names to their index in the score list

    2. -

  2. 2-d numpy array of scores, of which rows are indexed by label map dict (first return value)

    3. -
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-mmif.utils.sequence_helper.smooth_outlying_short_intervals(scores: List[float], min_spseq_size: int, min_snseq_size: int, min_score: float = 0.5)[source]
-

Given a list of scores, a score threshold, and smoothing parameters, -identify the intervals of “positive” scores by “trimming” the short -positive sequences (“spseq”) and short negative sequences (“snseq”). To -decide the positivity, first step is binarization of the scores by the -min_score threshold. Given Sr as “raw” input real-number scores -list, and min_score=0.5,

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Sr: [0.3, 0.6, 0.2, 0.8, 0.2, 0.9, 0.8, 0.5, 0.1, 0.5, 0.8, 0.3, 1.0, 0.7, 0.5, 0.5, 0.5, 0.8, 0.3, 0.6]
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the binarization is done by simply comparing each score to the -threshold to get S list of binary scores

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1.0 :                                     |                      
-0.9 :                |                    |                      
-0.8 :          |     |  |           |     |              |       
-0.7 :          |     |  |           |     |  |           |       
-0.6 :    |     |     |  |           |     |  |           |     | 
-0.5 :----+-----+-----+--+--+-----+--+-----+--+--+--+--+--+-----+-
-0.4 :    |     |     |  |  |     |  |     |  |  |  |  |  |     | 
-0.3 : |  |     |     |  |  |     |  |  |  |  |  |  |  |  |  |  | 
-0.2 : |  |  |  |  |  |  |  |     |  |  |  |  |  |  |  |  |  |  | 
-0.1 : |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | 
-0.0 +------------------------------------------------------------
-raw :.3 .6 .2 .8 .2 .9 .8 .5 .1 .5 .8 .3 1. .7 .5 .5 .5 .8 .3 .6
- S  : 0  1  0  1  0  1  1  0  0  0  1  0  1  1  0  1  1  1  0  1 
-
-
-
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Note that the size of a positive or negative sequence can be as small -as 1.

-

Then, here are examples of smoothing a list of binary scores into -intervals, by trimming “very short” (under thresholds) sequences of -positive or negative:

-
-

Note

-

legends:

-
    -

  • t is unit index (e.g. time index)

    • -

  • S is the list of binary scores (zeros and ones)

    • -

  • I is the list of intervals after smoothing

    • -
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    -

  1. with params min_spseq_size==1, min_snseq_size==4

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1]
-I: [0, 1--1--1--1--1--1--1--1--1--1--1--1, 0--0--0--0--0--0, 1]
-
    -
    -

    Explanation: min_snseq_size is used to smooth short sequences -of negative predictions. In this, zeros from t[7:10] are smoothed -into “one” I, while zeros from t[13:19] are kept as “zero” I. Note -that the “short” snseqs at the either ends (t[0:1]) are never -smoothed.

    -
    -
    2. -

  2. with params min_spseq_size==4, min_snseq_size==2

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1]
-I: [0, 1--1--1--1--1--1, 0--0--0--0--0--0--0--0--0--0--0--0--0]
-
    -
    -

    Explanation: min_spseq_size is used to smooth short sequences -of positive predictions. In this example, the spseqs of ones from -both t[10:13] and t[19:20] are smoothed. Note that the “short” -spseqs at the either ends (t[19:20]) are always smoothed.

    -
    -
    3. -

  3. with params min_spseq_size==4, min_snseq_size==4

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1]
-I: [0, 1--1--1--1--1--1--1--1--1--1--1--1--0--0--0--0--0--0--0]
-
    -
    -

    Explanation: When two threshold parameters are working together, -the algorithm will prioritize the smoothing of the snseqs over the -smoothing of the spseqs. Thus, in this example, the snseq t[7:10] -gets first smoothed “up” before the spseq t[10:13] is smoothed -“down”, resulting in a long final I.

    -
    -
    4. -

  4. with params min_spseq_size==4, min_snseq_size==4

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [1, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 1, 1]
-I: [1--1--1--1--1--1--1, 0--0--0--0, 1--1--1--1--1--1--1--1--1]
-
    -
    -

    Explanation: Since smoothing of snseqs is prioritized, short spseqs -at the beginning or the end can be kept.

    -
    -
    5. -

  5. with params min_spseq_size==1, min_snseq_size==1

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 1, 1]
-I: [0--0--0, 1--1--1--1, 0--0--0--0, 1--1--1--1, 0--0--0, 1--1]
-
    -
    -

    Explanation: When both width thresholds are set to 1, the algorithm -works essentially in the “stitching” only mode.

    -
    -
    6. -
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Parameters:
-
    -

  • scores – SORTED list of scores to be smoothed. The score list -is assumed to be “exhaust” the entire time or space of -the underlying document segment. -(Sorted by the start, and then by the end of anchors)

    • -

  • min_score – minimum threshold to use to discard -low-scored units (strictly less than)

    • -

  • min_spseq_size – minimum size of a positive sequence not to be -smoothed (greater or equal to)

    • -

  • min_snseq_size – minimum size of a negative sequence not to be -smoothed (greater or equal to)

    • -
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Returns:
-

list of tuples of start(inclusive)/end(exclusive) indices -of the “positive” sequences. Negative sequences (regardless of -their size) are not included in the output.

-
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- -
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-mmif.utils.sequence_helper.validate_labelset(annotations: Iterable[Annotation]) → List[str][source]
-

Simple check for a list of annotations to see if they have the same label set.

-
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Raise:
-

AttributeError if an element in the input list doesn’t have the labelset property

-
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Raise:
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ValueError if different labelset values are found

-
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Returns:
-

a list of the common labelset value (list of label names)

-
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- - - \ No newline at end of file diff --git a/docs/1.0.13/autodoc/mmif.vocabulary.html b/docs/1.0.13/autodoc/mmif.vocabulary.html deleted file mode 100644 index da1d13de..00000000 --- a/docs/1.0.13/autodoc/mmif.vocabulary.html +++ /dev/null @@ -1,319 +0,0 @@ - - - - - - - - - mmif.vocabulary module — mmif-python documentation - - - - - - - - - - - - - - - - - -
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mmif.vocabulary module

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mmif.vocabulary.annotation_types module

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-class mmif.vocabulary.annotation_types.AnnotationTypes(type_uri, fuzzymode=True)[source]
-

Bases: AnnotationTypesBase

-

This class contains the CLAMS annotation types -defined in the spec version 1.1.0 as class variables.

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-Alignment = http://mmif.clams.ai/vocabulary/Alignment/v1[source]
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-Annotation = http://mmif.clams.ai/vocabulary/Annotation/v6[source]
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-BoundingBox = http://mmif.clams.ai/vocabulary/BoundingBox/v5[source]
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-NamedEntity = http://mmif.clams.ai/vocabulary/NamedEntity/v1[source]
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-Paragraph = http://mmif.clams.ai/vocabulary/Paragraph/v1[source]
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-Polygon = http://mmif.clams.ai/vocabulary/Polygon/v5[source]
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-Relation = http://mmif.clams.ai/vocabulary/Relation/v5[source]
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-Sentence = http://mmif.clams.ai/vocabulary/Sentence/v1[source]
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-Span = http://mmif.clams.ai/vocabulary/Span/v5[source]
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-TimeFrame = http://mmif.clams.ai/vocabulary/TimeFrame/v6[source]
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-TimePoint = http://mmif.clams.ai/vocabulary/TimePoint/v5[source]
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-Token = http://mmif.clams.ai/vocabulary/Token/v1[source]
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-VerbChunk = http://mmif.clams.ai/vocabulary/VerbChunk/v1[source]
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-VideoObject = http://mmif.clams.ai/vocabulary/VideoObject/v5[source]
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mmif.vocabulary.document_types module

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-class mmif.vocabulary.document_types.DocumentTypes(type_uri, fuzzymode=True)[source]
-

Bases: DocumentTypesBase

-

This class contains the CLAMS document types -defined in the spec version 1.1.0 as class variables.

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-AudioDocument = http://mmif.clams.ai/vocabulary/AudioDocument/v1[source]
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-Document = http://mmif.clams.ai/vocabulary/Document/v1[source]
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-ImageDocument = http://mmif.clams.ai/vocabulary/ImageDocument/v1[source]
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-TextDocument = http://mmif.clams.ai/vocabulary/TextDocument/v1[source]
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-VideoDocument = http://mmif.clams.ai/vocabulary/VideoDocument/v1[source]
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- - - \ No newline at end of file diff --git a/docs/1.0.13/autodoc/mmif_docloc_http.html b/docs/1.0.13/autodoc/mmif_docloc_http.html deleted file mode 100644 index 32ee2a31..00000000 --- a/docs/1.0.13/autodoc/mmif_docloc_http.html +++ /dev/null @@ -1,179 +0,0 @@ - - - - - - - - - mmif_docloc_http package — mmif-python documentation - - - - - - - - - - - - - - - - -
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mmif_docloc_http package

-

MMIF document location helper module for http and https schemes. -If you want to write your own docloc scheme handler, please use the source code of this module as a reference. -See this plug-in section for more information.

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-mmif_docloc_http.resolve(docloc)[source]
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MMIF consumer

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A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the appliance documentation to learn more about the appliance.

-

MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance.

-
    -

  1. The code must be hosted on a public git repository (e.g. Github, Gitlab, …)

    2. -

  2. Must listen to 5000 port.

    3. -

  3. Must expose /display route .

    4. -

  4. /display router should response to GET requests.

    5. -

  5. In the GET request, a public URL of the input MMIF file is passed via file URL parameter.

    6. -

  6. On the codebase root, there must be a Dockerfile that can build a docker image that runs the web app.

    7. -
-

We provide an example consumer at https://github.com/clamsproject/mmif-visualizer.

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  • Welcome to mmif-python’s documentation!
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Welcome to mmif-python’s documentation!

-
-

MultiMedia Interchange Format

-

MMIF is a JSON(-LD)-based data format designed for transferring annotation data between computational analysis applications in CLAMS project.

-
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-

mmif-python

-

mmif-python is a Python implementation of the MMIF data format. -mmif-python provides various helper classes and functions to handle MMIF JSON in Python, -including ;

-
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  1. de-/serialization of MMIF internal data structures to/from JSON

    2. -

  2. validation of MMIF JSON

    3. -

  3. handling of CLAMS vocabulary types

    4. -

  4. navigation of MMIF object via various “search” methods (e.g. mmif.get_all_views_contain(vocab_type)))

    5. -
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For more …

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Contents

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API documentation:

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Indices and tables

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Getting Started

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Overview

-

MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for reproducibility, transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF website. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects.

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Prerequisites

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    -

  • Python: the latest mmif-python requires Python 3.8 or newer. We have no plan to support Python 2.7.

    • -
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Installation

-

Package mmif-python is distributed via the official PyPI. Users are supposed to pip-install to get latest release.

-
pip install mmif-python
-
-
-

This will install a package mmif to local python.

-

The MMIF format and specification is evolving over time, and mmif-python package will be updated along with the changes in MMIF format.

-
-

Note

-

MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and mmif-python versions, please take time to read our decision on the subject here. If you need to know which python SDK supports which specification version, see Target MMIF Versions page.

-
-
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MMIF Serialization

-

mmif.serialize.mmif.Mmif represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of mmif.serialize.model.MmifObject, including the mmif.serialize.mmif.Mmif. To start with an existing MMIF str, simple initiate a new Mmif object with the file.

-
import mmif
-from mmif import Mmif
-
-mmif_str = """{
-"metadata": {
-  "mmif": "http://mmif.clams.ai/1.0.0"
-},
-"documents": [
-  {
-    "@type": "http://mmif.clams.ai/vocabulary/VideoDocument/v1",
-    "properties": {
-      "id": "m1",
-      "mime": "video/mp4",
-      "location": "file:///var/archive/video-0012.mp4"
-    }
-  },
-  {
-    "@type": "http://mmif.clams.ai/vocabulary/TextDocument/v1",
-    "properties": {
-      "id": "m2",
-      "mime": "text/plain",
-      "location": "file:///var/archive/video-0012-transcript.txt"
-    }
-  }
-],
-"views": []}"""
-mmif_obj = Mmif(mmif_str)
-
-
-

Few notes;

-
    -

  1. MMIF does not carry the primary source files in it.

    2. -

  2. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version mmif-python implementation of the MMIF might not be able to load an unsupported version of MMIF string.

    3. -
-

When serializing back to str, call mmif.serialize.model.MmifObject.serialize() on the object.

-

To get subcomponents, you can use various getters implemented in subclasses. For example;

-
from mmif.vocabulary.document_types import DocumentTypes
-
-for video in mmif_obj.Mmif.get_documents_by_type(DocumentTypes.VideoDocument):
-  with open(video.location_path(), 'b') as in_video:
-    # do something with the video file
-
-
-

For a full list of available helper methods, please refer to the API documentation.

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mmif package

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mmif_docloc_http package

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Developing plugins for MMIF Python SDK

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Overview

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As MMIF JSON files can carry information about media document files without actually carrying file contents, file accessing modules in mmif Python package (distributed as mmif-python on PyPI) are designed to be lightweight and flexible so that it can work with additional “plugin” Python packages that can handle concrete file access.

-

This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF website. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects.

-

Developer can write simple plugins that can provide additional functionalities to mmif-python. For example, mmif-python does not provide any file access functionality beyond a local file system (with file scheme), but it can be extended with a plugin that can handle file access over different protocols (e.g. http, s3, ftp, etc).

-

This document contains information about how to write plugins for mmif-python.

-
-

Document Location Scheme Plugins

-

mmif.serialize.annotation.Document class has various methods to access parts of location property of the document. The location is in URI/IRI format (SCHEME://HOSTNAME/PATH, in a nutshell) and it has to be resolved to a local file for CLAMS Apps to process the local file to analyze and extract information about the media and its contents. The core mmif-python distribution only provides a default implementation that can handle file scheme URIs.

-

To add a document location handler plugin, you need to implement a Python “package” (do not confuse with PYPI distribution), that meets these requirements;

-
    -

  1. the package must be named mmif_docloc_<SCHEME>. For example, to implement a handler for s3 scheme, the package name must be mmif_docloc_s3. The prefix is important as it’s used in the plugin discovery process from the core mmif-python modules.

    2. -

  2. the top module of the package must have a function named resolve. The function must take a single argument, which is a str of the document location URI. The function must return a str of the local file path. For example, if the document location is s3://mybucket/myfile.mp4, a Python user should be able to to something like this;

    3. -
-
import mmif_docloc_s3
-resolved = mmif_docloc_s3.resolve('s3://mybucket/myfile.mp4')
-# then resolved must be a local file path that can be used to open the file
-
-
-

Here’s a minimal example codebase that you refer to when you develop a docloc plugin.

-

(However, before you start writing your own plugin for a specific URI scheme, checking if there’s already a PyPI distribution for the scheme might be a good idea.)

-
$ tree .
-.
-├── mmif_docloc_dummy
-│   └── __init__.py
-├── pyproject.toml
-└── setup.cfg
-
- $ cat pyproject.toml
-[build-system]
-requires = ["setuptools"]
-build-backend = "setuptools.build_meta"
-
-$ cat setup.cfg
-[metadata]
-name = mmif_docloc_dummy  # this name is IMPORTANT
-version = 0.0.1
-description = a plugin to mmif-pyhon to handle `dummy` location scheme
-
-
-

And the plugin code.

-
# mmif_docloc_dummy/__init__.py
-doc_types = {'video': 'mp4'}
-
-def resolve(docloc):
-    scheme = 'dummy'
-    if docloc.startswith(f'{scheme}://'):
-        doc_id, doc_type = docloc.split('.')
-        return f'/path/to/{doc_id}.{doc_types[doc_type]}'
-    else:
-        raise ValueError(f'cannot handle document location scheme: {docloc}')
-
-
-
-
-

Bulit-in Document Location Scheme Plugins

-

At the moment, mmif-python PyPI distribution ships a built-in docloc plugin that support both http and https schemes. -Take a look at mmif_docloc_http module for details.

-
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- - Other Versions - v: 1.0.13 - - -
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- - - \ No newline at end of file diff --git a/docs/1.0.13/py-modindex.html b/docs/1.0.13/py-modindex.html deleted file mode 100644 index a128c08f..00000000 --- a/docs/1.0.13/py-modindex.html +++ /dev/null @@ -1,223 +0,0 @@ - - - - - - - - Python Module Index — mmif-python documentation - - - - - - - - - - - - - - - - - - -
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Python Module Index

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- m
- mmif -
    - mmif.serialize.annotation -
    - mmif.serialize.mmif -
    - mmif.serialize.model -
    - mmif.serialize.view -
    - mmif.utils.sequence_helper -
    - mmif.utils.video_document_helper -
    - mmif.vocabulary.annotation_types -
    - mmif.vocabulary.document_types -
- mmif_docloc_http -
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0.5.2
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1.0.0
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1.0.1
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1.0.10
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8], "via": [4, 5, 6], "vid": 0, "video": [1, 6, 8], "video_doc": 1, "video_docu": 1, "video_document_help": 7, "videocaptur": 1, "videodocu": [1, 2, 6, 7], "videoobject": [2, 7], "view": [1, 6, 7], "view_id": 0, "view_obj": 0, "view_prefix": [0, 7], "viewmetadata": [0, 7], "viewmetadata_obj": 0, "visit": [6, 8], "visual": 4, "vocab_typ": 5, "vocabulari": [0, 5, 6, 7], "wa": 0, "wai": 0, "want": [0, 1, 3], "warn": [0, 1], "we": [0, 4, 6], "web": 4, "websit": [6, 8], "well": [0, 6, 8], "when": [0, 1, 6, 8], "where": 0, "whether": 0, "which": [0, 1, 6, 8], "while": 1, "width": 1, "within": 0, "without": [0, 8], "won": 0, "work": [0, 1, 8], "workflow": 6, "would": 0, "write": [0, 3, 8], "xist": 1, "you": [0, 1, 3, 6, 8], "your": [3, 8], "zero": [0, 1]}, "titles": ["mmif.serialize module", "mmif.utils module", "mmif.vocabulary module", "mmif_docloc_http package", "MMIF consumer", "Welcome to mmif-python\u2019s documentation!", "Getting Started", "mmif package", "Developing plugins for MMIF Python SDK", "Target MMIF Versions"], "titleterms": {"": 5, "For": 5, "annot": 0, "annotation_typ": 2, "api": 5, "bulit": 8, "consum": 4, "content": 5, "develop": 8, "document": [5, 8], "document_typ": 2, "format": 5, "get": 6, "indic": 5, "instal": 6, "interchang": 5, "locat": 8, "mmif": [0, 1, 2, 4, 5, 6, 7, 8, 9], "mmif_docloc_http": [3, 7], "model": 0, "modul": [0, 1, 2], "more": 5, "multimedia": 5, "overview": [6, 8], "packag": [3, 7], "plugin": 8, "prerequisit": 6, "python": [5, 8], "scheme": 8, "sdk": 8, "sequence_help": 1, "serial": [0, 6], "specif": 9, "start": 6, "tabl": 5, "target": 9, "util": 1, "version": 9, "video_document_help": 1, "view": 0, "vocabulari": 2, "welcom": 5}}) \ No newline at end of file diff --git a/docs/1.0.13/target-versions.html b/docs/1.0.13/target-versions.html deleted file mode 100644 index f0aa9ee0..00000000 --- a/docs/1.0.13/target-versions.html +++ /dev/null @@ -1,285 +0,0 @@ - - - - - - - - - Target MMIF Versions — mmif-python documentation - - - 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Target MMIF Versions

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This article provides targeting MMIF specification versions of different versions of mmif-python SDK.

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Target Specification Versions

mmif-python version

Target MMIF Specification

1.0.13

1.1.0

1.0.12

1.0.4

1.0.11

1.0.4

1.0.10.dev1

1.0.3

1.0.10

1.0.2

1.0.9

1.1.0

1.0.8

1.0.0

1.0.7

1.0.0

1.0.6

1.0.0

1.0.5

1.0.0

1.0.4

1.0.0

1.0.3

1.0.0

1.0.2

1.0.0

1.0.1

1.0.0

1.0.0

0.5.0

0.5.2

0.5.0

0.5.1

0.5.0

0.5.0

0.5.0

0.4.8

0.4.2

0.4.7

0.4.1

0.4.6

0.4.0

0.4.5

0.4.0

0.4.4

0.4.0

0.4.3

0.4.0

0.4.2

0.4.0

0.4.1

0.4.0

0.4.0

0.4.0

0.3.5

0.3.1

0.3.4

0.3.1

0.3.3

0.3.1

0.3.2

0.3.1

0.3.1

0.3.0

0.3.0

0.3.0

0.2.2

0.2.1

0.2.1

0.2.1

0.2.0

0.2.1

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0.3.0
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0.3.1
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0.3.2
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0.3.3
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0.3.4
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0.3.5
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0.4.0
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0.4.1
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0.4.2
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0.4.3
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0.4.4
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0.4.5
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0.4.6
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0.4.7
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0.4.8
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0.5.0
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0.5.1
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0.5.2
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1.0.0
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1.0.1
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1.0.10
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1.0.11
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1.0.12
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1.0.13
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1.0.14
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1.0.15
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1.0.16
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1.0.17
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1.0.18
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1.0.19
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1.0.2
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1.0.3
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1.0.4
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1.0.5
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1.0.6
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1.0.7
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1.0.8
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1.0.9
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1.1.0
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-mmif.serialize.model module ---------------------------- - -.. automodule:: mmif.serialize.model - :members: - :undoc-members: - :show-inheritance: - -mmif.serialize.mmif module --------------------------- - -.. automodule:: mmif.serialize.mmif - :members: - :undoc-members: - :show-inheritance: - -mmif.serialize.view module --------------------------- - -.. automodule:: mmif.serialize.view - :members: - :undoc-members: - :show-inheritance: - -mmif.serialize.annotation module --------------------------------- - -.. automodule:: mmif.serialize.annotation - :members: - :undoc-members: - :show-inheritance: - diff --git a/docs/1.0.14/_sources/autodoc/mmif.utils.rst.txt b/docs/1.0.14/_sources/autodoc/mmif.utils.rst.txt deleted file mode 100644 index 9a6ecc44..00000000 --- a/docs/1.0.14/_sources/autodoc/mmif.utils.rst.txt +++ /dev/null @@ -1,18 +0,0 @@ -mmif.utils module -================= - -mmif.utils.video_document_helper module ----------------------------------------- - -.. automodule:: mmif.utils.video_document_helper - :members: - :undoc-members: - :show-inheritance: - -mmif.utils.sequence_helper module ---------------------------------- - -.. automodule:: mmif.utils.sequence_helper - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/1.0.14/_sources/autodoc/mmif.vocabulary.rst.txt b/docs/1.0.14/_sources/autodoc/mmif.vocabulary.rst.txt deleted file mode 100644 index d250c6a3..00000000 --- a/docs/1.0.14/_sources/autodoc/mmif.vocabulary.rst.txt +++ /dev/null @@ -1,18 +0,0 @@ -mmif.vocabulary module -====================== - -mmif.vocabulary.annotation\_types module ----------------------------------------- - -.. automodule:: mmif.vocabulary.annotation_types - :members: - :undoc-members: - :show-inheritance: - -mmif.vocabulary.document\_types module --------------------------------------- - -.. automodule:: mmif.vocabulary.document_types - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/1.0.14/_sources/autodoc/mmif_docloc_http.rst.txt b/docs/1.0.14/_sources/autodoc/mmif_docloc_http.rst.txt deleted file mode 100644 index b76c8df5..00000000 --- a/docs/1.0.14/_sources/autodoc/mmif_docloc_http.rst.txt +++ /dev/null @@ -1,11 +0,0 @@ -mmif_docloc_http package -======================== - -MMIF document location helper module for `http` and `https` schemes. -If you want to write your own docloc scheme handler, please use the source code of this module as a reference. -See this :ref:`plug-in section ` for more information. - -.. automodule:: mmif_docloc_http - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/1.0.14/_sources/consumer-tutorial.rst.txt b/docs/1.0.14/_sources/consumer-tutorial.rst.txt deleted file mode 100644 index c54634e2..00000000 --- a/docs/1.0.14/_sources/consumer-tutorial.rst.txt +++ /dev/null @@ -1,17 +0,0 @@ -.. _consumer-tutorial: - -MMIF consumer -================================= - -A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the `appliance documentation `_ to learn more about the appliance. - -MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance. - -#. The code must be hosted on a public git repository (e.g. Github, Gitlab, ...) -#. Must listen to ``5000`` port. -#. Must expose ``/display`` route . -#. ``/display`` router should response to ``GET`` requests. -#. In the ``GET`` request, a public URL of the input MMIF file is passed via ``file`` URL parameter. -#. On the codebase root, there must be a ``Dockerfile`` that can build a `docker `_ image that runs the web app. - -We provide an example consumer at https://github.com/clamsproject/mmif-visualizer. diff --git a/docs/1.0.14/_sources/index.rst.txt b/docs/1.0.14/_sources/index.rst.txt deleted file mode 100644 index beb56aae..00000000 --- a/docs/1.0.14/_sources/index.rst.txt +++ /dev/null @@ -1,26 +0,0 @@ -Welcome to mmif-python's documentation! -======================================= - -.. mdinclude:: ../README.md - -.. toctree:: - :maxdepth: 2 - :caption: Contents - - introduction - plugins - target-versions - -.. toctree:: - :maxdepth: 2 - :caption: API documentation: - - modules - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/docs/1.0.14/_sources/introduction.rst.txt b/docs/1.0.14/_sources/introduction.rst.txt deleted file mode 100644 index cfd9eaf7..00000000 --- a/docs/1.0.14/_sources/introduction.rst.txt +++ /dev/null @@ -1,89 +0,0 @@ -.. _introduction: - -Getting Started -=============== - - -Overview ---------- - -MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for reproducibility, transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF website `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects. - -Prerequisites -------------- - -* `Python `_: the latest ``mmif-python`` requires Python 3.8 or newer. We have no plan to support `Python 2.7 `_. - -Installation ---------------- - -Package ``mmif-python`` is distributed via the official PyPI. Users are supposed to pip-install to get latest release. - -.. code-block:: bash - - pip install mmif-python - -This will install a package `mmif` to local python. - -The MMIF format and specification is evolving over time, and ``mmif-python`` package will be updated along with the changes in MMIF format. - -.. note:: MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and ``mmif-python`` versions, please take time to read our decision on the subject `here `_. If you need to know which python SDK supports which specification version, see :ref:`target-versions` page. - -MMIF Serialization ---------------------------- - -:class:`mmif.serialize.mmif.Mmif` represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of :class:`mmif.serialize.model.MmifObject`, including the :class:`mmif.serialize.mmif.Mmif`. To start with an existing MMIF :class:`str`, simple initiate a new ``Mmif`` object with the file. - -.. code-block:: python - - import mmif - from mmif import Mmif - - mmif_str = """{ - "metadata": { - "mmif": "http://mmif.clams.ai/1.0.0" - }, - "documents": [ - { - "@type": "http://mmif.clams.ai/vocabulary/VideoDocument/v1", - "properties": { - "id": "m1", - "mime": "video/mp4", - "location": "file:///var/archive/video-0012.mp4" - } - }, - { - "@type": "http://mmif.clams.ai/vocabulary/TextDocument/v1", - "properties": { - "id": "m2", - "mime": "text/plain", - "location": "file:///var/archive/video-0012-transcript.txt" - } - } - ], - "views": []}""" - mmif_obj = Mmif(mmif_str) - - -Few notes; - -#. MMIF does not carry the primary source files in it. -#. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version ``mmif-python`` implementation of the MMIF might not be able to load an unsupported version of MMIF string. - -When serializing back to :class:`str`, call :meth:`mmif.serialize.model.MmifObject.serialize` on the object. - -To get subcomponents, you can use various getters implemented in subclasses. For example; - -.. code-block:: python - - from mmif.vocabulary.document_types import DocumentTypes - - for video in mmif_obj.Mmif.get_documents_by_type(DocumentTypes.VideoDocument): - with open(video.location_path(), 'b') as in_video: - # do something with the video file - - -For a full list of available helper methods, please refer to :ref:`the API documentation `. - diff --git a/docs/1.0.14/_sources/modules.rst.txt b/docs/1.0.14/_sources/modules.rst.txt deleted file mode 100644 index 4bb9307d..00000000 --- a/docs/1.0.14/_sources/modules.rst.txt +++ /dev/null @@ -1,20 +0,0 @@ -.. _apidoc: - -mmif package -============ - -.. toctree:: - :maxdepth: 4 - - autodoc/mmif.serialize - autodoc/mmif.vocabulary - autodoc/mmif.utils - -mmif_docloc_http package -======================== - -.. toctree:: - :maxdepth: 2 - - autodoc/mmif_docloc_http - diff --git a/docs/1.0.14/_sources/plugins.rst.txt b/docs/1.0.14/_sources/plugins.rst.txt deleted file mode 100644 index 9907c495..00000000 --- a/docs/1.0.14/_sources/plugins.rst.txt +++ /dev/null @@ -1,83 +0,0 @@ -.. _plugins: - -Developing plugins for MMIF Python SDK -====================================== - - -Overview --------- - -As MMIF JSON files can carry information about media document files without actually carrying file contents, file accessing modules in ``mmif`` Python package (distributed as ``mmif-python`` on PyPI) are designed to be lightweight and flexible so that it can work with additional "plugin" Python packages that can handle concrete file access. - - -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF website `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects. - -Developer can write simple plugins that can provide additional functionalities to ``mmif-python``. For example, ``mmif-python`` does not provide any file access functionality beyond a local file system (with ``file`` scheme), but it can be extended with a plugin that can handle file access over different protocols (e.g. ``http``, ``s3``, ``ftp``, etc). - -This document contains information about how to write plugins for ``mmif-python``. - -.. _docloc_plugin: - -Document Location Scheme Plugins -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -:class:`mmif.serialize.annotation.Document` class has various methods to access parts of ``location`` property of the document. The location is in `URI/IRI format `_ (``SCHEME://HOSTNAME/PATH``, in a nutshell) and it has to be resolved to a local file for CLAMS Apps to process the local file to analyze and extract information about the media and its contents. The core ``mmif-python`` distribution only provides a default implementation that can handle ``file`` scheme URIs. - -To add a document location handler plugin, you need to implement a Python `"package" `_ (do not confuse with PYPI distribution), that meets these requirements; - -#. the package must be named ``mmif_docloc_``. For example, to implement a handler for ``s3`` scheme, the package name must be ``mmif_docloc_s3``. The prefix is important as it's used in the plugin discovery process from the core ``mmif-python`` modules. -#. the top module of the package must have a function named ``resolve``. The function must take a single argument, which is a :class:`str` of the document location URI. The function must return a :class:`str` of the local file path. For example, if the document location is ``s3://mybucket/myfile.mp4``, a Python user should be able to to something like this; - -.. code-block:: python - - import mmif_docloc_s3 - resolved = mmif_docloc_s3.resolve('s3://mybucket/myfile.mp4') - # then resolved must be a local file path that can be used to open the file - - -Here's a minimal example codebase that you refer to when you develop a ``docloc`` plugin. - -(However, before you start writing your own plugin for a specific URI scheme, checking `if there's already a PyPI distribution `_ for the scheme might be a good idea.) - -.. code-block:: sh - - $ tree . - . - ├── mmif_docloc_dummy - │ └── __init__.py - ├── pyproject.toml - └── setup.cfg - - $ cat pyproject.toml - [build-system] - requires = ["setuptools"] - build-backend = "setuptools.build_meta" - - $ cat setup.cfg - [metadata] - name = mmif_docloc_dummy # this name is IMPORTANT - version = 0.0.1 - description = a plugin to mmif-pyhon to handle `dummy` location scheme - - -And the plugin code. - -.. code-block:: python - - # mmif_docloc_dummy/__init__.py - doc_types = {'video': 'mp4'} - - def resolve(docloc): - scheme = 'dummy' - if docloc.startswith(f'{scheme}://'): - doc_id, doc_type = docloc.split('.') - return f'/path/to/{doc_id}.{doc_types[doc_type]}' - else: - raise ValueError(f'cannot handle document location scheme: {docloc}') - -Bulit-in Document Location Scheme Plugins -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -At the moment, ``mmif-python`` PyPI distribution ships a built-in *docloc* plugin that support both ``http`` and ``https`` schemes. -Take a look at :mod:`mmif_docloc_http` module for details. diff --git a/docs/1.0.14/_sources/target-versions.rst.txt b/docs/1.0.14/_sources/target-versions.rst.txt deleted file mode 100644 index 34216d3e..00000000 --- a/docs/1.0.14/_sources/target-versions.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _target-versions: - -Target MMIF Versions -==================== - -This article provides targeting MMIF specification versions of different versions of ``mmif-python`` SDK. - -.. csv-table:: Target Specification Versions - :file: target-versions.csv - :header-rows: 1 diff --git a/docs/1.0.14/_static/_sphinx_javascript_frameworks_compat.js b/docs/1.0.14/_static/_sphinx_javascript_frameworks_compat.js deleted file mode 100644 index 81415803..00000000 --- a/docs/1.0.14/_static/_sphinx_javascript_frameworks_compat.js +++ /dev/null @@ -1,123 +0,0 @@ -/* Compatability shim for jQuery and underscores.js. - * - * Copyright Sphinx contributors - * Released under the two clause BSD licence - */ - -/** - * small helper function to urldecode strings - * - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL - */ -jQuery.urldecode = function(x) { - if (!x) { - return x - } - return decodeURIComponent(x.replace(/\+/g, ' ')); -}; - -/** - * small helper function to urlencode strings - */ -jQuery.urlencode = encodeURIComponent; - -/** - * This function returns the parsed url parameters of the - * current request. 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- -/** - * Simple result scoring code. - */ -if (typeof Scorer === "undefined") { - var Scorer = { - // Implement the following function to further tweak the score for each result - // The function takes a result array [docname, title, anchor, descr, score, filename] - // and returns the new score. - /* - score: result => { - const [docname, title, anchor, descr, score, filename, kind] = result - return score - }, - */ - - // query matches the full name of an object - objNameMatch: 11, - // or matches in the last dotted part of the object name - objPartialMatch: 6, - // Additive scores depending on the priority of the object - objPrio: { - 0: 15, // used to be importantResults - 1: 5, // used to be objectResults - 2: -5, // used to be unimportantResults - }, - // Used when the priority is not in the mapping. - objPrioDefault: 0, - - // query found in title - title: 15, - partialTitle: 7, - // query found in terms - term: 5, - partialTerm: 2, - }; -} - -// Global search result kind enum, used by themes to style search results. -class SearchResultKind { - static get index() { return "index"; } - static get object() { return "object"; } - static get text() { return "text"; } - static get title() { return "title"; } -} - -const _removeChildren = (element) => { - while (element && element.lastChild) element.removeChild(element.lastChild); -}; - -/** - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping - */ -const _escapeRegExp = (string) => - string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string - -const _displayItem = (item, searchTerms, highlightTerms) => { - const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; - const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; - const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; - const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; - const contentRoot = document.documentElement.dataset.content_root; - - const [docName, title, anchor, descr, score, _filename, kind] = item; - - let listItem = document.createElement("li"); - // Add a class representing the item's type: - // can be used by a theme's CSS selector for styling - // See SearchResultKind for the class names. - listItem.classList.add(`kind-${kind}`); - let requestUrl; - let linkUrl; - if (docBuilder === "dirhtml") { - // dirhtml builder - let dirname = docName + "/"; - if (dirname.match(/\/index\/$/)) - dirname = dirname.substring(0, dirname.length - 6); - else if (dirname === "index/") dirname = ""; - requestUrl = contentRoot + dirname; - linkUrl = requestUrl; - } else { - // normal html builders - requestUrl = contentRoot + docName + docFileSuffix; - linkUrl = docName + docLinkSuffix; - } - let linkEl = listItem.appendChild(document.createElement("a")); - linkEl.href = linkUrl + anchor; - linkEl.dataset.score = score; - linkEl.innerHTML = title; - if (descr) { - listItem.appendChild(document.createElement("span")).innerHTML = - " (" + descr + ")"; - // highlight search terms in the description - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - } - else if (showSearchSummary) - fetch(requestUrl) - .then((responseData) => responseData.text()) - .then((data) => { - if (data) - listItem.appendChild( - Search.makeSearchSummary(data, searchTerms, anchor) - ); - // highlight search terms in the summary - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - }); - Search.output.appendChild(listItem); -}; -const _finishSearch = (resultCount) => { - Search.stopPulse(); - Search.title.innerText = _("Search Results"); - if (!resultCount) - Search.status.innerText = Documentation.gettext( - "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." - ); - else - Search.status.innerText = Documentation.ngettext( - "Search finished, found one page matching the search query.", - "Search finished, found ${resultCount} pages matching the search query.", - resultCount, - ).replace('${resultCount}', resultCount); -}; -const _displayNextItem = ( - results, - resultCount, - searchTerms, - highlightTerms, -) => { - // results left, load the summary and display it - // this is intended to be dynamic (don't sub resultsCount) - if (results.length) { - _displayItem(results.pop(), searchTerms, highlightTerms); - setTimeout( - () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), - 5 - ); - } - // search finished, update title and status message - else _finishSearch(resultCount); -}; -// Helper function used by query() to order search results. -// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. -// Order the results by score (in opposite order of appearance, since the -// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. -const _orderResultsByScoreThenName = (a, b) => { - const leftScore = a[4]; - const rightScore = b[4]; - if (leftScore === rightScore) { - // same score: sort alphabetically - const leftTitle = a[1].toLowerCase(); - const rightTitle = b[1].toLowerCase(); - if (leftTitle === rightTitle) return 0; - return leftTitle > rightTitle ? -1 : 1; // inverted is intentional - } - return leftScore > rightScore ? 1 : -1; -}; - -/** - * Default splitQuery function. Can be overridden in ``sphinx.search`` with a - * custom function per language. - * - * The regular expression works by splitting the string on consecutive characters - * that are not Unicode letters, numbers, underscores, or emoji characters. - * This is the same as ``\W+`` in Python, preserving the surrogate pair area. - */ -if (typeof splitQuery === "undefined") { - var splitQuery = (query) => query - .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) - .filter(term => term) // remove remaining empty strings -} - -/** - * Search Module - */ -const Search = { - _index: null, - _queued_query: null, - _pulse_status: -1, - - htmlToText: (htmlString, anchor) => { - const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - for (const removalQuery of [".headerlink", "script", "style"]) { - htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); - } - if (anchor) { - const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); - if (anchorContent) return anchorContent.textContent; - - console.warn( - `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` - ); - } - - // if anchor not specified or not found, fall back to main content - const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent) return docContent.textContent; - - console.warn( - "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." - ); - return ""; - }, - - init: () => { - const query = new URLSearchParams(window.location.search).get("q"); - document - .querySelectorAll('input[name="q"]') - .forEach((el) => (el.value = query)); - if (query) Search.performSearch(query); - }, - - loadIndex: (url) => - (document.body.appendChild(document.createElement("script")).src = url), - - setIndex: (index) => { - Search._index = index; - if (Search._queued_query !== null) { - const query = Search._queued_query; - Search._queued_query = null; - Search.query(query); - } - }, - - hasIndex: () => Search._index !== null, - - deferQuery: (query) => (Search._queued_query = query), - - stopPulse: () => (Search._pulse_status = -1), - - startPulse: () => { - if (Search._pulse_status >= 0) return; - - const pulse = () => { - Search._pulse_status = (Search._pulse_status + 1) % 4; - Search.dots.innerText = ".".repeat(Search._pulse_status); - if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); - }; - pulse(); - }, - - /** - * perform a search for something (or wait until index is loaded) - */ - performSearch: (query) => { - // create the required interface elements - const searchText = document.createElement("h2"); - searchText.textContent = _("Searching"); - const searchSummary = document.createElement("p"); - searchSummary.classList.add("search-summary"); - searchSummary.innerText = ""; - const searchList = document.createElement("ul"); - searchList.setAttribute("role", "list"); - searchList.classList.add("search"); - - const out = document.getElementById("search-results"); - Search.title = out.appendChild(searchText); - Search.dots = Search.title.appendChild(document.createElement("span")); - Search.status = out.appendChild(searchSummary); - Search.output = out.appendChild(searchList); - - const searchProgress = document.getElementById("search-progress"); - // Some themes don't use the search progress node - if (searchProgress) { - searchProgress.innerText = _("Preparing search..."); - } - Search.startPulse(); - - // index already loaded, the browser was quick! - if (Search.hasIndex()) Search.query(query); - else Search.deferQuery(query); - }, - - _parseQuery: (query) => { - // stem the search terms and add them to the correct list - const stemmer = new Stemmer(); - const searchTerms = new Set(); - const excludedTerms = new Set(); - const highlightTerms = new Set(); - const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); - splitQuery(query.trim()).forEach((queryTerm) => { - const queryTermLower = queryTerm.toLowerCase(); - - // maybe skip this "word" - // stopwords array is from language_data.js - if ( - stopwords.indexOf(queryTermLower) !== -1 || - queryTerm.match(/^\d+$/) - ) - return; - - // stem the word - let word = stemmer.stemWord(queryTermLower); - // select the correct list - if (word[0] === "-") excludedTerms.add(word.substr(1)); - else { - searchTerms.add(word); - highlightTerms.add(queryTermLower); - } - }); - - if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js - localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) - } - - // console.debug("SEARCH: searching for:"); - // console.info("required: ", [...searchTerms]); - // console.info("excluded: ", [...excludedTerms]); - - return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; - }, - - /** - * execute search (requires search index to be loaded) - */ - _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - - // Collect multiple result groups to be sorted separately and then ordered. - // Each is an array of [docname, title, anchor, descr, score, filename, kind]. - const normalResults = []; - const nonMainIndexResults = []; - - _removeChildren(document.getElementById("search-progress")); - - const queryLower = query.toLowerCase().trim(); - for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { - for (const [file, id] of foundTitles) { - const score = Math.round(Scorer.title * queryLower.length / title.length); - const boost = titles[file] === title ? 1 : 0; // add a boost for document titles - normalResults.push([ - docNames[file], - titles[file] !== title ? `${titles[file]} > ${title}` : title, - id !== null ? "#" + id : "", - null, - score + boost, - filenames[file], - SearchResultKind.title, - ]); - } - } - } - - // search for explicit entries in index directives - for (const [entry, foundEntries] of Object.entries(indexEntries)) { - if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id, isMain] of foundEntries) { - const score = Math.round(100 * queryLower.length / entry.length); - const result = [ - docNames[file], - titles[file], - id ? "#" + id : "", - null, - score, - filenames[file], - SearchResultKind.index, - ]; - if (isMain) { - normalResults.push(result); - } else { - nonMainIndexResults.push(result); - } - } - } - } - - // lookup as object - objectTerms.forEach((term) => - normalResults.push(...Search.performObjectSearch(term, objectTerms)) - ); - - // lookup as search terms in fulltext - normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); - - // let the scorer override scores with a custom scoring function - if (Scorer.score) { - normalResults.forEach((item) => (item[4] = Scorer.score(item))); - nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); - } - - // Sort each group of results by score and then alphabetically by name. - normalResults.sort(_orderResultsByScoreThenName); - nonMainIndexResults.sort(_orderResultsByScoreThenName); - - // Combine the result groups in (reverse) order. - // Non-main index entries are typically arbitrary cross-references, - // so display them after other results. - let results = [...nonMainIndexResults, ...normalResults]; - - // remove duplicate search results - // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept - let seen = new Set(); - results = results.reverse().reduce((acc, result) => { - let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); - if (!seen.has(resultStr)) { - acc.push(result); - seen.add(resultStr); - } - return acc; - }, []); - - return results.reverse(); - }, - - query: (query) => { - const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); - const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); - - // for debugging - //Search.lastresults = results.slice(); // a copy - // console.info("search results:", Search.lastresults); - - // print the results - _displayNextItem(results, results.length, searchTerms, highlightTerms); - }, - - /** - * search for object names - */ - performObjectSearch: (object, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const objects = Search._index.objects; - const objNames = Search._index.objnames; - const titles = Search._index.titles; - - const results = []; - - const objectSearchCallback = (prefix, match) => { - const name = match[4] - const fullname = (prefix ? prefix + "." : "") + name; - const fullnameLower = fullname.toLowerCase(); - if (fullnameLower.indexOf(object) < 0) return; - - let score = 0; - const parts = fullnameLower.split("."); - - // check for different match types: exact matches of full name or - // "last name" (i.e. last dotted part) - if (fullnameLower === object || parts.slice(-1)[0] === object) - score += Scorer.objNameMatch; - else if (parts.slice(-1)[0].indexOf(object) > -1) - score += Scorer.objPartialMatch; // matches in last name - - const objName = objNames[match[1]][2]; - const title = titles[match[0]]; - - // If more than one term searched for, we require other words to be - // found in the name/title/description - const otherTerms = new Set(objectTerms); - otherTerms.delete(object); - if (otherTerms.size > 0) { - const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); - if ( - [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) - ) - return; - } - - let anchor = match[3]; - if (anchor === "") anchor = fullname; - else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; - - const descr = objName + _(", in ") + title; - - // add custom score for some objects according to scorer - if (Scorer.objPrio.hasOwnProperty(match[2])) - score += Scorer.objPrio[match[2]]; - else score += Scorer.objPrioDefault; - - results.push([ - docNames[match[0]], - fullname, - "#" + anchor, - descr, - score, - filenames[match[0]], - SearchResultKind.object, - ]); - }; - Object.keys(objects).forEach((prefix) => - objects[prefix].forEach((array) => - objectSearchCallback(prefix, array) - ) - ); - return results; - }, - - /** - * search for full-text terms in the index - */ - performTermsSearch: (searchTerms, excludedTerms) => { - // prepare search - const terms = Search._index.terms; - const titleTerms = Search._index.titleterms; - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - - const scoreMap = new Map(); - const fileMap = new Map(); - - // perform the search on the required terms - searchTerms.forEach((word) => { - const files = []; - const arr = [ - { files: terms[word], score: Scorer.term }, - { files: titleTerms[word], score: Scorer.title }, - ]; - // add support for partial matches - if (word.length > 2) { - const escapedWord = _escapeRegExp(word); - if (!terms.hasOwnProperty(word)) { - Object.keys(terms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: terms[term], score: Scorer.partialTerm }); - }); - } - if (!titleTerms.hasOwnProperty(word)) { - Object.keys(titleTerms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); - }); - } - } - - // no match but word was a required one - if (arr.every((record) => record.files === undefined)) return; - - // found search word in contents - arr.forEach((record) => { - if (record.files === undefined) return; - - let recordFiles = record.files; - if (recordFiles.length === undefined) recordFiles = [recordFiles]; - files.push(...recordFiles); - - // set score for the word in each file - recordFiles.forEach((file) => { - if (!scoreMap.has(file)) scoreMap.set(file, {}); - scoreMap.get(file)[word] = record.score; - }); - }); - - // create the mapping - files.forEach((file) => { - if (!fileMap.has(file)) fileMap.set(file, [word]); - else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); - }); - }); - - // now check if the files don't contain excluded terms - const results = []; - for (const [file, wordList] of fileMap) { - // check if all requirements are matched - - // as search terms with length < 3 are discarded - const filteredTermCount = [...searchTerms].filter( - (term) => term.length > 2 - ).length; - if ( - wordList.length !== searchTerms.size && - wordList.length !== filteredTermCount - ) - continue; - - // ensure that none of the excluded terms is in the search result - if ( - [...excludedTerms].some( - (term) => - terms[term] === file || - titleTerms[term] === file || - (terms[term] || []).includes(file) || - (titleTerms[term] || []).includes(file) - ) - ) - break; - - // select one (max) score for the file. - const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); - // add result to the result list - results.push([ - docNames[file], - titles[file], - "", - null, - score, - filenames[file], - SearchResultKind.text, - ]); - } - return results; - }, - - /** - * helper function to return a node containing the - * search summary for a given text. keywords is a list - * of stemmed words. - */ - makeSearchSummary: (htmlText, keywords, anchor) => { - const text = Search.htmlToText(htmlText, anchor); - if (text === "") return null; - - const textLower = text.toLowerCase(); - const actualStartPosition = [...keywords] - .map((k) => textLower.indexOf(k.toLowerCase())) - .filter((i) => i > -1) - .slice(-1)[0]; - const startWithContext = Math.max(actualStartPosition - 120, 0); - - const top = startWithContext === 0 ? "" : "..."; - const tail = startWithContext + 240 < text.length ? "..." : ""; - - let summary = document.createElement("p"); - summary.classList.add("context"); - summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; - - return summary; - }, -}; - -_ready(Search.init); diff --git a/docs/1.0.14/_static/sphinx_highlight.js b/docs/1.0.14/_static/sphinx_highlight.js deleted file mode 100644 index 8a96c69a..00000000 --- a/docs/1.0.14/_static/sphinx_highlight.js +++ /dev/null @@ -1,154 +0,0 @@ -/* Highlighting utilities for Sphinx HTML documentation. */ -"use strict"; - -const SPHINX_HIGHLIGHT_ENABLED = true - -/** - * highlight a given string on a node by wrapping it in - * span elements with the given class name. - */ -const _highlight = (node, addItems, text, className) => { - if (node.nodeType === Node.TEXT_NODE) { - const val = node.nodeValue; - const parent = node.parentNode; - const pos = val.toLowerCase().indexOf(text); - if ( - pos >= 0 && - !parent.classList.contains(className) && - !parent.classList.contains("nohighlight") - ) { - let span; - - const closestNode = parent.closest("body, svg, foreignObject"); - const isInSVG = closestNode && closestNode.matches("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.classList.add(className); - } - - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - const rest = document.createTextNode(val.substr(pos + text.length)); - parent.insertBefore( - span, - parent.insertBefore( - rest, - node.nextSibling - ) - ); - node.nodeValue = val.substr(0, pos); - /* There may be more occurrences of search term in this node. So call this - * function recursively on the remaining fragment. - */ - _highlight(rest, addItems, text, className); - - if (isInSVG) { - const rect = document.createElementNS( - "http://www.w3.org/2000/svg", - "rect" - ); - const bbox = parent.getBBox(); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute("class", className); - addItems.push({ parent: parent, target: rect }); - } - } - } else if (node.matches && !node.matches("button, select, textarea")) { - node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); - } -}; -const _highlightText = (thisNode, text, className) => { - let addItems = []; - _highlight(thisNode, addItems, text, className); - addItems.forEach((obj) => - obj.parent.insertAdjacentElement("beforebegin", obj.target) - ); -}; - -/** - * Small JavaScript module for the documentation. - */ -const SphinxHighlight = { - - /** - * highlight the search words provided in localstorage in the text - */ - highlightSearchWords: () => { - if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight - - // get and clear terms from localstorage - const url = new URL(window.location); - const highlight = - localStorage.getItem("sphinx_highlight_terms") - || url.searchParams.get("highlight") - || ""; - localStorage.removeItem("sphinx_highlight_terms") - url.searchParams.delete("highlight"); - window.history.replaceState({}, "", url); - - // get individual terms from highlight string - const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); - if (terms.length === 0) return; // nothing to do - - // There should never be more than one element matching "div.body" - const divBody = document.querySelectorAll("div.body"); - const body = divBody.length ? divBody[0] : document.querySelector("body"); - window.setTimeout(() => { - terms.forEach((term) => _highlightText(body, term, "highlighted")); - }, 10); - - const searchBox = document.getElementById("searchbox"); - if (searchBox === null) return; - searchBox.appendChild( - document - .createRange() - .createContextualFragment( - '

' + - '' + - _("Hide Search Matches") + - "

" - ) - ); - }, - - /** - * helper function to hide the search marks again - */ - hideSearchWords: () => { - document - .querySelectorAll("#searchbox .highlight-link") - .forEach((el) => el.remove()); - document - .querySelectorAll("span.highlighted") - .forEach((el) => el.classList.remove("highlighted")); - localStorage.removeItem("sphinx_highlight_terms") - }, - - initEscapeListener: () => { - // only install a listener if it is really needed - if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; - - document.addEventListener("keydown", (event) => { - // bail for input elements - if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; - // bail with special keys - if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; - if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { - SphinxHighlight.hideSearchWords(); - event.preventDefault(); - } - }); - }, -}; - -_ready(() => { - /* Do not call highlightSearchWords() when we are on the search page. - * It will highlight words from the *previous* search query. - */ - if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); - SphinxHighlight.initEscapeListener(); -}); diff --git a/docs/1.0.14/autodoc/mmif.serialize.html b/docs/1.0.14/autodoc/mmif.serialize.html deleted file mode 100644 index 88546fc4..00000000 --- a/docs/1.0.14/autodoc/mmif.serialize.html +++ /dev/null @@ -1,1412 +0,0 @@ - - - - - - - - - mmif.serialize module — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
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mmif.serialize module

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mmif.serialize.model module

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The model module contains the classes used to represent an -abstract MMIF object as a live Python object.

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The MmifObject class or one of its derivatives is subclassed by -all other classes defined in this SDK, except for MmifObjectEncoder.

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These objects are generally instantiated from JSON, either as a string -or as an already-loaded Python dictionary. This base class provides the -core functionality for deserializing MMIF JSON data into live objects -and serializing live objects into MMIF JSON data. Specialized behavior -for the different components of MMIF is added in the subclasses.

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-class mmif.serialize.model.DataDict(mmif_obj: bytes | str | dict | None = None)[source]
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Bases: MmifObject, Generic[T, S]

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-empty()[source]
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-get(key: T, default=None) → S | None[source]
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-items()[source]
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-keys()[source]
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-update(other, overwrite)[source]
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-values()[source]
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-class mmif.serialize.model.DataList(mmif_obj: bytes | str | list | None = None)[source]
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Bases: MmifObject, Generic[T]

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The DataList class is an abstraction that represents the -various lists found in a MMIF file, such as documents, subdocuments, -views, and annotations.

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Parameters:
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mmif_obj (Union[str, list]) – the data that the list contains

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-append(value, overwrite)[source]
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-deserialize(mmif_json: str | list) → None[source]
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Passes the input data into the internal deserializer.

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-empty()[source]
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-get(key: str) → T | None[source]
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Standard dictionary-style get() method, albeit with no default -parameter. Relies on the implementation of __getitem__.

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Will return None if the key is not found.

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Parameters:
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key – the key to search for

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Returns:
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the value matching that key

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-class mmif.serialize.model.MmifObject(mmif_obj: bytes | str | dict | None = None)[source]
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Bases: object

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Abstract superclass for MMIF related key-value pair objects.

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Any MMIF object can be initialized as an empty placeholder or -an actual representation with a JSON formatted string or equivalent -dict object argument.

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This superclass has four specially designed instance variables, and these -variable names cannot be used as attribute names for MMIF objects.

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    -

  1. _unnamed_attributes: -Only can be either None or an empty dictionary. If it’s set to None, -it means the class won’t take any Additional Attributes in the -JSON schema sense. If it’s an empty dict, users can throw any k-v -pairs to the class, as long as the key is not a “reserved” name, -and those additional attributes will be stored in this dict while -in memory.

    2. -

  2. _attribute_classes: -This is a dict from a key name to a specific python class to use for -deserialize the value. Note that a key name in this dict does NOT -have to be a named attribute, but is recommended to be one.

    3. -

  3. _required_attributes: -This is a simple list of names of attributes that are required in -the object. When serialize, an object will skip its empty (e.g. -zero-length, or None) attributes unless they are in this list. -Otherwise, the serialized JSON string would have empty -representations (e.g. "", []).

    4. -

  4. _exclude_from_diff: -This is a simple list of names of attributes that should be excluded -from the diff calculation in __eq__.

    5. -
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# TODO (krim @ 8/17/20): this dict is however, a duplicate with the type hints in the class definition. -Maybe there is a better way to utilize type hints (e.g. getting them -as a programmatically), but for now developers should be careful to -add types to hints as well as to this dict.

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Also note that those special attributes MUST be set in the __init__() -before calling super method, otherwise deserialization will not work.

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And also, a subclass that has one or more named attributes, it must -set those attributes in the __init__() before calling super method. -When serializing a MmifObject, all empty attributes will be ignored, -so for optional named attributes, you must leave the values empty -(len == 0), but NOT None. Any None-valued named attributes will cause -issues with current implementation.

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Parameters:
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mmif_obj – JSON string or dict to initialize an object. -If not given, an empty object will be initialized, sometimes with -an ID value automatically generated, based on its parent object.

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-deserialize(mmif_json: str | dict) → None[source]
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Takes a JSON-formatted string or a simple dict that’s json-loaded from -such a string as an input and populates object’s fields with the values -specified in the input.

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Parameters:
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mmif_json – JSON-formatted string or dict from such a string -that represents a MMIF object

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-disallow_additional_properties() → None[source]
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Call this method in __init__() to prevent the insertion -of unnamed attributes after initialization.

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-id_delimiter: ClassVar[str] = ':'[source]
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-static is_empty(obj) → bool[source]
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return True if the obj is None or “emtpy”. The emptiness first defined as -having zero length. But for objects that lack __len__ method, we need -additional check.

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-reserved_names: Set[str] = {'_attribute_classes', '_exclude_from_diff', '_required_attributes', '_unnamed_attributes', 'reserved_names'}[source]
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-serialize(pretty: bool = False) → str[source]
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Generates JSON representation of an object.

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Parameters:
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pretty – If True, returns string representation with indentation.

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Returns:
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JSON string of the object.

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-set_additional_property(key: str, value: Any) → None[source]
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Method to set values in _unnamed_attributes.

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Parameters:
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    -

  • key – the attribute name

    • -

  • value – the desired value

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Returns:
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None

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Raise:
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AttributeError if additional properties are disallowed by disallow_additional_properties()

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-view_prefix: ClassVar[str] = 'v_'[source]
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-class mmif.serialize.model.MmifObjectEncoder(*, skipkeys=False, ensure_ascii=True, check_circular=True, allow_nan=True, sort_keys=False, indent=None, separators=None, default=None)[source]
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Bases: JSONEncoder

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Encoder class to define behaviors of de-/serialization

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-default(obj: MmifObject)[source]
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Overrides default encoding behavior to prioritize MmifObject.serialize().

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mmif.serialize.mmif module

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The mmif module contains the classes used to represent a full MMIF -file as a live Python object.

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See the specification docs and the JSON Schema file for more information.

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-class mmif.serialize.mmif.Mmif(mmif_obj: bytes | str | dict | None = None, *, validate: bool = True)[source]
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Bases: MmifObject

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MmifObject that represents a full MMIF file.

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Parameters:
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  • mmif_obj – the JSON data

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  • validate – whether to validate the data against the MMIF JSON schema.

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-add_document(document: Document, overwrite=False) → None[source]
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Appends a Document object to the documents list.

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Fails if there is already a document with the same ID in the MMIF object.

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Parameters:
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  • document – the Document object to add

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  • overwrite – if set to True, will overwrite -an existing view with the same ID

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Returns:
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None

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-add_view(view: View, overwrite=False) → None[source]
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Appends a View object to the views list.

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Fails if there is already a view with the same ID in the MMIF object.

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Parameters:
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  • view – the Document object to add

    • -

  • overwrite – if set to True, will overwrite -an existing view with the same ID

    • -
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Returns:
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None

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-generate_capital_annotations()[source]
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Automatically convert any “pending” temporary properties from -Document objects to Annotation objects . The generated Annotation -objects are then added to the last View in the views lists.

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See https://github.com/clamsproject/mmif-python/issues/226 for rationale -behind this behavior and discussion.

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-get_alignments(at_type1: str | TypesBase, at_type2: str | TypesBase) → Dict[str, List[Annotation]][source]
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Finds views where alignments between two given annotation types occurred.

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Returns:
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a dict that keyed by view IDs (str) and has lists of alignment Annotation objects as values.

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-get_all_views_contain(at_types: TypesBase | str | List[str | TypesBase]) → List[View][source]
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Returns the list of all views in the MMIF if given types -are present in that view’s ‘contains’ metadata.

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Parameters:
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at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

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Returns:
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the list of views that contain the type

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-get_all_views_with_error() → List[View][source]
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Returns the list of all views in the MMIF that have errors.

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Returns:
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the list of views that contain errors but no annotations

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-get_document_by_id(doc_id: str) → Document[source]
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Finds a Document object with the given ID.

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Parameters:
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doc_id – the ID to search for

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Returns:
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a reference to the corresponding document, if it exists

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Raises:
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KeyError – if there is no corresponding document

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-get_document_location(m_type: DocumentTypes | str, path_only=False) → str | None[source]
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Method to get the location of first document of given type.

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Parameters:
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m_type – the type to search for

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Returns:
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the value of the location field in the corresponding document

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-get_documents_by_app(app_id: str) → List[Document][source]
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Method to get all documents object queries by its originated app name.

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Parameters:
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app_id – the app name to search for

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Returns:
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a list of documents matching the requested app name, or an empty list if the app not found

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-get_documents_by_property(prop_key: str, prop_value: str) → List[Document][source]
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Method to retrieve documents by an arbitrary key-value pair in the document properties objects.

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Parameters:
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    -

  • prop_key – the metadata key to search for

    • -

  • prop_value – the metadata value to match

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Returns:
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a list of documents matching the requested metadata key-value pair

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-get_documents_by_type(doc_type: str | DocumentTypes) → List[Document][source]
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Method to get all documents where the type matches a particular document type, which should be one of the CLAMS document types.

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Parameters:
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doc_type – the type of documents to search for, must be one of Document type defined in the CLAMS vocabulary.

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Returns:
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a list of documents matching the requested type, or an empty list if none found.

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-get_documents_in_view(vid: str | None = None) → List[Document][source]
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Method to get all documents object queries by a view id.

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Parameters:
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vid – the source view ID to search for

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Returns:
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a list of documents matching the requested source view ID, or an empty list if the view not found

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-get_documents_locations(m_type: DocumentTypes | str, path_only=False) → List[str | None][source]
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This method returns the file paths of documents of given type. -Only top-level documents have locations, so we only check them.

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Parameters:
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m_type – the type to search for

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Returns:
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a list of the values of the location fields in the corresponding documents

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-get_end(annotation: Annotation) → int | float[source]
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An alias to get_anchor_point method with start=False.

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-get_last_error() → str | None[source]
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Returns the last error message found in the views.

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Returns:
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the error message in human-readable format, or None if no error is found

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-get_start(annotation: Annotation) → int | float[source]
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An alias to get_anchor_point method with start=True.

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-get_view_by_id(req_view_id: str) → View[source]
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Finds a View object with the given ID.

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Parameters:
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req_view_id – the ID to search for

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Returns:
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a reference to the corresponding view, if it exists

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Raises:
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Exception – if there is no corresponding view

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-get_view_contains(at_types: TypesBase | str | List[str | TypesBase]) → View | None[source]
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Returns the last view appended that contains the given -types in its ‘contains’ metadata.

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Parameters:
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at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

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Returns:
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the view, or None if the type is not found

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-get_view_with_error() → View | None[source]
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Returns the last view appended that contains an error.

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Returns:
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the view, or None if no error is found

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-get_views_contain(at_types: TypesBase | str | List[str | TypesBase]) → List[View][source]
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Returns the list of all views in the MMIF if given types -are present in that view’s ‘contains’ metadata.

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Parameters:
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at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

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Returns:
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the list of views that contain the type

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-get_views_for_document(doc_id: str) → List[View][source]
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Returns the list of all views that have annotations anchored on a particular document. -Note that when the document is inside a view (generated during the pipeline’s running), -doc_id must be prefixed with the view_id.

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-get_views_with_error() → List[View][source]
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Returns the list of all views in the MMIF that have errors.

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Returns:
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the list of views that contain errors but no annotations

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-new_view() → View[source]
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Creates an empty view with a new ID and appends it to the views list.

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Returns:
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a reference to the new View object

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-new_view_id() → str[source]
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Fetches an ID for a new view.

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Returns:
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the ID

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-sanitize()[source]
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Sanitizes a Mmif object by running some safeguards. -Concretely, it performs the following before returning the JSON string.

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  1. validating output using built-in MMIF jsonschema

    2. -

  2. remove non-existing annotation types from contains metadata

    3. -
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-serialize(pretty: bool = False, sanitize: bool = False, autogenerate_capital_annotations=True) → str[source]
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Serializes the MMIF object to a JSON string.

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Parameters:
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    -

  • sanitize – If True, performs some sanitization of before returning -the JSON string. See sanitize() for details.

    • -

  • autogenerate_capital_annotations – If True, automatically convert -any “pending” temporary properties from Document objects to -Annotation objects. See generate_capital_annotations() for -details.

    • -

  • pretty – If True, returns string representation with indentation.

    • -
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Returns:
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JSON string of the MMIF object.

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-static validate(json_str: bytes | str | dict) → None[source]
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Validates a MMIF JSON object against the MMIF Schema. -Note that this method operates before processing by MmifObject._load_str, -so it expects @ and not _ for the JSON-LD @-keys.

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Raises:
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jsonschema.exceptions.ValidationError – if the input fails validation

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Parameters:
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json_str – a MMIF JSON dict or string

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Returns:
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None

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mmif.serialize.view module

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The view module contains the classes used to represent a MMIF view -as a live Python object.

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In MMIF, views are created by apps in a pipeline that are annotating -data that was previously present in the MMIF file.

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-class mmif.serialize.view.Contain(mmif_obj: bytes | str | dict | None = None)[source]
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Bases: DataDict[str, str]

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Contain object that represents the metadata of a single -annotation type in the contains metadata of a MMIF view.

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-class mmif.serialize.view.View(view_obj: bytes | str | dict | None = None)[source]
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Bases: MmifObject

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View object that represents a single view in a MMIF file.

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A view is identified by an ID, and contains certain metadata, -a list of annotations, and potentially a JSON-LD @context -IRI.

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If view_obj is not provided, an empty View will be generated.

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Parameters:
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view_obj – the JSON data that defines the view

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-add_annotation(annotation: Annotation, overwrite=False) → Annotation[source]
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Adds an annotation to the current view.

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Fails if there is already an annotation with the same ID -in the view, unless overwrite is set to True.

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Parameters:
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Raises:
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KeyError – if overwrite is set to False and -an annotation with the same ID exists -in the view

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Returns:
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the same Annotation object passed in as annotation

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-add_document(document: Document, overwrite=False) → Annotation[source]
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Appends a Document object to the annotations list.

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Fails if there is already a document with the same ID in the annotations list.

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Parameters:
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    -

  • document – the Document object to add

    • -

  • overwrite – if set to True, will overwrite -an existing view with the same ID

    • -
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Returns:
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None

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-get_annotation_by_id(ann_id) → Annotation[source]
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-get_annotations(at_type: str | TypesBase | None = None, **properties) → Generator[Annotation, None, None][source]
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Look for certain annotations in this view, specified by parameters

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Parameters:
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    -

  • at_type – @type of the annotations to look for. When this is None, any @type will match.

    • -

  • properties – properties of the annotations to look for. When given more than one property, all properties must match. Note that annotation type metadata are specified in the contains view metadata, not in individual annotation objects.

    • -
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-get_document_by_id(doc_id) → Document[source]
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-get_documents() → List[Document][source]
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-get_error() → str | None[source]
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Get the “text” representation of the error occurred during -processing. Text representation is supposed to be human-readable. -When ths view does not have any error, returns None.

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-has_error() → bool[source]
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-has_warnings()[source]
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-new_annotation(at_type: str | TypesBase, aid: str | None = None, overwrite=False, **properties) → Annotation[source]
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Generates a new mmif.serialize.annotation.Annotation -object and adds it to the current view.

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Fails if there is already an annotation with the same ID -in the view, unless overwrite is set to True.

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Parameters:
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    -

  • at_type – the desired @type of the annotation.

    • -

  • aid – the desired ID of the annotation, when not given, -the mmif SDK tries to automatically generate an ID based on -Annotation type and existing annotations in the view.

    • -

  • overwrite – if set to True, will overwrite an -existing annotation with the same ID.

    • -
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Raises:
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KeyError – if overwrite is set to False and -an annotation with the same ID exists -in the view.

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Returns:
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the generated mmif.serialize.annotation.Annotation

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-new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
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Adds a new element to the contains metadata.

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Parameters:
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    -

  • at_type – the @type of the annotation type being added

    • -

  • contains_metadata – any metadata associated with the annotation type

    • -
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Returns:
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the generated Contain object

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-new_textdocument(text: str, lang: str = 'en', did: str | None = None, overwrite=False, **properties) → Document[source]
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Generates a new mmif.serialize.annotation.Document -object, particularly typed as TextDocument and adds it to the current view.

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Fails if there is already a text document with the same ID -in the view, unless overwrite is set to True.

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Parameters:
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    -

  • text – text content of the new document

    • -

  • lang – ISO 639-1 code of the language used in the new document

    • -

  • did – the desired ID of the document, when not given, -the mmif SDK tries to automatically generate an ID based on -Annotation type and existing documents in the view.

    • -

  • overwrite – if set to True, will overwrite an -existing document with the same ID

    • -
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Raises:
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KeyError – if overwrite is set to False and -an document with the same ID exists -in the view

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Returns:
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the generated mmif.serialize.annotation.Document

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- -
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-set_error(err_message: str, err_trace: str) → None[source]
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- -
- -
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-class mmif.serialize.view.ViewMetadata(viewmetadata_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-

ViewMetadata object that represents the metadata object within a MMIF view.

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Parameters:
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viewmetadata_obj – the JSON data that defines the metadata

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-add_app_configuration(config_key: str, config_value: str | int | float | bool | None | List[str | int | float | bool | None]) → None[source]
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Add a configuration key-value pair to the app_configuration dictionary.

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- -
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-add_contain(contain: Contain, at_type: str | TypesBase) → None[source]
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- -
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-add_parameter(param_key: str, param_value: str)[source]
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Add a single runtime parameter to the view metadata. Note that parameter value must be a string.

-
- -
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-add_parameters(**runtime_params: str)[source]
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Add runtime parameters as a batch (dict) to the view metadata. Note that parameter values must be strings.

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- -
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-add_warnings(*warnings: Warning)[source]
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- -
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-emtpy_warnings()[source]
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- -
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-get_app_configuration(config_key: str) → str | int | float | bool | None | List[str | int | float | bool | None][source]
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Get a configuration value from the app_configuration dictionary.

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- -
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-get_error_as_text() → str[source]
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- -
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-get_parameter(param_key: str) → str[source]
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Get a runtime parameter from the view metadata.

-
- -
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-has_error() → bool[source]
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- -
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-has_warnings()[source]
-
- -
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-new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
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Adds a new element to the contains dictionary.

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Parameters:
-
    -

  • at_type – the @type of the annotation type being added

    • -

  • contains_metadata – any metadata associated with the annotation type

    • -
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Returns:
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the generated Contain object

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- -
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-set_error(message: str, stack_trace: str)[source]
-
- -
- -
-
-

mmif.serialize.annotation module

-

The annotation module contains the classes used to represent a -MMIF annotation as a live Python object.

-

In MMIF, annotations are created by apps in a pipeline as a part -of a view. For documentation on how views are represented, see -mmif.serialize.view.

-
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-class mmif.serialize.annotation.Annotation(anno_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-

MmifObject that represents an annotation in a MMIF view.

-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]]) → None[source]
-

Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

-
- -
-
-property at_type: TypesBase[source]
-
- -
-
-static check_prop_value_is_simple_enough(value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]]) → bool[source]
-
- -
-
-get(prop_name: str) → AnnotationProperties | str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]][source]
-

A special getter for Annotation properties. This is to allow for -directly accessing properties without having to go through the -properties object, or view-level annotation properties encoded in the -view.metadata.contains dict. Note that the regular props will take -the priority over the ephemeral props when there are conflicts.

-
- -
-
-get_property(prop_name: str) → AnnotationProperties | str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]][source]
-

A special getter for Annotation properties. This is to allow for -directly accessing properties without having to go through the -properties object, or view-level annotation properties encoded in the -view.metadata.contains dict. Note that the regular props will take -the priority over the ephemeral props when there are conflicts.

-
- -
-
-property id: str[source]
-
- -
-
-is_document()[source]
-
- -
-
-is_type(at_type: str | TypesBase) → bool[source]
-

Check if the @type of this object matches.

-
- -
-
-property long_id: str[source]
-
- -
-
-property parent: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.AnnotationProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject, MutableMapping[str, T]

-

AnnotationProperties object that represents the -properties object within a MMIF annotation.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
- -
-
-class mmif.serialize.annotation.Document(doc_obj: bytes | str | dict | None = None)[source]
-

Bases: Annotation

-

Document object that represents a single document in a MMIF file.

-

A document is identified by an ID, and contains certain attributes -and potentially contains the contents of the document itself, -metadata about how the document was created, and/or a list of -subdocuments grouped together logically.

-

If document_obj is not provided, an empty Document will be generated.

-
-
Parameters:
-

document_obj – the JSON data that defines the document

-
-
-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None]) → None[source]
-

Adds a property to the document’s properties.

-

Unlike the parent Annotation class, added properties of a -Document object can be lost during serialization unless it belongs -to somewhere in a Mmif object. This is because we want to keep -Document object as “read-only” as possible. Thus, if you want to add -a property to a Document object,

-
    -

  • add the document to a Mmif object (either in the documents list or -in a view from the views list), or

    • -

  • directly write to Document.properties instead of using this method -(which is not recommended).

    • -
-

With the former method, the SDK will record the added property as a -Annotation annotation object, separate from the original Document -object. See Mmif.generate_capital_annotations() for more.

-

A few notes to keep in mind:

-
    -

  1. You can’t overwrite an existing property of a Document object.

    2. -

  2. A MMIF can have multiple Annotation objects with the same -property name but different values. When this happens, the SDK will -only keep the latest value (in order of appearances in views list) of -the property, effectively overwriting the previous values.

    3. -
-
- -
-
-get(prop_name)[source]
-

A special getter for Document properties. The major difference from -the super class’s Annotation.get() method is that Document -class has one more set of “pending” properties, that are added after -the Document object is created and will be serialized as a separate -Annotation object of which @type = Annotation. The -pending properties will take the priority over the regular properties -when there are conflicts.

-
- -
-
-get_property(prop_name)[source]
-

A special getter for Document properties. The major difference from -the super class’s Annotation.get() method is that Document -class has one more set of “pending” properties, that are added after -the Document object is created and will be serialized as a separate -Annotation object of which @type = Annotation. The -pending properties will take the priority over the regular properties -when there are conflicts.

-
- -
-
-property location: str | None[source]
-

location property must be a legitimate URI. That is, should the document be a local file -then the file:// scheme must be used. -Returns None when no location is set.

-
- -
-
-location_address() → str | None[source]
-

Retrieves the full address from the document location URI. -Returns None when no location is set.

-
- -
-
-location_path(nonexist_ok=True) → str | None[source]
-

Retrieves a path that’s resolved to a pathname in the local file system. -To obtain the original value of the “path” part in the location string -(before resolving), use properties.location_path_literal method. -Returns None when no location is set.

-
-
Parameters:
-

nonexist_ok – if False, raise FileNotFoundError when the resolved path doesn’t exist

-
-
-
- -
-
-location_scheme() → str | None[source]
-

Retrieves URI scheme of the document location. -Returns None when no location is set.

-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.DocumentProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: AnnotationProperties

-

DocumentProperties object that represents the -properties object within a MMIF document.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
-
-property location: str | None[source]
-

location property must be a legitimate URI. That is, should the document be a local file -then the file:// scheme must be used. -Returns None when no location is set.

-
- -
-
-location_address() → str | None[source]
-

Retrieves the full address from the document location URI. -Returns None when no location is set.

-
- -
-
-location_path() → str | None[source]
-
- -
-
-location_path_literal() → str | None[source]
-

Retrieves only path name of the document location (hostname is ignored). -Returns None when no location is set.

-
- -
-
-location_path_resolved(nonexist_ok=True) → str | None[source]
-

Retrieves only path name of the document location (hostname is ignored), -and then try to resolve the path name in the local file system. -This method should be used when the document scheme is file or empty. -For other schemes, users should install mmif-locdoc-<scheme> plugin.

-

Returns None when no location is set. -Raise ValueError when no code found to resolve the given location scheme.

-
- -
-
-location_scheme() → str | None[source]
-

Retrieves URI scheme of the document location. -Returns None when no location is set.

-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.Text(text_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-
-
-property lang: str[source]
-
- -
-
-property value: str[source]
-
- -
- -
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 1.0.14 - - -
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- - - \ No newline at end of file diff --git a/docs/1.0.14/autodoc/mmif.utils.html b/docs/1.0.14/autodoc/mmif.utils.html deleted file mode 100644 index 66558d6f..00000000 --- a/docs/1.0.14/autodoc/mmif.utils.html +++ /dev/null @@ -1,578 +0,0 @@ - - - - - - - - - mmif.utils module — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.utils module

-
-

mmif.utils.video_document_helper module

-
-
-mmif.utils.video_document_helper.capture(video_document: Document)[source]
-

Captures a video file using OpenCV and adds fps, frame count, and duration as properties to the document.

-
-
Parameters:
-

video_document – Document instance that holds a video document ("@type": ".../VideoDocument/...")

-
-
Returns:
-

OpenCV VideoCapture object

-
-
-
- -
-
-mmif.utils.video_document_helper.convert_timeframe(mmif: Mmif, time_frame: Annotation, out_unit: str) → Tuple[int | float | str, int | float | str][source]
-

Converts start and end points in a TimeFrame annotation a different time unit.

-
-
Parameters:
-
    -

  • mmif – Mmif instance

    • -

  • time_frame – Annotation instance that holds a time interval annotation ("@type": ".../TimeFrame/...")

    • -

  • out_unit – time unit to which the point is converted

    • -
-
-
Returns:
-

tuple of frame numbers (integer) or seconds/milliseconds (float) of input start and end

-
-
-
- -
-
-mmif.utils.video_document_helper.convert_timepoint(mmif: Mmif, timepoint: Annotation, out_unit: str) → int | float | str[source]
-

Converts a time point included in an annotation to a different time unit. -The input annotation must have timePoint property.

-
-
Parameters:
-
    -

  • mmif – input MMIF to obtain fps and input timeunit

    • -

  • timepoint – Annotation instance with timePoint property

    • -

  • out_unit – time unit to which the point is converted (frames, seconds, milliseconds)

    • -
-
-
Returns:
-

frame number (integer) or second/millisecond (float) of input timepoint

-
-
-
- -
-
-mmif.utils.video_document_helper.extract_frames_as_images(video_document: Document, framenums: List[int], as_PIL: bool = False)[source]
-

Extracts frames from a video document as a list of numpy.ndarray. -Use with sample_frames() function to get the list of frame numbers first.

-
-
Parameters:
-
    -

  • video_document – Document instance that holds a video document ("@type": ".../VideoDocument/...")

    • -

  • framenums – integers representing the frame numbers to extract

    • -

  • as_PIL – return PIL.Image.Image instead of ndarray

    • -
-
-
Returns:
-

frames as a list of ndarray or Image

-
-
-
- -
-
-mmif.utils.video_document_helper.extract_mid_frame(mmif: Mmif, time_frame: Annotation, as_PIL: bool = False)[source]
-

Extracts the middle frame of a time interval annotation as a numpy ndarray.

-
-
Parameters:
-
    -

  • mmif – Mmif instance

    • -

  • time_frame – Annotation instance that holds a time interval annotation ("@type": ".../TimeFrame/...")

    • -

  • as_PIL – return Image instead of ndarray

    • -
-
-
Returns:
-

frame as a numpy.ndarray or PIL.Image.Image

-
-
-
- -
-
-mmif.utils.video_document_helper.framenum_to_millisecond(video_doc: Document, frame: int)[source]
-

Converts a frame number to a millisecond value.

-
- -
-
-mmif.utils.video_document_helper.framenum_to_second(video_doc: Document, frame: int)[source]
-

Converts a frame number to a second value.

-
- -
-
-mmif.utils.video_document_helper.get_annotation_property(mmif, annotation, prop_name)[source]
-
-

Deprecated since version 1.0.8: Use mmif.serialize.annotation.Annotation.get_property() method instead.

-
-

Get a property value from an annotation. If the property is not found in the annotation, it will look up the metadata of the annotation’s parent view and return the value from there. -xisting

-
- -
-
-mmif.utils.video_document_helper.get_framerate(video_document: Document) → float[source]
-

Gets the frame rate of a video document. First by checking the fps property of the document, then by capturing the video.

-
-
Parameters:
-

video_document – Document instance that holds a video document ("@type": ".../VideoDocument/...")

-
-
Returns:
-

frames per second as a float, rounded to 2 decimal places

-
-
-
- -
-
-mmif.utils.video_document_helper.get_mid_framenum(mmif: Mmif, time_frame: Annotation)[source]
-

Calculates the middle frame number of a time interval annotation.

-
-
Parameters:
-
    -

  • mmif – Mmif instance

    • -

  • time_frame – Annotation instance that holds a time interval annotation ("@type": ".../TimeFrame/...")

    • -
-
-
Returns:
-

middle frame number as an integer

-
-
-
- -
-
-mmif.utils.video_document_helper.millisecond_to_framenum(video_doc: Document, millisecond: float) → int[source]
-

Converts a millisecond value to a frame number.

-
- -
-
-mmif.utils.video_document_helper.sample_frames(start_frame: int, end_frame: int, sample_rate: float = 1) → List[int][source]
-

Helper function to sample frames from a time interval. -Can also be used as a “cutoff” function when used with start_frame==0 and sample_rate==1.

-
-
Parameters:
-
    -

  • start_frame – start frame of the interval

    • -

  • end_frame – end frame of the interval

    • -

  • sample_rate – sampling rate (or step) to configure how often to take a frame, default is 1, meaning all consecutive frames are sampled

    • -
-
-
-
- -
-
-mmif.utils.video_document_helper.second_to_framenum(video_doc: Document, second) → int[source]
-

Converts a second value to a frame number.

-
- -
-
-

mmif.utils.sequence_helper module

-

This module provides helpers for handling sequence labeling. Specifically, it provides

-
    -

  • a generalized label re-mapper for “post-binning” of labels

    • -

  • conversion from a list of CLAMS annotations (with classification props) into a list of reals (scores by labels), can be combined with the label re-mapper mentioned above

    • -

  • mmif.utils.sequence_helper.smooth_outlying_short_intervals(): a simple smoothing algorithm by trimming “short” outlier sequences

    • -
-

However, it DOES NOT provide

-
    -

  • direct conversion between CLAMS annotations. For example, it does not directly handle stitching of TimePoint into TimeFrames.

    • -

  • support for multi-class scenario, such as handling of _competing_ subsequence or overlapping labels.

    • -
-

Some functions can use optional external libraries (e.g., numpy) for better performance. -Hence, if you see a warning about missing optional packages, you might want to install them by running pip install mmif-python[seq].

-
-
-mmif.utils.sequence_helper.build_label_remapper(src_labels: List[str], dst_labels: Dict[str, str | int | float | bool | None]) → Dict[str, str | int | float | bool | None][source]
-

Build a label remapper dictionary from source and destination labels.

-
-
Parameters:
-
    -

  • src_labels – a list of all labels on the source side

    • -

  • dst_labels – a dict from source labels to destination labels. -Source labels not in this dict will be remapped to a negative label (-).

    • -
-
-
Returns:
-

a dict that exhaustively maps source labels to destination labels

-
-
-
- -
-
-mmif.utils.sequence_helper.build_score_lists(classifications: ~typing.List[~typing.Dict], label_remapper: ~typing.Dict, score_remap_op: ~typing.Callable[[...], float] = <built-in function max>) → Tuple[Dict[str, int], numpy.ndarray][source]
-

Build lists of scores indexed by the label names.

-
-
Parameters:
-
    -

  • classifications – list of dictionaries of classification results, taken from input annotation objects

    • -

  • label_remapper – a dictionary that maps source label names to destination label names (formerly “postbin”)

    • -

  • score_remap_op – a function to remap the scores from multiple source labels binned to a destination label -common choices are max, min, or sum

    • -
-
-
Returns:
-

    -

  1. a dictionary that maps label names to their index in the score list

    2. -

  2. 2-d numpy array of scores, of which rows are indexed by label map dict (first return value)

    3. -
-

-
-
-
- -
-
-mmif.utils.sequence_helper.smooth_outlying_short_intervals(scores: List[float], min_spseq_size: int, min_snseq_size: int, min_score: float = 0.5)[source]
-

Given a list of scores, a score threshold, and smoothing parameters, -identify the intervals of “positive” scores by “trimming” the short -positive sequences (“spseq”) and short negative sequences (“snseq”). To -decide the positivity, first step is binarization of the scores by the -min_score threshold. Given Sr as “raw” input real-number scores -list, and min_score=0.5,

-
-
Sr: [0.3, 0.6, 0.2, 0.8, 0.2, 0.9, 0.8, 0.5, 0.1, 0.5, 0.8, 0.3, 1.0, 0.7, 0.5, 0.5, 0.5, 0.8, 0.3, 0.6]
-
-
-
-

the binarization is done by simply comparing each score to the -threshold to get S list of binary scores

-
-
1.0 :                                     |                      
-0.9 :                |                    |                      
-0.8 :          |     |  |           |     |              |       
-0.7 :          |     |  |           |     |  |           |       
-0.6 :    |     |     |  |           |     |  |           |     | 
-0.5 :----+-----+-----+--+--+-----+--+-----+--+--+--+--+--+-----+-
-0.4 :    |     |     |  |  |     |  |     |  |  |  |  |  |     | 
-0.3 : |  |     |     |  |  |     |  |  |  |  |  |  |  |  |  |  | 
-0.2 : |  |  |  |  |  |  |  |     |  |  |  |  |  |  |  |  |  |  | 
-0.1 : |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | 
-0.0 +------------------------------------------------------------
-raw :.3 .6 .2 .8 .2 .9 .8 .5 .1 .5 .8 .3 1. .7 .5 .5 .5 .8 .3 .6
- S  : 0  1  0  1  0  1  1  0  0  0  1  0  1  1  0  1  1  1  0  1 
-
-
-
-

Note that the size of a positive or negative sequence can be as small -as 1.

-

Then, here are examples of smoothing a list of binary scores into -intervals, by trimming “very short” (under thresholds) sequences of -positive or negative:

-
-

Note

-

legends:

-
    -

  • t is unit index (e.g. time index)

    • -

  • S is the list of binary scores (zeros and ones)

    • -

  • I is the list of intervals after smoothing

    • -
-
-
    -

  1. with params min_spseq_size==1, min_snseq_size==4

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1]
-I: [0, 1--1--1--1--1--1--1--1--1--1--1--1, 0--0--0--0--0--0, 1]
-
    -
    -

    Explanation: min_snseq_size is used to smooth short sequences -of negative predictions. In this, zeros from t[7:10] are smoothed -into “one” I, while zeros from t[13:19] are kept as “zero” I. Note -that the “short” snseqs at the either ends (t[0:1]) are never -smoothed.

    -
    -
    2. -

  2. with params min_spseq_size==4, min_snseq_size==2

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1]
-I: [0, 1--1--1--1--1--1, 0--0--0--0--0--0--0--0--0--0--0--0--0]
-
    -
    -

    Explanation: min_spseq_size is used to smooth short sequences -of positive predictions. In this example, the spseqs of ones from -both t[10:13] and t[19:20] are smoothed. Note that the “short” -spseqs at the either ends (t[19:20]) are always smoothed.

    -
    -
    3. -

  3. with params min_spseq_size==4, min_snseq_size==4

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1]
-I: [0, 1--1--1--1--1--1--1--1--1--1--1--1--0--0--0--0--0--0--0]
-
    -
    -

    Explanation: When two threshold parameters are working together, -the algorithm will prioritize the smoothing of the snseqs over the -smoothing of the spseqs. Thus, in this example, the snseq t[7:10] -gets first smoothed “up” before the spseq t[10:13] is smoothed -“down”, resulting in a long final I.

    -
    -
    4. -

  4. with params min_spseq_size==4, min_snseq_size==4

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [1, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 1, 1]
-I: [1--1--1--1--1--1--1, 0--0--0--0, 1--1--1--1--1--1--1--1--1]
-
    -
    -

    Explanation: Since smoothing of snseqs is prioritized, short spseqs -at the beginning or the end can be kept.

    -
    -
    5. -

  5. with params min_spseq_size==1, min_snseq_size==1

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 1, 1]
-I: [0--0--0, 1--1--1--1, 0--0--0--0, 1--1--1--1, 0--0--0, 1--1]
-
    -
    -

    Explanation: When both width thresholds are set to 1, the algorithm -works essentially in the “stitching” only mode.

    -
    -
    6. -
-
-
Parameters:
-
    -

  • scores – SORTED list of scores to be smoothed. The score list -is assumed to be “exhaust” the entire time or space of -the underlying document segment. -(Sorted by the start, and then by the end of anchors)

    • -

  • min_score – minimum threshold to use to discard -low-scored units (strictly less than)

    • -

  • min_spseq_size – minimum size of a positive sequence not to be -smoothed (greater or equal to)

    • -

  • min_snseq_size – minimum size of a negative sequence not to be -smoothed (greater or equal to)

    • -
-
-
Returns:
-

list of tuples of start(inclusive)/end(exclusive) indices -of the “positive” sequences. Negative sequences (regardless of -their size) are not included in the output.

-
-
-
- -
-
-mmif.utils.sequence_helper.validate_labelset(annotations: Iterable[Annotation]) → List[str][source]
-

Simple check for a list of annotations to see if they have the same label set.

-
-
Raise:
-

AttributeError if an element in the input list doesn’t have the labelset property

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ValueError if different labelset values are found

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a list of the common labelset value (list of label names)

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- - - \ No newline at end of file diff --git a/docs/1.0.14/autodoc/mmif.vocabulary.html b/docs/1.0.14/autodoc/mmif.vocabulary.html deleted file mode 100644 index 2b7a230f..00000000 --- a/docs/1.0.14/autodoc/mmif.vocabulary.html +++ /dev/null @@ -1,319 +0,0 @@ - - - - - - - - - mmif.vocabulary module — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
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mmif.vocabulary module

-
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mmif.vocabulary.annotation_types module

-
-
-class mmif.vocabulary.annotation_types.AnnotationTypes(type_uri, fuzzymode=True)[source]
-

Bases: AnnotationTypesBase

-

This class contains the CLAMS annotation types -defined in the spec version 1.1.0 as class variables.

-
-
-Alignment = http://mmif.clams.ai/vocabulary/Alignment/v1[source]
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- -
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-Annotation = http://mmif.clams.ai/vocabulary/Annotation/v6[source]
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-BoundingBox = http://mmif.clams.ai/vocabulary/BoundingBox/v5[source]
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-Chapter = http://mmif.clams.ai/vocabulary/Chapter/v6[source]
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-Interval = http://mmif.clams.ai/vocabulary/Interval/v5[source]
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-NamedEntity = http://mmif.clams.ai/vocabulary/NamedEntity/v1[source]
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-NounChunk = http://mmif.clams.ai/vocabulary/NounChunk/v1[source]
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-Paragraph = http://mmif.clams.ai/vocabulary/Paragraph/v1[source]
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-Polygon = http://mmif.clams.ai/vocabulary/Polygon/v5[source]
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-Region = http://mmif.clams.ai/vocabulary/Region/v5[source]
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-Relation = http://mmif.clams.ai/vocabulary/Relation/v5[source]
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-Sentence = http://mmif.clams.ai/vocabulary/Sentence/v1[source]
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-Span = http://mmif.clams.ai/vocabulary/Span/v5[source]
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-TimeFrame = http://mmif.clams.ai/vocabulary/TimeFrame/v6[source]
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-TimePoint = http://mmif.clams.ai/vocabulary/TimePoint/v5[source]
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-Token = http://mmif.clams.ai/vocabulary/Token/v1[source]
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-VerbChunk = http://mmif.clams.ai/vocabulary/VerbChunk/v1[source]
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-VideoObject = http://mmif.clams.ai/vocabulary/VideoObject/v5[source]
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- -
- -
-
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mmif.vocabulary.document_types module

-
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-class mmif.vocabulary.document_types.DocumentTypes(type_uri, fuzzymode=True)[source]
-

Bases: DocumentTypesBase

-

This class contains the CLAMS document types -defined in the spec version 1.1.0 as class variables.

-
-
-AudioDocument = http://mmif.clams.ai/vocabulary/AudioDocument/v1[source]
-
- -
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-Document = http://mmif.clams.ai/vocabulary/Document/v1[source]
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-ImageDocument = http://mmif.clams.ai/vocabulary/ImageDocument/v1[source]
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-TextDocument = http://mmif.clams.ai/vocabulary/TextDocument/v1[source]
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-VideoDocument = http://mmif.clams.ai/vocabulary/VideoDocument/v1[source]
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- - - \ No newline at end of file diff --git a/docs/1.0.14/autodoc/mmif_docloc_http.html b/docs/1.0.14/autodoc/mmif_docloc_http.html deleted file mode 100644 index b7ef9f8e..00000000 --- a/docs/1.0.14/autodoc/mmif_docloc_http.html +++ /dev/null @@ -1,179 +0,0 @@ - - - - - - - - - mmif_docloc_http package — mmif-python documentation - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif_docloc_http package

-

MMIF document location helper module for http and https schemes. -If you want to write your own docloc scheme handler, please use the source code of this module as a reference. -See this plug-in section for more information.

-
-
-mmif_docloc_http.resolve(docloc)[source]
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- -
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  • MMIF consumer
    • -
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MMIF consumer

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A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the appliance documentation to learn more about the appliance.

-

MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance.

-
    -

  1. The code must be hosted on a public git repository (e.g. Github, Gitlab, …)

    2. -

  2. Must listen to 5000 port.

    3. -

  3. Must expose /display route .

    4. -

  4. /display router should response to GET requests.

    5. -

  5. In the GET request, a public URL of the input MMIF file is passed via file URL parameter.

    6. -

  6. On the codebase root, there must be a Dockerfile that can build a docker image that runs the web app.

    7. -
-

We provide an example consumer at https://github.com/clamsproject/mmif-visualizer.

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    • -
  • -
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Index

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- A - | B - | C - | D - | E - | F - | G - | H - | I - | K - | L - | M - | N - | P - | R - | S - | T - | U - | V - -
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- - -
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  • Welcome to mmif-python’s documentation!
    • -
  • -
    • -
-
-
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-
- -
-

Welcome to mmif-python’s documentation!

-
-

MultiMedia Interchange Format

-

MMIF is a JSON(-LD)-based data format designed for transferring annotation data between computational analysis applications in CLAMS project.

-
-
-

mmif-python

-

mmif-python is a Python implementation of the MMIF data format. -mmif-python provides various helper classes and functions to handle MMIF JSON in Python, -including ;

-
    -

  1. de-/serialization of MMIF internal data structures to/from JSON

    2. -

  2. validation of MMIF JSON

    3. -

  3. handling of CLAMS vocabulary types

    4. -

  4. navigation of MMIF object via various “search” methods (e.g. mmif.get_all_views_contain(vocab_type)))

    5. -
-
-
-

For more …

- -
-

Contents

- -
-
-

API documentation:

- -
-
-
-
-

Indices and tables

- -
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- - -
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  • Getting Started
    • -
  • -
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Getting Started

-
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Overview

-

MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for reproducibility, transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF website. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects.

-
-
-

Prerequisites

-
    -

  • Python: the latest mmif-python requires Python 3.8 or newer. We have no plan to support Python 2.7.

    • -
-
-
-

Installation

-

Package mmif-python is distributed via the official PyPI. Users are supposed to pip-install to get latest release.

-
pip install mmif-python
-
-
-

This will install a package mmif to local python.

-

The MMIF format and specification is evolving over time, and mmif-python package will be updated along with the changes in MMIF format.

-
-

Note

-

MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and mmif-python versions, please take time to read our decision on the subject here. If you need to know which python SDK supports which specification version, see Target MMIF Versions page.

-
-
-
-

MMIF Serialization

-

mmif.serialize.mmif.Mmif represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of mmif.serialize.model.MmifObject, including the mmif.serialize.mmif.Mmif. To start with an existing MMIF str, simple initiate a new Mmif object with the file.

-
import mmif
-from mmif import Mmif
-
-mmif_str = """{
-"metadata": {
-  "mmif": "http://mmif.clams.ai/1.0.0"
-},
-"documents": [
-  {
-    "@type": "http://mmif.clams.ai/vocabulary/VideoDocument/v1",
-    "properties": {
-      "id": "m1",
-      "mime": "video/mp4",
-      "location": "file:///var/archive/video-0012.mp4"
-    }
-  },
-  {
-    "@type": "http://mmif.clams.ai/vocabulary/TextDocument/v1",
-    "properties": {
-      "id": "m2",
-      "mime": "text/plain",
-      "location": "file:///var/archive/video-0012-transcript.txt"
-    }
-  }
-],
-"views": []}"""
-mmif_obj = Mmif(mmif_str)
-
-
-

Few notes;

-
    -

  1. MMIF does not carry the primary source files in it.

    2. -

  2. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version mmif-python implementation of the MMIF might not be able to load an unsupported version of MMIF string.

    3. -
-

When serializing back to str, call mmif.serialize.model.MmifObject.serialize() on the object.

-

To get subcomponents, you can use various getters implemented in subclasses. For example;

-
from mmif.vocabulary.document_types import DocumentTypes
-
-for video in mmif_obj.Mmif.get_documents_by_type(DocumentTypes.VideoDocument):
-  with open(video.location_path(), 'b') as in_video:
-    # do something with the video file
-
-
-

For a full list of available helper methods, please refer to the API documentation.

-
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mmif package

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mmif_docloc_http package

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  • Developing plugins for MMIF Python SDK
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Developing plugins for MMIF Python SDK

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Overview

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As MMIF JSON files can carry information about media document files without actually carrying file contents, file accessing modules in mmif Python package (distributed as mmif-python on PyPI) are designed to be lightweight and flexible so that it can work with additional “plugin” Python packages that can handle concrete file access.

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This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF website. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects.

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Developer can write simple plugins that can provide additional functionalities to mmif-python. For example, mmif-python does not provide any file access functionality beyond a local file system (with file scheme), but it can be extended with a plugin that can handle file access over different protocols (e.g. http, s3, ftp, etc).

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This document contains information about how to write plugins for mmif-python.

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Document Location Scheme Plugins

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mmif.serialize.annotation.Document class has various methods to access parts of location property of the document. The location is in URI/IRI format (SCHEME://HOSTNAME/PATH, in a nutshell) and it has to be resolved to a local file for CLAMS Apps to process the local file to analyze and extract information about the media and its contents. The core mmif-python distribution only provides a default implementation that can handle file scheme URIs.

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To add a document location handler plugin, you need to implement a Python “package” (do not confuse with PYPI distribution), that meets these requirements;

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  1. the package must be named mmif_docloc_<SCHEME>. For example, to implement a handler for s3 scheme, the package name must be mmif_docloc_s3. The prefix is important as it’s used in the plugin discovery process from the core mmif-python modules.

    2. -

  2. the top module of the package must have a function named resolve. The function must take a single argument, which is a str of the document location URI. The function must return a str of the local file path. For example, if the document location is s3://mybucket/myfile.mp4, a Python user should be able to to something like this;

    3. -
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import mmif_docloc_s3
-resolved = mmif_docloc_s3.resolve('s3://mybucket/myfile.mp4')
-# then resolved must be a local file path that can be used to open the file
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Here’s a minimal example codebase that you refer to when you develop a docloc plugin.

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(However, before you start writing your own plugin for a specific URI scheme, checking if there’s already a PyPI distribution for the scheme might be a good idea.)

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$ tree .
-.
-├── mmif_docloc_dummy
-│   └── __init__.py
-├── pyproject.toml
-└── setup.cfg
-
- $ cat pyproject.toml
-[build-system]
-requires = ["setuptools"]
-build-backend = "setuptools.build_meta"
-
-$ cat setup.cfg
-[metadata]
-name = mmif_docloc_dummy  # this name is IMPORTANT
-version = 0.0.1
-description = a plugin to mmif-pyhon to handle `dummy` location scheme
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And the plugin code.

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# mmif_docloc_dummy/__init__.py
-doc_types = {'video': 'mp4'}
-
-def resolve(docloc):
-    scheme = 'dummy'
-    if docloc.startswith(f'{scheme}://'):
-        doc_id, doc_type = docloc.split('.')
-        return f'/path/to/{doc_id}.{doc_types[doc_type]}'
-    else:
-        raise ValueError(f'cannot handle document location scheme: {docloc}')
-
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Bulit-in Document Location Scheme Plugins

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At the moment, mmif-python PyPI distribution ships a built-in docloc plugin that support both http and https schemes. -Take a look at mmif_docloc_http module for details.

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- - - - - - - - \ No newline at end of file diff --git a/docs/1.0.14/searchindex.js b/docs/1.0.14/searchindex.js deleted file mode 100644 index 48ad4445..00000000 --- a/docs/1.0.14/searchindex.js +++ /dev/null @@ -1 +0,0 @@ -Search.setIndex({"alltitles": {"API documentation:": [[5, null]], "Bulit-in Document Location Scheme Plugins": [[8, "bulit-in-document-location-scheme-plugins"]], "Contents": [[5, null]], "Developing plugins for MMIF Python SDK": [[8, null]], "Document Location Scheme Plugins": [[8, "document-location-scheme-plugins"]], "For more \u2026": [[5, "for-more"]], "Getting Started": [[6, null]], "Indices and tables": [[5, "indices-and-tables"]], "Installation": [[6, "installation"]], "MMIF Serialization": [[6, "mmif-serialization"]], "MMIF consumer": [[4, null]], "MultiMedia Interchange Format": [[5, "multimedia-interchange-format"]], "Overview": [[6, "overview"], [8, "overview"]], "Prerequisites": [[6, "prerequisites"]], "Target MMIF Versions": [[9, null]], "Target 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  • Target MMIF Versions
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Target MMIF Versions

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This article provides targeting MMIF specification versions of different versions of mmif-python SDK.

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Target Specification Versions

mmif-python version

Target MMIF Specification

1.0.14

1.1.0

1.0.13

1.0.4

1.0.12

1.0.4

1.0.11

1.0.4

1.0.10.dev1

1.0.3

1.0.10

1.0.2

1.0.9

1.1.0

1.0.8

1.0.0

1.0.7

1.0.0

1.0.6

1.0.0

1.0.5

1.0.0

1.0.4

1.0.0

1.0.3

1.0.0

1.0.2

1.0.0

1.0.1

1.0.0

1.0.0

0.5.0

0.5.2

0.5.0

0.5.1

0.5.0

0.5.0

0.5.0

0.4.8

0.4.2

0.4.7

0.4.1

0.4.6

0.4.0

0.4.5

0.4.0

0.4.4

0.4.0

0.4.3

0.4.0

0.4.2

0.4.0

0.4.1

0.4.0

0.4.0

0.4.0

0.3.5

0.3.1

0.3.4

0.3.1

0.3.3

0.3.1

0.3.2

0.3.1

0.3.1

0.3.0

0.3.0

0.3.0

0.2.2

0.2.1

0.2.1

0.2.1

0.2.0

0.2.1

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0.3.0
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0.3.1
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0.3.2
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0.3.3
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0.3.4
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0.3.5
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0.4.0
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0.4.1
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0.4.2
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0.4.3
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0.4.4
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0.4.5
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0.4.6
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0.4.7
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0.4.8
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0.5.0
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0.5.1
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0.5.2
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1.0.0
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1.0.1
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1.0.10
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1.0.11
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1.0.12
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1.0.13
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1.0.14
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1.0.15
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1.0.16
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1.0.17
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1.0.18
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1.0.19
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1.0.2
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1.0.3
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1.0.4
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1.0.5
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1.0.6
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1.0.7
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1.0.8
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1.0.9
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-mmif.serialize.model module ---------------------------- - -.. automodule:: mmif.serialize.model - :members: - :undoc-members: - :show-inheritance: - -mmif.serialize.mmif module --------------------------- - -.. automodule:: mmif.serialize.mmif - :members: - :undoc-members: - :show-inheritance: - -mmif.serialize.view module --------------------------- - -.. automodule:: mmif.serialize.view - :members: - :undoc-members: - :show-inheritance: - -mmif.serialize.annotation module --------------------------------- - -.. automodule:: mmif.serialize.annotation - :members: - :undoc-members: - :show-inheritance: - diff --git a/docs/1.0.15/_sources/autodoc/mmif.utils.rst.txt b/docs/1.0.15/_sources/autodoc/mmif.utils.rst.txt deleted file mode 100644 index 9a6ecc44..00000000 --- a/docs/1.0.15/_sources/autodoc/mmif.utils.rst.txt +++ /dev/null @@ -1,18 +0,0 @@ -mmif.utils module -================= - -mmif.utils.video_document_helper module ----------------------------------------- - -.. automodule:: mmif.utils.video_document_helper - :members: - :undoc-members: - :show-inheritance: - -mmif.utils.sequence_helper module ---------------------------------- - -.. automodule:: mmif.utils.sequence_helper - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/1.0.15/_sources/autodoc/mmif.vocabulary.rst.txt b/docs/1.0.15/_sources/autodoc/mmif.vocabulary.rst.txt deleted file mode 100644 index d250c6a3..00000000 --- a/docs/1.0.15/_sources/autodoc/mmif.vocabulary.rst.txt +++ /dev/null @@ -1,18 +0,0 @@ -mmif.vocabulary module -====================== - -mmif.vocabulary.annotation\_types module ----------------------------------------- - -.. automodule:: mmif.vocabulary.annotation_types - :members: - :undoc-members: - :show-inheritance: - -mmif.vocabulary.document\_types module --------------------------------------- - -.. automodule:: mmif.vocabulary.document_types - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/1.0.15/_sources/autodoc/mmif_docloc_http.rst.txt b/docs/1.0.15/_sources/autodoc/mmif_docloc_http.rst.txt deleted file mode 100644 index b76c8df5..00000000 --- a/docs/1.0.15/_sources/autodoc/mmif_docloc_http.rst.txt +++ /dev/null @@ -1,11 +0,0 @@ -mmif_docloc_http package -======================== - -MMIF document location helper module for `http` and `https` schemes. -If you want to write your own docloc scheme handler, please use the source code of this module as a reference. -See this :ref:`plug-in section ` for more information. - -.. automodule:: mmif_docloc_http - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/1.0.15/_sources/consumer-tutorial.rst.txt b/docs/1.0.15/_sources/consumer-tutorial.rst.txt deleted file mode 100644 index c54634e2..00000000 --- a/docs/1.0.15/_sources/consumer-tutorial.rst.txt +++ /dev/null @@ -1,17 +0,0 @@ -.. _consumer-tutorial: - -MMIF consumer -================================= - -A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the `appliance documentation `_ to learn more about the appliance. - -MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance. - -#. The code must be hosted on a public git repository (e.g. Github, Gitlab, ...) -#. Must listen to ``5000`` port. -#. Must expose ``/display`` route . -#. ``/display`` router should response to ``GET`` requests. -#. In the ``GET`` request, a public URL of the input MMIF file is passed via ``file`` URL parameter. -#. On the codebase root, there must be a ``Dockerfile`` that can build a `docker `_ image that runs the web app. - -We provide an example consumer at https://github.com/clamsproject/mmif-visualizer. diff --git a/docs/1.0.15/_sources/index.rst.txt b/docs/1.0.15/_sources/index.rst.txt deleted file mode 100644 index beb56aae..00000000 --- a/docs/1.0.15/_sources/index.rst.txt +++ /dev/null @@ -1,26 +0,0 @@ -Welcome to mmif-python's documentation! -======================================= - -.. mdinclude:: ../README.md - -.. toctree:: - :maxdepth: 2 - :caption: Contents - - introduction - plugins - target-versions - -.. toctree:: - :maxdepth: 2 - :caption: API documentation: - - modules - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/docs/1.0.15/_sources/introduction.rst.txt b/docs/1.0.15/_sources/introduction.rst.txt deleted file mode 100644 index cfd9eaf7..00000000 --- a/docs/1.0.15/_sources/introduction.rst.txt +++ /dev/null @@ -1,89 +0,0 @@ -.. _introduction: - -Getting Started -=============== - - -Overview ---------- - -MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for reproducibility, transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF website `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects. - -Prerequisites -------------- - -* `Python `_: the latest ``mmif-python`` requires Python 3.8 or newer. We have no plan to support `Python 2.7 `_. - -Installation ---------------- - -Package ``mmif-python`` is distributed via the official PyPI. Users are supposed to pip-install to get latest release. - -.. code-block:: bash - - pip install mmif-python - -This will install a package `mmif` to local python. - -The MMIF format and specification is evolving over time, and ``mmif-python`` package will be updated along with the changes in MMIF format. - -.. note:: MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and ``mmif-python`` versions, please take time to read our decision on the subject `here `_. If you need to know which python SDK supports which specification version, see :ref:`target-versions` page. - -MMIF Serialization ---------------------------- - -:class:`mmif.serialize.mmif.Mmif` represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of :class:`mmif.serialize.model.MmifObject`, including the :class:`mmif.serialize.mmif.Mmif`. To start with an existing MMIF :class:`str`, simple initiate a new ``Mmif`` object with the file. - -.. code-block:: python - - import mmif - from mmif import Mmif - - mmif_str = """{ - "metadata": { - "mmif": "http://mmif.clams.ai/1.0.0" - }, - "documents": [ - { - "@type": "http://mmif.clams.ai/vocabulary/VideoDocument/v1", - "properties": { - "id": "m1", - "mime": "video/mp4", - "location": "file:///var/archive/video-0012.mp4" - } - }, - { - "@type": "http://mmif.clams.ai/vocabulary/TextDocument/v1", - "properties": { - "id": "m2", - "mime": "text/plain", - "location": "file:///var/archive/video-0012-transcript.txt" - } - } - ], - "views": []}""" - mmif_obj = Mmif(mmif_str) - - -Few notes; - -#. MMIF does not carry the primary source files in it. -#. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version ``mmif-python`` implementation of the MMIF might not be able to load an unsupported version of MMIF string. - -When serializing back to :class:`str`, call :meth:`mmif.serialize.model.MmifObject.serialize` on the object. - -To get subcomponents, you can use various getters implemented in subclasses. For example; - -.. code-block:: python - - from mmif.vocabulary.document_types import DocumentTypes - - for video in mmif_obj.Mmif.get_documents_by_type(DocumentTypes.VideoDocument): - with open(video.location_path(), 'b') as in_video: - # do something with the video file - - -For a full list of available helper methods, please refer to :ref:`the API documentation `. - diff --git a/docs/1.0.15/_sources/modules.rst.txt b/docs/1.0.15/_sources/modules.rst.txt deleted file mode 100644 index 4bb9307d..00000000 --- a/docs/1.0.15/_sources/modules.rst.txt +++ /dev/null @@ -1,20 +0,0 @@ -.. _apidoc: - -mmif package -============ - -.. toctree:: - :maxdepth: 4 - - autodoc/mmif.serialize - autodoc/mmif.vocabulary - autodoc/mmif.utils - -mmif_docloc_http package -======================== - -.. toctree:: - :maxdepth: 2 - - autodoc/mmif_docloc_http - diff --git a/docs/1.0.15/_sources/plugins.rst.txt b/docs/1.0.15/_sources/plugins.rst.txt deleted file mode 100644 index 9907c495..00000000 --- a/docs/1.0.15/_sources/plugins.rst.txt +++ /dev/null @@ -1,83 +0,0 @@ -.. _plugins: - -Developing plugins for MMIF Python SDK -====================================== - - -Overview --------- - -As MMIF JSON files can carry information about media document files without actually carrying file contents, file accessing modules in ``mmif`` Python package (distributed as ``mmif-python`` on PyPI) are designed to be lightweight and flexible so that it can work with additional "plugin" Python packages that can handle concrete file access. - - -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF website `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects. - -Developer can write simple plugins that can provide additional functionalities to ``mmif-python``. For example, ``mmif-python`` does not provide any file access functionality beyond a local file system (with ``file`` scheme), but it can be extended with a plugin that can handle file access over different protocols (e.g. ``http``, ``s3``, ``ftp``, etc). - -This document contains information about how to write plugins for ``mmif-python``. - -.. _docloc_plugin: - -Document Location Scheme Plugins -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -:class:`mmif.serialize.annotation.Document` class has various methods to access parts of ``location`` property of the document. The location is in `URI/IRI format `_ (``SCHEME://HOSTNAME/PATH``, in a nutshell) and it has to be resolved to a local file for CLAMS Apps to process the local file to analyze and extract information about the media and its contents. The core ``mmif-python`` distribution only provides a default implementation that can handle ``file`` scheme URIs. - -To add a document location handler plugin, you need to implement a Python `"package" `_ (do not confuse with PYPI distribution), that meets these requirements; - -#. the package must be named ``mmif_docloc_``. For example, to implement a handler for ``s3`` scheme, the package name must be ``mmif_docloc_s3``. The prefix is important as it's used in the plugin discovery process from the core ``mmif-python`` modules. -#. the top module of the package must have a function named ``resolve``. The function must take a single argument, which is a :class:`str` of the document location URI. The function must return a :class:`str` of the local file path. For example, if the document location is ``s3://mybucket/myfile.mp4``, a Python user should be able to to something like this; - -.. code-block:: python - - import mmif_docloc_s3 - resolved = mmif_docloc_s3.resolve('s3://mybucket/myfile.mp4') - # then resolved must be a local file path that can be used to open the file - - -Here's a minimal example codebase that you refer to when you develop a ``docloc`` plugin. - -(However, before you start writing your own plugin for a specific URI scheme, checking `if there's already a PyPI distribution `_ for the scheme might be a good idea.) - -.. code-block:: sh - - $ tree . - . - ├── mmif_docloc_dummy - │ └── __init__.py - ├── pyproject.toml - └── setup.cfg - - $ cat pyproject.toml - [build-system] - requires = ["setuptools"] - build-backend = "setuptools.build_meta" - - $ cat setup.cfg - [metadata] - name = mmif_docloc_dummy # this name is IMPORTANT - version = 0.0.1 - description = a plugin to mmif-pyhon to handle `dummy` location scheme - - -And the plugin code. - -.. code-block:: python - - # mmif_docloc_dummy/__init__.py - doc_types = {'video': 'mp4'} - - def resolve(docloc): - scheme = 'dummy' - if docloc.startswith(f'{scheme}://'): - doc_id, doc_type = docloc.split('.') - return f'/path/to/{doc_id}.{doc_types[doc_type]}' - else: - raise ValueError(f'cannot handle document location scheme: {docloc}') - -Bulit-in Document Location Scheme Plugins -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -At the moment, ``mmif-python`` PyPI distribution ships a built-in *docloc* plugin that support both ``http`` and ``https`` schemes. -Take a look at :mod:`mmif_docloc_http` module for details. diff --git a/docs/1.0.15/_sources/target-versions.rst.txt b/docs/1.0.15/_sources/target-versions.rst.txt deleted file mode 100644 index 34216d3e..00000000 --- a/docs/1.0.15/_sources/target-versions.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _target-versions: - -Target MMIF Versions -==================== - -This article provides targeting MMIF specification versions of different versions of ``mmif-python`` SDK. - -.. csv-table:: Target Specification Versions - :file: target-versions.csv - :header-rows: 1 diff --git a/docs/1.0.15/_static/_sphinx_javascript_frameworks_compat.js b/docs/1.0.15/_static/_sphinx_javascript_frameworks_compat.js deleted file mode 100644 index 81415803..00000000 --- a/docs/1.0.15/_static/_sphinx_javascript_frameworks_compat.js +++ /dev/null @@ -1,123 +0,0 @@ -/* Compatability shim for jQuery and underscores.js. - * - * Copyright Sphinx contributors - * Released under the two clause BSD licence - */ - -/** - * small helper function to urldecode strings - * - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL - */ -jQuery.urldecode = function(x) { - if (!x) { - return x - } - return decodeURIComponent(x.replace(/\+/g, ' ')); -}; - -/** - * small helper function to urlencode strings - */ -jQuery.urlencode = encodeURIComponent; - -/** - * This function returns the parsed url parameters of the - * current request. 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- document.dispatchEvent(event); - }); -}); \ No newline at end of file diff --git a/docs/1.0.15/_static/language_data.js b/docs/1.0.15/_static/language_data.js deleted file mode 100644 index c7fe6c6f..00000000 --- a/docs/1.0.15/_static/language_data.js +++ /dev/null @@ -1,192 +0,0 @@ -/* - * This script contains the language-specific data used by searchtools.js, - * namely the list of stopwords, stemmer, scorer and splitter. - */ - -var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"]; - - -/* Non-minified version is copied as a separate JS file, if available */ - -/** - * Porter Stemmer - */ -var Stemmer = function() { - - var step2list = { - ational: 'ate', - tional: 'tion', - enci: 'ence', - anci: 'ance', - izer: 'ize', - bli: 'ble', - alli: 'al', - entli: 'ent', - eli: 'e', - ousli: 'ous', - ization: 'ize', - ation: 'ate', - ator: 'ate', - alism: 'al', - iveness: 'ive', - fulness: 'ful', - ousness: 'ous', - aliti: 'al', - iviti: 'ive', - biliti: 'ble', - logi: 'log' - }; 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- -/** - * Simple result scoring code. - */ -if (typeof Scorer === "undefined") { - var Scorer = { - // Implement the following function to further tweak the score for each result - // The function takes a result array [docname, title, anchor, descr, score, filename] - // and returns the new score. - /* - score: result => { - const [docname, title, anchor, descr, score, filename, kind] = result - return score - }, - */ - - // query matches the full name of an object - objNameMatch: 11, - // or matches in the last dotted part of the object name - objPartialMatch: 6, - // Additive scores depending on the priority of the object - objPrio: { - 0: 15, // used to be importantResults - 1: 5, // used to be objectResults - 2: -5, // used to be unimportantResults - }, - // Used when the priority is not in the mapping. - objPrioDefault: 0, - - // query found in title - title: 15, - partialTitle: 7, - // query found in terms - term: 5, - partialTerm: 2, - }; -} - -// Global search result kind enum, used by themes to style search results. -class SearchResultKind { - static get index() { return "index"; } - static get object() { return "object"; } - static get text() { return "text"; } - static get title() { return "title"; } -} - -const _removeChildren = (element) => { - while (element && element.lastChild) element.removeChild(element.lastChild); -}; - -/** - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping - */ -const _escapeRegExp = (string) => - string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string - -const _displayItem = (item, searchTerms, highlightTerms) => { - const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; - const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; - const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; - const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; - const contentRoot = document.documentElement.dataset.content_root; - - const [docName, title, anchor, descr, score, _filename, kind] = item; - - let listItem = document.createElement("li"); - // Add a class representing the item's type: - // can be used by a theme's CSS selector for styling - // See SearchResultKind for the class names. - listItem.classList.add(`kind-${kind}`); - let requestUrl; - let linkUrl; - if (docBuilder === "dirhtml") { - // dirhtml builder - let dirname = docName + "/"; - if (dirname.match(/\/index\/$/)) - dirname = dirname.substring(0, dirname.length - 6); - else if (dirname === "index/") dirname = ""; - requestUrl = contentRoot + dirname; - linkUrl = requestUrl; - } else { - // normal html builders - requestUrl = contentRoot + docName + docFileSuffix; - linkUrl = docName + docLinkSuffix; - } - let linkEl = listItem.appendChild(document.createElement("a")); - linkEl.href = linkUrl + anchor; - linkEl.dataset.score = score; - linkEl.innerHTML = title; - if (descr) { - listItem.appendChild(document.createElement("span")).innerHTML = - " (" + descr + ")"; - // highlight search terms in the description - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - } - else if (showSearchSummary) - fetch(requestUrl) - .then((responseData) => responseData.text()) - .then((data) => { - if (data) - listItem.appendChild( - Search.makeSearchSummary(data, searchTerms, anchor) - ); 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Please make sure that all words are spelled correctly and that you've selected enough categories." - ); - else - Search.status.innerText = Documentation.ngettext( - "Search finished, found one page matching the search query.", - "Search finished, found ${resultCount} pages matching the search query.", - resultCount, - ).replace('${resultCount}', resultCount); -}; -const _displayNextItem = ( - results, - resultCount, - searchTerms, - highlightTerms, -) => { - // results left, load the summary and display it - // this is intended to be dynamic (don't sub resultsCount) - if (results.length) { - _displayItem(results.pop(), searchTerms, highlightTerms); - setTimeout( - () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), - 5 - ); - } - // search finished, update title and status message - else _finishSearch(resultCount); -}; -// Helper function used by query() to order search results. -// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. -// Order the results by score (in opposite order of appearance, since the -// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. -const _orderResultsByScoreThenName = (a, b) => { - const leftScore = a[4]; - const rightScore = b[4]; - if (leftScore === rightScore) { - // same score: sort alphabetically - const leftTitle = a[1].toLowerCase(); - const rightTitle = b[1].toLowerCase(); - if (leftTitle === rightTitle) return 0; - return leftTitle > rightTitle ? -1 : 1; // inverted is intentional - } - return leftScore > rightScore ? 1 : -1; -}; - -/** - * Default splitQuery function. Can be overridden in ``sphinx.search`` with a - * custom function per language. - * - * The regular expression works by splitting the string on consecutive characters - * that are not Unicode letters, numbers, underscores, or emoji characters. - * This is the same as ``\W+`` in Python, preserving the surrogate pair area. - */ -if (typeof splitQuery === "undefined") { - var splitQuery = (query) => query - .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) - .filter(term => term) // remove remaining empty strings -} - -/** - * Search Module - */ -const Search = { - _index: null, - _queued_query: null, - _pulse_status: -1, - - htmlToText: (htmlString, anchor) => { - const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - for (const removalQuery of [".headerlink", "script", "style"]) { - htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); - } - if (anchor) { - const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); - if (anchorContent) return anchorContent.textContent; - - console.warn( - `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` - ); - } - - // if anchor not specified or not found, fall back to main content - const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent) return docContent.textContent; - - console.warn( - "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." - ); - return ""; - }, - - init: () => { - const query = new URLSearchParams(window.location.search).get("q"); - document - .querySelectorAll('input[name="q"]') - .forEach((el) => (el.value = query)); - if (query) Search.performSearch(query); - }, - - loadIndex: (url) => - (document.body.appendChild(document.createElement("script")).src = url), - - setIndex: (index) => { - Search._index = index; - if (Search._queued_query !== null) { - const query = Search._queued_query; - Search._queued_query = null; - Search.query(query); - } - }, - - hasIndex: () => Search._index !== null, - - deferQuery: (query) => (Search._queued_query = query), - - stopPulse: () => (Search._pulse_status = -1), - - startPulse: () => { - if (Search._pulse_status >= 0) return; - - const pulse = () => { - Search._pulse_status = (Search._pulse_status + 1) % 4; - Search.dots.innerText = ".".repeat(Search._pulse_status); - if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); - }; - pulse(); - }, - - /** - * perform a search for something (or wait until index is loaded) - */ - performSearch: (query) => { - // create the required interface elements - const searchText = document.createElement("h2"); - searchText.textContent = _("Searching"); - const searchSummary = document.createElement("p"); - searchSummary.classList.add("search-summary"); - searchSummary.innerText = ""; - const searchList = document.createElement("ul"); - searchList.setAttribute("role", "list"); - searchList.classList.add("search"); - - const out = document.getElementById("search-results"); - Search.title = out.appendChild(searchText); - Search.dots = Search.title.appendChild(document.createElement("span")); - Search.status = out.appendChild(searchSummary); - Search.output = out.appendChild(searchList); - - const searchProgress = document.getElementById("search-progress"); - // Some themes don't use the search progress node - if (searchProgress) { - searchProgress.innerText = _("Preparing search..."); - } - Search.startPulse(); - - // index already loaded, the browser was quick! - if (Search.hasIndex()) Search.query(query); - else Search.deferQuery(query); - }, - - _parseQuery: (query) => { - // stem the search terms and add them to the correct list - const stemmer = new Stemmer(); - const searchTerms = new Set(); - const excludedTerms = new Set(); - const highlightTerms = new Set(); - const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); - splitQuery(query.trim()).forEach((queryTerm) => { - const queryTermLower = queryTerm.toLowerCase(); - - // maybe skip this "word" - // stopwords array is from language_data.js - if ( - stopwords.indexOf(queryTermLower) !== -1 || - queryTerm.match(/^\d+$/) - ) - return; - - // stem the word - let word = stemmer.stemWord(queryTermLower); - // select the correct list - if (word[0] === "-") excludedTerms.add(word.substr(1)); - else { - searchTerms.add(word); - highlightTerms.add(queryTermLower); - } - }); - - if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js - localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) - } - - // console.debug("SEARCH: searching for:"); - // console.info("required: ", [...searchTerms]); - // console.info("excluded: ", [...excludedTerms]); - - return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; - }, - - /** - * execute search (requires search index to be loaded) - */ - _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - - // Collect multiple result groups to be sorted separately and then ordered. - // Each is an array of [docname, title, anchor, descr, score, filename, kind]. - const normalResults = []; - const nonMainIndexResults = []; - - _removeChildren(document.getElementById("search-progress")); - - const queryLower = query.toLowerCase().trim(); - for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { - for (const [file, id] of foundTitles) { - const score = Math.round(Scorer.title * queryLower.length / title.length); - const boost = titles[file] === title ? 1 : 0; // add a boost for document titles - normalResults.push([ - docNames[file], - titles[file] !== title ? `${titles[file]} > ${title}` : title, - id !== null ? "#" + id : "", - null, - score + boost, - filenames[file], - SearchResultKind.title, - ]); - } - } - } - - // search for explicit entries in index directives - for (const [entry, foundEntries] of Object.entries(indexEntries)) { - if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id, isMain] of foundEntries) { - const score = Math.round(100 * queryLower.length / entry.length); - const result = [ - docNames[file], - titles[file], - id ? "#" + id : "", - null, - score, - filenames[file], - SearchResultKind.index, - ]; - if (isMain) { - normalResults.push(result); - } else { - nonMainIndexResults.push(result); - } - } - } - } - - // lookup as object - objectTerms.forEach((term) => - normalResults.push(...Search.performObjectSearch(term, objectTerms)) - ); - - // lookup as search terms in fulltext - normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); - - // let the scorer override scores with a custom scoring function - if (Scorer.score) { - normalResults.forEach((item) => (item[4] = Scorer.score(item))); - nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); - } - - // Sort each group of results by score and then alphabetically by name. - normalResults.sort(_orderResultsByScoreThenName); - nonMainIndexResults.sort(_orderResultsByScoreThenName); - - // Combine the result groups in (reverse) order. - // Non-main index entries are typically arbitrary cross-references, - // so display them after other results. - let results = [...nonMainIndexResults, ...normalResults]; - - // remove duplicate search results - // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept - let seen = new Set(); - results = results.reverse().reduce((acc, result) => { - let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); - if (!seen.has(resultStr)) { - acc.push(result); - seen.add(resultStr); - } - return acc; - }, []); - - return results.reverse(); - }, - - query: (query) => { - const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); - const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); - - // for debugging - //Search.lastresults = results.slice(); // a copy - // console.info("search results:", Search.lastresults); - - // print the results - _displayNextItem(results, results.length, searchTerms, highlightTerms); - }, - - /** - * search for object names - */ - performObjectSearch: (object, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const objects = Search._index.objects; - const objNames = Search._index.objnames; - const titles = Search._index.titles; - - const results = []; - - const objectSearchCallback = (prefix, match) => { - const name = match[4] - const fullname = (prefix ? prefix + "." : "") + name; - const fullnameLower = fullname.toLowerCase(); - if (fullnameLower.indexOf(object) < 0) return; - - let score = 0; - const parts = fullnameLower.split("."); - - // check for different match types: exact matches of full name or - // "last name" (i.e. last dotted part) - if (fullnameLower === object || parts.slice(-1)[0] === object) - score += Scorer.objNameMatch; - else if (parts.slice(-1)[0].indexOf(object) > -1) - score += Scorer.objPartialMatch; // matches in last name - - const objName = objNames[match[1]][2]; - const title = titles[match[0]]; - - // If more than one term searched for, we require other words to be - // found in the name/title/description - const otherTerms = new Set(objectTerms); - otherTerms.delete(object); - if (otherTerms.size > 0) { - const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); - if ( - [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) - ) - return; - } - - let anchor = match[3]; - if (anchor === "") anchor = fullname; - else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; - - const descr = objName + _(", in ") + title; - - // add custom score for some objects according to scorer - if (Scorer.objPrio.hasOwnProperty(match[2])) - score += Scorer.objPrio[match[2]]; - else score += Scorer.objPrioDefault; - - results.push([ - docNames[match[0]], - fullname, - "#" + anchor, - descr, - score, - filenames[match[0]], - SearchResultKind.object, - ]); - }; - Object.keys(objects).forEach((prefix) => - objects[prefix].forEach((array) => - objectSearchCallback(prefix, array) - ) - ); - return results; - }, - - /** - * search for full-text terms in the index - */ - performTermsSearch: (searchTerms, excludedTerms) => { - // prepare search - const terms = Search._index.terms; - const titleTerms = Search._index.titleterms; - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - - const scoreMap = new Map(); - const fileMap = new Map(); - - // perform the search on the required terms - searchTerms.forEach((word) => { - const files = []; - const arr = [ - { files: terms[word], score: Scorer.term }, - { files: titleTerms[word], score: Scorer.title }, - ]; - // add support for partial matches - if (word.length > 2) { - const escapedWord = _escapeRegExp(word); - if (!terms.hasOwnProperty(word)) { - Object.keys(terms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: terms[term], score: Scorer.partialTerm }); - }); - } - if (!titleTerms.hasOwnProperty(word)) { - Object.keys(titleTerms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); - }); - } - } - - // no match but word was a required one - if (arr.every((record) => record.files === undefined)) return; - - // found search word in contents - arr.forEach((record) => { - if (record.files === undefined) return; - - let recordFiles = record.files; - if (recordFiles.length === undefined) recordFiles = [recordFiles]; - files.push(...recordFiles); - - // set score for the word in each file - recordFiles.forEach((file) => { - if (!scoreMap.has(file)) scoreMap.set(file, {}); - scoreMap.get(file)[word] = record.score; - }); - }); - - // create the mapping - files.forEach((file) => { - if (!fileMap.has(file)) fileMap.set(file, [word]); - else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); - }); - }); - - // now check if the files don't contain excluded terms - const results = []; - for (const [file, wordList] of fileMap) { - // check if all requirements are matched - - // as search terms with length < 3 are discarded - const filteredTermCount = [...searchTerms].filter( - (term) => term.length > 2 - ).length; - if ( - wordList.length !== searchTerms.size && - wordList.length !== filteredTermCount - ) - continue; - - // ensure that none of the excluded terms is in the search result - if ( - [...excludedTerms].some( - (term) => - terms[term] === file || - titleTerms[term] === file || - (terms[term] || []).includes(file) || - (titleTerms[term] || []).includes(file) - ) - ) - break; - - // select one (max) score for the file. - const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); - // add result to the result list - results.push([ - docNames[file], - titles[file], - "", - null, - score, - filenames[file], - SearchResultKind.text, - ]); - } - return results; - }, - - /** - * helper function to return a node containing the - * search summary for a given text. keywords is a list - * of stemmed words. - */ - makeSearchSummary: (htmlText, keywords, anchor) => { - const text = Search.htmlToText(htmlText, anchor); - if (text === "") return null; - - const textLower = text.toLowerCase(); - const actualStartPosition = [...keywords] - .map((k) => textLower.indexOf(k.toLowerCase())) - .filter((i) => i > -1) - .slice(-1)[0]; - const startWithContext = Math.max(actualStartPosition - 120, 0); - - const top = startWithContext === 0 ? "" : "..."; - const tail = startWithContext + 240 < text.length ? "..." : ""; - - let summary = document.createElement("p"); - summary.classList.add("context"); - summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; - - return summary; - }, -}; - -_ready(Search.init); diff --git a/docs/1.0.15/_static/sphinx_highlight.js b/docs/1.0.15/_static/sphinx_highlight.js deleted file mode 100644 index 8a96c69a..00000000 --- a/docs/1.0.15/_static/sphinx_highlight.js +++ /dev/null @@ -1,154 +0,0 @@ -/* Highlighting utilities for Sphinx HTML documentation. */ -"use strict"; - -const SPHINX_HIGHLIGHT_ENABLED = true - -/** - * highlight a given string on a node by wrapping it in - * span elements with the given class name. - */ -const _highlight = (node, addItems, text, className) => { - if (node.nodeType === Node.TEXT_NODE) { - const val = node.nodeValue; - const parent = node.parentNode; - const pos = val.toLowerCase().indexOf(text); - if ( - pos >= 0 && - !parent.classList.contains(className) && - !parent.classList.contains("nohighlight") - ) { - let span; - - const closestNode = parent.closest("body, svg, foreignObject"); - const isInSVG = closestNode && closestNode.matches("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.classList.add(className); - } - - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - const rest = document.createTextNode(val.substr(pos + text.length)); - parent.insertBefore( - span, - parent.insertBefore( - rest, - node.nextSibling - ) - ); - node.nodeValue = val.substr(0, pos); - /* There may be more occurrences of search term in this node. So call this - * function recursively on the remaining fragment. - */ - _highlight(rest, addItems, text, className); - - if (isInSVG) { - const rect = document.createElementNS( - "http://www.w3.org/2000/svg", - "rect" - ); - const bbox = parent.getBBox(); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute("class", className); - addItems.push({ parent: parent, target: rect }); - } - } - } else if (node.matches && !node.matches("button, select, textarea")) { - node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); - } -}; -const _highlightText = (thisNode, text, className) => { - let addItems = []; - _highlight(thisNode, addItems, text, className); - addItems.forEach((obj) => - obj.parent.insertAdjacentElement("beforebegin", obj.target) - ); -}; - -/** - * Small JavaScript module for the documentation. - */ -const SphinxHighlight = { - - /** - * highlight the search words provided in localstorage in the text - */ - highlightSearchWords: () => { - if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight - - // get and clear terms from localstorage - const url = new URL(window.location); - const highlight = - localStorage.getItem("sphinx_highlight_terms") - || url.searchParams.get("highlight") - || ""; - localStorage.removeItem("sphinx_highlight_terms") - url.searchParams.delete("highlight"); - window.history.replaceState({}, "", url); - - // get individual terms from highlight string - const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); - if (terms.length === 0) return; // nothing to do - - // There should never be more than one element matching "div.body" - const divBody = document.querySelectorAll("div.body"); - const body = divBody.length ? divBody[0] : document.querySelector("body"); - window.setTimeout(() => { - terms.forEach((term) => _highlightText(body, term, "highlighted")); - }, 10); - - const searchBox = document.getElementById("searchbox"); - if (searchBox === null) return; - searchBox.appendChild( - document - .createRange() - .createContextualFragment( - '

' + - '' + - _("Hide Search Matches") + - "

" - ) - ); - }, - - /** - * helper function to hide the search marks again - */ - hideSearchWords: () => { - document - .querySelectorAll("#searchbox .highlight-link") - .forEach((el) => el.remove()); - document - .querySelectorAll("span.highlighted") - .forEach((el) => el.classList.remove("highlighted")); - localStorage.removeItem("sphinx_highlight_terms") - }, - - initEscapeListener: () => { - // only install a listener if it is really needed - if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; - - document.addEventListener("keydown", (event) => { - // bail for input elements - if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; - // bail with special keys - if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; - if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { - SphinxHighlight.hideSearchWords(); - event.preventDefault(); - } - }); - }, -}; - -_ready(() => { - /* Do not call highlightSearchWords() when we are on the search page. - * It will highlight words from the *previous* search query. - */ - if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); - SphinxHighlight.initEscapeListener(); -}); diff --git a/docs/1.0.15/autodoc/mmif.serialize.html b/docs/1.0.15/autodoc/mmif.serialize.html deleted file mode 100644 index d3d818fd..00000000 --- a/docs/1.0.15/autodoc/mmif.serialize.html +++ /dev/null @@ -1,1412 +0,0 @@ - - - - - - - - - mmif.serialize module — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.serialize module

-
-

mmif.serialize.model module

-

The model module contains the classes used to represent an -abstract MMIF object as a live Python object.

-

The MmifObject class or one of its derivatives is subclassed by -all other classes defined in this SDK, except for MmifObjectEncoder.

-

These objects are generally instantiated from JSON, either as a string -or as an already-loaded Python dictionary. This base class provides the -core functionality for deserializing MMIF JSON data into live objects -and serializing live objects into MMIF JSON data. Specialized behavior -for the different components of MMIF is added in the subclasses.

-
-
-class mmif.serialize.model.DataDict(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject, Generic[T, S]

-
-
-empty()[source]
-
- -
-
-get(key: T, default=None) → S | None[source]
-
- -
-
-items()[source]
-
- -
-
-keys()[source]
-
- -
-
-update(other, overwrite)[source]
-
- -
-
-values()[source]
-
- -
- -
-
-class mmif.serialize.model.DataList(mmif_obj: bytes | str | list | None = None)[source]
-

Bases: MmifObject, Generic[T]

-

The DataList class is an abstraction that represents the -various lists found in a MMIF file, such as documents, subdocuments, -views, and annotations.

-
-
Parameters:
-

mmif_obj (Union[str, list]) – the data that the list contains

-
-
-
-
-append(value, overwrite)[source]
-
- -
-
-deserialize(mmif_json: str | list) → None[source]
-

Passes the input data into the internal deserializer.

-
- -
-
-empty()[source]
-
- -
-
-get(key: str) → T | None[source]
-

Standard dictionary-style get() method, albeit with no default -parameter. Relies on the implementation of __getitem__.

-

Will return None if the key is not found.

-
-
Parameters:
-

key – the key to search for

-
-
Returns:
-

the value matching that key

-
-
-
- -
- -
-
-class mmif.serialize.model.MmifObject(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: object

-

Abstract superclass for MMIF related key-value pair objects.

-

Any MMIF object can be initialized as an empty placeholder or -an actual representation with a JSON formatted string or equivalent -dict object argument.

-

This superclass has four specially designed instance variables, and these -variable names cannot be used as attribute names for MMIF objects.

-
    -

  1. _unnamed_attributes: -Only can be either None or an empty dictionary. If it’s set to None, -it means the class won’t take any Additional Attributes in the -JSON schema sense. If it’s an empty dict, users can throw any k-v -pairs to the class, as long as the key is not a “reserved” name, -and those additional attributes will be stored in this dict while -in memory.

    2. -

  2. _attribute_classes: -This is a dict from a key name to a specific python class to use for -deserialize the value. Note that a key name in this dict does NOT -have to be a named attribute, but is recommended to be one.

    3. -

  3. _required_attributes: -This is a simple list of names of attributes that are required in -the object. When serialize, an object will skip its empty (e.g. -zero-length, or None) attributes unless they are in this list. -Otherwise, the serialized JSON string would have empty -representations (e.g. "", []).

    4. -

  4. _exclude_from_diff: -This is a simple list of names of attributes that should be excluded -from the diff calculation in __eq__.

    5. -
-

# TODO (krim @ 8/17/20): this dict is however, a duplicate with the type hints in the class definition. -Maybe there is a better way to utilize type hints (e.g. getting them -as a programmatically), but for now developers should be careful to -add types to hints as well as to this dict.

-

Also note that those special attributes MUST be set in the __init__() -before calling super method, otherwise deserialization will not work.

-

And also, a subclass that has one or more named attributes, it must -set those attributes in the __init__() before calling super method. -When serializing a MmifObject, all empty attributes will be ignored, -so for optional named attributes, you must leave the values empty -(len == 0), but NOT None. Any None-valued named attributes will cause -issues with current implementation.

-
-
Parameters:
-

mmif_obj – JSON string or dict to initialize an object. -If not given, an empty object will be initialized, sometimes with -an ID value automatically generated, based on its parent object.

-
-
-
-
-deserialize(mmif_json: str | dict) → None[source]
-

Takes a JSON-formatted string or a simple dict that’s json-loaded from -such a string as an input and populates object’s fields with the values -specified in the input.

-
-
Parameters:
-

mmif_json – JSON-formatted string or dict from such a string -that represents a MMIF object

-
-
-
- -
-
-disallow_additional_properties() → None[source]
-

Call this method in __init__() to prevent the insertion -of unnamed attributes after initialization.

-
- -
-
-id_delimiter: ClassVar[str] = ':'[source]
-
- -
-
-static is_empty(obj) → bool[source]
-

return True if the obj is None or “emtpy”. The emptiness first defined as -having zero length. But for objects that lack __len__ method, we need -additional check.

-
- -
-
-reserved_names: Set[str] = {'_attribute_classes', '_exclude_from_diff', '_required_attributes', '_unnamed_attributes', 'reserved_names'}[source]
-
- -
-
-serialize(pretty: bool = False) → str[source]
-

Generates JSON representation of an object.

-
-
Parameters:
-

pretty – If True, returns string representation with indentation.

-
-
Returns:
-

JSON string of the object.

-
-
-
- -
-
-set_additional_property(key: str, value: Any) → None[source]
-

Method to set values in _unnamed_attributes.

-
-
Parameters:
-
    -

  • key – the attribute name

    • -

  • value – the desired value

    • -
-
-
Returns:
-

None

-
-
Raise:
-

AttributeError if additional properties are disallowed by disallow_additional_properties()

-
-
-
- -
-
-view_prefix: ClassVar[str] = 'v_'[source]
-
- -
- -
-
-class mmif.serialize.model.MmifObjectEncoder(*, skipkeys=False, ensure_ascii=True, check_circular=True, allow_nan=True, sort_keys=False, indent=None, separators=None, default=None)[source]
-

Bases: JSONEncoder

-

Encoder class to define behaviors of de-/serialization

-
-
-default(obj: MmifObject)[source]
-

Overrides default encoding behavior to prioritize MmifObject.serialize().

-
- -
- -
-
-

mmif.serialize.mmif module

-

The mmif module contains the classes used to represent a full MMIF -file as a live Python object.

-

See the specification docs and the JSON Schema file for more information.

-
-
-class mmif.serialize.mmif.Mmif(mmif_obj: bytes | str | dict | None = None, *, validate: bool = True)[source]
-

Bases: MmifObject

-

MmifObject that represents a full MMIF file.

-
-
Parameters:
-
    -

  • mmif_obj – the JSON data

    • -

  • validate – whether to validate the data against the MMIF JSON schema.

    • -
-
-
-
-
-add_document(document: Document, overwrite=False) → None[source]
-

Appends a Document object to the documents list.

-

Fails if there is already a document with the same ID in the MMIF object.

-
-
Parameters:
-
    -

  • document – the Document object to add

    • -

  • overwrite – if set to True, will overwrite -an existing view with the same ID

    • -
-
-
Returns:
-

None

-
-
-
- -
-
-add_view(view: View, overwrite=False) → None[source]
-

Appends a View object to the views list.

-

Fails if there is already a view with the same ID in the MMIF object.

-
-
Parameters:
-
    -

  • view – the Document object to add

    • -

  • overwrite – if set to True, will overwrite -an existing view with the same ID

    • -
-
-
Returns:
-

None

-
-
-
- -
-
-generate_capital_annotations()[source]
-

Automatically convert any “pending” temporary properties from -Document objects to Annotation objects . The generated Annotation -objects are then added to the last View in the views lists.

-

See https://github.com/clamsproject/mmif-python/issues/226 for rationale -behind this behavior and discussion.

-
- -
-
-get_alignments(at_type1: str | TypesBase, at_type2: str | TypesBase) → Dict[str, List[Annotation]][source]
-

Finds views where alignments between two given annotation types occurred.

-
-
Returns:
-

a dict that keyed by view IDs (str) and has lists of alignment Annotation objects as values.

-
-
-
- -
-
-get_all_views_contain(at_types: TypesBase | str | List[str | TypesBase]) → List[View][source]
-

Returns the list of all views in the MMIF if given types -are present in that view’s ‘contains’ metadata.

-
-
Parameters:
-

at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

-
-
Returns:
-

the list of views that contain the type

-
-
-
- -
-
-get_all_views_with_error() → List[View][source]
-

Returns the list of all views in the MMIF that have errors.

-
-
Returns:
-

the list of views that contain errors but no annotations

-
-
-
- -
-
-get_document_by_id(doc_id: str) → Document[source]
-

Finds a Document object with the given ID.

-
-
Parameters:
-

doc_id – the ID to search for

-
-
Returns:
-

a reference to the corresponding document, if it exists

-
-
Raises:
-

KeyError – if there is no corresponding document

-
-
-
- -
-
-get_document_location(m_type: DocumentTypes | str, path_only=False) → str | None[source]
-

Method to get the location of first document of given type.

-
-
Parameters:
-

m_type – the type to search for

-
-
Returns:
-

the value of the location field in the corresponding document

-
-
-
- -
-
-get_documents_by_app(app_id: str) → List[Document][source]
-

Method to get all documents object queries by its originated app name.

-
-
Parameters:
-

app_id – the app name to search for

-
-
Returns:
-

a list of documents matching the requested app name, or an empty list if the app not found

-
-
-
- -
-
-get_documents_by_property(prop_key: str, prop_value: str) → List[Document][source]
-

Method to retrieve documents by an arbitrary key-value pair in the document properties objects.

-
-
Parameters:
-
    -

  • prop_key – the metadata key to search for

    • -

  • prop_value – the metadata value to match

    • -
-
-
Returns:
-

a list of documents matching the requested metadata key-value pair

-
-
-
- -
-
-get_documents_by_type(doc_type: str | DocumentTypes) → List[Document][source]
-

Method to get all documents where the type matches a particular document type, which should be one of the CLAMS document types.

-
-
Parameters:
-

doc_type – the type of documents to search for, must be one of Document type defined in the CLAMS vocabulary.

-
-
Returns:
-

a list of documents matching the requested type, or an empty list if none found.

-
-
-
- -
-
-get_documents_in_view(vid: str | None = None) → List[Document][source]
-

Method to get all documents object queries by a view id.

-
-
Parameters:
-

vid – the source view ID to search for

-
-
Returns:
-

a list of documents matching the requested source view ID, or an empty list if the view not found

-
-
-
- -
-
-get_documents_locations(m_type: DocumentTypes | str, path_only=False) → List[str | None][source]
-

This method returns the file paths of documents of given type. -Only top-level documents have locations, so we only check them.

-
-
Parameters:
-

m_type – the type to search for

-
-
Returns:
-

a list of the values of the location fields in the corresponding documents

-
-
-
- -
-
-get_end(annotation: Annotation) → int | float[source]
-

An alias to get_anchor_point method with start=False.

-
- -
-
-get_last_error() → str | None[source]
-

Returns the last error message found in the views.

-
-
Returns:
-

the error message in human-readable format, or None if no error is found

-
-
-
- -
-
-get_start(annotation: Annotation) → int | float[source]
-

An alias to get_anchor_point method with start=True.

-
- -
-
-get_view_by_id(req_view_id: str) → View[source]
-

Finds a View object with the given ID.

-
-
Parameters:
-

req_view_id – the ID to search for

-
-
Returns:
-

a reference to the corresponding view, if it exists

-
-
Raises:
-

Exception – if there is no corresponding view

-
-
-
- -
-
-get_view_contains(at_types: TypesBase | str | List[str | TypesBase]) → View | None[source]
-

Returns the last view appended that contains the given -types in its ‘contains’ metadata.

-
-
Parameters:
-

at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

-
-
Returns:
-

the view, or None if the type is not found

-
-
-
- -
-
-get_view_with_error() → View | None[source]
-

Returns the last view appended that contains an error.

-
-
Returns:
-

the view, or None if no error is found

-
-
-
- -
-
-get_views_contain(at_types: TypesBase | str | List[str | TypesBase]) → List[View][source]
-

Returns the list of all views in the MMIF if given types -are present in that view’s ‘contains’ metadata.

-
-
Parameters:
-

at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

-
-
Returns:
-

the list of views that contain the type

-
-
-
- -
-
-get_views_for_document(doc_id: str) → List[View][source]
-

Returns the list of all views that have annotations anchored on a particular document. -Note that when the document is inside a view (generated during the pipeline’s running), -doc_id must be prefixed with the view_id.

-
- -
-
-get_views_with_error() → List[View][source]
-

Returns the list of all views in the MMIF that have errors.

-
-
Returns:
-

the list of views that contain errors but no annotations

-
-
-
- -
-
-new_view() → View[source]
-

Creates an empty view with a new ID and appends it to the views list.

-
-
Returns:
-

a reference to the new View object

-
-
-
- -
-
-new_view_id() → str[source]
-

Fetches an ID for a new view.

-
-
Returns:
-

the ID

-
-
-
- -
-
-sanitize()[source]
-

Sanitizes a Mmif object by running some safeguards. -Concretely, it performs the following before returning the JSON string.

-
    -

  1. validating output using built-in MMIF jsonschema

    2. -

  2. remove non-existing annotation types from contains metadata

    3. -
-
- -
-
-serialize(pretty: bool = False, sanitize: bool = False, autogenerate_capital_annotations=True) → str[source]
-

Serializes the MMIF object to a JSON string.

-
-
Parameters:
-
    -

  • sanitize – If True, performs some sanitization of before returning -the JSON string. See sanitize() for details.

    • -

  • autogenerate_capital_annotations – If True, automatically convert -any “pending” temporary properties from Document objects to -Annotation objects. See generate_capital_annotations() for -details.

    • -

  • pretty – If True, returns string representation with indentation.

    • -
-
-
Returns:
-

JSON string of the MMIF object.

-
-
-
- -
-
-static validate(json_str: bytes | str | dict) → None[source]
-

Validates a MMIF JSON object against the MMIF Schema. -Note that this method operates before processing by MmifObject._load_str, -so it expects @ and not _ for the JSON-LD @-keys.

-
-
Raises:
-

jsonschema.exceptions.ValidationError – if the input fails validation

-
-
Parameters:
-

json_str – a MMIF JSON dict or string

-
-
Returns:
-

None

-
-
-
- -
- -
-
-

mmif.serialize.view module

-

The view module contains the classes used to represent a MMIF view -as a live Python object.

-

In MMIF, views are created by apps in a pipeline that are annotating -data that was previously present in the MMIF file.

-
-
-class mmif.serialize.view.Contain(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: DataDict[str, str]

-

Contain object that represents the metadata of a single -annotation type in the contains metadata of a MMIF view.

-
- -
-
-class mmif.serialize.view.View(view_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-

View object that represents a single view in a MMIF file.

-

A view is identified by an ID, and contains certain metadata, -a list of annotations, and potentially a JSON-LD @context -IRI.

-

If view_obj is not provided, an empty View will be generated.

-
-
Parameters:
-

view_obj – the JSON data that defines the view

-
-
-
-
-add_annotation(annotation: Annotation, overwrite=False) → Annotation[source]
-

Adds an annotation to the current view.

-

Fails if there is already an annotation with the same ID -in the view, unless overwrite is set to True.

-
-
Parameters:
-
-
-
Raises:
-

KeyError – if overwrite is set to False and -an annotation with the same ID exists -in the view

-
-
Returns:
-

the same Annotation object passed in as annotation

-
-
-
- -
-
-add_document(document: Document, overwrite=False) → Annotation[source]
-

Appends a Document object to the annotations list.

-

Fails if there is already a document with the same ID in the annotations list.

-
-
Parameters:
-
    -

  • document – the Document object to add

    • -

  • overwrite – if set to True, will overwrite -an existing view with the same ID

    • -
-
-
Returns:
-

None

-
-
-
- -
-
-get_annotation_by_id(ann_id) → Annotation[source]
-
- -
-
-get_annotations(at_type: str | TypesBase | None = None, **properties) → Generator[Annotation, None, None][source]
-

Look for certain annotations in this view, specified by parameters

-
-
Parameters:
-
    -

  • at_type – @type of the annotations to look for. When this is None, any @type will match.

    • -

  • properties – properties of the annotations to look for. When given more than one property, all properties must match. Note that annotation type metadata are specified in the contains view metadata, not in individual annotation objects.

    • -
-
-
-
- -
-
-get_document_by_id(doc_id) → Document[source]
-
- -
-
-get_documents() → List[Document][source]
-
- -
-
-get_error() → str | None[source]
-

Get the “text” representation of the error occurred during -processing. Text representation is supposed to be human-readable. -When ths view does not have any error, returns None.

-
- -
-
-has_error() → bool[source]
-
- -
-
-has_warnings()[source]
-
- -
-
-new_annotation(at_type: str | TypesBase, aid: str | None = None, overwrite=False, **properties) → Annotation[source]
-

Generates a new mmif.serialize.annotation.Annotation -object and adds it to the current view.

-

Fails if there is already an annotation with the same ID -in the view, unless overwrite is set to True.

-
-
Parameters:
-
    -

  • at_type – the desired @type of the annotation.

    • -

  • aid – the desired ID of the annotation, when not given, -the mmif SDK tries to automatically generate an ID based on -Annotation type and existing annotations in the view.

    • -

  • overwrite – if set to True, will overwrite an -existing annotation with the same ID.

    • -
-
-
Raises:
-

KeyError – if overwrite is set to False and -an annotation with the same ID exists -in the view.

-
-
Returns:
-

the generated mmif.serialize.annotation.Annotation

-
-
-
- -
-
-new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
-

Adds a new element to the contains metadata.

-
-
Parameters:
-
    -

  • at_type – the @type of the annotation type being added

    • -

  • contains_metadata – any metadata associated with the annotation type

    • -
-
-
Returns:
-

the generated Contain object

-
-
-
- -
-
-new_textdocument(text: str, lang: str = 'en', did: str | None = None, overwrite=False, **properties) → Document[source]
-

Generates a new mmif.serialize.annotation.Document -object, particularly typed as TextDocument and adds it to the current view.

-

Fails if there is already a text document with the same ID -in the view, unless overwrite is set to True.

-
-
Parameters:
-
    -

  • text – text content of the new document

    • -

  • lang – ISO 639-1 code of the language used in the new document

    • -

  • did – the desired ID of the document, when not given, -the mmif SDK tries to automatically generate an ID based on -Annotation type and existing documents in the view.

    • -

  • overwrite – if set to True, will overwrite an -existing document with the same ID

    • -
-
-
Raises:
-

KeyError – if overwrite is set to False and -an document with the same ID exists -in the view

-
-
Returns:
-

the generated mmif.serialize.annotation.Document

-
-
-
- -
-
-set_error(err_message: str, err_trace: str) → None[source]
-
- -
- -
-
-class mmif.serialize.view.ViewMetadata(viewmetadata_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-

ViewMetadata object that represents the metadata object within a MMIF view.

-
-
Parameters:
-

viewmetadata_obj – the JSON data that defines the metadata

-
-
-
-
-add_app_configuration(config_key: str, config_value: str | int | float | bool | None | List[str | int | float | bool | None]) → None[source]
-

Add a configuration key-value pair to the app_configuration dictionary.

-
- -
-
-add_contain(contain: Contain, at_type: str | TypesBase) → None[source]
-
- -
-
-add_parameter(param_key: str, param_value: str)[source]
-

Add a single runtime parameter to the view metadata. Note that parameter value must be a string.

-
- -
-
-add_parameters(**runtime_params: str)[source]
-

Add runtime parameters as a batch (dict) to the view metadata. Note that parameter values must be strings.

-
- -
-
-add_warnings(*warnings: Warning)[source]
-
- -
-
-emtpy_warnings()[source]
-
- -
-
-get_app_configuration(config_key: str) → str | int | float | bool | None | List[str | int | float | bool | None][source]
-

Get a configuration value from the app_configuration dictionary.

-
- -
-
-get_error_as_text() → str[source]
-
- -
-
-get_parameter(param_key: str) → str[source]
-

Get a runtime parameter from the view metadata.

-
- -
-
-has_error() → bool[source]
-
- -
-
-has_warnings()[source]
-
- -
-
-new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
-

Adds a new element to the contains dictionary.

-
-
Parameters:
-
    -

  • at_type – the @type of the annotation type being added

    • -

  • contains_metadata – any metadata associated with the annotation type

    • -
-
-
Returns:
-

the generated Contain object

-
-
-
- -
-
-set_error(message: str, stack_trace: str)[source]
-
- -
- -
-
-

mmif.serialize.annotation module

-

The annotation module contains the classes used to represent a -MMIF annotation as a live Python object.

-

In MMIF, annotations are created by apps in a pipeline as a part -of a view. For documentation on how views are represented, see -mmif.serialize.view.

-
-
-class mmif.serialize.annotation.Annotation(anno_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-

MmifObject that represents an annotation in a MMIF view.

-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]]) → None[source]
-

Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

-
- -
-
-property at_type: TypesBase[source]
-
- -
-
-static check_prop_value_is_simple_enough(value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]]) → bool[source]
-
- -
-
-get(prop_name: str) → AnnotationProperties | str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]][source]
-

A special getter for Annotation properties. This is to allow for -directly accessing properties without having to go through the -properties object, or view-level annotation properties encoded in the -view.metadata.contains dict. Note that the regular props will take -the priority over the ephemeral props when there are conflicts.

-
- -
-
-get_property(prop_name: str) → AnnotationProperties | str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]][source]
-

A special getter for Annotation properties. This is to allow for -directly accessing properties without having to go through the -properties object, or view-level annotation properties encoded in the -view.metadata.contains dict. Note that the regular props will take -the priority over the ephemeral props when there are conflicts.

-
- -
-
-property id: str[source]
-
- -
-
-is_document()[source]
-
- -
-
-is_type(at_type: str | TypesBase) → bool[source]
-

Check if the @type of this object matches.

-
- -
-
-property long_id: str[source]
-
- -
-
-property parent: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.AnnotationProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject, MutableMapping[str, T]

-

AnnotationProperties object that represents the -properties object within a MMIF annotation.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
- -
-
-class mmif.serialize.annotation.Document(doc_obj: bytes | str | dict | None = None)[source]
-

Bases: Annotation

-

Document object that represents a single document in a MMIF file.

-

A document is identified by an ID, and contains certain attributes -and potentially contains the contents of the document itself, -metadata about how the document was created, and/or a list of -subdocuments grouped together logically.

-

If document_obj is not provided, an empty Document will be generated.

-
-
Parameters:
-

document_obj – the JSON data that defines the document

-
-
-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None]) → None[source]
-

Adds a property to the document’s properties.

-

Unlike the parent Annotation class, added properties of a -Document object can be lost during serialization unless it belongs -to somewhere in a Mmif object. This is because we want to keep -Document object as “read-only” as possible. Thus, if you want to add -a property to a Document object,

-
    -

  • add the document to a Mmif object (either in the documents list or -in a view from the views list), or

    • -

  • directly write to Document.properties instead of using this method -(which is not recommended).

    • -
-

With the former method, the SDK will record the added property as a -Annotation annotation object, separate from the original Document -object. See Mmif.generate_capital_annotations() for more.

-

A few notes to keep in mind:

-
    -

  1. You can’t overwrite an existing property of a Document object.

    2. -

  2. A MMIF can have multiple Annotation objects with the same -property name but different values. When this happens, the SDK will -only keep the latest value (in order of appearances in views list) of -the property, effectively overwriting the previous values.

    3. -
-
- -
-
-get(prop_name)[source]
-

A special getter for Document properties. The major difference from -the super class’s Annotation.get() method is that Document -class has one more set of “pending” properties, that are added after -the Document object is created and will be serialized as a separate -Annotation object of which @type = Annotation. The -pending properties will take the priority over the regular properties -when there are conflicts.

-
- -
-
-get_property(prop_name)[source]
-

A special getter for Document properties. The major difference from -the super class’s Annotation.get() method is that Document -class has one more set of “pending” properties, that are added after -the Document object is created and will be serialized as a separate -Annotation object of which @type = Annotation. The -pending properties will take the priority over the regular properties -when there are conflicts.

-
- -
-
-property location: str | None[source]
-

location property must be a legitimate URI. That is, should the document be a local file -then the file:// scheme must be used. -Returns None when no location is set.

-
- -
-
-location_address() → str | None[source]
-

Retrieves the full address from the document location URI. -Returns None when no location is set.

-
- -
-
-location_path(nonexist_ok=True) → str | None[source]
-

Retrieves a path that’s resolved to a pathname in the local file system. -To obtain the original value of the “path” part in the location string -(before resolving), use properties.location_path_literal method. -Returns None when no location is set.

-
-
Parameters:
-

nonexist_ok – if False, raise FileNotFoundError when the resolved path doesn’t exist

-
-
-
- -
-
-location_scheme() → str | None[source]
-

Retrieves URI scheme of the document location. -Returns None when no location is set.

-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.DocumentProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: AnnotationProperties

-

DocumentProperties object that represents the -properties object within a MMIF document.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
-
-property location: str | None[source]
-

location property must be a legitimate URI. That is, should the document be a local file -then the file:// scheme must be used. -Returns None when no location is set.

-
- -
-
-location_address() → str | None[source]
-

Retrieves the full address from the document location URI. -Returns None when no location is set.

-
- -
-
-location_path() → str | None[source]
-
- -
-
-location_path_literal() → str | None[source]
-

Retrieves only path name of the document location (hostname is ignored). -Returns None when no location is set.

-
- -
-
-location_path_resolved(nonexist_ok=True) → str | None[source]
-

Retrieves only path name of the document location (hostname is ignored), -and then try to resolve the path name in the local file system. -This method should be used when the document scheme is file or empty. -For other schemes, users should install mmif-locdoc-<scheme> plugin.

-

Returns None when no location is set. -Raise ValueError when no code found to resolve the given location scheme.

-
- -
-
-location_scheme() → str | None[source]
-

Retrieves URI scheme of the document location. -Returns None when no location is set.

-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.Text(text_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-
-
-property lang: str[source]
-
- -
-
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- - - \ No newline at end of file diff --git a/docs/1.0.15/autodoc/mmif.utils.html b/docs/1.0.15/autodoc/mmif.utils.html deleted file mode 100644 index b9a76ffe..00000000 --- a/docs/1.0.15/autodoc/mmif.utils.html +++ /dev/null @@ -1,615 +0,0 @@ - - - - - - - - - mmif.utils module — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
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- -
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- -
-

mmif.utils module

-
-

mmif.utils.video_document_helper module

-
-
-mmif.utils.video_document_helper.capture(video_document: Document)[source]
-

Captures a video file using OpenCV and adds fps, frame count, and duration as properties to the document.

-
-
Parameters:
-

video_document – Document instance that holds a video document ("@type": ".../VideoDocument/...")

-
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Returns:
-

OpenCV VideoCapture object

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- -
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-mmif.utils.video_document_helper.convert_timeframe(mmif: Mmif, time_frame: Annotation, out_unit: str) → Tuple[int | float | str, int | float | str][source]
-

Converts start and end points in a TimeFrame annotation a different time unit.

-
-
Parameters:
-
    -

  • mmif – Mmif instance

    • -

  • time_frame – Annotation instance that holds a time interval annotation ("@type": ".../TimeFrame/...")

    • -

  • out_unit – time unit to which the point is converted

    • -
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Returns:
-

tuple of frame numbers (integer) or seconds/milliseconds (float) of input start and end

-
-
-
- -
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-mmif.utils.video_document_helper.convert_timepoint(mmif: Mmif, timepoint: Annotation, out_unit: str) → int | float | str[source]
-

Converts a time point included in an annotation to a different time unit. -The input annotation must have timePoint property.

-
-
Parameters:
-
    -

  • mmif – input MMIF to obtain fps and input timeunit

    • -

  • timepoint – Annotation instance with timePoint property

    • -

  • out_unit – time unit to which the point is converted (frames, seconds, milliseconds)

    • -
-
-
Returns:
-

frame number (integer) or second/millisecond (float) of input timepoint

-
-
-
- -
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-mmif.utils.video_document_helper.extract_frames_as_images(video_document: Document, framenums: List[int], as_PIL: bool = False)[source]
-

Extracts frames from a video document as a list of numpy.ndarray. -Use with sample_frames() function to get the list of frame numbers first.

-
-
Parameters:
-
    -

  • video_document – Document instance that holds a video document ("@type": ".../VideoDocument/...")

    • -

  • framenums – integers representing the frame numbers to extract

    • -

  • as_PIL – return PIL.Image.Image instead of ndarray

    • -
-
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Returns:
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frames as a list of ndarray or Image

-
-
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- -
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-mmif.utils.video_document_helper.extract_mid_frame(mmif: Mmif, time_frame: Annotation, as_PIL: bool = False)[source]
-

Extracts the middle frame of a time interval annotation as a numpy ndarray.

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-
Parameters:
-
    -

  • mmif – Mmif instance

    • -

  • time_frame – Annotation instance that holds a time interval annotation ("@type": ".../TimeFrame/...")

    • -

  • as_PIL – return Image instead of ndarray

    • -
-
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Returns:
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frame as a numpy.ndarray or PIL.Image.Image

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-
- -
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-mmif.utils.video_document_helper.extract_representative_frame(mmif: Mmif, time_frame: Annotation, as_PIL: bool = False)[source]
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Extracts the representative frame of an annotation as a numpy ndarray or PIL Image.

-
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Parameters:
-
    -

  • mmif – Mmif instance

    • -

  • time_frame – Annotation instance that holds a time interval annotation ("@type": ".../TimeFrame/...")

    • -

  • as_PIL – return Image instead of ndarray

    • -
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Returns:
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frame as a numpy.ndarray or PIL.Image.Image

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- -
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-mmif.utils.video_document_helper.framenum_to_millisecond(video_doc: Document, frame: int)[source]
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Converts a frame number to a millisecond value.

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- -
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-mmif.utils.video_document_helper.framenum_to_second(video_doc: Document, frame: int)[source]
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Converts a frame number to a second value.

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- -
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-mmif.utils.video_document_helper.get_annotation_property(mmif, annotation, prop_name)[source]
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-

Deprecated since version 1.0.8: Use mmif.serialize.annotation.Annotation.get_property() method instead.

-
-

Get a property value from an annotation. If the property is not found in the annotation, it will look up the metadata of the annotation’s parent view and return the value from there. -xisting

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- -
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-mmif.utils.video_document_helper.get_framerate(video_document: Document) → float[source]
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Gets the frame rate of a video document. First by checking the fps property of the document, then by capturing the video.

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Parameters:
-

video_document – Document instance that holds a video document ("@type": ".../VideoDocument/...")

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Returns:
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frames per second as a float, rounded to 2 decimal places

-
-
-
- -
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-mmif.utils.video_document_helper.get_mid_framenum(mmif: Mmif, time_frame: Annotation)[source]
-

Calculates the middle frame number of a time interval annotation.

-
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Parameters:
-
    -

  • mmif – Mmif instance

    • -

  • time_frame – Annotation instance that holds a time interval annotation ("@type": ".../TimeFrame/...")

    • -
-
-
Returns:
-

middle frame number as an integer

-
-
-
- -
-
-mmif.utils.video_document_helper.get_representative_framenum(mmif: Mmif, time_frame: Annotation)[source]
-

Calculates the representative frame number from an annotation.

-
-
Parameters:
-
    -

  • mmif – Mmif instance

    • -

  • time_frame – Annotation instance that holds a time interval annotation containing a representatives property ("@type": ".../TimeFrame/...")

    • -
-
-
Returns:
-

representative frame number as an integer

-
-
-
- -
-
-mmif.utils.video_document_helper.millisecond_to_framenum(video_doc: Document, millisecond: float) → int[source]
-

Converts a millisecond value to a frame number.

-
- -
-
-mmif.utils.video_document_helper.sample_frames(start_frame: int, end_frame: int, sample_rate: float = 1) → List[int][source]
-

Helper function to sample frames from a time interval. -Can also be used as a “cutoff” function when used with start_frame==0 and sample_rate==1.

-
-
Parameters:
-
    -

  • start_frame – start frame of the interval

    • -

  • end_frame – end frame of the interval

    • -

  • sample_rate – sampling rate (or step) to configure how often to take a frame, default is 1, meaning all consecutive frames are sampled

    • -
-
-
-
- -
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-mmif.utils.video_document_helper.second_to_framenum(video_doc: Document, second) → int[source]
-

Converts a second value to a frame number.

-
- -
-
-

mmif.utils.sequence_helper module

-

This module provides helpers for handling sequence labeling. Specifically, it provides

-
    -

  • a generalized label re-mapper for “post-binning” of labels

    • -

  • conversion from a list of CLAMS annotations (with classification props) into a list of reals (scores by labels), can be combined with the label re-mapper mentioned above

    • -

  • mmif.utils.sequence_helper.smooth_outlying_short_intervals(): a simple smoothing algorithm by trimming “short” outlier sequences

    • -
-

However, it DOES NOT provide

-
    -

  • direct conversion between CLAMS annotations. For example, it does not directly handle stitching of TimePoint into TimeFrames.

    • -

  • support for multi-class scenario, such as handling of _competing_ subsequence or overlapping labels.

    • -
-

Some functions can use optional external libraries (e.g., numpy) for better performance. -Hence, if you see a warning about missing optional packages, you might want to install them by running pip install mmif-python[seq].

-
-
-mmif.utils.sequence_helper.build_label_remapper(src_labels: List[str], dst_labels: Dict[str, str | int | float | bool | None]) → Dict[str, str | int | float | bool | None][source]
-

Build a label remapper dictionary from source and destination labels.

-
-
Parameters:
-
    -

  • src_labels – a list of all labels on the source side

    • -

  • dst_labels – a dict from source labels to destination labels. -Source labels not in this dict will be remapped to a negative label (-).

    • -
-
-
Returns:
-

a dict that exhaustively maps source labels to destination labels

-
-
-
- -
-
-mmif.utils.sequence_helper.build_score_lists(classifications: ~typing.List[~typing.Dict], label_remapper: ~typing.Dict, score_remap_op: ~typing.Callable[[...], float] = <built-in function max>) → Tuple[Dict[str, int], numpy.ndarray][source]
-

Build lists of scores indexed by the label names.

-
-
Parameters:
-
    -

  • classifications – list of dictionaries of classification results, taken from input annotation objects

    • -

  • label_remapper – a dictionary that maps source label names to destination label names (formerly “postbin”)

    • -

  • score_remap_op – a function to remap the scores from multiple source labels binned to a destination label -common choices are max, min, or sum

    • -
-
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Returns:
-

    -

  1. a dictionary that maps label names to their index in the score list

    2. -

  2. 2-d numpy array of scores, of which rows are indexed by label map dict (first return value)

    3. -
-

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- -
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-mmif.utils.sequence_helper.smooth_outlying_short_intervals(scores: List[float], min_spseq_size: int, min_snseq_size: int, min_score: float = 0.5)[source]
-

Given a list of scores, a score threshold, and smoothing parameters, -identify the intervals of “positive” scores by “trimming” the short -positive sequences (“spseq”) and short negative sequences (“snseq”). To -decide the positivity, first step is binarization of the scores by the -min_score threshold. Given Sr as “raw” input real-number scores -list, and min_score=0.5,

-
-
Sr: [0.3, 0.6, 0.2, 0.8, 0.2, 0.9, 0.8, 0.5, 0.1, 0.5, 0.8, 0.3, 1.0, 0.7, 0.5, 0.5, 0.5, 0.8, 0.3, 0.6]
-
-
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the binarization is done by simply comparing each score to the -threshold to get S list of binary scores

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1.0 :                                     |                      
-0.9 :                |                    |                      
-0.8 :          |     |  |           |     |              |       
-0.7 :          |     |  |           |     |  |           |       
-0.6 :    |     |     |  |           |     |  |           |     | 
-0.5 :----+-----+-----+--+--+-----+--+-----+--+--+--+--+--+-----+-
-0.4 :    |     |     |  |  |     |  |     |  |  |  |  |  |     | 
-0.3 : |  |     |     |  |  |     |  |  |  |  |  |  |  |  |  |  | 
-0.2 : |  |  |  |  |  |  |  |     |  |  |  |  |  |  |  |  |  |  | 
-0.1 : |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | 
-0.0 +------------------------------------------------------------
-raw :.3 .6 .2 .8 .2 .9 .8 .5 .1 .5 .8 .3 1. .7 .5 .5 .5 .8 .3 .6
- S  : 0  1  0  1  0  1  1  0  0  0  1  0  1  1  0  1  1  1  0  1 
-
-
-
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Note that the size of a positive or negative sequence can be as small -as 1.

-

Then, here are examples of smoothing a list of binary scores into -intervals, by trimming “very short” (under thresholds) sequences of -positive or negative:

-
-

Note

-

legends:

-
    -

  • t is unit index (e.g. time index)

    • -

  • S is the list of binary scores (zeros and ones)

    • -

  • I is the list of intervals after smoothing

    • -
-
-
    -

  1. with params min_spseq_size==1, min_snseq_size==4

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1]
-I: [0, 1--1--1--1--1--1--1--1--1--1--1--1, 0--0--0--0--0--0, 1]
-
    -
    -

    Explanation: min_snseq_size is used to smooth short sequences -of negative predictions. In this, zeros from t[7:10] are smoothed -into “one” I, while zeros from t[13:19] are kept as “zero” I. Note -that the “short” snseqs at the either ends (t[0:1]) are never -smoothed.

    -
    -
    2. -

  2. with params min_spseq_size==4, min_snseq_size==2

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1]
-I: [0, 1--1--1--1--1--1, 0--0--0--0--0--0--0--0--0--0--0--0--0]
-
    -
    -

    Explanation: min_spseq_size is used to smooth short sequences -of positive predictions. In this example, the spseqs of ones from -both t[10:13] and t[19:20] are smoothed. Note that the “short” -spseqs at the either ends (t[19:20]) are always smoothed.

    -
    -
    3. -

  3. with params min_spseq_size==4, min_snseq_size==4

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1]
-I: [0, 1--1--1--1--1--1--1--1--1--1--1--1--0--0--0--0--0--0--0]
-
    -
    -

    Explanation: When two threshold parameters are working together, -the algorithm will prioritize the smoothing of the snseqs over the -smoothing of the spseqs. Thus, in this example, the snseq t[7:10] -gets first smoothed “up” before the spseq t[10:13] is smoothed -“down”, resulting in a long final I.

    -
    -
    4. -

  4. with params min_spseq_size==4, min_snseq_size==4

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [1, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 1, 1]
-I: [1--1--1--1--1--1--1, 0--0--0--0, 1--1--1--1--1--1--1--1--1]
-
    -
    -

    Explanation: Since smoothing of snseqs is prioritized, short spseqs -at the beginning or the end can be kept.

    -
    -
    5. -

  5. with params min_spseq_size==1, min_snseq_size==1

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 1, 1]
-I: [0--0--0, 1--1--1--1, 0--0--0--0, 1--1--1--1, 0--0--0, 1--1]
-
    -
    -

    Explanation: When both width thresholds are set to 1, the algorithm -works essentially in the “stitching” only mode.

    -
    -
    6. -
-
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Parameters:
-
    -

  • scores – SORTED list of scores to be smoothed. The score list -is assumed to be “exhaust” the entire time or space of -the underlying document segment. -(Sorted by the start, and then by the end of anchors)

    • -

  • min_score – minimum threshold to use to discard -low-scored units (strictly less than)

    • -

  • min_spseq_size – minimum size of a positive sequence not to be -smoothed (greater or equal to)

    • -

  • min_snseq_size – minimum size of a negative sequence not to be -smoothed (greater or equal to)

    • -
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Returns:
-

list of tuples of start(inclusive)/end(exclusive) indices -of the “positive” sequences. Negative sequences (regardless of -their size) are not included in the output.

-
-
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- -
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-mmif.utils.sequence_helper.validate_labelset(annotations: Iterable[Annotation]) → List[str][source]
-

Simple check for a list of annotations to see if they have the same label set.

-
-
Raise:
-

AttributeError if an element in the input list doesn’t have the labelset property

-
-
Raise:
-

ValueError if different labelset values are found

-
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Returns:
-

a list of the common labelset value (list of label names)

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- - - \ No newline at end of file diff --git a/docs/1.0.15/autodoc/mmif.vocabulary.html b/docs/1.0.15/autodoc/mmif.vocabulary.html deleted file mode 100644 index 924abc5f..00000000 --- a/docs/1.0.15/autodoc/mmif.vocabulary.html +++ /dev/null @@ -1,319 +0,0 @@ - - - - - - - - - mmif.vocabulary module — mmif-python documentation - - - - - - - - - - - - - - - - - -
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mmif.vocabulary module

-
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mmif.vocabulary.annotation_types module

-
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-class mmif.vocabulary.annotation_types.AnnotationTypes(type_uri, fuzzymode=True)[source]
-

Bases: AnnotationTypesBase

-

This class contains the CLAMS annotation types -defined in the spec version 1.1.0 as class variables.

-
-
-Alignment = http://mmif.clams.ai/vocabulary/Alignment/v1[source]
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-Annotation = http://mmif.clams.ai/vocabulary/Annotation/v6[source]
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-BoundingBox = http://mmif.clams.ai/vocabulary/BoundingBox/v5[source]
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-Chapter = http://mmif.clams.ai/vocabulary/Chapter/v6[source]
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-Interval = http://mmif.clams.ai/vocabulary/Interval/v5[source]
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-NamedEntity = http://mmif.clams.ai/vocabulary/NamedEntity/v1[source]
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-NounChunk = http://mmif.clams.ai/vocabulary/NounChunk/v1[source]
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-Paragraph = http://mmif.clams.ai/vocabulary/Paragraph/v1[source]
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-Polygon = http://mmif.clams.ai/vocabulary/Polygon/v5[source]
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-Region = http://mmif.clams.ai/vocabulary/Region/v5[source]
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-Relation = http://mmif.clams.ai/vocabulary/Relation/v5[source]
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-Sentence = http://mmif.clams.ai/vocabulary/Sentence/v1[source]
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-Span = http://mmif.clams.ai/vocabulary/Span/v5[source]
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-TimeFrame = http://mmif.clams.ai/vocabulary/TimeFrame/v6[source]
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-TimePoint = http://mmif.clams.ai/vocabulary/TimePoint/v5[source]
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-Token = http://mmif.clams.ai/vocabulary/Token/v1[source]
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-VerbChunk = http://mmif.clams.ai/vocabulary/VerbChunk/v1[source]
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-VideoObject = http://mmif.clams.ai/vocabulary/VideoObject/v5[source]
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- -
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mmif.vocabulary.document_types module

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-class mmif.vocabulary.document_types.DocumentTypes(type_uri, fuzzymode=True)[source]
-

Bases: DocumentTypesBase

-

This class contains the CLAMS document types -defined in the spec version 1.1.0 as class variables.

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-AudioDocument = http://mmif.clams.ai/vocabulary/AudioDocument/v1[source]
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-Document = http://mmif.clams.ai/vocabulary/Document/v1[source]
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- -
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-ImageDocument = http://mmif.clams.ai/vocabulary/ImageDocument/v1[source]
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- -
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-TextDocument = http://mmif.clams.ai/vocabulary/TextDocument/v1[source]
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-VideoDocument = http://mmif.clams.ai/vocabulary/VideoDocument/v1[source]
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- - -
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- -
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mmif_docloc_http package

-

MMIF document location helper module for http and https schemes. -If you want to write your own docloc scheme handler, please use the source code of this module as a reference. -See this plug-in section for more information.

-
-
-mmif_docloc_http.resolve(docloc)[source]
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  • MMIF consumer
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MMIF consumer

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A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the appliance documentation to learn more about the appliance.

-

MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance.

-
    -

  1. The code must be hosted on a public git repository (e.g. Github, Gitlab, …)

    2. -

  2. Must listen to 5000 port.

    3. -

  3. Must expose /display route .

    4. -

  4. /display router should response to GET requests.

    5. -

  5. In the GET request, a public URL of the input MMIF file is passed via file URL parameter.

    6. -

  6. On the codebase root, there must be a Dockerfile that can build a docker image that runs the web app.

    7. -
-

We provide an example consumer at https://github.com/clamsproject/mmif-visualizer.

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  • Welcome to mmif-python’s documentation!
    • -
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Welcome to mmif-python’s documentation!

-
-

MultiMedia Interchange Format

-

MMIF is a JSON(-LD)-based data format designed for transferring annotation data between computational analysis applications in CLAMS project.

-
-
-

mmif-python

-

mmif-python is a Python implementation of the MMIF data format. -mmif-python provides various helper classes and functions to handle MMIF JSON in Python, -including ;

-
    -

  1. de-/serialization of MMIF internal data structures to/from JSON

    2. -

  2. validation of MMIF JSON

    3. -

  3. handling of CLAMS vocabulary types

    4. -

  4. navigation of MMIF object via various “search” methods (e.g. mmif.get_all_views_contain(vocab_type)))

    5. -
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For more …

- -
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Contents

- -
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API documentation:

- -
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Indices and tables

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    • -
  • -
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Getting Started

-
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Overview

-

MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for reproducibility, transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF website. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects.

-
-
-

Prerequisites

-
    -

  • Python: the latest mmif-python requires Python 3.8 or newer. We have no plan to support Python 2.7.

    • -
-
-
-

Installation

-

Package mmif-python is distributed via the official PyPI. Users are supposed to pip-install to get latest release.

-
pip install mmif-python
-
-
-

This will install a package mmif to local python.

-

The MMIF format and specification is evolving over time, and mmif-python package will be updated along with the changes in MMIF format.

-
-

Note

-

MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and mmif-python versions, please take time to read our decision on the subject here. If you need to know which python SDK supports which specification version, see Target MMIF Versions page.

-
-
-
-

MMIF Serialization

-

mmif.serialize.mmif.Mmif represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of mmif.serialize.model.MmifObject, including the mmif.serialize.mmif.Mmif. To start with an existing MMIF str, simple initiate a new Mmif object with the file.

-
import mmif
-from mmif import Mmif
-
-mmif_str = """{
-"metadata": {
-  "mmif": "http://mmif.clams.ai/1.0.0"
-},
-"documents": [
-  {
-    "@type": "http://mmif.clams.ai/vocabulary/VideoDocument/v1",
-    "properties": {
-      "id": "m1",
-      "mime": "video/mp4",
-      "location": "file:///var/archive/video-0012.mp4"
-    }
-  },
-  {
-    "@type": "http://mmif.clams.ai/vocabulary/TextDocument/v1",
-    "properties": {
-      "id": "m2",
-      "mime": "text/plain",
-      "location": "file:///var/archive/video-0012-transcript.txt"
-    }
-  }
-],
-"views": []}"""
-mmif_obj = Mmif(mmif_str)
-
-
-

Few notes;

-
    -

  1. MMIF does not carry the primary source files in it.

    2. -

  2. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version mmif-python implementation of the MMIF might not be able to load an unsupported version of MMIF string.

    3. -
-

When serializing back to str, call mmif.serialize.model.MmifObject.serialize() on the object.

-

To get subcomponents, you can use various getters implemented in subclasses. For example;

-
from mmif.vocabulary.document_types import DocumentTypes
-
-for video in mmif_obj.Mmif.get_documents_by_type(DocumentTypes.VideoDocument):
-  with open(video.location_path(), 'b') as in_video:
-    # do something with the video file
-
-
-

For a full list of available helper methods, please refer to the API documentation.

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mmif package

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mmif_docloc_http package

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Developing plugins for MMIF Python SDK

-
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Overview

-

As MMIF JSON files can carry information about media document files without actually carrying file contents, file accessing modules in mmif Python package (distributed as mmif-python on PyPI) are designed to be lightweight and flexible so that it can work with additional “plugin” Python packages that can handle concrete file access.

-

This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF website. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects.

-

Developer can write simple plugins that can provide additional functionalities to mmif-python. For example, mmif-python does not provide any file access functionality beyond a local file system (with file scheme), but it can be extended with a plugin that can handle file access over different protocols (e.g. http, s3, ftp, etc).

-

This document contains information about how to write plugins for mmif-python.

-
-

Document Location Scheme Plugins

-

mmif.serialize.annotation.Document class has various methods to access parts of location property of the document. The location is in URI/IRI format (SCHEME://HOSTNAME/PATH, in a nutshell) and it has to be resolved to a local file for CLAMS Apps to process the local file to analyze and extract information about the media and its contents. The core mmif-python distribution only provides a default implementation that can handle file scheme URIs.

-

To add a document location handler plugin, you need to implement a Python “package” (do not confuse with PYPI distribution), that meets these requirements;

-
    -

  1. the package must be named mmif_docloc_<SCHEME>. For example, to implement a handler for s3 scheme, the package name must be mmif_docloc_s3. The prefix is important as it’s used in the plugin discovery process from the core mmif-python modules.

    2. -

  2. the top module of the package must have a function named resolve. The function must take a single argument, which is a str of the document location URI. The function must return a str of the local file path. For example, if the document location is s3://mybucket/myfile.mp4, a Python user should be able to to something like this;

    3. -
-
import mmif_docloc_s3
-resolved = mmif_docloc_s3.resolve('s3://mybucket/myfile.mp4')
-# then resolved must be a local file path that can be used to open the file
-
-
-

Here’s a minimal example codebase that you refer to when you develop a docloc plugin.

-

(However, before you start writing your own plugin for a specific URI scheme, checking if there’s already a PyPI distribution for the scheme might be a good idea.)

-
$ tree .
-.
-├── mmif_docloc_dummy
-│   └── __init__.py
-├── pyproject.toml
-└── setup.cfg
-
- $ cat pyproject.toml
-[build-system]
-requires = ["setuptools"]
-build-backend = "setuptools.build_meta"
-
-$ cat setup.cfg
-[metadata]
-name = mmif_docloc_dummy  # this name is IMPORTANT
-version = 0.0.1
-description = a plugin to mmif-pyhon to handle `dummy` location scheme
-
-
-

And the plugin code.

-
# mmif_docloc_dummy/__init__.py
-doc_types = {'video': 'mp4'}
-
-def resolve(docloc):
-    scheme = 'dummy'
-    if docloc.startswith(f'{scheme}://'):
-        doc_id, doc_type = docloc.split('.')
-        return f'/path/to/{doc_id}.{doc_types[doc_type]}'
-    else:
-        raise ValueError(f'cannot handle document location scheme: {docloc}')
-
-
-
-
-

Bulit-in Document Location Scheme Plugins

-

At the moment, mmif-python PyPI distribution ships a built-in docloc plugin that support both http and https schemes. -Take a look at mmif_docloc_http module for details.

-
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Python Module Index

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8], "where": 0, "whether": 0, "which": [0, 1, 6, 8], "while": [0, 1], "width": 1, "within": 0, "without": [0, 8], "won": 0, "work": [0, 1, 8], "workflow": 6, "would": 0, "write": [0, 3, 8], "xist": 1, "you": [0, 1, 3, 6, 8], "your": [3, 8], "zero": [0, 1]}, "titles": ["mmif.serialize module", "mmif.utils module", "mmif.vocabulary module", "mmif_docloc_http package", "MMIF consumer", "Welcome to mmif-python\u2019s documentation!", "Getting Started", "mmif package", "Developing plugins for MMIF Python SDK", "Target MMIF Versions"], "titleterms": {"": 5, "For": 5, "annot": 0, "annotation_typ": 2, "api": 5, "bulit": 8, "consum": 4, "content": 5, "develop": 8, "document": [5, 8], "document_typ": 2, "format": 5, "get": 6, "indic": 5, "instal": 6, "interchang": 5, "locat": 8, "mmif": [0, 1, 2, 4, 5, 6, 7, 8, 9], "mmif_docloc_http": [3, 7], "model": 0, "modul": [0, 1, 2], "more": 5, "multimedia": 5, "overview": [6, 8], "packag": [3, 7], "plugin": 8, "prerequisit": 6, "python": [5, 8], "scheme": 8, "sdk": 8, "sequence_help": 1, "serial": [0, 6], "specif": 9, "start": 6, "tabl": 5, "target": 9, "util": 1, "version": 9, "video_document_help": 1, "view": 0, "vocabulari": 2, "welcom": 5}}) \ No newline at end of file diff --git a/docs/1.0.15/target-versions.html b/docs/1.0.15/target-versions.html deleted file mode 100644 index e828591e..00000000 --- a/docs/1.0.15/target-versions.html +++ /dev/null @@ -1,291 +0,0 @@ - - - - - - - - - Target MMIF Versions — mmif-python documentation - - - - - - - - - - - - - - - - - -
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  • Target MMIF Versions
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Target MMIF Versions

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This article provides targeting MMIF specification versions of different versions of mmif-python SDK.

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Target Specification Versions

mmif-python version

Target MMIF Specification

1.0.15

1.1.0

1.0.14

1.0.4

1.0.13

1.0.4

1.0.12

1.0.4

1.0.11

1.0.4

1.0.10.dev1

1.0.3

1.0.10

1.0.2

1.0.9

1.1.0

1.0.8

1.0.0

1.0.7

1.0.0

1.0.6

1.0.0

1.0.5

1.0.0

1.0.4

1.0.0

1.0.3

1.0.0

1.0.2

1.0.0

1.0.1

1.0.0

1.0.0

0.5.0

0.5.2

0.5.0

0.5.1

0.5.0

0.5.0

0.5.0

0.4.8

0.4.2

0.4.7

0.4.1

0.4.6

0.4.0

0.4.5

0.4.0

0.4.4

0.4.0

0.4.3

0.4.0

0.4.2

0.4.0

0.4.1

0.4.0

0.4.0

0.4.0

0.3.5

0.3.1

0.3.4

0.3.1

0.3.3

0.3.1

0.3.2

0.3.1

0.3.1

0.3.0

0.3.0

0.3.0

0.2.2

0.2.1

0.2.1

0.2.1

0.2.0

0.2.1

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0.3.0
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0.3.1
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0.3.2
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0.3.3
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0.3.4
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0.3.5
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0.4.0
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0.4.1
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0.4.2
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0.4.3
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0.4.4
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0.4.5
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0.4.6
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0.4.7
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0.4.8
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0.5.0
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0.5.1
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0.5.2
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1.0.0
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1.0.1
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1.0.10
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1.0.11
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1.0.12
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1.0.13
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1.0.14
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1.0.15
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1.0.16
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1.0.17
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1.0.18
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1.0.19
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1.0.2
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1.0.3
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1.0.4
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1.0.5
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1.0.6
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1.0.7
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1.0.8
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1.0.9
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1.1.0
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-mmif.serialize.model module ---------------------------- - -.. automodule:: mmif.serialize.model - :members: - :undoc-members: - :show-inheritance: - -mmif.serialize.mmif module --------------------------- - -.. automodule:: mmif.serialize.mmif - :members: - :undoc-members: - :show-inheritance: - -mmif.serialize.view module --------------------------- - -.. automodule:: mmif.serialize.view - :members: - :undoc-members: - :show-inheritance: - -mmif.serialize.annotation module --------------------------------- - -.. automodule:: mmif.serialize.annotation - :members: - :undoc-members: - :show-inheritance: - diff --git a/docs/1.0.16/_sources/autodoc/mmif.utils.rst.txt b/docs/1.0.16/_sources/autodoc/mmif.utils.rst.txt deleted file mode 100644 index 9a6ecc44..00000000 --- a/docs/1.0.16/_sources/autodoc/mmif.utils.rst.txt +++ /dev/null @@ -1,18 +0,0 @@ -mmif.utils module -================= - -mmif.utils.video_document_helper module ----------------------------------------- - -.. automodule:: mmif.utils.video_document_helper - :members: - :undoc-members: - :show-inheritance: - -mmif.utils.sequence_helper module ---------------------------------- - -.. automodule:: mmif.utils.sequence_helper - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/1.0.16/_sources/autodoc/mmif.vocabulary.rst.txt b/docs/1.0.16/_sources/autodoc/mmif.vocabulary.rst.txt deleted file mode 100644 index d250c6a3..00000000 --- a/docs/1.0.16/_sources/autodoc/mmif.vocabulary.rst.txt +++ /dev/null @@ -1,18 +0,0 @@ -mmif.vocabulary module -====================== - -mmif.vocabulary.annotation\_types module ----------------------------------------- - -.. automodule:: mmif.vocabulary.annotation_types - :members: - :undoc-members: - :show-inheritance: - -mmif.vocabulary.document\_types module --------------------------------------- - -.. automodule:: mmif.vocabulary.document_types - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/1.0.16/_sources/autodoc/mmif_docloc_http.rst.txt b/docs/1.0.16/_sources/autodoc/mmif_docloc_http.rst.txt deleted file mode 100644 index b76c8df5..00000000 --- a/docs/1.0.16/_sources/autodoc/mmif_docloc_http.rst.txt +++ /dev/null @@ -1,11 +0,0 @@ -mmif_docloc_http package -======================== - -MMIF document location helper module for `http` and `https` schemes. -If you want to write your own docloc scheme handler, please use the source code of this module as a reference. -See this :ref:`plug-in section ` for more information. - -.. automodule:: mmif_docloc_http - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/1.0.16/_sources/consumer-tutorial.rst.txt b/docs/1.0.16/_sources/consumer-tutorial.rst.txt deleted file mode 100644 index c54634e2..00000000 --- a/docs/1.0.16/_sources/consumer-tutorial.rst.txt +++ /dev/null @@ -1,17 +0,0 @@ -.. _consumer-tutorial: - -MMIF consumer -================================= - -A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the `appliance documentation `_ to learn more about the appliance. - -MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance. - -#. The code must be hosted on a public git repository (e.g. Github, Gitlab, ...) -#. Must listen to ``5000`` port. -#. Must expose ``/display`` route . -#. ``/display`` router should response to ``GET`` requests. -#. In the ``GET`` request, a public URL of the input MMIF file is passed via ``file`` URL parameter. -#. On the codebase root, there must be a ``Dockerfile`` that can build a `docker `_ image that runs the web app. - -We provide an example consumer at https://github.com/clamsproject/mmif-visualizer. diff --git a/docs/1.0.16/_sources/index.rst.txt b/docs/1.0.16/_sources/index.rst.txt deleted file mode 100644 index beb56aae..00000000 --- a/docs/1.0.16/_sources/index.rst.txt +++ /dev/null @@ -1,26 +0,0 @@ -Welcome to mmif-python's documentation! -======================================= - -.. mdinclude:: ../README.md - -.. toctree:: - :maxdepth: 2 - :caption: Contents - - introduction - plugins - target-versions - -.. toctree:: - :maxdepth: 2 - :caption: API documentation: - - modules - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/docs/1.0.16/_sources/introduction.rst.txt b/docs/1.0.16/_sources/introduction.rst.txt deleted file mode 100644 index cfd9eaf7..00000000 --- a/docs/1.0.16/_sources/introduction.rst.txt +++ /dev/null @@ -1,89 +0,0 @@ -.. _introduction: - -Getting Started -=============== - - -Overview ---------- - -MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for reproducibility, transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF website `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects. - -Prerequisites -------------- - -* `Python `_: the latest ``mmif-python`` requires Python 3.8 or newer. We have no plan to support `Python 2.7 `_. - -Installation ---------------- - -Package ``mmif-python`` is distributed via the official PyPI. Users are supposed to pip-install to get latest release. - -.. code-block:: bash - - pip install mmif-python - -This will install a package `mmif` to local python. - -The MMIF format and specification is evolving over time, and ``mmif-python`` package will be updated along with the changes in MMIF format. - -.. note:: MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and ``mmif-python`` versions, please take time to read our decision on the subject `here `_. If you need to know which python SDK supports which specification version, see :ref:`target-versions` page. - -MMIF Serialization ---------------------------- - -:class:`mmif.serialize.mmif.Mmif` represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of :class:`mmif.serialize.model.MmifObject`, including the :class:`mmif.serialize.mmif.Mmif`. To start with an existing MMIF :class:`str`, simple initiate a new ``Mmif`` object with the file. - -.. code-block:: python - - import mmif - from mmif import Mmif - - mmif_str = """{ - "metadata": { - "mmif": "http://mmif.clams.ai/1.0.0" - }, - "documents": [ - { - "@type": "http://mmif.clams.ai/vocabulary/VideoDocument/v1", - "properties": { - "id": "m1", - "mime": "video/mp4", - "location": "file:///var/archive/video-0012.mp4" - } - }, - { - "@type": "http://mmif.clams.ai/vocabulary/TextDocument/v1", - "properties": { - "id": "m2", - "mime": "text/plain", - "location": "file:///var/archive/video-0012-transcript.txt" - } - } - ], - "views": []}""" - mmif_obj = Mmif(mmif_str) - - -Few notes; - -#. MMIF does not carry the primary source files in it. -#. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version ``mmif-python`` implementation of the MMIF might not be able to load an unsupported version of MMIF string. - -When serializing back to :class:`str`, call :meth:`mmif.serialize.model.MmifObject.serialize` on the object. - -To get subcomponents, you can use various getters implemented in subclasses. For example; - -.. code-block:: python - - from mmif.vocabulary.document_types import DocumentTypes - - for video in mmif_obj.Mmif.get_documents_by_type(DocumentTypes.VideoDocument): - with open(video.location_path(), 'b') as in_video: - # do something with the video file - - -For a full list of available helper methods, please refer to :ref:`the API documentation `. - diff --git a/docs/1.0.16/_sources/modules.rst.txt b/docs/1.0.16/_sources/modules.rst.txt deleted file mode 100644 index 4bb9307d..00000000 --- a/docs/1.0.16/_sources/modules.rst.txt +++ /dev/null @@ -1,20 +0,0 @@ -.. _apidoc: - -mmif package -============ - -.. toctree:: - :maxdepth: 4 - - autodoc/mmif.serialize - autodoc/mmif.vocabulary - autodoc/mmif.utils - -mmif_docloc_http package -======================== - -.. toctree:: - :maxdepth: 2 - - autodoc/mmif_docloc_http - diff --git a/docs/1.0.16/_sources/plugins.rst.txt b/docs/1.0.16/_sources/plugins.rst.txt deleted file mode 100644 index 9907c495..00000000 --- a/docs/1.0.16/_sources/plugins.rst.txt +++ /dev/null @@ -1,83 +0,0 @@ -.. _plugins: - -Developing plugins for MMIF Python SDK -====================================== - - -Overview --------- - -As MMIF JSON files can carry information about media document files without actually carrying file contents, file accessing modules in ``mmif`` Python package (distributed as ``mmif-python`` on PyPI) are designed to be lightweight and flexible so that it can work with additional "plugin" Python packages that can handle concrete file access. - - -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF website `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects. - -Developer can write simple plugins that can provide additional functionalities to ``mmif-python``. For example, ``mmif-python`` does not provide any file access functionality beyond a local file system (with ``file`` scheme), but it can be extended with a plugin that can handle file access over different protocols (e.g. ``http``, ``s3``, ``ftp``, etc). - -This document contains information about how to write plugins for ``mmif-python``. - -.. _docloc_plugin: - -Document Location Scheme Plugins -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -:class:`mmif.serialize.annotation.Document` class has various methods to access parts of ``location`` property of the document. The location is in `URI/IRI format `_ (``SCHEME://HOSTNAME/PATH``, in a nutshell) and it has to be resolved to a local file for CLAMS Apps to process the local file to analyze and extract information about the media and its contents. The core ``mmif-python`` distribution only provides a default implementation that can handle ``file`` scheme URIs. - -To add a document location handler plugin, you need to implement a Python `"package" `_ (do not confuse with PYPI distribution), that meets these requirements; - -#. the package must be named ``mmif_docloc_``. For example, to implement a handler for ``s3`` scheme, the package name must be ``mmif_docloc_s3``. The prefix is important as it's used in the plugin discovery process from the core ``mmif-python`` modules. -#. the top module of the package must have a function named ``resolve``. The function must take a single argument, which is a :class:`str` of the document location URI. The function must return a :class:`str` of the local file path. For example, if the document location is ``s3://mybucket/myfile.mp4``, a Python user should be able to to something like this; - -.. code-block:: python - - import mmif_docloc_s3 - resolved = mmif_docloc_s3.resolve('s3://mybucket/myfile.mp4') - # then resolved must be a local file path that can be used to open the file - - -Here's a minimal example codebase that you refer to when you develop a ``docloc`` plugin. - -(However, before you start writing your own plugin for a specific URI scheme, checking `if there's already a PyPI distribution `_ for the scheme might be a good idea.) - -.. code-block:: sh - - $ tree . - . - ├── mmif_docloc_dummy - │ └── __init__.py - ├── pyproject.toml - └── setup.cfg - - $ cat pyproject.toml - [build-system] - requires = ["setuptools"] - build-backend = "setuptools.build_meta" - - $ cat setup.cfg - [metadata] - name = mmif_docloc_dummy # this name is IMPORTANT - version = 0.0.1 - description = a plugin to mmif-pyhon to handle `dummy` location scheme - - -And the plugin code. - -.. code-block:: python - - # mmif_docloc_dummy/__init__.py - doc_types = {'video': 'mp4'} - - def resolve(docloc): - scheme = 'dummy' - if docloc.startswith(f'{scheme}://'): - doc_id, doc_type = docloc.split('.') - return f'/path/to/{doc_id}.{doc_types[doc_type]}' - else: - raise ValueError(f'cannot handle document location scheme: {docloc}') - -Bulit-in Document Location Scheme Plugins -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -At the moment, ``mmif-python`` PyPI distribution ships a built-in *docloc* plugin that support both ``http`` and ``https`` schemes. -Take a look at :mod:`mmif_docloc_http` module for details. diff --git a/docs/1.0.16/_sources/target-versions.rst.txt b/docs/1.0.16/_sources/target-versions.rst.txt deleted file mode 100644 index 34216d3e..00000000 --- a/docs/1.0.16/_sources/target-versions.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _target-versions: - -Target MMIF Versions -==================== - -This article provides targeting MMIF specification versions of different versions of ``mmif-python`` SDK. - -.. csv-table:: Target Specification Versions - :file: target-versions.csv - :header-rows: 1 diff --git a/docs/1.0.16/_static/_sphinx_javascript_frameworks_compat.js b/docs/1.0.16/_static/_sphinx_javascript_frameworks_compat.js deleted file mode 100644 index 81415803..00000000 --- a/docs/1.0.16/_static/_sphinx_javascript_frameworks_compat.js +++ /dev/null @@ -1,123 +0,0 @@ -/* Compatability shim for jQuery and underscores.js. - * - * Copyright Sphinx contributors - * Released under the two clause BSD licence - */ - -/** - * small helper function to urldecode strings - * - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL - */ -jQuery.urldecode = function(x) { - if (!x) { - return x - } - return decodeURIComponent(x.replace(/\+/g, ' ')); -}; - -/** - * small helper function to urlencode strings - */ -jQuery.urlencode = encodeURIComponent; - -/** - * This function returns the parsed url parameters of the - * current request. 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- -/** - * Simple result scoring code. - */ -if (typeof Scorer === "undefined") { - var Scorer = { - // Implement the following function to further tweak the score for each result - // The function takes a result array [docname, title, anchor, descr, score, filename] - // and returns the new score. - /* - score: result => { - const [docname, title, anchor, descr, score, filename, kind] = result - return score - }, - */ - - // query matches the full name of an object - objNameMatch: 11, - // or matches in the last dotted part of the object name - objPartialMatch: 6, - // Additive scores depending on the priority of the object - objPrio: { - 0: 15, // used to be importantResults - 1: 5, // used to be objectResults - 2: -5, // used to be unimportantResults - }, - // Used when the priority is not in the mapping. - objPrioDefault: 0, - - // query found in title - title: 15, - partialTitle: 7, - // query found in terms - term: 5, - partialTerm: 2, - }; -} - -// Global search result kind enum, used by themes to style search results. -class SearchResultKind { - static get index() { return "index"; } - static get object() { return "object"; } - static get text() { return "text"; } - static get title() { return "title"; } -} - -const _removeChildren = (element) => { - while (element && element.lastChild) element.removeChild(element.lastChild); -}; - -/** - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping - */ -const _escapeRegExp = (string) => - string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string - -const _displayItem = (item, searchTerms, highlightTerms) => { - const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; - const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; - const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; - const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; - const contentRoot = document.documentElement.dataset.content_root; - - const [docName, title, anchor, descr, score, _filename, kind] = item; - - let listItem = document.createElement("li"); - // Add a class representing the item's type: - // can be used by a theme's CSS selector for styling - // See SearchResultKind for the class names. - listItem.classList.add(`kind-${kind}`); - let requestUrl; - let linkUrl; - if (docBuilder === "dirhtml") { - // dirhtml builder - let dirname = docName + "/"; - if (dirname.match(/\/index\/$/)) - dirname = dirname.substring(0, dirname.length - 6); - else if (dirname === "index/") dirname = ""; - requestUrl = contentRoot + dirname; - linkUrl = requestUrl; - } else { - // normal html builders - requestUrl = contentRoot + docName + docFileSuffix; - linkUrl = docName + docLinkSuffix; - } - let linkEl = listItem.appendChild(document.createElement("a")); - linkEl.href = linkUrl + anchor; - linkEl.dataset.score = score; - linkEl.innerHTML = title; - if (descr) { - listItem.appendChild(document.createElement("span")).innerHTML = - " (" + descr + ")"; - // highlight search terms in the description - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - } - else if (showSearchSummary) - fetch(requestUrl) - .then((responseData) => responseData.text()) - .then((data) => { - if (data) - listItem.appendChild( - Search.makeSearchSummary(data, searchTerms, anchor) - ); - // highlight search terms in the summary - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - }); - Search.output.appendChild(listItem); -}; -const _finishSearch = (resultCount) => { - Search.stopPulse(); - Search.title.innerText = _("Search Results"); - if (!resultCount) - Search.status.innerText = Documentation.gettext( - "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." - ); - else - Search.status.innerText = Documentation.ngettext( - "Search finished, found one page matching the search query.", - "Search finished, found ${resultCount} pages matching the search query.", - resultCount, - ).replace('${resultCount}', resultCount); -}; -const _displayNextItem = ( - results, - resultCount, - searchTerms, - highlightTerms, -) => { - // results left, load the summary and display it - // this is intended to be dynamic (don't sub resultsCount) - if (results.length) { - _displayItem(results.pop(), searchTerms, highlightTerms); - setTimeout( - () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), - 5 - ); - } - // search finished, update title and status message - else _finishSearch(resultCount); -}; -// Helper function used by query() to order search results. -// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. -// Order the results by score (in opposite order of appearance, since the -// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. -const _orderResultsByScoreThenName = (a, b) => { - const leftScore = a[4]; - const rightScore = b[4]; - if (leftScore === rightScore) { - // same score: sort alphabetically - const leftTitle = a[1].toLowerCase(); - const rightTitle = b[1].toLowerCase(); - if (leftTitle === rightTitle) return 0; - return leftTitle > rightTitle ? -1 : 1; // inverted is intentional - } - return leftScore > rightScore ? 1 : -1; -}; - -/** - * Default splitQuery function. Can be overridden in ``sphinx.search`` with a - * custom function per language. - * - * The regular expression works by splitting the string on consecutive characters - * that are not Unicode letters, numbers, underscores, or emoji characters. - * This is the same as ``\W+`` in Python, preserving the surrogate pair area. - */ -if (typeof splitQuery === "undefined") { - var splitQuery = (query) => query - .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) - .filter(term => term) // remove remaining empty strings -} - -/** - * Search Module - */ -const Search = { - _index: null, - _queued_query: null, - _pulse_status: -1, - - htmlToText: (htmlString, anchor) => { - const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - for (const removalQuery of [".headerlink", "script", "style"]) { - htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); - } - if (anchor) { - const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); - if (anchorContent) return anchorContent.textContent; - - console.warn( - `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` - ); - } - - // if anchor not specified or not found, fall back to main content - const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent) return docContent.textContent; - - console.warn( - "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." - ); - return ""; - }, - - init: () => { - const query = new URLSearchParams(window.location.search).get("q"); - document - .querySelectorAll('input[name="q"]') - .forEach((el) => (el.value = query)); - if (query) Search.performSearch(query); - }, - - loadIndex: (url) => - (document.body.appendChild(document.createElement("script")).src = url), - - setIndex: (index) => { - Search._index = index; - if (Search._queued_query !== null) { - const query = Search._queued_query; - Search._queued_query = null; - Search.query(query); - } - }, - - hasIndex: () => Search._index !== null, - - deferQuery: (query) => (Search._queued_query = query), - - stopPulse: () => (Search._pulse_status = -1), - - startPulse: () => { - if (Search._pulse_status >= 0) return; - - const pulse = () => { - Search._pulse_status = (Search._pulse_status + 1) % 4; - Search.dots.innerText = ".".repeat(Search._pulse_status); - if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); - }; - pulse(); - }, - - /** - * perform a search for something (or wait until index is loaded) - */ - performSearch: (query) => { - // create the required interface elements - const searchText = document.createElement("h2"); - searchText.textContent = _("Searching"); - const searchSummary = document.createElement("p"); - searchSummary.classList.add("search-summary"); - searchSummary.innerText = ""; - const searchList = document.createElement("ul"); - searchList.setAttribute("role", "list"); - searchList.classList.add("search"); - - const out = document.getElementById("search-results"); - Search.title = out.appendChild(searchText); - Search.dots = Search.title.appendChild(document.createElement("span")); - Search.status = out.appendChild(searchSummary); - Search.output = out.appendChild(searchList); - - const searchProgress = document.getElementById("search-progress"); - // Some themes don't use the search progress node - if (searchProgress) { - searchProgress.innerText = _("Preparing search..."); - } - Search.startPulse(); - - // index already loaded, the browser was quick! - if (Search.hasIndex()) Search.query(query); - else Search.deferQuery(query); - }, - - _parseQuery: (query) => { - // stem the search terms and add them to the correct list - const stemmer = new Stemmer(); - const searchTerms = new Set(); - const excludedTerms = new Set(); - const highlightTerms = new Set(); - const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); - splitQuery(query.trim()).forEach((queryTerm) => { - const queryTermLower = queryTerm.toLowerCase(); - - // maybe skip this "word" - // stopwords array is from language_data.js - if ( - stopwords.indexOf(queryTermLower) !== -1 || - queryTerm.match(/^\d+$/) - ) - return; - - // stem the word - let word = stemmer.stemWord(queryTermLower); - // select the correct list - if (word[0] === "-") excludedTerms.add(word.substr(1)); - else { - searchTerms.add(word); - highlightTerms.add(queryTermLower); - } - }); - - if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js - localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) - } - - // console.debug("SEARCH: searching for:"); - // console.info("required: ", [...searchTerms]); - // console.info("excluded: ", [...excludedTerms]); - - return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; - }, - - /** - * execute search (requires search index to be loaded) - */ - _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - - // Collect multiple result groups to be sorted separately and then ordered. - // Each is an array of [docname, title, anchor, descr, score, filename, kind]. - const normalResults = []; - const nonMainIndexResults = []; - - _removeChildren(document.getElementById("search-progress")); - - const queryLower = query.toLowerCase().trim(); - for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { - for (const [file, id] of foundTitles) { - const score = Math.round(Scorer.title * queryLower.length / title.length); - const boost = titles[file] === title ? 1 : 0; // add a boost for document titles - normalResults.push([ - docNames[file], - titles[file] !== title ? `${titles[file]} > ${title}` : title, - id !== null ? "#" + id : "", - null, - score + boost, - filenames[file], - SearchResultKind.title, - ]); - } - } - } - - // search for explicit entries in index directives - for (const [entry, foundEntries] of Object.entries(indexEntries)) { - if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id, isMain] of foundEntries) { - const score = Math.round(100 * queryLower.length / entry.length); - const result = [ - docNames[file], - titles[file], - id ? "#" + id : "", - null, - score, - filenames[file], - SearchResultKind.index, - ]; - if (isMain) { - normalResults.push(result); - } else { - nonMainIndexResults.push(result); - } - } - } - } - - // lookup as object - objectTerms.forEach((term) => - normalResults.push(...Search.performObjectSearch(term, objectTerms)) - ); - - // lookup as search terms in fulltext - normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); - - // let the scorer override scores with a custom scoring function - if (Scorer.score) { - normalResults.forEach((item) => (item[4] = Scorer.score(item))); - nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); - } - - // Sort each group of results by score and then alphabetically by name. - normalResults.sort(_orderResultsByScoreThenName); - nonMainIndexResults.sort(_orderResultsByScoreThenName); - - // Combine the result groups in (reverse) order. - // Non-main index entries are typically arbitrary cross-references, - // so display them after other results. - let results = [...nonMainIndexResults, ...normalResults]; - - // remove duplicate search results - // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept - let seen = new Set(); - results = results.reverse().reduce((acc, result) => { - let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); - if (!seen.has(resultStr)) { - acc.push(result); - seen.add(resultStr); - } - return acc; - }, []); - - return results.reverse(); - }, - - query: (query) => { - const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); - const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); - - // for debugging - //Search.lastresults = results.slice(); // a copy - // console.info("search results:", Search.lastresults); - - // print the results - _displayNextItem(results, results.length, searchTerms, highlightTerms); - }, - - /** - * search for object names - */ - performObjectSearch: (object, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const objects = Search._index.objects; - const objNames = Search._index.objnames; - const titles = Search._index.titles; - - const results = []; - - const objectSearchCallback = (prefix, match) => { - const name = match[4] - const fullname = (prefix ? prefix + "." : "") + name; - const fullnameLower = fullname.toLowerCase(); - if (fullnameLower.indexOf(object) < 0) return; - - let score = 0; - const parts = fullnameLower.split("."); - - // check for different match types: exact matches of full name or - // "last name" (i.e. last dotted part) - if (fullnameLower === object || parts.slice(-1)[0] === object) - score += Scorer.objNameMatch; - else if (parts.slice(-1)[0].indexOf(object) > -1) - score += Scorer.objPartialMatch; // matches in last name - - const objName = objNames[match[1]][2]; - const title = titles[match[0]]; - - // If more than one term searched for, we require other words to be - // found in the name/title/description - const otherTerms = new Set(objectTerms); - otherTerms.delete(object); - if (otherTerms.size > 0) { - const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); - if ( - [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) - ) - return; - } - - let anchor = match[3]; - if (anchor === "") anchor = fullname; - else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; - - const descr = objName + _(", in ") + title; - - // add custom score for some objects according to scorer - if (Scorer.objPrio.hasOwnProperty(match[2])) - score += Scorer.objPrio[match[2]]; - else score += Scorer.objPrioDefault; - - results.push([ - docNames[match[0]], - fullname, - "#" + anchor, - descr, - score, - filenames[match[0]], - SearchResultKind.object, - ]); - }; - Object.keys(objects).forEach((prefix) => - objects[prefix].forEach((array) => - objectSearchCallback(prefix, array) - ) - ); - return results; - }, - - /** - * search for full-text terms in the index - */ - performTermsSearch: (searchTerms, excludedTerms) => { - // prepare search - const terms = Search._index.terms; - const titleTerms = Search._index.titleterms; - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - - const scoreMap = new Map(); - const fileMap = new Map(); - - // perform the search on the required terms - searchTerms.forEach((word) => { - const files = []; - const arr = [ - { files: terms[word], score: Scorer.term }, - { files: titleTerms[word], score: Scorer.title }, - ]; - // add support for partial matches - if (word.length > 2) { - const escapedWord = _escapeRegExp(word); - if (!terms.hasOwnProperty(word)) { - Object.keys(terms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: terms[term], score: Scorer.partialTerm }); - }); - } - if (!titleTerms.hasOwnProperty(word)) { - Object.keys(titleTerms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); - }); - } - } - - // no match but word was a required one - if (arr.every((record) => record.files === undefined)) return; - - // found search word in contents - arr.forEach((record) => { - if (record.files === undefined) return; - - let recordFiles = record.files; - if (recordFiles.length === undefined) recordFiles = [recordFiles]; - files.push(...recordFiles); - - // set score for the word in each file - recordFiles.forEach((file) => { - if (!scoreMap.has(file)) scoreMap.set(file, {}); - scoreMap.get(file)[word] = record.score; - }); - }); - - // create the mapping - files.forEach((file) => { - if (!fileMap.has(file)) fileMap.set(file, [word]); - else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); - }); - }); - - // now check if the files don't contain excluded terms - const results = []; - for (const [file, wordList] of fileMap) { - // check if all requirements are matched - - // as search terms with length < 3 are discarded - const filteredTermCount = [...searchTerms].filter( - (term) => term.length > 2 - ).length; - if ( - wordList.length !== searchTerms.size && - wordList.length !== filteredTermCount - ) - continue; - - // ensure that none of the excluded terms is in the search result - if ( - [...excludedTerms].some( - (term) => - terms[term] === file || - titleTerms[term] === file || - (terms[term] || []).includes(file) || - (titleTerms[term] || []).includes(file) - ) - ) - break; - - // select one (max) score for the file. - const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); - // add result to the result list - results.push([ - docNames[file], - titles[file], - "", - null, - score, - filenames[file], - SearchResultKind.text, - ]); - } - return results; - }, - - /** - * helper function to return a node containing the - * search summary for a given text. keywords is a list - * of stemmed words. - */ - makeSearchSummary: (htmlText, keywords, anchor) => { - const text = Search.htmlToText(htmlText, anchor); - if (text === "") return null; - - const textLower = text.toLowerCase(); - const actualStartPosition = [...keywords] - .map((k) => textLower.indexOf(k.toLowerCase())) - .filter((i) => i > -1) - .slice(-1)[0]; - const startWithContext = Math.max(actualStartPosition - 120, 0); - - const top = startWithContext === 0 ? "" : "..."; - const tail = startWithContext + 240 < text.length ? "..." : ""; - - let summary = document.createElement("p"); - summary.classList.add("context"); - summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; - - return summary; - }, -}; - -_ready(Search.init); diff --git a/docs/1.0.16/_static/sphinx_highlight.js b/docs/1.0.16/_static/sphinx_highlight.js deleted file mode 100644 index 8a96c69a..00000000 --- a/docs/1.0.16/_static/sphinx_highlight.js +++ /dev/null @@ -1,154 +0,0 @@ -/* Highlighting utilities for Sphinx HTML documentation. */ -"use strict"; - -const SPHINX_HIGHLIGHT_ENABLED = true - -/** - * highlight a given string on a node by wrapping it in - * span elements with the given class name. - */ -const _highlight = (node, addItems, text, className) => { - if (node.nodeType === Node.TEXT_NODE) { - const val = node.nodeValue; - const parent = node.parentNode; - const pos = val.toLowerCase().indexOf(text); - if ( - pos >= 0 && - !parent.classList.contains(className) && - !parent.classList.contains("nohighlight") - ) { - let span; - - const closestNode = parent.closest("body, svg, foreignObject"); - const isInSVG = closestNode && closestNode.matches("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.classList.add(className); - } - - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - const rest = document.createTextNode(val.substr(pos + text.length)); - parent.insertBefore( - span, - parent.insertBefore( - rest, - node.nextSibling - ) - ); - node.nodeValue = val.substr(0, pos); - /* There may be more occurrences of search term in this node. So call this - * function recursively on the remaining fragment. - */ - _highlight(rest, addItems, text, className); - - if (isInSVG) { - const rect = document.createElementNS( - "http://www.w3.org/2000/svg", - "rect" - ); - const bbox = parent.getBBox(); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute("class", className); - addItems.push({ parent: parent, target: rect }); - } - } - } else if (node.matches && !node.matches("button, select, textarea")) { - node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); - } -}; -const _highlightText = (thisNode, text, className) => { - let addItems = []; - _highlight(thisNode, addItems, text, className); - addItems.forEach((obj) => - obj.parent.insertAdjacentElement("beforebegin", obj.target) - ); -}; - -/** - * Small JavaScript module for the documentation. - */ -const SphinxHighlight = { - - /** - * highlight the search words provided in localstorage in the text - */ - highlightSearchWords: () => { - if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight - - // get and clear terms from localstorage - const url = new URL(window.location); - const highlight = - localStorage.getItem("sphinx_highlight_terms") - || url.searchParams.get("highlight") - || ""; - localStorage.removeItem("sphinx_highlight_terms") - url.searchParams.delete("highlight"); - window.history.replaceState({}, "", url); - - // get individual terms from highlight string - const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); - if (terms.length === 0) return; // nothing to do - - // There should never be more than one element matching "div.body" - const divBody = document.querySelectorAll("div.body"); - const body = divBody.length ? divBody[0] : document.querySelector("body"); - window.setTimeout(() => { - terms.forEach((term) => _highlightText(body, term, "highlighted")); - }, 10); - - const searchBox = document.getElementById("searchbox"); - if (searchBox === null) return; - searchBox.appendChild( - document - .createRange() - .createContextualFragment( - '

' + - '' + - _("Hide Search Matches") + - "

" - ) - ); - }, - - /** - * helper function to hide the search marks again - */ - hideSearchWords: () => { - document - .querySelectorAll("#searchbox .highlight-link") - .forEach((el) => el.remove()); - document - .querySelectorAll("span.highlighted") - .forEach((el) => el.classList.remove("highlighted")); - localStorage.removeItem("sphinx_highlight_terms") - }, - - initEscapeListener: () => { - // only install a listener if it is really needed - if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; - - document.addEventListener("keydown", (event) => { - // bail for input elements - if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; - // bail with special keys - if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; - if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { - SphinxHighlight.hideSearchWords(); - event.preventDefault(); - } - }); - }, -}; - -_ready(() => { - /* Do not call highlightSearchWords() when we are on the search page. - * It will highlight words from the *previous* search query. - */ - if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); - SphinxHighlight.initEscapeListener(); -}); diff --git a/docs/1.0.16/autodoc/mmif.serialize.html b/docs/1.0.16/autodoc/mmif.serialize.html deleted file mode 100644 index f6d26282..00000000 --- a/docs/1.0.16/autodoc/mmif.serialize.html +++ /dev/null @@ -1,1432 +0,0 @@ - - - - - - - - - mmif.serialize module — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.serialize module

-
-

mmif.serialize.model module

-

The model module contains the classes used to represent an -abstract MMIF object as a live Python object.

-

The MmifObject class or one of its derivatives is subclassed by -all other classes defined in this SDK, except for MmifObjectEncoder.

-

These objects are generally instantiated from JSON, either as a string -or as an already-loaded Python dictionary. This base class provides the -core functionality for deserializing MMIF JSON data into live objects -and serializing live objects into MMIF JSON data. Specialized behavior -for the different components of MMIF is added in the subclasses.

-
-
-class mmif.serialize.model.DataDict(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject, Generic[T, S]

-
-
-empty()[source]
-
- -
-
-get(key: T, default=None) → S | None[source]
-
- -
-
-items()[source]
-
- -
-
-keys()[source]
-
- -
-
-update(other, overwrite)[source]
-
- -
-
-values()[source]
-
- -
- -
-
-class mmif.serialize.model.DataList(mmif_obj: bytes | str | list | None = None)[source]
-

Bases: MmifObject, Generic[T]

-

The DataList class is an abstraction that represents the -various lists found in a MMIF file, such as documents, subdocuments, -views, and annotations.

-
-
Parameters:
-

mmif_obj (Union[str, list]) – the data that the list contains

-
-
-
-
-append(value, overwrite)[source]
-
- -
-
-deserialize(mmif_json: str | list) → None[source]
-

Passes the input data into the internal deserializer.

-
- -
-
-empty()[source]
-
- -
-
-get(key: str) → T | None[source]
-

Standard dictionary-style get() method, albeit with no default -parameter. Relies on the implementation of __getitem__.

-

Will return None if the key is not found.

-
-
Parameters:
-

key – the key to search for

-
-
Returns:
-

the value matching that key

-
-
-
- -
- -
-
-class mmif.serialize.model.MmifObject(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: object

-

Abstract superclass for MMIF related key-value pair objects.

-

Any MMIF object can be initialized as an empty placeholder or -an actual representation with a JSON formatted string or equivalent -dict object argument.

-

This superclass has four specially designed instance variables, and these -variable names cannot be used as attribute names for MMIF objects.

-
    -

  1. _unnamed_attributes: -Only can be either None or an empty dictionary. If it’s set to None, -it means the class won’t take any Additional Attributes in the -JSON schema sense. If it’s an empty dict, users can throw any k-v -pairs to the class, as long as the key is not a “reserved” name, -and those additional attributes will be stored in this dict while -in memory.

    2. -

  2. _attribute_classes: -This is a dict from a key name to a specific python class to use for -deserialize the value. Note that a key name in this dict does NOT -have to be a named attribute, but is recommended to be one.

    3. -

  3. _required_attributes: -This is a simple list of names of attributes that are required in -the object. When serialize, an object will skip its empty (e.g. -zero-length, or None) attributes unless they are in this list. -Otherwise, the serialized JSON string would have empty -representations (e.g. "", []).

    4. -

  4. _exclude_from_diff: -This is a simple list of names of attributes that should be excluded -from the diff calculation in __eq__.

    5. -
-

# TODO (krim @ 8/17/20): this dict is however, a duplicate with the type hints in the class definition. -Maybe there is a better way to utilize type hints (e.g. getting them -as a programmatically), but for now developers should be careful to -add types to hints as well as to this dict.

-

Also note that those special attributes MUST be set in the __init__() -before calling super method, otherwise deserialization will not work.

-

And also, a subclass that has one or more named attributes, it must -set those attributes in the __init__() before calling super method. -When serializing a MmifObject, all empty attributes will be ignored, -so for optional named attributes, you must leave the values empty -(len == 0), but NOT None. Any None-valued named attributes will cause -issues with current implementation.

-
-
Parameters:
-

mmif_obj – JSON string or dict to initialize an object. -If not given, an empty object will be initialized, sometimes with -an ID value automatically generated, based on its parent object.

-
-
-
-
-deserialize(mmif_json: str | dict) → None[source]
-

Takes a JSON-formatted string or a simple dict that’s json-loaded from -such a string as an input and populates object’s fields with the values -specified in the input.

-
-
Parameters:
-

mmif_json – JSON-formatted string or dict from such a string -that represents a MMIF object

-
-
-
- -
-
-disallow_additional_properties() → None[source]
-

Call this method in __init__() to prevent the insertion -of unnamed attributes after initialization.

-
- -
-
-id_delimiter: ClassVar[str] = ':'[source]
-
- -
-
-static is_empty(obj) → bool[source]
-

return True if the obj is None or “emtpy”. The emptiness first defined as -having zero length. But for objects that lack __len__ method, we need -additional check.

-
- -
-
-reserved_names: Set[str] = {'_attribute_classes', '_exclude_from_diff', '_required_attributes', '_unnamed_attributes', 'reserved_names'}[source]
-
- -
-
-serialize(pretty: bool = False) → str[source]
-

Generates JSON representation of an object.

-
-
Parameters:
-

pretty – If True, returns string representation with indentation.

-
-
Returns:
-

JSON string of the object.

-
-
-
- -
-
-set_additional_property(key: str, value: Any) → None[source]
-

Method to set values in _unnamed_attributes.

-
-
Parameters:
-
    -

  • key – the attribute name

    • -

  • value – the desired value

    • -
-
-
Returns:
-

None

-
-
Raise:
-

AttributeError if additional properties are disallowed by disallow_additional_properties()

-
-
-
- -
-
-view_prefix: ClassVar[str] = 'v_'[source]
-
- -
- -
-
-class mmif.serialize.model.MmifObjectEncoder(*, skipkeys=False, ensure_ascii=True, check_circular=True, allow_nan=True, sort_keys=False, indent=None, separators=None, default=None)[source]
-

Bases: JSONEncoder

-

Encoder class to define behaviors of de-/serialization

-
-
-default(obj: MmifObject)[source]
-

Overrides default encoding behavior to prioritize MmifObject.serialize().

-
- -
- -
-
-

mmif.serialize.mmif module

-

The mmif module contains the classes used to represent a full MMIF -file as a live Python object.

-

See the specification docs and the JSON Schema file for more information.

-
-
-class mmif.serialize.mmif.Mmif(mmif_obj: bytes | str | dict | None = None, *, validate: bool = True)[source]
-

Bases: MmifObject

-

MmifObject that represents a full MMIF file.

-
-
Parameters:
-
    -

  • mmif_obj – the JSON data

    • -

  • validate – whether to validate the data against the MMIF JSON schema.

    • -
-
-
-
-
-add_document(document: Document, overwrite=False) → None[source]
-

Appends a Document object to the documents list.

-

Fails if there is already a document with the same ID in the MMIF object.

-
-
Parameters:
-
    -

  • document – the Document object to add

    • -

  • overwrite – if set to True, will overwrite -an existing view with the same ID

    • -
-
-
Returns:
-

None

-
-
-
- -
-
-add_view(view: View, overwrite=False) → None[source]
-

Appends a View object to the views list.

-

Fails if there is already a view with the same ID in the MMIF object.

-
-
Parameters:
-
    -

  • view – the Document object to add

    • -

  • overwrite – if set to True, will overwrite -an existing view with the same ID

    • -
-
-
Returns:
-

None

-
-
-
- -
-
-generate_capital_annotations()[source]
-

Automatically convert any “pending” temporary properties from -Document objects to Annotation objects . The generated Annotation -objects are then added to the last View in the views lists.

-

See https://github.com/clamsproject/mmif-python/issues/226 for rationale -behind this behavior and discussion.

-
- -
-
-get_alignments(at_type1: str | TypesBase, at_type2: str | TypesBase) → Dict[str, List[Annotation]][source]
-

Finds views where alignments between two given annotation types occurred.

-
-
Returns:
-

a dict that keyed by view IDs (str) and has lists of alignment Annotation objects as values.

-
-
-
- -
-
-get_all_views_contain(at_types: TypesBase | str | List[str | TypesBase]) → List[View][source]
-

Returns the list of all views in the MMIF if given types -are present in that view’s ‘contains’ metadata.

-
-
Parameters:
-

at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

-
-
Returns:
-

the list of views that contain the type

-
-
-
- -
-
-get_all_views_with_error() → List[View][source]
-

Returns the list of all views in the MMIF that have errors.

-
-
Returns:
-

the list of views that contain errors but no annotations

-
-
-
- -
-
-get_annotations_between_time(start: int, end: int, time_unit: str = 'milliseconds') → Iterator[Annotation][source]
-

Version: 1.0 -Returns all ‘Token’ annotations aligned with ‘TimeFrame’ annotations sorted by start time within start and end time -Note: this function only works for mmif object obtained from Whisper-wrapper

-
-
Parameters:
-
    -

  • start – the start time

    • -

  • end – the end time

    • -

  • time_unit – the time unit, either string “milliseconds” or “seconds”, defaults to “milliseconds”

    • -
-
-
Returns:
-

a generator of ‘Token’ annotations

-
-
-
- -
-
-get_document_by_id(doc_id: str) → Document[source]
-

Finds a Document object with the given ID.

-
-
Parameters:
-

doc_id – the ID to search for

-
-
Returns:
-

a reference to the corresponding document, if it exists

-
-
Raises:
-

KeyError – if there is no corresponding document

-
-
-
- -
-
-get_document_location(m_type: DocumentTypes | str, path_only=False) → str | None[source]
-

Method to get the location of first document of given type.

-
-
Parameters:
-

m_type – the type to search for

-
-
Returns:
-

the value of the location field in the corresponding document

-
-
-
- -
-
-get_documents_by_app(app_id: str) → List[Document][source]
-

Method to get all documents object queries by its originated app name.

-
-
Parameters:
-

app_id – the app name to search for

-
-
Returns:
-

a list of documents matching the requested app name, or an empty list if the app not found

-
-
-
- -
-
-get_documents_by_property(prop_key: str, prop_value: str) → List[Document][source]
-

Method to retrieve documents by an arbitrary key-value pair in the document properties objects.

-
-
Parameters:
-
    -

  • prop_key – the metadata key to search for

    • -

  • prop_value – the metadata value to match

    • -
-
-
Returns:
-

a list of documents matching the requested metadata key-value pair

-
-
-
- -
-
-get_documents_by_type(doc_type: str | DocumentTypes) → List[Document][source]
-

Method to get all documents where the type matches a particular document type, which should be one of the CLAMS document types.

-
-
Parameters:
-

doc_type – the type of documents to search for, must be one of Document type defined in the CLAMS vocabulary.

-
-
Returns:
-

a list of documents matching the requested type, or an empty list if none found.

-
-
-
- -
-
-get_documents_in_view(vid: str | None = None) → List[Document][source]
-

Method to get all documents object queries by a view id.

-
-
Parameters:
-

vid – the source view ID to search for

-
-
Returns:
-

a list of documents matching the requested source view ID, or an empty list if the view not found

-
-
-
- -
-
-get_documents_locations(m_type: DocumentTypes | str, path_only=False) → List[str | None][source]
-

This method returns the file paths of documents of given type. -Only top-level documents have locations, so we only check them.

-
-
Parameters:
-

m_type – the type to search for

-
-
Returns:
-

a list of the values of the location fields in the corresponding documents

-
-
-
- -
-
-get_end(annotation: Annotation) → int | float[source]
-

An alias to get_anchor_point method with start=False.

-
- -
-
-get_last_error() → str | None[source]
-

Returns the last error message found in the views.

-
-
Returns:
-

the error message in human-readable format, or None if no error is found

-
-
-
- -
-
-get_start(annotation: Annotation) → int | float[source]
-

An alias to get_anchor_point method with start=True.

-
- -
-
-get_view_by_id(req_view_id: str) → View[source]
-

Finds a View object with the given ID.

-
-
Parameters:
-

req_view_id – the ID to search for

-
-
Returns:
-

a reference to the corresponding view, if it exists

-
-
Raises:
-

Exception – if there is no corresponding view

-
-
-
- -
-
-get_view_contains(at_types: TypesBase | str | List[str | TypesBase]) → View | None[source]
-

Returns the last view appended that contains the given -types in its ‘contains’ metadata.

-
-
Parameters:
-

at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

-
-
Returns:
-

the view, or None if the type is not found

-
-
-
- -
-
-get_view_with_error() → View | None[source]
-

Returns the last view appended that contains an error.

-
-
Returns:
-

the view, or None if no error is found

-
-
-
- -
-
-get_views_contain(at_types: TypesBase | str | List[str | TypesBase]) → List[View][source]
-

Returns the list of all views in the MMIF if given types -are present in that view’s ‘contains’ metadata.

-
-
Parameters:
-

at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

-
-
Returns:
-

the list of views that contain the type

-
-
-
- -
-
-get_views_for_document(doc_id: str) → List[View][source]
-

Returns the list of all views that have annotations anchored on a particular document. -Note that when the document is inside a view (generated during the pipeline’s running), -doc_id must be prefixed with the view_id.

-
- -
-
-get_views_with_error() → List[View][source]
-

Returns the list of all views in the MMIF that have errors.

-
-
Returns:
-

the list of views that contain errors but no annotations

-
-
-
- -
-
-new_view() → View[source]
-

Creates an empty view with a new ID and appends it to the views list.

-
-
Returns:
-

a reference to the new View object

-
-
-
- -
-
-new_view_id() → str[source]
-

Fetches an ID for a new view.

-
-
Returns:
-

the ID

-
-
-
- -
-
-sanitize()[source]
-

Sanitizes a Mmif object by running some safeguards. -Concretely, it performs the following before returning the JSON string.

-
    -

  1. validating output using built-in MMIF jsonschema

    2. -

  2. remove non-existing annotation types from contains metadata

    3. -
-
- -
-
-serialize(pretty: bool = False, sanitize: bool = False, autogenerate_capital_annotations=True) → str[source]
-

Serializes the MMIF object to a JSON string.

-
-
Parameters:
-
    -

  • sanitize – If True, performs some sanitization of before returning -the JSON string. See sanitize() for details.

    • -

  • autogenerate_capital_annotations – If True, automatically convert -any “pending” temporary properties from Document objects to -Annotation objects. See generate_capital_annotations() for -details.

    • -

  • pretty – If True, returns string representation with indentation.

    • -
-
-
Returns:
-

JSON string of the MMIF object.

-
-
-
- -
-
-static validate(json_str: bytes | str | dict) → None[source]
-

Validates a MMIF JSON object against the MMIF Schema. -Note that this method operates before processing by MmifObject._load_str, -so it expects @ and not _ for the JSON-LD @-keys.

-
-
Raises:
-

jsonschema.exceptions.ValidationError – if the input fails validation

-
-
Parameters:
-

json_str – a MMIF JSON dict or string

-
-
Returns:
-

None

-
-
-
- -
- -
-
-

mmif.serialize.view module

-

The view module contains the classes used to represent a MMIF view -as a live Python object.

-

In MMIF, views are created by apps in a pipeline that are annotating -data that was previously present in the MMIF file.

-
-
-class mmif.serialize.view.Contain(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: DataDict[str, str]

-

Contain object that represents the metadata of a single -annotation type in the contains metadata of a MMIF view.

-
- -
-
-class mmif.serialize.view.View(view_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-

View object that represents a single view in a MMIF file.

-

A view is identified by an ID, and contains certain metadata, -a list of annotations, and potentially a JSON-LD @context -IRI.

-

If view_obj is not provided, an empty View will be generated.

-
-
Parameters:
-

view_obj – the JSON data that defines the view

-
-
-
-
-add_annotation(annotation: Annotation, overwrite=False) → Annotation[source]
-

Adds an annotation to the current view.

-

Fails if there is already an annotation with the same ID -in the view, unless overwrite is set to True.

-
-
Parameters:
-
-
-
Raises:
-

KeyError – if overwrite is set to False and -an annotation with the same ID exists -in the view

-
-
Returns:
-

the same Annotation object passed in as annotation

-
-
-
- -
-
-add_document(document: Document, overwrite=False) → Annotation[source]
-

Appends a Document object to the annotations list.

-

Fails if there is already a document with the same ID in the annotations list.

-
-
Parameters:
-
    -

  • document – the Document object to add

    • -

  • overwrite – if set to True, will overwrite -an existing view with the same ID

    • -
-
-
Returns:
-

None

-
-
-
- -
-
-get_annotation_by_id(ann_id) → Annotation[source]
-
- -
-
-get_annotations(at_type: str | TypesBase | None = None, **properties) → Generator[Annotation, None, None][source]
-

Look for certain annotations in this view, specified by parameters

-
-
Parameters:
-
    -

  • at_type – @type of the annotations to look for. When this is None, any @type will match.

    • -

  • properties – properties of the annotations to look for. When given more than one property, all properties must match. Note that annotation type metadata are specified in the contains view metadata, not in individual annotation objects.

    • -
-
-
-
- -
-
-get_document_by_id(doc_id) → Document[source]
-
- -
-
-get_documents() → List[Document][source]
-
- -
-
-get_error() → str | None[source]
-

Get the “text” representation of the error occurred during -processing. Text representation is supposed to be human-readable. -When ths view does not have any error, returns None.

-
- -
-
-has_error() → bool[source]
-
- -
-
-has_warnings()[source]
-
- -
-
-new_annotation(at_type: str | TypesBase, aid: str | None = None, overwrite=False, **properties) → Annotation[source]
-

Generates a new mmif.serialize.annotation.Annotation -object and adds it to the current view.

-

Fails if there is already an annotation with the same ID -in the view, unless overwrite is set to True.

-
-
Parameters:
-
    -

  • at_type – the desired @type of the annotation.

    • -

  • aid – the desired ID of the annotation, when not given, -the mmif SDK tries to automatically generate an ID based on -Annotation type and existing annotations in the view.

    • -

  • overwrite – if set to True, will overwrite an -existing annotation with the same ID.

    • -
-
-
Raises:
-

KeyError – if overwrite is set to False and -an annotation with the same ID exists -in the view.

-
-
Returns:
-

the generated mmif.serialize.annotation.Annotation

-
-
-
- -
-
-new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
-

Adds a new element to the contains metadata.

-
-
Parameters:
-
    -

  • at_type – the @type of the annotation type being added

    • -

  • contains_metadata – any metadata associated with the annotation type

    • -
-
-
Returns:
-

the generated Contain object

-
-
-
- -
-
-new_textdocument(text: str, lang: str = 'en', did: str | None = None, overwrite=False, **properties) → Document[source]
-

Generates a new mmif.serialize.annotation.Document -object, particularly typed as TextDocument and adds it to the current view.

-

Fails if there is already a text document with the same ID -in the view, unless overwrite is set to True.

-
-
Parameters:
-
    -

  • text – text content of the new document

    • -

  • lang – ISO 639-1 code of the language used in the new document

    • -

  • did – the desired ID of the document, when not given, -the mmif SDK tries to automatically generate an ID based on -Annotation type and existing documents in the view.

    • -

  • overwrite – if set to True, will overwrite an -existing document with the same ID

    • -
-
-
Raises:
-

KeyError – if overwrite is set to False and -an document with the same ID exists -in the view

-
-
Returns:
-

the generated mmif.serialize.annotation.Document

-
-
-
- -
-
-set_error(err_message: str, err_trace: str) → None[source]
-
- -
- -
-
-class mmif.serialize.view.ViewMetadata(viewmetadata_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-

ViewMetadata object that represents the metadata object within a MMIF view.

-
-
Parameters:
-

viewmetadata_obj – the JSON data that defines the metadata

-
-
-
-
-add_app_configuration(config_key: str, config_value: str | int | float | bool | None | List[str | int | float | bool | None]) → None[source]
-

Add a configuration key-value pair to the app_configuration dictionary.

-
- -
-
-add_contain(contain: Contain, at_type: str | TypesBase) → None[source]
-
- -
-
-add_parameter(param_key: str, param_value: str)[source]
-

Add a single runtime parameter to the view metadata. Note that parameter value must be a string.

-
- -
-
-add_parameters(**runtime_params: str)[source]
-

Add runtime parameters as a batch (dict) to the view metadata. Note that parameter values must be strings.

-
- -
-
-add_warnings(*warnings: Warning)[source]
-
- -
-
-emtpy_warnings()[source]
-
- -
-
-get_app_configuration(config_key: str) → str | int | float | bool | None | List[str | int | float | bool | None][source]
-

Get a configuration value from the app_configuration dictionary.

-
- -
-
-get_error_as_text() → str[source]
-
- -
-
-get_parameter(param_key: str) → str[source]
-

Get a runtime parameter from the view metadata.

-
- -
-
-has_error() → bool[source]
-
- -
-
-has_warnings()[source]
-
- -
-
-new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
-

Adds a new element to the contains dictionary.

-
-
Parameters:
-
    -

  • at_type – the @type of the annotation type being added

    • -

  • contains_metadata – any metadata associated with the annotation type

    • -
-
-
Returns:
-

the generated Contain object

-
-
-
- -
-
-set_error(message: str, stack_trace: str)[source]
-
- -
- -
-
-

mmif.serialize.annotation module

-

The annotation module contains the classes used to represent a -MMIF annotation as a live Python object.

-

In MMIF, annotations are created by apps in a pipeline as a part -of a view. For documentation on how views are represented, see -mmif.serialize.view.

-
-
-class mmif.serialize.annotation.Annotation(anno_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-

MmifObject that represents an annotation in a MMIF view.

-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]]) → None[source]
-

Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

-
- -
-
-property at_type: TypesBase[source]
-
- -
-
-static check_prop_value_is_simple_enough(value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]]) → bool[source]
-
- -
-
-get(prop_name: str) → AnnotationProperties | str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]][source]
-

A special getter for Annotation properties. This is to allow for -directly accessing properties without having to go through the -properties object, or view-level annotation properties encoded in the -view.metadata.contains dict. Note that the regular props will take -the priority over the ephemeral props when there are conflicts.

-
- -
-
-get_property(prop_name: str) → AnnotationProperties | str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]][source]
-

A special getter for Annotation properties. This is to allow for -directly accessing properties without having to go through the -properties object, or view-level annotation properties encoded in the -view.metadata.contains dict. Note that the regular props will take -the priority over the ephemeral props when there are conflicts.

-
- -
-
-property id: str[source]
-
- -
-
-is_document()[source]
-
- -
-
-is_type(at_type: str | TypesBase) → bool[source]
-

Check if the @type of this object matches.

-
- -
-
-property long_id: str[source]
-
- -
-
-property parent: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.AnnotationProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject, MutableMapping[str, T]

-

AnnotationProperties object that represents the -properties object within a MMIF annotation.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
- -
-
-class mmif.serialize.annotation.Document(doc_obj: bytes | str | dict | None = None)[source]
-

Bases: Annotation

-

Document object that represents a single document in a MMIF file.

-

A document is identified by an ID, and contains certain attributes -and potentially contains the contents of the document itself, -metadata about how the document was created, and/or a list of -subdocuments grouped together logically.

-

If document_obj is not provided, an empty Document will be generated.

-
-
Parameters:
-

document_obj – the JSON data that defines the document

-
-
-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None]) → None[source]
-

Adds a property to the document’s properties.

-

Unlike the parent Annotation class, added properties of a -Document object can be lost during serialization unless it belongs -to somewhere in a Mmif object. This is because we want to keep -Document object as “read-only” as possible. Thus, if you want to add -a property to a Document object,

-
    -

  • add the document to a Mmif object (either in the documents list or -in a view from the views list), or

    • -

  • directly write to Document.properties instead of using this method -(which is not recommended).

    • -
-

With the former method, the SDK will record the added property as a -Annotation annotation object, separate from the original Document -object. See Mmif.generate_capital_annotations() for more.

-

A few notes to keep in mind:

-
    -

  1. You can’t overwrite an existing property of a Document object.

    2. -

  2. A MMIF can have multiple Annotation objects with the same -property name but different values. When this happens, the SDK will -only keep the latest value (in order of appearances in views list) of -the property, effectively overwriting the previous values.

    3. -
-
- -
-
-get(prop_name)[source]
-

A special getter for Document properties. The major difference from -the super class’s Annotation.get() method is that Document -class has one more set of “pending” properties, that are added after -the Document object is created and will be serialized as a separate -Annotation object of which @type = Annotation. The -pending properties will take the priority over the regular properties -when there are conflicts.

-
- -
-
-get_property(prop_name)[source]
-

A special getter for Document properties. The major difference from -the super class’s Annotation.get() method is that Document -class has one more set of “pending” properties, that are added after -the Document object is created and will be serialized as a separate -Annotation object of which @type = Annotation. The -pending properties will take the priority over the regular properties -when there are conflicts.

-
- -
-
-property location: str | None[source]
-

location property must be a legitimate URI. That is, should the document be a local file -then the file:// scheme must be used. -Returns None when no location is set.

-
- -
-
-location_address() → str | None[source]
-

Retrieves the full address from the document location URI. -Returns None when no location is set.

-
- -
-
-location_path(nonexist_ok=True) → str | None[source]
-

Retrieves a path that’s resolved to a pathname in the local file system. -To obtain the original value of the “path” part in the location string -(before resolving), use properties.location_path_literal method. -Returns None when no location is set.

-
-
Parameters:
-

nonexist_ok – if False, raise FileNotFoundError when the resolved path doesn’t exist

-
-
-
- -
-
-location_scheme() → str | None[source]
-

Retrieves URI scheme of the document location. -Returns None when no location is set.

-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.DocumentProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: AnnotationProperties

-

DocumentProperties object that represents the -properties object within a MMIF document.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
-
-property location: str | None[source]
-

location property must be a legitimate URI. That is, should the document be a local file -then the file:// scheme must be used. -Returns None when no location is set.

-
- -
-
-location_address() → str | None[source]
-

Retrieves the full address from the document location URI. -Returns None when no location is set.

-
- -
-
-location_path() → str | None[source]
-
- -
-
-location_path_literal() → str | None[source]
-

Retrieves only path name of the document location (hostname is ignored). -Returns None when no location is set.

-
- -
-
-location_path_resolved(nonexist_ok=True) → str | None[source]
-

Retrieves only path name of the document location (hostname is ignored), -and then try to resolve the path name in the local file system. -This method should be used when the document scheme is file or empty. -For other schemes, users should install mmif-locdoc-<scheme> plugin.

-

Returns None when no location is set. -Raise ValueError when no code found to resolve the given location scheme.

-
- -
-
-location_scheme() → str | None[source]
-

Retrieves URI scheme of the document location. -Returns None when no location is set.

-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.Text(text_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-
-
-property lang: str[source]
-
- -
-
-property value: str[source]
-
- -
- -
-
- - -
-
- -
-
-
-
- -
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- - - \ No newline at end of file diff --git a/docs/1.0.16/autodoc/mmif.utils.html b/docs/1.0.16/autodoc/mmif.utils.html deleted file mode 100644 index beaf1184..00000000 --- a/docs/1.0.16/autodoc/mmif.utils.html +++ /dev/null @@ -1,615 +0,0 @@ - - - - - - - - - mmif.utils module — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.utils module

-
-

mmif.utils.video_document_helper module

-
-
-mmif.utils.video_document_helper.capture(video_document: Document)[source]
-

Captures a video file using OpenCV and adds fps, frame count, and duration as properties to the document.

-
-
Parameters:
-

video_document – Document instance that holds a video document ("@type": ".../VideoDocument/...")

-
-
Returns:
-

OpenCV VideoCapture object

-
-
-
- -
-
-mmif.utils.video_document_helper.convert_timeframe(mmif: Mmif, time_frame: Annotation, out_unit: str) → Tuple[int | float | str, int | float | str][source]
-

Converts start and end points in a TimeFrame annotation a different time unit.

-
-
Parameters:
-
    -

  • mmif – Mmif instance

    • -

  • time_frame – Annotation instance that holds a time interval annotation ("@type": ".../TimeFrame/...")

    • -

  • out_unit – time unit to which the point is converted

    • -
-
-
Returns:
-

tuple of frame numbers (integer) or seconds/milliseconds (float) of input start and end

-
-
-
- -
-
-mmif.utils.video_document_helper.convert_timepoint(mmif: Mmif, timepoint: Annotation, out_unit: str) → int | float | str[source]
-

Converts a time point included in an annotation to a different time unit. -The input annotation must have timePoint property.

-
-
Parameters:
-
    -

  • mmif – input MMIF to obtain fps and input timeunit

    • -

  • timepoint – Annotation instance with timePoint property

    • -

  • out_unit – time unit to which the point is converted (frames, seconds, milliseconds)

    • -
-
-
Returns:
-

frame number (integer) or second/millisecond (float) of input timepoint

-
-
-
- -
-
-mmif.utils.video_document_helper.extract_frames_as_images(video_document: Document, framenums: List[int], as_PIL: bool = False)[source]
-

Extracts frames from a video document as a list of numpy.ndarray. -Use with sample_frames() function to get the list of frame numbers first.

-
-
Parameters:
-
    -

  • video_document – Document instance that holds a video document ("@type": ".../VideoDocument/...")

    • -

  • framenums – integers representing the frame numbers to extract

    • -

  • as_PIL – return PIL.Image.Image instead of ndarray

    • -
-
-
Returns:
-

frames as a list of ndarray or Image

-
-
-
- -
-
-mmif.utils.video_document_helper.extract_mid_frame(mmif: Mmif, time_frame: Annotation, as_PIL: bool = False)[source]
-

Extracts the middle frame of a time interval annotation as a numpy ndarray.

-
-
Parameters:
-
    -

  • mmif – Mmif instance

    • -

  • time_frame – Annotation instance that holds a time interval annotation ("@type": ".../TimeFrame/...")

    • -

  • as_PIL – return Image instead of ndarray

    • -
-
-
Returns:
-

frame as a numpy.ndarray or PIL.Image.Image

-
-
-
- -
-
-mmif.utils.video_document_helper.extract_representative_frame(mmif: Mmif, time_frame: Annotation, as_PIL: bool = False)[source]
-

Extracts the representative frame of an annotation as a numpy ndarray or PIL Image.

-
-
Parameters:
-
    -

  • mmif – Mmif instance

    • -

  • time_frame – Annotation instance that holds a time interval annotation ("@type": ".../TimeFrame/...")

    • -

  • as_PIL – return Image instead of ndarray

    • -
-
-
Returns:
-

frame as a numpy.ndarray or PIL.Image.Image

-
-
-
- -
-
-mmif.utils.video_document_helper.framenum_to_millisecond(video_doc: Document, frame: int)[source]
-

Converts a frame number to a millisecond value.

-
- -
-
-mmif.utils.video_document_helper.framenum_to_second(video_doc: Document, frame: int)[source]
-

Converts a frame number to a second value.

-
- -
-
-mmif.utils.video_document_helper.get_annotation_property(mmif, annotation, prop_name)[source]
-
-

Deprecated since version 1.0.8: Use mmif.serialize.annotation.Annotation.get_property() method instead.

-
-

Get a property value from an annotation. If the property is not found in the annotation, it will look up the metadata of the annotation’s parent view and return the value from there. -xisting

-
- -
-
-mmif.utils.video_document_helper.get_framerate(video_document: Document) → float[source]
-

Gets the frame rate of a video document. First by checking the fps property of the document, then by capturing the video.

-
-
Parameters:
-

video_document – Document instance that holds a video document ("@type": ".../VideoDocument/...")

-
-
Returns:
-

frames per second as a float, rounded to 2 decimal places

-
-
-
- -
-
-mmif.utils.video_document_helper.get_mid_framenum(mmif: Mmif, time_frame: Annotation)[source]
-

Calculates the middle frame number of a time interval annotation.

-
-
Parameters:
-
    -

  • mmif – Mmif instance

    • -

  • time_frame – Annotation instance that holds a time interval annotation ("@type": ".../TimeFrame/...")

    • -
-
-
Returns:
-

middle frame number as an integer

-
-
-
- -
-
-mmif.utils.video_document_helper.get_representative_framenum(mmif: Mmif, time_frame: Annotation)[source]
-

Calculates the representative frame number from an annotation.

-
-
Parameters:
-
    -

  • mmif – Mmif instance

    • -

  • time_frame – Annotation instance that holds a time interval annotation containing a representatives property ("@type": ".../TimeFrame/...")

    • -
-
-
Returns:
-

representative frame number as an integer

-
-
-
- -
-
-mmif.utils.video_document_helper.millisecond_to_framenum(video_doc: Document, millisecond: float) → int[source]
-

Converts a millisecond value to a frame number.

-
- -
-
-mmif.utils.video_document_helper.sample_frames(start_frame: int, end_frame: int, sample_rate: float = 1) → List[int][source]
-

Helper function to sample frames from a time interval. -Can also be used as a “cutoff” function when used with start_frame==0 and sample_rate==1.

-
-
Parameters:
-
    -

  • start_frame – start frame of the interval

    • -

  • end_frame – end frame of the interval

    • -

  • sample_rate – sampling rate (or step) to configure how often to take a frame, default is 1, meaning all consecutive frames are sampled

    • -
-
-
-
- -
-
-mmif.utils.video_document_helper.second_to_framenum(video_doc: Document, second) → int[source]
-

Converts a second value to a frame number.

-
- -
-
-

mmif.utils.sequence_helper module

-

This module provides helpers for handling sequence labeling. Specifically, it provides

-
    -

  • a generalized label re-mapper for “post-binning” of labels

    • -

  • conversion from a list of CLAMS annotations (with classification props) into a list of reals (scores by labels), can be combined with the label re-mapper mentioned above

    • -

  • mmif.utils.sequence_helper.smooth_outlying_short_intervals(): a simple smoothing algorithm by trimming “short” outlier sequences

    • -
-

However, it DOES NOT provide

-
    -

  • direct conversion between CLAMS annotations. For example, it does not directly handle stitching of TimePoint into TimeFrames.

    • -

  • support for multi-class scenario, such as handling of _competing_ subsequence or overlapping labels.

    • -
-

Some functions can use optional external libraries (e.g., numpy) for better performance. -Hence, if you see a warning about missing optional packages, you might want to install them by running pip install mmif-python[seq].

-
-
-mmif.utils.sequence_helper.build_label_remapper(src_labels: List[str], dst_labels: Dict[str, str | int | float | bool | None]) → Dict[str, str | int | float | bool | None][source]
-

Build a label remapper dictionary from source and destination labels.

-
-
Parameters:
-
    -

  • src_labels – a list of all labels on the source side

    • -

  • dst_labels – a dict from source labels to destination labels. -Source labels not in this dict will be remapped to a negative label (-).

    • -
-
-
Returns:
-

a dict that exhaustively maps source labels to destination labels

-
-
-
- -
-
-mmif.utils.sequence_helper.build_score_lists(classifications: ~typing.List[~typing.Dict], label_remapper: ~typing.Dict, score_remap_op: ~typing.Callable[[...], float] = <built-in function max>) → Tuple[Dict[str, int], numpy.ndarray][source]
-

Build lists of scores indexed by the label names.

-
-
Parameters:
-
    -

  • classifications – list of dictionaries of classification results, taken from input annotation objects

    • -

  • label_remapper – a dictionary that maps source label names to destination label names (formerly “postbin”)

    • -

  • score_remap_op – a function to remap the scores from multiple source labels binned to a destination label -common choices are max, min, or sum

    • -
-
-
Returns:
-

    -

  1. a dictionary that maps label names to their index in the score list

    2. -

  2. 2-d numpy array of scores, of which rows are indexed by label map dict (first return value)

    3. -
-

-
-
-
- -
-
-mmif.utils.sequence_helper.smooth_outlying_short_intervals(scores: List[float], min_spseq_size: int, min_snseq_size: int, min_score: float = 0.5)[source]
-

Given a list of scores, a score threshold, and smoothing parameters, -identify the intervals of “positive” scores by “trimming” the short -positive sequences (“spseq”) and short negative sequences (“snseq”). To -decide the positivity, first step is binarization of the scores by the -min_score threshold. Given Sr as “raw” input real-number scores -list, and min_score=0.5,

-
-
Sr: [0.3, 0.6, 0.2, 0.8, 0.2, 0.9, 0.8, 0.5, 0.1, 0.5, 0.8, 0.3, 1.0, 0.7, 0.5, 0.5, 0.5, 0.8, 0.3, 0.6]
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the binarization is done by simply comparing each score to the -threshold to get S list of binary scores

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1.0 :                                     |                      
-0.9 :                |                    |                      
-0.8 :          |     |  |           |     |              |       
-0.7 :          |     |  |           |     |  |           |       
-0.6 :    |     |     |  |           |     |  |           |     | 
-0.5 :----+-----+-----+--+--+-----+--+-----+--+--+--+--+--+-----+-
-0.4 :    |     |     |  |  |     |  |     |  |  |  |  |  |     | 
-0.3 : |  |     |     |  |  |     |  |  |  |  |  |  |  |  |  |  | 
-0.2 : |  |  |  |  |  |  |  |     |  |  |  |  |  |  |  |  |  |  | 
-0.1 : |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | 
-0.0 +------------------------------------------------------------
-raw :.3 .6 .2 .8 .2 .9 .8 .5 .1 .5 .8 .3 1. .7 .5 .5 .5 .8 .3 .6
- S  : 0  1  0  1  0  1  1  0  0  0  1  0  1  1  0  1  1  1  0  1 
-
-
-
-

Note that the size of a positive or negative sequence can be as small -as 1.

-

Then, here are examples of smoothing a list of binary scores into -intervals, by trimming “very short” (under thresholds) sequences of -positive or negative:

-
-

Note

-

legends:

-
    -

  • t is unit index (e.g. time index)

    • -

  • S is the list of binary scores (zeros and ones)

    • -

  • I is the list of intervals after smoothing

    • -
-
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    -

  1. with params min_spseq_size==1, min_snseq_size==4

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1]
-I: [0, 1--1--1--1--1--1--1--1--1--1--1--1, 0--0--0--0--0--0, 1]
-
    -
    -

    Explanation: min_snseq_size is used to smooth short sequences -of negative predictions. In this, zeros from t[7:10] are smoothed -into “one” I, while zeros from t[13:19] are kept as “zero” I. Note -that the “short” snseqs at the either ends (t[0:1]) are never -smoothed.

    -
    -
    2. -

  2. with params min_spseq_size==4, min_snseq_size==2

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1]
-I: [0, 1--1--1--1--1--1, 0--0--0--0--0--0--0--0--0--0--0--0--0]
-
    -
    -

    Explanation: min_spseq_size is used to smooth short sequences -of positive predictions. In this example, the spseqs of ones from -both t[10:13] and t[19:20] are smoothed. Note that the “short” -spseqs at the either ends (t[19:20]) are always smoothed.

    -
    -
    3. -

  3. with params min_spseq_size==4, min_snseq_size==4

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1]
-I: [0, 1--1--1--1--1--1--1--1--1--1--1--1--0--0--0--0--0--0--0]
-
    -
    -

    Explanation: When two threshold parameters are working together, -the algorithm will prioritize the smoothing of the snseqs over the -smoothing of the spseqs. Thus, in this example, the snseq t[7:10] -gets first smoothed “up” before the spseq t[10:13] is smoothed -“down”, resulting in a long final I.

    -
    -
    4. -

  4. with params min_spseq_size==4, min_snseq_size==4

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [1, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 1, 1]
-I: [1--1--1--1--1--1--1, 0--0--0--0, 1--1--1--1--1--1--1--1--1]
-
    -
    -

    Explanation: Since smoothing of snseqs is prioritized, short spseqs -at the beginning or the end can be kept.

    -
    -
    5. -

  5. with params min_spseq_size==1, min_snseq_size==1

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 1, 1]
-I: [0--0--0, 1--1--1--1, 0--0--0--0, 1--1--1--1, 0--0--0, 1--1]
-
    -
    -

    Explanation: When both width thresholds are set to 1, the algorithm -works essentially in the “stitching” only mode.

    -
    -
    6. -
-
-
Parameters:
-
    -

  • scores – SORTED list of scores to be smoothed. The score list -is assumed to be “exhaust” the entire time or space of -the underlying document segment. -(Sorted by the start, and then by the end of anchors)

    • -

  • min_score – minimum threshold to use to discard -low-scored units (strictly less than)

    • -

  • min_spseq_size – minimum size of a positive sequence not to be -smoothed (greater or equal to)

    • -

  • min_snseq_size – minimum size of a negative sequence not to be -smoothed (greater or equal to)

    • -
-
-
Returns:
-

list of tuples of start(inclusive)/end(exclusive) indices -of the “positive” sequences. Negative sequences (regardless of -their size) are not included in the output.

-
-
-
- -
-
-mmif.utils.sequence_helper.validate_labelset(annotations: Iterable[Annotation]) → List[str][source]
-

Simple check for a list of annotations to see if they have the same label set.

-
-
Raise:
-

AttributeError if an element in the input list doesn’t have the labelset property

-
-
Raise:
-

ValueError if different labelset values are found

-
-
Returns:
-

a list of the common labelset value (list of label names)

-
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- - - \ No newline at end of file diff --git a/docs/1.0.16/autodoc/mmif.vocabulary.html b/docs/1.0.16/autodoc/mmif.vocabulary.html deleted file mode 100644 index e8c3c5da..00000000 --- a/docs/1.0.16/autodoc/mmif.vocabulary.html +++ /dev/null @@ -1,319 +0,0 @@ - - - - - - - - - mmif.vocabulary module — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
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- -
-

mmif.vocabulary module

-
-

mmif.vocabulary.annotation_types module

-
-
-class mmif.vocabulary.annotation_types.AnnotationTypes(type_uri, fuzzymode=True)[source]
-

Bases: AnnotationTypesBase

-

This class contains the CLAMS annotation types -defined in the spec version 1.1.0 as class variables.

-
-
-Alignment = http://mmif.clams.ai/vocabulary/Alignment/v1[source]
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- -
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-Annotation = http://mmif.clams.ai/vocabulary/Annotation/v6[source]
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-BoundingBox = http://mmif.clams.ai/vocabulary/BoundingBox/v5[source]
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-Chapter = http://mmif.clams.ai/vocabulary/Chapter/v6[source]
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-Interval = http://mmif.clams.ai/vocabulary/Interval/v5[source]
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-NamedEntity = http://mmif.clams.ai/vocabulary/NamedEntity/v1[source]
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-NounChunk = http://mmif.clams.ai/vocabulary/NounChunk/v1[source]
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-Paragraph = http://mmif.clams.ai/vocabulary/Paragraph/v1[source]
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-Polygon = http://mmif.clams.ai/vocabulary/Polygon/v5[source]
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-Region = http://mmif.clams.ai/vocabulary/Region/v5[source]
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-Relation = http://mmif.clams.ai/vocabulary/Relation/v5[source]
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-Sentence = http://mmif.clams.ai/vocabulary/Sentence/v1[source]
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-Span = http://mmif.clams.ai/vocabulary/Span/v5[source]
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-TimeFrame = http://mmif.clams.ai/vocabulary/TimeFrame/v6[source]
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-TimePoint = http://mmif.clams.ai/vocabulary/TimePoint/v5[source]
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-Token = http://mmif.clams.ai/vocabulary/Token/v1[source]
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-VerbChunk = http://mmif.clams.ai/vocabulary/VerbChunk/v1[source]
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-VideoObject = http://mmif.clams.ai/vocabulary/VideoObject/v5[source]
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- -
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mmif.vocabulary.document_types module

-
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-class mmif.vocabulary.document_types.DocumentTypes(type_uri, fuzzymode=True)[source]
-

Bases: DocumentTypesBase

-

This class contains the CLAMS document types -defined in the spec version 1.1.0 as class variables.

-
-
-AudioDocument = http://mmif.clams.ai/vocabulary/AudioDocument/v1[source]
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-Document = http://mmif.clams.ai/vocabulary/Document/v1[source]
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-ImageDocument = http://mmif.clams.ai/vocabulary/ImageDocument/v1[source]
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-TextDocument = http://mmif.clams.ai/vocabulary/TextDocument/v1[source]
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-VideoDocument = http://mmif.clams.ai/vocabulary/VideoDocument/v1[source]
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- - - \ No newline at end of file diff --git a/docs/1.0.16/autodoc/mmif_docloc_http.html b/docs/1.0.16/autodoc/mmif_docloc_http.html deleted file mode 100644 index aacdd4a8..00000000 --- a/docs/1.0.16/autodoc/mmif_docloc_http.html +++ /dev/null @@ -1,179 +0,0 @@ - - - - - - - - - mmif_docloc_http package — mmif-python documentation - - - - - - - - - - - - - - - - -
- - -
- -
-
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- -
-
-
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- -
-

mmif_docloc_http package

-

MMIF document location helper module for http and https schemes. -If you want to write your own docloc scheme handler, please use the source code of this module as a reference. -See this plug-in section for more information.

-
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-mmif_docloc_http.resolve(docloc)[source]
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- - - \ No newline at end of file diff --git a/docs/1.0.16/consumer-tutorial.html b/docs/1.0.16/consumer-tutorial.html deleted file mode 100644 index 3e2bc495..00000000 --- a/docs/1.0.16/consumer-tutorial.html +++ /dev/null @@ -1,172 +0,0 @@ - - - - - - - - - MMIF consumer — mmif-python documentation - - - - - - - - - - - - - - - -
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  • MMIF consumer
    • -
  • -
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MMIF consumer

-

A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the appliance documentation to learn more about the appliance.

-

MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance.

-
    -

  1. The code must be hosted on a public git repository (e.g. Github, Gitlab, …)

    2. -

  2. Must listen to 5000 port.

    3. -

  3. Must expose /display route .

    4. -

  4. /display router should response to GET requests.

    5. -

  5. In the GET request, a public URL of the input MMIF file is passed via file URL parameter.

    6. -

  6. On the codebase root, there must be a Dockerfile that can build a docker image that runs the web app.

    7. -
-

We provide an example consumer at https://github.com/clamsproject/mmif-visualizer.

-
- - -
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- - Other Versions - v: 1.0.16 - - -
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  • Index
    • -
  • -
    • -
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Index

- -
- A - | B - | C - | D - | E - | F - | G - | H - | I - | K - | L - | M - | N - | P - | R - | S - | T - | U - | V - -
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- - -
- -
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    • -
  • Welcome to mmif-python’s documentation!
    • -
  • -
    • -
-
-
-
-
- -
-

Welcome to mmif-python’s documentation!

-
-

MultiMedia Interchange Format

-

MMIF is a JSON(-LD)-based data format designed for transferring annotation data between computational analysis applications in CLAMS project.

-
-
-

mmif-python

-

mmif-python is a Python implementation of the MMIF data format. -mmif-python provides various helper classes and functions to handle MMIF JSON in Python, -including ;

-
    -

  1. de-/serialization of MMIF internal data structures to/from JSON

    2. -

  2. validation of MMIF JSON

    3. -

  3. handling of CLAMS vocabulary types

    4. -

  4. navigation of MMIF object via various “search” methods (e.g. mmif.get_all_views_contain(vocab_type)))

    5. -
-
-
-

For more …

- -
-

Contents

- -
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-

API documentation:

- -
-
-
-
-

Indices and tables

- -
- - -
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- -
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- - Other Versions - v: 1.0.16 - - -
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  • Getting Started
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Getting Started

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Overview

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MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for reproducibility, transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF website. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects.

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Prerequisites

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  • Python: the latest mmif-python requires Python 3.8 or newer. We have no plan to support Python 2.7.

    • -
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Installation

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Package mmif-python is distributed via the official PyPI. Users are supposed to pip-install to get latest release.

-
pip install mmif-python
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This will install a package mmif to local python.

-

The MMIF format and specification is evolving over time, and mmif-python package will be updated along with the changes in MMIF format.

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Note

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MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and mmif-python versions, please take time to read our decision on the subject here. If you need to know which python SDK supports which specification version, see Target MMIF Versions page.

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MMIF Serialization

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mmif.serialize.mmif.Mmif represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of mmif.serialize.model.MmifObject, including the mmif.serialize.mmif.Mmif. To start with an existing MMIF str, simple initiate a new Mmif object with the file.

-
import mmif
-from mmif import Mmif
-
-mmif_str = """{
-"metadata": {
-  "mmif": "http://mmif.clams.ai/1.0.0"
-},
-"documents": [
-  {
-    "@type": "http://mmif.clams.ai/vocabulary/VideoDocument/v1",
-    "properties": {
-      "id": "m1",
-      "mime": "video/mp4",
-      "location": "file:///var/archive/video-0012.mp4"
-    }
-  },
-  {
-    "@type": "http://mmif.clams.ai/vocabulary/TextDocument/v1",
-    "properties": {
-      "id": "m2",
-      "mime": "text/plain",
-      "location": "file:///var/archive/video-0012-transcript.txt"
-    }
-  }
-],
-"views": []}"""
-mmif_obj = Mmif(mmif_str)
-
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Few notes;

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    -

  1. MMIF does not carry the primary source files in it.

    2. -

  2. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version mmif-python implementation of the MMIF might not be able to load an unsupported version of MMIF string.

    3. -
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When serializing back to str, call mmif.serialize.model.MmifObject.serialize() on the object.

-

To get subcomponents, you can use various getters implemented in subclasses. For example;

-
from mmif.vocabulary.document_types import DocumentTypes
-
-for video in mmif_obj.Mmif.get_documents_by_type(DocumentTypes.VideoDocument):
-  with open(video.location_path(), 'b') as in_video:
-    # do something with the video file
-
-
-

For a full list of available helper methods, please refer to the API documentation.

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mmif_docloc_http package

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Developing plugins for MMIF Python SDK

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Overview

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As MMIF JSON files can carry information about media document files without actually carrying file contents, file accessing modules in mmif Python package (distributed as mmif-python on PyPI) are designed to be lightweight and flexible so that it can work with additional “plugin” Python packages that can handle concrete file access.

-

This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF website. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects.

-

Developer can write simple plugins that can provide additional functionalities to mmif-python. For example, mmif-python does not provide any file access functionality beyond a local file system (with file scheme), but it can be extended with a plugin that can handle file access over different protocols (e.g. http, s3, ftp, etc).

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This document contains information about how to write plugins for mmif-python.

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Document Location Scheme Plugins

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mmif.serialize.annotation.Document class has various methods to access parts of location property of the document. The location is in URI/IRI format (SCHEME://HOSTNAME/PATH, in a nutshell) and it has to be resolved to a local file for CLAMS Apps to process the local file to analyze and extract information about the media and its contents. The core mmif-python distribution only provides a default implementation that can handle file scheme URIs.

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To add a document location handler plugin, you need to implement a Python “package” (do not confuse with PYPI distribution), that meets these requirements;

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    -

  1. the package must be named mmif_docloc_<SCHEME>. For example, to implement a handler for s3 scheme, the package name must be mmif_docloc_s3. The prefix is important as it’s used in the plugin discovery process from the core mmif-python modules.

    2. -

  2. the top module of the package must have a function named resolve. The function must take a single argument, which is a str of the document location URI. The function must return a str of the local file path. For example, if the document location is s3://mybucket/myfile.mp4, a Python user should be able to to something like this;

    3. -
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import mmif_docloc_s3
-resolved = mmif_docloc_s3.resolve('s3://mybucket/myfile.mp4')
-# then resolved must be a local file path that can be used to open the file
-
-
-

Here’s a minimal example codebase that you refer to when you develop a docloc plugin.

-

(However, before you start writing your own plugin for a specific URI scheme, checking if there’s already a PyPI distribution for the scheme might be a good idea.)

-
$ tree .
-.
-├── mmif_docloc_dummy
-│   └── __init__.py
-├── pyproject.toml
-└── setup.cfg
-
- $ cat pyproject.toml
-[build-system]
-requires = ["setuptools"]
-build-backend = "setuptools.build_meta"
-
-$ cat setup.cfg
-[metadata]
-name = mmif_docloc_dummy  # this name is IMPORTANT
-version = 0.0.1
-description = a plugin to mmif-pyhon to handle `dummy` location scheme
-
-
-

And the plugin code.

-
# mmif_docloc_dummy/__init__.py
-doc_types = {'video': 'mp4'}
-
-def resolve(docloc):
-    scheme = 'dummy'
-    if docloc.startswith(f'{scheme}://'):
-        doc_id, doc_type = docloc.split('.')
-        return f'/path/to/{doc_id}.{doc_types[doc_type]}'
-    else:
-        raise ValueError(f'cannot handle document location scheme: {docloc}')
-
-
-
-
-

Bulit-in Document Location Scheme Plugins

-

At the moment, mmif-python PyPI distribution ships a built-in docloc plugin that support both http and https schemes. -Take a look at mmif_docloc_http module for details.

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Python Module Index

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- mmif -
    - mmif.serialize.annotation -
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    - mmif.utils.sequence_helper -
    - mmif.utils.video_document_helper -
    - mmif.vocabulary.annotation_types -
    - mmif.vocabulary.document_types -
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"mmif.serialize.mmif.Mmif.add_view", false]], "add_warnings() (mmif.serialize.view.viewmetadata method)": [[0, "mmif.serialize.view.ViewMetadata.add_warnings", false]], "alignment (mmif.vocabulary.annotation_types.annotationtypes attribute)": [[2, "mmif.vocabulary.annotation_types.AnnotationTypes.Alignment", false]], "annotation (class in mmif.serialize.annotation)": [[0, "mmif.serialize.annotation.Annotation", false]], "annotation (mmif.vocabulary.annotation_types.annotationtypes attribute)": [[2, "mmif.vocabulary.annotation_types.AnnotationTypes.Annotation", false]], "annotationproperties (class in mmif.serialize.annotation)": [[0, "mmif.serialize.annotation.AnnotationProperties", false]], "annotationtypes (class in mmif.vocabulary.annotation_types)": [[2, "mmif.vocabulary.annotation_types.AnnotationTypes", false]], "append() (mmif.serialize.model.datalist method)": [[0, "mmif.serialize.model.DataList.append", false]], "at_type (mmif.serialize.annotation.annotation property)": [[0, 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0, "split": 8, "spseq": 1, "sr": 1, "src_label": 1, "stack_trac": 0, "standard": 0, "start": [0, 1, 5, 8], "start_fram": 1, "startswith": 8, "static": 0, "step": 1, "stitch": 1, "store": 0, "str": [0, 1, 6, 8], "strictli": 1, "string": [0, 6], "structur": 5, "style": 0, "subclass": [0, 6], "subcompon": 6, "subdocu": 0, "subject": 6, "subsequ": 1, "sum": 1, "super": 0, "superclass": 0, "support": [1, 6, 8], "suppos": [0, 6], "system": [0, 8], "t": [0, 1], "take": [0, 1, 6, 8], "taken": 1, "target": [5, 6], "temporari": 0, "text": [0, 6, 7], "text_languag": [0, 7], "text_obj": 0, "text_valu": [0, 7], "textdocu": [0, 2, 6, 7], "th": 0, "than": [0, 1], "thei": [0, 1], "them": [0, 1], "thi": [0, 1, 2, 3, 4, 6, 8, 9], "those": 0, "threshold": 1, "through": 0, "throw": 0, "thu": [0, 1], "time": [0, 1, 6], "time_fram": 1, "time_unit": 0, "timefram": [0, 1, 2, 7], "timepoint": [1, 2, 7], "timeunit": 1, "todo": 0, "togeth": [0, 1], "token": [0, 2, 7], "toml": 8, "top": [0, 6, 8], "transcript": 6, "transfer": 5, "transpar": 6, "tree": 8, "tri": 0, "trim": 1, "true": [0, 2], "try": 0, "tupl": 1, "turn": 4, "two": [0, 1], "txt": 6, "type": [0, 1, 2, 5, 6], "type_uri": 2, "typesbas": 0, "under": 1, "underli": 1, "union": 0, "unit": [0, 1], "unless": 0, "unlik": 0, "unnam": 0, "unsupport": 6, "up": 1, "updat": [0, 6, 7], "uri": [0, 8], "url": 4, "us": [0, 1, 3, 6, 8], "user": [0, 6, 8], "util": [0, 5, 7], "v": 0, "v1": [2, 6], "v5": 2, "v6": 2, "v_": 0, "valid": [0, 5, 7], "validate_labelset": [1, 7], "validationerror": 0, "valu": [0, 1, 7], "valueerror": [0, 1, 8], "var": 6, "variabl": [0, 2], "variou": [0, 5, 6, 8], "verbchunk": [2, 7], "veri": 1, "version": [0, 1, 2, 5, 6, 8], "via": [4, 5, 6], "vid": 0, "video": [1, 6, 8], "video_doc": 1, "video_docu": 1, "video_document_help": 7, "videocaptur": 1, "videodocu": [1, 2, 6, 7], "videoobject": [2, 7], "view": [1, 6, 7], "view_id": 0, "view_obj": 0, "view_prefix": [0, 7], "viewmetadata": [0, 7], "viewmetadata_obj": 0, "visit": [6, 8], "visual": 4, "vocab_typ": 5, "vocabulari": [0, 5, 6, 7], "wa": 0, "wai": 0, "want": [0, 1, 3], "warn": [0, 1], "we": [0, 4, 6], "web": 4, "websit": [6, 8], "well": [0, 6, 8], "when": [0, 1, 6, 8], "where": 0, "whether": 0, "which": [0, 1, 6, 8], "while": [0, 1], "whisper": 0, "width": 1, "within": 0, "without": [0, 8], "won": 0, "work": [0, 1, 8], "workflow": 6, "would": 0, "wrapper": 0, "write": [0, 3, 8], "xist": 1, "you": [0, 1, 3, 6, 8], "your": [3, 8], "zero": [0, 1]}, "titles": ["mmif.serialize module", "mmif.utils module", "mmif.vocabulary module", "mmif_docloc_http package", "MMIF consumer", "Welcome to mmif-python\u2019s documentation!", "Getting Started", "mmif package", "Developing plugins for MMIF Python SDK", "Target MMIF Versions"], "titleterms": {"": 5, "For": 5, "annot": 0, "annotation_typ": 2, "api": 5, "bulit": 8, "consum": 4, "content": 5, "develop": 8, "document": [5, 8], "document_typ": 2, "format": 5, "get": 6, "indic": 5, "instal": 6, "interchang": 5, "locat": 8, "mmif": [0, 1, 2, 4, 5, 6, 7, 8, 9], "mmif_docloc_http": [3, 7], "model": 0, "modul": [0, 1, 2], "more": 5, "multimedia": 5, "overview": [6, 8], "packag": [3, 7], "plugin": 8, "prerequisit": 6, "python": [5, 8], "scheme": 8, "sdk": 8, "sequence_help": 1, "serial": [0, 6], "specif": 9, "start": 6, "tabl": 5, "target": 9, "util": 1, "version": 9, "video_document_help": 1, "view": 0, "vocabulari": 2, "welcom": 5}}) \ No newline at end of file diff --git a/docs/1.0.16/target-versions.html b/docs/1.0.16/target-versions.html deleted file mode 100644 index dcab3e52..00000000 --- a/docs/1.0.16/target-versions.html +++ /dev/null @@ -1,294 +0,0 @@ - - - - - - - - - Target MMIF Versions — mmif-python documentation - - - - - - - - - - - - - - - - - -
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Target MMIF Versions

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This article provides targeting MMIF specification versions of different versions of mmif-python SDK.

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Target Specification Versions

mmif-python version

Target MMIF Specification

1.0.16

1.1.0

1.0.15

1.0.4

1.0.14

1.0.4

1.0.13

1.0.4

1.0.12

1.0.4

1.0.11

1.0.4

1.0.10.dev1

1.0.3

1.0.10

1.0.2

1.0.9

1.1.0

1.0.8

1.0.0

1.0.7

1.0.0

1.0.6

1.0.0

1.0.5

1.0.0

1.0.4

1.0.0

1.0.3

1.0.0

1.0.2

1.0.0

1.0.1

1.0.0

1.0.0

0.5.0

0.5.2

0.5.0

0.5.1

0.5.0

0.5.0

0.5.0

0.4.8

0.4.2

0.4.7

0.4.1

0.4.6

0.4.0

0.4.5

0.4.0

0.4.4

0.4.0

0.4.3

0.4.0

0.4.2

0.4.0

0.4.1

0.4.0

0.4.0

0.4.0

0.3.5

0.3.1

0.3.4

0.3.1

0.3.3

0.3.1

0.3.2

0.3.1

0.3.1

0.3.0

0.3.0

0.3.0

0.2.2

0.2.1

0.2.1

0.2.1

0.2.0

0.2.1

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0.3.0
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0.3.1
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0.3.2
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0.3.3
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0.3.4
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0.3.5
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0.4.0
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0.4.1
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0.4.2
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0.4.3
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0.4.4
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0.4.5
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0.4.6
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0.4.7
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0.4.8
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0.5.0
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0.5.1
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0.5.2
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1.0.0
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1.0.1
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1.0.10
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1.0.11
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1.0.12
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1.0.13
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1.0.14
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1.0.15
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1.0.16
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1.0.17
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1.0.18
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1.0.19
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1.0.2
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1.0.3
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1.0.4
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1.0.5
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1.0.6
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1.0.7
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1.0.8
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1.0.9
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1.1.0
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-mmif.serialize.model module ---------------------------- - -.. automodule:: mmif.serialize.model - :members: - :undoc-members: - :show-inheritance: - -mmif.serialize.mmif module --------------------------- - -.. automodule:: mmif.serialize.mmif - :members: - :undoc-members: - :show-inheritance: - -mmif.serialize.view module --------------------------- - -.. automodule:: mmif.serialize.view - :members: - :undoc-members: - :show-inheritance: - -mmif.serialize.annotation module --------------------------------- - -.. automodule:: mmif.serialize.annotation - :members: - :undoc-members: - :show-inheritance: - diff --git a/docs/1.0.17/_sources/autodoc/mmif.utils.rst.txt b/docs/1.0.17/_sources/autodoc/mmif.utils.rst.txt deleted file mode 100644 index 9a6ecc44..00000000 --- a/docs/1.0.17/_sources/autodoc/mmif.utils.rst.txt +++ /dev/null @@ -1,18 +0,0 @@ -mmif.utils module -================= - -mmif.utils.video_document_helper module ----------------------------------------- - -.. automodule:: mmif.utils.video_document_helper - :members: - :undoc-members: - :show-inheritance: - -mmif.utils.sequence_helper module ---------------------------------- - -.. automodule:: mmif.utils.sequence_helper - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/1.0.17/_sources/autodoc/mmif.vocabulary.rst.txt b/docs/1.0.17/_sources/autodoc/mmif.vocabulary.rst.txt deleted file mode 100644 index d250c6a3..00000000 --- a/docs/1.0.17/_sources/autodoc/mmif.vocabulary.rst.txt +++ /dev/null @@ -1,18 +0,0 @@ -mmif.vocabulary module -====================== - -mmif.vocabulary.annotation\_types module ----------------------------------------- - -.. automodule:: mmif.vocabulary.annotation_types - :members: - :undoc-members: - :show-inheritance: - -mmif.vocabulary.document\_types module --------------------------------------- - -.. automodule:: mmif.vocabulary.document_types - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/1.0.17/_sources/autodoc/mmif_docloc_http.rst.txt b/docs/1.0.17/_sources/autodoc/mmif_docloc_http.rst.txt deleted file mode 100644 index b76c8df5..00000000 --- a/docs/1.0.17/_sources/autodoc/mmif_docloc_http.rst.txt +++ /dev/null @@ -1,11 +0,0 @@ -mmif_docloc_http package -======================== - -MMIF document location helper module for `http` and `https` schemes. -If you want to write your own docloc scheme handler, please use the source code of this module as a reference. -See this :ref:`plug-in section ` for more information. - -.. automodule:: mmif_docloc_http - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/1.0.17/_sources/consumer-tutorial.rst.txt b/docs/1.0.17/_sources/consumer-tutorial.rst.txt deleted file mode 100644 index c54634e2..00000000 --- a/docs/1.0.17/_sources/consumer-tutorial.rst.txt +++ /dev/null @@ -1,17 +0,0 @@ -.. _consumer-tutorial: - -MMIF consumer -================================= - -A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the `appliance documentation `_ to learn more about the appliance. - -MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance. - -#. The code must be hosted on a public git repository (e.g. Github, Gitlab, ...) -#. Must listen to ``5000`` port. -#. Must expose ``/display`` route . -#. ``/display`` router should response to ``GET`` requests. -#. In the ``GET`` request, a public URL of the input MMIF file is passed via ``file`` URL parameter. -#. On the codebase root, there must be a ``Dockerfile`` that can build a `docker `_ image that runs the web app. - -We provide an example consumer at https://github.com/clamsproject/mmif-visualizer. diff --git a/docs/1.0.17/_sources/index.rst.txt b/docs/1.0.17/_sources/index.rst.txt deleted file mode 100644 index beb56aae..00000000 --- a/docs/1.0.17/_sources/index.rst.txt +++ /dev/null @@ -1,26 +0,0 @@ -Welcome to mmif-python's documentation! -======================================= - -.. mdinclude:: ../README.md - -.. toctree:: - :maxdepth: 2 - :caption: Contents - - introduction - plugins - target-versions - -.. toctree:: - :maxdepth: 2 - :caption: API documentation: - - modules - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/docs/1.0.17/_sources/introduction.rst.txt b/docs/1.0.17/_sources/introduction.rst.txt deleted file mode 100644 index cfd9eaf7..00000000 --- a/docs/1.0.17/_sources/introduction.rst.txt +++ /dev/null @@ -1,89 +0,0 @@ -.. _introduction: - -Getting Started -=============== - - -Overview ---------- - -MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for reproducibility, transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF website `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects. - -Prerequisites -------------- - -* `Python `_: the latest ``mmif-python`` requires Python 3.8 or newer. We have no plan to support `Python 2.7 `_. - -Installation ---------------- - -Package ``mmif-python`` is distributed via the official PyPI. Users are supposed to pip-install to get latest release. - -.. code-block:: bash - - pip install mmif-python - -This will install a package `mmif` to local python. - -The MMIF format and specification is evolving over time, and ``mmif-python`` package will be updated along with the changes in MMIF format. - -.. note:: MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and ``mmif-python`` versions, please take time to read our decision on the subject `here `_. If you need to know which python SDK supports which specification version, see :ref:`target-versions` page. - -MMIF Serialization ---------------------------- - -:class:`mmif.serialize.mmif.Mmif` represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of :class:`mmif.serialize.model.MmifObject`, including the :class:`mmif.serialize.mmif.Mmif`. To start with an existing MMIF :class:`str`, simple initiate a new ``Mmif`` object with the file. - -.. code-block:: python - - import mmif - from mmif import Mmif - - mmif_str = """{ - "metadata": { - "mmif": "http://mmif.clams.ai/1.0.0" - }, - "documents": [ - { - "@type": "http://mmif.clams.ai/vocabulary/VideoDocument/v1", - "properties": { - "id": "m1", - "mime": "video/mp4", - "location": "file:///var/archive/video-0012.mp4" - } - }, - { - "@type": "http://mmif.clams.ai/vocabulary/TextDocument/v1", - "properties": { - "id": "m2", - "mime": "text/plain", - "location": "file:///var/archive/video-0012-transcript.txt" - } - } - ], - "views": []}""" - mmif_obj = Mmif(mmif_str) - - -Few notes; - -#. MMIF does not carry the primary source files in it. -#. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version ``mmif-python`` implementation of the MMIF might not be able to load an unsupported version of MMIF string. - -When serializing back to :class:`str`, call :meth:`mmif.serialize.model.MmifObject.serialize` on the object. - -To get subcomponents, you can use various getters implemented in subclasses. For example; - -.. code-block:: python - - from mmif.vocabulary.document_types import DocumentTypes - - for video in mmif_obj.Mmif.get_documents_by_type(DocumentTypes.VideoDocument): - with open(video.location_path(), 'b') as in_video: - # do something with the video file - - -For a full list of available helper methods, please refer to :ref:`the API documentation `. - diff --git a/docs/1.0.17/_sources/modules.rst.txt b/docs/1.0.17/_sources/modules.rst.txt deleted file mode 100644 index 4bb9307d..00000000 --- a/docs/1.0.17/_sources/modules.rst.txt +++ /dev/null @@ -1,20 +0,0 @@ -.. _apidoc: - -mmif package -============ - -.. toctree:: - :maxdepth: 4 - - autodoc/mmif.serialize - autodoc/mmif.vocabulary - autodoc/mmif.utils - -mmif_docloc_http package -======================== - -.. toctree:: - :maxdepth: 2 - - autodoc/mmif_docloc_http - diff --git a/docs/1.0.17/_sources/plugins.rst.txt b/docs/1.0.17/_sources/plugins.rst.txt deleted file mode 100644 index 9907c495..00000000 --- a/docs/1.0.17/_sources/plugins.rst.txt +++ /dev/null @@ -1,83 +0,0 @@ -.. _plugins: - -Developing plugins for MMIF Python SDK -====================================== - - -Overview --------- - -As MMIF JSON files can carry information about media document files without actually carrying file contents, file accessing modules in ``mmif`` Python package (distributed as ``mmif-python`` on PyPI) are designed to be lightweight and flexible so that it can work with additional "plugin" Python packages that can handle concrete file access. - - -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF website `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects. - -Developer can write simple plugins that can provide additional functionalities to ``mmif-python``. For example, ``mmif-python`` does not provide any file access functionality beyond a local file system (with ``file`` scheme), but it can be extended with a plugin that can handle file access over different protocols (e.g. ``http``, ``s3``, ``ftp``, etc). - -This document contains information about how to write plugins for ``mmif-python``. - -.. _docloc_plugin: - -Document Location Scheme Plugins -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -:class:`mmif.serialize.annotation.Document` class has various methods to access parts of ``location`` property of the document. The location is in `URI/IRI format `_ (``SCHEME://HOSTNAME/PATH``, in a nutshell) and it has to be resolved to a local file for CLAMS Apps to process the local file to analyze and extract information about the media and its contents. The core ``mmif-python`` distribution only provides a default implementation that can handle ``file`` scheme URIs. - -To add a document location handler plugin, you need to implement a Python `"package" `_ (do not confuse with PYPI distribution), that meets these requirements; - -#. the package must be named ``mmif_docloc_``. For example, to implement a handler for ``s3`` scheme, the package name must be ``mmif_docloc_s3``. The prefix is important as it's used in the plugin discovery process from the core ``mmif-python`` modules. -#. the top module of the package must have a function named ``resolve``. The function must take a single argument, which is a :class:`str` of the document location URI. The function must return a :class:`str` of the local file path. For example, if the document location is ``s3://mybucket/myfile.mp4``, a Python user should be able to to something like this; - -.. code-block:: python - - import mmif_docloc_s3 - resolved = mmif_docloc_s3.resolve('s3://mybucket/myfile.mp4') - # then resolved must be a local file path that can be used to open the file - - -Here's a minimal example codebase that you refer to when you develop a ``docloc`` plugin. - -(However, before you start writing your own plugin for a specific URI scheme, checking `if there's already a PyPI distribution `_ for the scheme might be a good idea.) - -.. code-block:: sh - - $ tree . - . - ├── mmif_docloc_dummy - │ └── __init__.py - ├── pyproject.toml - └── setup.cfg - - $ cat pyproject.toml - [build-system] - requires = ["setuptools"] - build-backend = "setuptools.build_meta" - - $ cat setup.cfg - [metadata] - name = mmif_docloc_dummy # this name is IMPORTANT - version = 0.0.1 - description = a plugin to mmif-pyhon to handle `dummy` location scheme - - -And the plugin code. - -.. code-block:: python - - # mmif_docloc_dummy/__init__.py - doc_types = {'video': 'mp4'} - - def resolve(docloc): - scheme = 'dummy' - if docloc.startswith(f'{scheme}://'): - doc_id, doc_type = docloc.split('.') - return f'/path/to/{doc_id}.{doc_types[doc_type]}' - else: - raise ValueError(f'cannot handle document location scheme: {docloc}') - -Bulit-in Document Location Scheme Plugins -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -At the moment, ``mmif-python`` PyPI distribution ships a built-in *docloc* plugin that support both ``http`` and ``https`` schemes. -Take a look at :mod:`mmif_docloc_http` module for details. diff --git a/docs/1.0.17/_sources/target-versions.rst.txt b/docs/1.0.17/_sources/target-versions.rst.txt deleted file mode 100644 index 34216d3e..00000000 --- a/docs/1.0.17/_sources/target-versions.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _target-versions: - -Target MMIF Versions -==================== - -This article provides targeting MMIF specification versions of different versions of ``mmif-python`` SDK. - -.. csv-table:: Target Specification Versions - :file: target-versions.csv - :header-rows: 1 diff --git a/docs/1.0.17/_static/_sphinx_javascript_frameworks_compat.js b/docs/1.0.17/_static/_sphinx_javascript_frameworks_compat.js deleted file mode 100644 index 81415803..00000000 --- a/docs/1.0.17/_static/_sphinx_javascript_frameworks_compat.js +++ /dev/null @@ -1,123 +0,0 @@ -/* Compatability shim for jQuery and underscores.js. - * - * Copyright Sphinx contributors - * Released under the two clause BSD licence - */ - -/** - * small helper function to urldecode strings - * - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL - */ -jQuery.urldecode = function(x) { - if (!x) { - return x - } - return decodeURIComponent(x.replace(/\+/g, ' ')); -}; - -/** - * small helper function to urlencode strings - */ -jQuery.urlencode = encodeURIComponent; - -/** - * This function returns the parsed url parameters of the - * current request. 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- -/** - * Simple result scoring code. - */ -if (typeof Scorer === "undefined") { - var Scorer = { - // Implement the following function to further tweak the score for each result - // The function takes a result array [docname, title, anchor, descr, score, filename] - // and returns the new score. - /* - score: result => { - const [docname, title, anchor, descr, score, filename, kind] = result - return score - }, - */ - - // query matches the full name of an object - objNameMatch: 11, - // or matches in the last dotted part of the object name - objPartialMatch: 6, - // Additive scores depending on the priority of the object - objPrio: { - 0: 15, // used to be importantResults - 1: 5, // used to be objectResults - 2: -5, // used to be unimportantResults - }, - // Used when the priority is not in the mapping. - objPrioDefault: 0, - - // query found in title - title: 15, - partialTitle: 7, - // query found in terms - term: 5, - partialTerm: 2, - }; -} - -// Global search result kind enum, used by themes to style search results. -class SearchResultKind { - static get index() { return "index"; } - static get object() { return "object"; } - static get text() { return "text"; } - static get title() { return "title"; } -} - -const _removeChildren = (element) => { - while (element && element.lastChild) element.removeChild(element.lastChild); -}; - -/** - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping - */ -const _escapeRegExp = (string) => - string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string - -const _displayItem = (item, searchTerms, highlightTerms) => { - const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; - const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; - const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; - const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; - const contentRoot = document.documentElement.dataset.content_root; - - const [docName, title, anchor, descr, score, _filename, kind] = item; - - let listItem = document.createElement("li"); - // Add a class representing the item's type: - // can be used by a theme's CSS selector for styling - // See SearchResultKind for the class names. - listItem.classList.add(`kind-${kind}`); - let requestUrl; - let linkUrl; - if (docBuilder === "dirhtml") { - // dirhtml builder - let dirname = docName + "/"; - if (dirname.match(/\/index\/$/)) - dirname = dirname.substring(0, dirname.length - 6); - else if (dirname === "index/") dirname = ""; - requestUrl = contentRoot + dirname; - linkUrl = requestUrl; - } else { - // normal html builders - requestUrl = contentRoot + docName + docFileSuffix; - linkUrl = docName + docLinkSuffix; - } - let linkEl = listItem.appendChild(document.createElement("a")); - linkEl.href = linkUrl + anchor; - linkEl.dataset.score = score; - linkEl.innerHTML = title; - if (descr) { - listItem.appendChild(document.createElement("span")).innerHTML = - " (" + descr + ")"; - // highlight search terms in the description - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - } - else if (showSearchSummary) - fetch(requestUrl) - .then((responseData) => responseData.text()) - .then((data) => { - if (data) - listItem.appendChild( - Search.makeSearchSummary(data, searchTerms, anchor) - ); - // highlight search terms in the summary - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - }); - Search.output.appendChild(listItem); -}; -const _finishSearch = (resultCount) => { - Search.stopPulse(); - Search.title.innerText = _("Search Results"); - if (!resultCount) - Search.status.innerText = Documentation.gettext( - "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." - ); - else - Search.status.innerText = Documentation.ngettext( - "Search finished, found one page matching the search query.", - "Search finished, found ${resultCount} pages matching the search query.", - resultCount, - ).replace('${resultCount}', resultCount); -}; -const _displayNextItem = ( - results, - resultCount, - searchTerms, - highlightTerms, -) => { - // results left, load the summary and display it - // this is intended to be dynamic (don't sub resultsCount) - if (results.length) { - _displayItem(results.pop(), searchTerms, highlightTerms); - setTimeout( - () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), - 5 - ); - } - // search finished, update title and status message - else _finishSearch(resultCount); -}; -// Helper function used by query() to order search results. -// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. -// Order the results by score (in opposite order of appearance, since the -// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. -const _orderResultsByScoreThenName = (a, b) => { - const leftScore = a[4]; - const rightScore = b[4]; - if (leftScore === rightScore) { - // same score: sort alphabetically - const leftTitle = a[1].toLowerCase(); - const rightTitle = b[1].toLowerCase(); - if (leftTitle === rightTitle) return 0; - return leftTitle > rightTitle ? -1 : 1; // inverted is intentional - } - return leftScore > rightScore ? 1 : -1; -}; - -/** - * Default splitQuery function. Can be overridden in ``sphinx.search`` with a - * custom function per language. - * - * The regular expression works by splitting the string on consecutive characters - * that are not Unicode letters, numbers, underscores, or emoji characters. - * This is the same as ``\W+`` in Python, preserving the surrogate pair area. - */ -if (typeof splitQuery === "undefined") { - var splitQuery = (query) => query - .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) - .filter(term => term) // remove remaining empty strings -} - -/** - * Search Module - */ -const Search = { - _index: null, - _queued_query: null, - _pulse_status: -1, - - htmlToText: (htmlString, anchor) => { - const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - for (const removalQuery of [".headerlink", "script", "style"]) { - htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); - } - if (anchor) { - const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); - if (anchorContent) return anchorContent.textContent; - - console.warn( - `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` - ); - } - - // if anchor not specified or not found, fall back to main content - const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent) return docContent.textContent; - - console.warn( - "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." - ); - return ""; - }, - - init: () => { - const query = new URLSearchParams(window.location.search).get("q"); - document - .querySelectorAll('input[name="q"]') - .forEach((el) => (el.value = query)); - if (query) Search.performSearch(query); - }, - - loadIndex: (url) => - (document.body.appendChild(document.createElement("script")).src = url), - - setIndex: (index) => { - Search._index = index; - if (Search._queued_query !== null) { - const query = Search._queued_query; - Search._queued_query = null; - Search.query(query); - } - }, - - hasIndex: () => Search._index !== null, - - deferQuery: (query) => (Search._queued_query = query), - - stopPulse: () => (Search._pulse_status = -1), - - startPulse: () => { - if (Search._pulse_status >= 0) return; - - const pulse = () => { - Search._pulse_status = (Search._pulse_status + 1) % 4; - Search.dots.innerText = ".".repeat(Search._pulse_status); - if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); - }; - pulse(); - }, - - /** - * perform a search for something (or wait until index is loaded) - */ - performSearch: (query) => { - // create the required interface elements - const searchText = document.createElement("h2"); - searchText.textContent = _("Searching"); - const searchSummary = document.createElement("p"); - searchSummary.classList.add("search-summary"); - searchSummary.innerText = ""; - const searchList = document.createElement("ul"); - searchList.setAttribute("role", "list"); - searchList.classList.add("search"); - - const out = document.getElementById("search-results"); - Search.title = out.appendChild(searchText); - Search.dots = Search.title.appendChild(document.createElement("span")); - Search.status = out.appendChild(searchSummary); - Search.output = out.appendChild(searchList); - - const searchProgress = document.getElementById("search-progress"); - // Some themes don't use the search progress node - if (searchProgress) { - searchProgress.innerText = _("Preparing search..."); - } - Search.startPulse(); - - // index already loaded, the browser was quick! - if (Search.hasIndex()) Search.query(query); - else Search.deferQuery(query); - }, - - _parseQuery: (query) => { - // stem the search terms and add them to the correct list - const stemmer = new Stemmer(); - const searchTerms = new Set(); - const excludedTerms = new Set(); - const highlightTerms = new Set(); - const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); - splitQuery(query.trim()).forEach((queryTerm) => { - const queryTermLower = queryTerm.toLowerCase(); - - // maybe skip this "word" - // stopwords array is from language_data.js - if ( - stopwords.indexOf(queryTermLower) !== -1 || - queryTerm.match(/^\d+$/) - ) - return; - - // stem the word - let word = stemmer.stemWord(queryTermLower); - // select the correct list - if (word[0] === "-") excludedTerms.add(word.substr(1)); - else { - searchTerms.add(word); - highlightTerms.add(queryTermLower); - } - }); - - if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js - localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) - } - - // console.debug("SEARCH: searching for:"); - // console.info("required: ", [...searchTerms]); - // console.info("excluded: ", [...excludedTerms]); - - return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; - }, - - /** - * execute search (requires search index to be loaded) - */ - _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - - // Collect multiple result groups to be sorted separately and then ordered. - // Each is an array of [docname, title, anchor, descr, score, filename, kind]. - const normalResults = []; - const nonMainIndexResults = []; - - _removeChildren(document.getElementById("search-progress")); - - const queryLower = query.toLowerCase().trim(); - for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { - for (const [file, id] of foundTitles) { - const score = Math.round(Scorer.title * queryLower.length / title.length); - const boost = titles[file] === title ? 1 : 0; // add a boost for document titles - normalResults.push([ - docNames[file], - titles[file] !== title ? `${titles[file]} > ${title}` : title, - id !== null ? "#" + id : "", - null, - score + boost, - filenames[file], - SearchResultKind.title, - ]); - } - } - } - - // search for explicit entries in index directives - for (const [entry, foundEntries] of Object.entries(indexEntries)) { - if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id, isMain] of foundEntries) { - const score = Math.round(100 * queryLower.length / entry.length); - const result = [ - docNames[file], - titles[file], - id ? "#" + id : "", - null, - score, - filenames[file], - SearchResultKind.index, - ]; - if (isMain) { - normalResults.push(result); - } else { - nonMainIndexResults.push(result); - } - } - } - } - - // lookup as object - objectTerms.forEach((term) => - normalResults.push(...Search.performObjectSearch(term, objectTerms)) - ); - - // lookup as search terms in fulltext - normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); - - // let the scorer override scores with a custom scoring function - if (Scorer.score) { - normalResults.forEach((item) => (item[4] = Scorer.score(item))); - nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); - } - - // Sort each group of results by score and then alphabetically by name. - normalResults.sort(_orderResultsByScoreThenName); - nonMainIndexResults.sort(_orderResultsByScoreThenName); - - // Combine the result groups in (reverse) order. - // Non-main index entries are typically arbitrary cross-references, - // so display them after other results. - let results = [...nonMainIndexResults, ...normalResults]; - - // remove duplicate search results - // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept - let seen = new Set(); - results = results.reverse().reduce((acc, result) => { - let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); - if (!seen.has(resultStr)) { - acc.push(result); - seen.add(resultStr); - } - return acc; - }, []); - - return results.reverse(); - }, - - query: (query) => { - const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); - const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); - - // for debugging - //Search.lastresults = results.slice(); // a copy - // console.info("search results:", Search.lastresults); - - // print the results - _displayNextItem(results, results.length, searchTerms, highlightTerms); - }, - - /** - * search for object names - */ - performObjectSearch: (object, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const objects = Search._index.objects; - const objNames = Search._index.objnames; - const titles = Search._index.titles; - - const results = []; - - const objectSearchCallback = (prefix, match) => { - const name = match[4] - const fullname = (prefix ? prefix + "." : "") + name; - const fullnameLower = fullname.toLowerCase(); - if (fullnameLower.indexOf(object) < 0) return; - - let score = 0; - const parts = fullnameLower.split("."); - - // check for different match types: exact matches of full name or - // "last name" (i.e. last dotted part) - if (fullnameLower === object || parts.slice(-1)[0] === object) - score += Scorer.objNameMatch; - else if (parts.slice(-1)[0].indexOf(object) > -1) - score += Scorer.objPartialMatch; // matches in last name - - const objName = objNames[match[1]][2]; - const title = titles[match[0]]; - - // If more than one term searched for, we require other words to be - // found in the name/title/description - const otherTerms = new Set(objectTerms); - otherTerms.delete(object); - if (otherTerms.size > 0) { - const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); - if ( - [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) - ) - return; - } - - let anchor = match[3]; - if (anchor === "") anchor = fullname; - else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; - - const descr = objName + _(", in ") + title; - - // add custom score for some objects according to scorer - if (Scorer.objPrio.hasOwnProperty(match[2])) - score += Scorer.objPrio[match[2]]; - else score += Scorer.objPrioDefault; - - results.push([ - docNames[match[0]], - fullname, - "#" + anchor, - descr, - score, - filenames[match[0]], - SearchResultKind.object, - ]); - }; - Object.keys(objects).forEach((prefix) => - objects[prefix].forEach((array) => - objectSearchCallback(prefix, array) - ) - ); - return results; - }, - - /** - * search for full-text terms in the index - */ - performTermsSearch: (searchTerms, excludedTerms) => { - // prepare search - const terms = Search._index.terms; - const titleTerms = Search._index.titleterms; - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - - const scoreMap = new Map(); - const fileMap = new Map(); - - // perform the search on the required terms - searchTerms.forEach((word) => { - const files = []; - const arr = [ - { files: terms[word], score: Scorer.term }, - { files: titleTerms[word], score: Scorer.title }, - ]; - // add support for partial matches - if (word.length > 2) { - const escapedWord = _escapeRegExp(word); - if (!terms.hasOwnProperty(word)) { - Object.keys(terms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: terms[term], score: Scorer.partialTerm }); - }); - } - if (!titleTerms.hasOwnProperty(word)) { - Object.keys(titleTerms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); - }); - } - } - - // no match but word was a required one - if (arr.every((record) => record.files === undefined)) return; - - // found search word in contents - arr.forEach((record) => { - if (record.files === undefined) return; - - let recordFiles = record.files; - if (recordFiles.length === undefined) recordFiles = [recordFiles]; - files.push(...recordFiles); - - // set score for the word in each file - recordFiles.forEach((file) => { - if (!scoreMap.has(file)) scoreMap.set(file, {}); - scoreMap.get(file)[word] = record.score; - }); - }); - - // create the mapping - files.forEach((file) => { - if (!fileMap.has(file)) fileMap.set(file, [word]); - else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); - }); - }); - - // now check if the files don't contain excluded terms - const results = []; - for (const [file, wordList] of fileMap) { - // check if all requirements are matched - - // as search terms with length < 3 are discarded - const filteredTermCount = [...searchTerms].filter( - (term) => term.length > 2 - ).length; - if ( - wordList.length !== searchTerms.size && - wordList.length !== filteredTermCount - ) - continue; - - // ensure that none of the excluded terms is in the search result - if ( - [...excludedTerms].some( - (term) => - terms[term] === file || - titleTerms[term] === file || - (terms[term] || []).includes(file) || - (titleTerms[term] || []).includes(file) - ) - ) - break; - - // select one (max) score for the file. - const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); - // add result to the result list - results.push([ - docNames[file], - titles[file], - "", - null, - score, - filenames[file], - SearchResultKind.text, - ]); - } - return results; - }, - - /** - * helper function to return a node containing the - * search summary for a given text. keywords is a list - * of stemmed words. - */ - makeSearchSummary: (htmlText, keywords, anchor) => { - const text = Search.htmlToText(htmlText, anchor); - if (text === "") return null; - - const textLower = text.toLowerCase(); - const actualStartPosition = [...keywords] - .map((k) => textLower.indexOf(k.toLowerCase())) - .filter((i) => i > -1) - .slice(-1)[0]; - const startWithContext = Math.max(actualStartPosition - 120, 0); - - const top = startWithContext === 0 ? "" : "..."; - const tail = startWithContext + 240 < text.length ? "..." : ""; - - let summary = document.createElement("p"); - summary.classList.add("context"); - summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; - - return summary; - }, -}; - -_ready(Search.init); diff --git a/docs/1.0.17/_static/sphinx_highlight.js b/docs/1.0.17/_static/sphinx_highlight.js deleted file mode 100644 index 8a96c69a..00000000 --- a/docs/1.0.17/_static/sphinx_highlight.js +++ /dev/null @@ -1,154 +0,0 @@ -/* Highlighting utilities for Sphinx HTML documentation. */ -"use strict"; - -const SPHINX_HIGHLIGHT_ENABLED = true - -/** - * highlight a given string on a node by wrapping it in - * span elements with the given class name. - */ -const _highlight = (node, addItems, text, className) => { - if (node.nodeType === Node.TEXT_NODE) { - const val = node.nodeValue; - const parent = node.parentNode; - const pos = val.toLowerCase().indexOf(text); - if ( - pos >= 0 && - !parent.classList.contains(className) && - !parent.classList.contains("nohighlight") - ) { - let span; - - const closestNode = parent.closest("body, svg, foreignObject"); - const isInSVG = closestNode && closestNode.matches("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.classList.add(className); - } - - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - const rest = document.createTextNode(val.substr(pos + text.length)); - parent.insertBefore( - span, - parent.insertBefore( - rest, - node.nextSibling - ) - ); - node.nodeValue = val.substr(0, pos); - /* There may be more occurrences of search term in this node. So call this - * function recursively on the remaining fragment. - */ - _highlight(rest, addItems, text, className); - - if (isInSVG) { - const rect = document.createElementNS( - "http://www.w3.org/2000/svg", - "rect" - ); - const bbox = parent.getBBox(); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute("class", className); - addItems.push({ parent: parent, target: rect }); - } - } - } else if (node.matches && !node.matches("button, select, textarea")) { - node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); - } -}; -const _highlightText = (thisNode, text, className) => { - let addItems = []; - _highlight(thisNode, addItems, text, className); - addItems.forEach((obj) => - obj.parent.insertAdjacentElement("beforebegin", obj.target) - ); -}; - -/** - * Small JavaScript module for the documentation. - */ -const SphinxHighlight = { - - /** - * highlight the search words provided in localstorage in the text - */ - highlightSearchWords: () => { - if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight - - // get and clear terms from localstorage - const url = new URL(window.location); - const highlight = - localStorage.getItem("sphinx_highlight_terms") - || url.searchParams.get("highlight") - || ""; - localStorage.removeItem("sphinx_highlight_terms") - url.searchParams.delete("highlight"); - window.history.replaceState({}, "", url); - - // get individual terms from highlight string - const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); - if (terms.length === 0) return; // nothing to do - - // There should never be more than one element matching "div.body" - const divBody = document.querySelectorAll("div.body"); - const body = divBody.length ? divBody[0] : document.querySelector("body"); - window.setTimeout(() => { - terms.forEach((term) => _highlightText(body, term, "highlighted")); - }, 10); - - const searchBox = document.getElementById("searchbox"); - if (searchBox === null) return; - searchBox.appendChild( - document - .createRange() - .createContextualFragment( - '

' + - '' + - _("Hide Search Matches") + - "

" - ) - ); - }, - - /** - * helper function to hide the search marks again - */ - hideSearchWords: () => { - document - .querySelectorAll("#searchbox .highlight-link") - .forEach((el) => el.remove()); - document - .querySelectorAll("span.highlighted") - .forEach((el) => el.classList.remove("highlighted")); - localStorage.removeItem("sphinx_highlight_terms") - }, - - initEscapeListener: () => { - // only install a listener if it is really needed - if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; - - document.addEventListener("keydown", (event) => { - // bail for input elements - if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; - // bail with special keys - if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; - if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { - SphinxHighlight.hideSearchWords(); - event.preventDefault(); - } - }); - }, -}; - -_ready(() => { - /* Do not call highlightSearchWords() when we are on the search page. - * It will highlight words from the *previous* search query. - */ - if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); - SphinxHighlight.initEscapeListener(); -}); diff --git a/docs/1.0.17/autodoc/mmif.serialize.html b/docs/1.0.17/autodoc/mmif.serialize.html deleted file mode 100644 index 3e08f83b..00000000 --- a/docs/1.0.17/autodoc/mmif.serialize.html +++ /dev/null @@ -1,1469 +0,0 @@ - - - - - - - - - mmif.serialize module — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
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mmif.serialize module

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mmif.serialize.model module

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The model module contains the classes used to represent an -abstract MMIF object as a live Python object.

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The MmifObject class or one of its derivatives is subclassed by -all other classes defined in this SDK, except for MmifObjectEncoder.

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These objects are generally instantiated from JSON, either as a string -or as an already-loaded Python dictionary. This base class provides the -core functionality for deserializing MMIF JSON data into live objects -and serializing live objects into MMIF JSON data. Specialized behavior -for the different components of MMIF is added in the subclasses.

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-class mmif.serialize.model.DataDict(mmif_obj: bytes | str | dict | None = None, *_)[source]
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Bases: MmifObject, Generic[T, S]

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-empty()[source]
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-get(key: T, default=None) → S | None[source]
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-items()[source]
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-keys()[source]
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-update(other, overwrite)[source]
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-values()[source]
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-class mmif.serialize.model.DataList(mmif_obj: bytes | str | list | None = None, *_)[source]
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Bases: MmifObject, Generic[T]

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The DataList class is an abstraction that represents the -various lists found in a MMIF file, such as documents, subdocuments, -views, and annotations.

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Parameters:
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mmif_obj (Union[str, list]) – the data that the list contains

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-append(value, overwrite)[source]
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-deserialize(mmif_json: str | list) → None[source]
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Passes the input data into the internal deserializer.

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-empty()[source]
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-get(key: str) → T | None[source]
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Standard dictionary-style get() method, albeit with no default -parameter. Relies on the implementation of __getitem__.

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Will return None if the key is not found.

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Parameters:
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key – the key to search for

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Returns:
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the value matching that key

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-class mmif.serialize.model.MmifObject(mmif_obj: bytes | str | dict | None = None, *_)[source]
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Bases: object

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Abstract superclass for MMIF related key-value pair objects.

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Any MMIF object can be initialized as an empty placeholder or -an actual representation with a JSON formatted string or equivalent -dict object argument.

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This superclass has four specially designed instance variables, and these -variable names cannot be used as attribute names for MMIF objects.

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  1. _unnamed_attributes: -Only can be either None or an empty dictionary. If it’s set to None, -it means the class won’t take any Additional Attributes in the -JSON schema sense. If it’s an empty dict, users can throw any k-v -pairs to the class, as long as the key is not a “reserved” name, -and those additional attributes will be stored in this dict while -in memory.

    2. -

  2. _attribute_classes: -This is a dict from a key name to a specific python class to use for -deserialize the value. Note that a key name in this dict does NOT -have to be a named attribute, but is recommended to be one.

    3. -

  3. _required_attributes: -This is a simple list of names of attributes that are required in -the object. When serialize, an object will skip its empty (e.g. -zero-length, or None) attributes unless they are in this list. -Otherwise, the serialized JSON string would have empty -representations (e.g. "", []).

    4. -

  4. _exclude_from_diff: -This is a simple list of names of attributes that should be excluded -from the diff calculation in __eq__.

    5. -
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# TODO (krim @ 8/17/20): this dict is however, a duplicate with the type hints in the class definition. -Maybe there is a better way to utilize type hints (e.g. getting them -as a programmatically), but for now developers should be careful to -add types to hints as well as to this dict.

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Also note that those special attributes MUST be set in the __init__() -before calling super method, otherwise deserialization will not work.

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And also, a subclass that has one or more named attributes, it must -set those attributes in the __init__() before calling super method. -When serializing a MmifObject, all empty attributes will be ignored, -so for optional named attributes, you must leave the values empty -(len == 0), but NOT None. Any None-valued named attributes will cause -issues with current implementation.

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Parameters:
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mmif_obj – JSON string or dict to initialize an object. -If not given, an empty object will be initialized, sometimes with -an ID value automatically generated, based on its parent object.

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-deserialize(mmif_json: str | dict) → None[source]
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Takes a JSON-formatted string or a simple dict that’s json-loaded from -such a string as an input and populates object’s fields with the values -specified in the input.

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Parameters:
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mmif_json – JSON-formatted string or dict from such a string -that represents a MMIF object

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-disallow_additional_properties() → None[source]
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Call this method in __init__() to prevent the insertion -of unnamed attributes after initialization.

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-id_delimiter: ClassVar[str] = ':'[source]
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-static is_empty(obj) → bool[source]
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return True if the obj is None or “emtpy”. The emptiness first defined as -having zero length. But for objects that lack __len__ method, we need -additional check.

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-reserved_names: Set[str] = {'_attribute_classes', '_exclude_from_diff', '_required_attributes', '_unnamed_attributes', 'reserved_names'}[source]
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-serialize(pretty: bool = False) → str[source]
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Generates JSON representation of an object.

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Parameters:
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pretty – If True, returns string representation with indentation.

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Returns:
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JSON string of the object.

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-set_additional_property(key: str, value: Any) → None[source]
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Method to set values in _unnamed_attributes.

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Parameters:
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  • key – the attribute name

    • -

  • value – the desired value

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Returns:
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None

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Raise:
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AttributeError if additional properties are disallowed by disallow_additional_properties()

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-view_prefix: ClassVar[str] = 'v_'[source]
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-class mmif.serialize.model.MmifObjectEncoder(*, skipkeys=False, ensure_ascii=True, check_circular=True, allow_nan=True, sort_keys=False, indent=None, separators=None, default=None)[source]
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Bases: JSONEncoder

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Encoder class to define behaviors of de-/serialization

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-default(obj: MmifObject)[source]
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Overrides default encoding behavior to prioritize MmifObject.serialize().

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mmif.serialize.mmif module

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The mmif module contains the classes used to represent a full MMIF -file as a live Python object.

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See the specification docs and the JSON Schema file for more information.

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-class mmif.serialize.mmif.Mmif(mmif_obj: bytes | str | dict | None = None, *, validate: bool = True)[source]
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Bases: MmifObject

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MmifObject that represents a full MMIF file.

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Parameters:
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  • mmif_obj – the JSON data

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  • validate – whether to validate the data against the MMIF JSON schema.

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-add_document(document: Document, overwrite=False) → None[source]
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Appends a Document object to the documents list.

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Fails if there is already a document with the same ID in the MMIF object.

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Parameters:
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  • document – the Document object to add

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  • overwrite – if set to True, will overwrite -an existing view with the same ID

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Returns:
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None

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-add_view(view: View, overwrite=False) → None[source]
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Appends a View object to the views list.

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Fails if there is already a view with the same ID in the MMIF object.

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Parameters:
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  • view – the Document object to add

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  • overwrite – if set to True, will overwrite -an existing view with the same ID

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Returns:
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None

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-generate_capital_annotations()[source]
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Automatically convert any “pending” temporary properties from -Document objects to Annotation objects . The generated Annotation -objects are then added to the last View in the views lists.

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See https://github.com/clamsproject/mmif-python/issues/226 for rationale -behind this behavior and discussion.

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-get_alignments(at_type1: str | TypesBase, at_type2: str | TypesBase) → Dict[str, List[Annotation]][source]
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Finds views where alignments between two given annotation types occurred.

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Returns:
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a dict that keyed by view IDs (str) and has lists of alignment Annotation objects as values.

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-get_all_views_contain(*at_types: TypesBase | str) → List[View][source]
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Returns the list of all views in the MMIF if given types -are present in that view’s ‘contains’ metadata.

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Parameters:
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at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

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Returns:
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the list of views that contain the type

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-get_all_views_with_error() → List[View][source]
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Returns the list of all views in the MMIF that have errors.

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Returns:
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the list of views that contain errors but no annotations

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-get_annotations_between_time(start: int | float, end: int | float, time_unit: str = 'ms', at_types: List[str | TypesBase] = []) → Iterator[Annotation][source]
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Finds annotations that are anchored between the given time points.

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Parameters:
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  • start – the start time point in the unit of input_unit

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  • end – the end time point in the unit of input_unit

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  • time_unit – the unit of the input time points. Default is ms.

    • -

  • at_types – a list of annotation types to filter with. Any type in this list will be included in the return.

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Returns:
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an iterator of Annotation objects that are anchored between the given time points

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-get_document_by_id(doc_id: str) → Document[source]
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Finds a Document object with the given ID.

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Parameters:
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doc_id – the ID to search for

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Returns:
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a reference to the corresponding document, if it exists

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Raises:
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KeyError – if there is no corresponding document

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-get_document_location(m_type: DocumentTypes | str, path_only=False) → str | None[source]
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Method to get the location of first document of given type.

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Parameters:
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m_type – the type to search for

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Returns:
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the value of the location field in the corresponding document

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-get_documents_by_app(app_id: str) → List[Document][source]
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Method to get all documents object queries by its originated app name.

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Parameters:
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app_id – the app name to search for

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Returns:
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a list of documents matching the requested app name, or an empty list if the app not found

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-get_documents_by_property(prop_key: str, prop_value: str) → List[Document][source]
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Method to retrieve documents by an arbitrary key-value pair in the document properties objects.

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Parameters:
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  • prop_key – the metadata key to search for

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  • prop_value – the metadata value to match

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Returns:
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a list of documents matching the requested metadata key-value pair

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-get_documents_by_type(doc_type: str | DocumentTypes) → List[Document][source]
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Method to get all documents where the type matches a particular document type, which should be one of the CLAMS document types.

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Parameters:
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doc_type – the type of documents to search for, must be one of Document type defined in the CLAMS vocabulary.

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Returns:
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a list of documents matching the requested type, or an empty list if none found.

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-get_documents_in_view(vid: str | None = None) → List[Document][source]
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Method to get all documents object queries by a view id.

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Parameters:
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vid – the source view ID to search for

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Returns:
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a list of documents matching the requested source view ID, or an empty list if the view not found

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-get_documents_locations(m_type: DocumentTypes | str, path_only=False) → List[str | None][source]
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This method returns the file paths of documents of given type. -Only top-level documents have locations, so we only check them.

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Parameters:
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m_type – the type to search for

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Returns:
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a list of the values of the location fields in the corresponding documents

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-get_end(annotation: Annotation) → int | float[source]
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An alias to get_anchor_point method with start=False.

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-get_last_error() → str | None[source]
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Returns the last error message found in the views.

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Returns:
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the error message in human-readable format, or None if no error is found

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-get_start(annotation: Annotation) → int | float[source]
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An alias to get_anchor_point method with start=True.

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-get_view_by_id(req_view_id: str) → View[source]
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Finds a View object with the given ID.

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Parameters:
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req_view_id – the ID to search for

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Returns:
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a reference to the corresponding view, if it exists

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Raises:
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Exception – if there is no corresponding view

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-get_view_contains(at_types: TypesBase | str | List[str | TypesBase]) → View | None[source]
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Returns the last view appended that contains the given -types in its ‘contains’ metadata.

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Parameters:
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at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

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Returns:
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the view, or None if the type is not found

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-get_view_with_error() → View | None[source]
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Returns the last view appended that contains an error.

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Returns:
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the view, or None if no error is found

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-get_views_contain(*at_types: TypesBase | str) → List[View][source]
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Returns the list of all views in the MMIF if given types -are present in that view’s ‘contains’ metadata.

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Parameters:
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at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

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Returns:
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the list of views that contain the type

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-get_views_for_document(doc_id: str) → List[View][source]
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Returns the list of all views that have annotations anchored on a particular document. -Note that when the document is inside a view (generated during the pipeline’s running), -doc_id must be prefixed with the view_id.

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-get_views_with_error() → List[View][source]
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Returns the list of all views in the MMIF that have errors.

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Returns:
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the list of views that contain errors but no annotations

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-new_view() → View[source]
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Creates an empty view with a new ID and appends it to the views list.

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Returns:
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a reference to the new View object

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-new_view_id() → str[source]
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Fetches an ID for a new view.

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Returns:
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the ID

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-sanitize()[source]
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Sanitizes a Mmif object by running some safeguards. -Concretely, it performs the following before returning the JSON string.

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  1. validating output using built-in MMIF jsonschema

    2. -

  2. remove non-existing annotation types from contains metadata

    3. -
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-serialize(pretty: bool = False, sanitize: bool = False, autogenerate_capital_annotations=True) → str[source]
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Serializes the MMIF object to a JSON string.

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Parameters:
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  • sanitize – If True, performs some sanitization of before returning -the JSON string. See sanitize() for details.

    • -

  • autogenerate_capital_annotations – If True, automatically convert -any “pending” temporary properties from Document objects to -Annotation objects. See generate_capital_annotations() for -details.

    • -

  • pretty – If True, returns string representation with indentation.

    • -
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Returns:
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JSON string of the MMIF object.

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-static validate(json_str: bytes | str | dict) → None[source]
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Validates a MMIF JSON object against the MMIF Schema. -Note that this method operates before processing by MmifObject._load_str, -so it expects @ and not _ for the JSON-LD @-keys.

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Raises:
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jsonschema.exceptions.ValidationError – if the input fails validation

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Parameters:
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json_str – a MMIF JSON dict or string

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Returns:
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None

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mmif.serialize.view module

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The view module contains the classes used to represent a MMIF view -as a live Python object.

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In MMIF, views are created by apps in a pipeline that are annotating -data that was previously present in the MMIF file.

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-class mmif.serialize.view.Contain(mmif_obj: bytes | str | dict | None = None, *_)[source]
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Bases: DataDict[str, str]

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Contain object that represents the metadata of a single -annotation type in the contains metadata of a MMIF view.

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-class mmif.serialize.view.View(view_obj: bytes | str | dict | None = None, parent_mmif=None, *_)[source]
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Bases: MmifObject

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View object that represents a single view in a MMIF file.

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A view is identified by an ID, and contains certain metadata, -a list of annotations, and potentially a JSON-LD @context -IRI.

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If view_obj is not provided, an empty View will be generated.

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Parameters:
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view_obj – the JSON data that defines the view

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-add_annotation(annotation: Annotation, overwrite=False) → Annotation[source]
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Adds an annotation to the current view.

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Fails if there is already an annotation with the same ID -in the view, unless overwrite is set to True.

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Parameters:
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Raises:
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KeyError – if overwrite is set to False and -an annotation with the same ID exists -in the view

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Returns:
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the same Annotation object passed in as annotation

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-add_document(document: Document, overwrite=False) → Annotation[source]
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Appends a Document object to the annotations list.

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Fails if there is already a document with the same ID in the annotations list.

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Parameters:
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  • document – the Document object to add

    • -

  • overwrite – if set to True, will overwrite -an existing view with the same ID

    • -
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Returns:
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None

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-get_annotation_by_id(ann_id) → Annotation[source]
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-get_annotations(at_type: str | TypesBase | None = None, **properties) → Generator[Annotation, None, None][source]
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Look for certain annotations in this view, specified by parameters

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Parameters:
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    -

  • at_type – @type of the annotations to look for. When this is None, any @type will match.

    • -

  • properties – properties of the annotations to look for. When given more than one property, all properties must match. Note that annotation type metadata are specified in the contains view metadata, not in individual annotation objects.

    • -
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-get_document_by_id(doc_id) → Document[source]
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-get_documents() → List[Document][source]
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-get_error() → str | None[source]
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Get the “text” representation of the error occurred during -processing. Text representation is supposed to be human-readable. -When ths view does not have any error, returns None.

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-has_error() → bool[source]
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-has_warnings()[source]
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-new_annotation(at_type: str | TypesBase, aid: str | None = None, overwrite=False, **properties) → Annotation[source]
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Generates a new mmif.serialize.annotation.Annotation -object and adds it to the current view.

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Fails if there is already an annotation with the same ID -in the view, unless overwrite is set to True.

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Parameters:
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    -

  • at_type – the desired @type of the annotation.

    • -

  • aid – the desired ID of the annotation, when not given, -the mmif SDK tries to automatically generate an ID based on -Annotation type and existing annotations in the view.

    • -

  • overwrite – if set to True, will overwrite an -existing annotation with the same ID.

    • -
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Raises:
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KeyError – if overwrite is set to False and -an annotation with the same ID exists -in the view.

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Returns:
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the generated mmif.serialize.annotation.Annotation

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-new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
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Adds a new element to the contains metadata.

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Parameters:
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    -

  • at_type – the @type of the annotation type being added

    • -

  • contains_metadata – any metadata associated with the annotation type

    • -
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Returns:
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the generated Contain object

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-new_textdocument(text: str, lang: str = 'en', did: str | None = None, overwrite=False, **properties) → Document[source]
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Generates a new mmif.serialize.annotation.Document -object, particularly typed as TextDocument and adds it to the current view.

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Fails if there is already a text document with the same ID -in the view, unless overwrite is set to True.

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Parameters:
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    -

  • text – text content of the new document

    • -

  • lang – ISO 639-1 code of the language used in the new document

    • -

  • did – the desired ID of the document, when not given, -the mmif SDK tries to automatically generate an ID based on -Annotation type and existing documents in the view.

    • -

  • overwrite – if set to True, will overwrite an -existing document with the same ID

    • -
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Raises:
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KeyError – if overwrite is set to False and -an document with the same ID exists -in the view

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Returns:
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the generated mmif.serialize.annotation.Document

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-set_error(err_message: str, err_trace: str) → None[source]
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- -
- -
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-class mmif.serialize.view.ViewMetadata(viewmetadata_obj: bytes | str | dict | None = None, *_)[source]
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Bases: MmifObject

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ViewMetadata object that represents the metadata object within a MMIF view.

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Parameters:
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viewmetadata_obj – the JSON data that defines the metadata

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-add_app_configuration(config_key: str, config_value: str | int | float | bool | None | List[str | int | float | bool | None]) → None[source]
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Add a configuration key-value pair to the app_configuration dictionary.

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- -
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-add_contain(contain: Contain, at_type: str | TypesBase) → None[source]
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- -
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-add_parameter(param_key: str, param_value: str)[source]
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Add a single runtime parameter to the view metadata. Note that parameter value must be a string.

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-add_parameters(**runtime_params: str)[source]
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Add runtime parameters as a batch (dict) to the view metadata. Note that parameter values must be strings.

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-add_warnings(*warnings: Warning)[source]
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- -
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-emtpy_warnings()[source]
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- -
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-get_app_configuration(config_key: str) → str | int | float | bool | None | List[str | int | float | bool | None][source]
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Get a configuration value from the app_configuration dictionary.

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-get_error_as_text() → str[source]
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-get_parameter(param_key: str) → str[source]
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Get a runtime parameter from the view metadata.

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-has_error() → bool[source]
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- -
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-has_warnings()[source]
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- -
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-new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
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Adds a new element to the contains dictionary.

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Parameters:
-
    -

  • at_type – the @type of the annotation type being added

    • -

  • contains_metadata – any metadata associated with the annotation type

    • -
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Returns:
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the generated Contain object

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- -
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-set_error(message: str, stack_trace: str)[source]
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- -
- -
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-

mmif.serialize.annotation module

-

The annotation module contains the classes used to represent a -MMIF annotation as a live Python object.

-

In MMIF, annotations are created by apps in a pipeline as a part -of a view. For documentation on how views are represented, see -mmif.serialize.view.

-
-
-class mmif.serialize.annotation.Annotation(anno_obj: bytes | str | dict | None = None, *_)[source]
-

Bases: MmifObject

-

MmifObject that represents an annotation in a MMIF view.

-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]]) → None[source]
-

Adds a property to the annotation’s properties.

-
-
Parameters:
-
    -

  • name – the name of the property

    • -

  • value – the property’s desired value

    • -
-
-
Returns:
-

None

-
-
-
- -
-
-aligned_to_by(alignment: Annotation) → Annotation | None[source]
-

Retrieves the other side of Alignment annotation that has this annotation on one side.

-
-
Parameters:
-

alignment – Alignment annotation that has this annotation on one side

-
-
Returns:
-

the annotation that this annotation is aligned to (other side of Alignment), -or None if this annotation is not used in the Alignment.

-
-
-
- -
-
-property at_type: TypesBase[source]
-
- -
-
-static check_prop_value_is_simple_enough(value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]]) → bool[source]
-
- -
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-get(prop_name: str) → AnnotationProperties | str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]][source]
-

A special getter for Annotation properties. This is to allow for -directly accessing properties without having to go through the -properties object, or view-level annotation properties encoded in the -view.metadata.contains dict. Note that the regular props will take -the priority over the ephemeral props when there are conflicts.

-
- -
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-get_all_aligned() → Iterator[Annotation][source]
-

Generator to iterate through all alignments and aligned annotations. Note that this generator will yield -the Alignment annotations as well. Every odd-numbered yield will be an Alignment annotation, and every -even-numbered yield will be the aligned annotation. If there’s a specific annotation type that you’re looking -for, you need to filter the generated results outside.

-
-
Returns:
-

yields the alignment annotation and the aligned annotation. -The order is decided by the order of appearance of Alignment annotations in the MMIF

-
-
-
- -
-
-get_property(prop_name: str) → AnnotationProperties | str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]][source]
-

A special getter for Annotation properties. This is to allow for -directly accessing properties without having to go through the -properties object, or view-level annotation properties encoded in the -view.metadata.contains dict. Note that the regular props will take -the priority over the ephemeral props when there are conflicts.

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- -
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-property id: str[source]
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- -
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-is_document()[source]
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- -
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-is_type(at_type: str | TypesBase) → bool[source]
-

Check if the @type of this object matches.

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- -
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-property long_id: str[source]
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- -
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-property parent: str[source]
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- -
- -
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-class mmif.serialize.annotation.AnnotationProperties(mmif_obj: bytes | str | dict | None = None, *_)[source]
-

Bases: MmifObject, MutableMapping[str, T]

-

AnnotationProperties object that represents the -properties object within a MMIF annotation.

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-
Parameters:
-

mmif_obj – the JSON data that defines the properties

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- -
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-class mmif.serialize.annotation.Document(doc_obj: bytes | str | dict | None = None, *_)[source]
-

Bases: Annotation

-

Document object that represents a single document in a MMIF file.

-

A document is identified by an ID, and contains certain attributes -and potentially contains the contents of the document itself, -metadata about how the document was created, and/or a list of -subdocuments grouped together logically.

-

If document_obj is not provided, an empty Document will be generated.

-
-
Parameters:
-

document_obj – the JSON data that defines the document

-
-
-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None]) → None[source]
-

Adds a property to the document’s properties.

-

Unlike the parent Annotation class, added properties of a -Document object can be lost during serialization unless it belongs -to somewhere in a Mmif object. This is because we want to keep -Document object as “read-only” as possible. Thus, if you want to add -a property to a Document object,

-
    -

  • add the document to a Mmif object (either in the documents list or -in a view from the views list), or

    • -

  • directly write to Document.properties instead of using this method -(which is not recommended).

    • -
-

With the former method, the SDK will record the added property as a -Annotation annotation object, separate from the original Document -object. See Mmif.generate_capital_annotations() for more.

-

A few notes to keep in mind:

-
    -

  1. You can’t overwrite an existing property of a Document object.

    2. -

  2. A MMIF can have multiple Annotation objects with the same -property name but different values. When this happens, the SDK will -only keep the latest value (in order of appearances in views list) of -the property, effectively overwriting the previous values.

    3. -
-
- -
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-get(prop_name)[source]
-

A special getter for Document properties. The major difference from -the super class’s Annotation.get() method is that Document -class has one more set of “pending” properties, that are added after -the Document object is created and will be serialized as a separate -Annotation object of which @type = Annotation. The -pending properties will take the priority over the regular properties -when there are conflicts.

-
- -
-
-get_property(prop_name)[source]
-

A special getter for Document properties. The major difference from -the super class’s Annotation.get() method is that Document -class has one more set of “pending” properties, that are added after -the Document object is created and will be serialized as a separate -Annotation object of which @type = Annotation. The -pending properties will take the priority over the regular properties -when there are conflicts.

-
- -
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-property location: str | None[source]
-

location property must be a legitimate URI. That is, should the document be a local file -then the file:// scheme must be used. -Returns None when no location is set.

-
- -
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-location_address() → str | None[source]
-

Retrieves the full address from the document location URI. -Returns None when no location is set.

-
- -
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-location_path(nonexist_ok=True) → str | None[source]
-

Retrieves a path that’s resolved to a pathname in the local file system. -To obtain the original value of the “path” part in the location string -(before resolving), use properties.location_path_literal method. -Returns None when no location is set.

-
-
Parameters:
-

nonexist_ok – if False, raise FileNotFoundError when the resolved path doesn’t exist

-
-
-
- -
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-location_scheme() → str | None[source]
-

Retrieves URI scheme of the document location. -Returns None when no location is set.

-
- -
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-property text_language: str[source]
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- -
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-property text_value: str[source]
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- -
- -
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-class mmif.serialize.annotation.DocumentProperties(mmif_obj: bytes | str | dict | None = None, *_)[source]
-

Bases: AnnotationProperties

-

DocumentProperties object that represents the -properties object within a MMIF document.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
-
-property location: str | None[source]
-

location property must be a legitimate URI. That is, should the document be a local file -then the file:// scheme must be used. -Returns None when no location is set.

-
- -
-
-location_address() → str | None[source]
-

Retrieves the full address from the document location URI. -Returns None when no location is set.

-
- -
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-location_path() → str | None[source]
-
- -
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-location_path_literal() → str | None[source]
-

Retrieves only path name of the document location (hostname is ignored). -Returns None when no location is set.

-
- -
-
-location_path_resolved(nonexist_ok=True) → str | None[source]
-

Retrieves only path name of the document location (hostname is ignored), -and then try to resolve the path name in the local file system. -This method should be used when the document scheme is file or empty. -For other schemes, users should install mmif-locdoc-<scheme> plugin.

-

Returns None when no location is set. -Raise ValueError when no code found to resolve the given location scheme.

-
- -
-
-location_scheme() → str | None[source]
-

Retrieves URI scheme of the document location. -Returns None when no location is set.

-
- -
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-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
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-class mmif.serialize.annotation.Text(text_obj: bytes | str | dict | None = None, *_)[source]
-

Bases: MmifObject

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-property lang: str[source]
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- -
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-property value: str[source]
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- -
- -
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- - Other Versions - v: 1.0.17 - - -
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- - - \ No newline at end of file diff --git a/docs/1.0.17/autodoc/mmif.utils.html b/docs/1.0.17/autodoc/mmif.utils.html deleted file mode 100644 index cb216ad7..00000000 --- a/docs/1.0.17/autodoc/mmif.utils.html +++ /dev/null @@ -1,615 +0,0 @@ - - - - - - - - - mmif.utils module — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
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- -
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- -
-

mmif.utils module

-
-

mmif.utils.video_document_helper module

-
-
-mmif.utils.video_document_helper.capture(video_document: Document)[source]
-

Captures a video file using OpenCV and adds fps, frame count, and duration as properties to the document.

-
-
Parameters:
-

video_document – Document instance that holds a video document ("@type": ".../VideoDocument/...")

-
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Returns:
-

OpenCV VideoCapture object

-
-
-
- -
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-mmif.utils.video_document_helper.convert_timeframe(mmif: Mmif, time_frame: Annotation, out_unit: str) → Tuple[int | float | str, int | float | str][source]
-

Converts start and end points in a TimeFrame annotation a different time unit.

-
-
Parameters:
-
    -

  • mmif – Mmif instance

    • -

  • time_frame – Annotation instance that holds a time interval annotation ("@type": ".../TimeFrame/...")

    • -

  • out_unit – time unit to which the point is converted

    • -
-
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Returns:
-

tuple of frame numbers, seconds/milliseconds, or ISO notation of TimeFrame’s start and end

-
-
-
- -
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-mmif.utils.video_document_helper.convert_timepoint(mmif: Mmif, timepoint: Annotation, out_unit: str) → int | float | str[source]
-

Converts a time point included in an annotation to a different time unit. -The input annotation must have timePoint property.

-
-
Parameters:
-
    -

  • mmif – input MMIF to obtain fps and input timeunit

    • -

  • timepoint – Annotation instance with timePoint property

    • -

  • out_unit – time unit to which the point is converted (frames, seconds, milliseconds)

    • -
-
-
Returns:
-

frame number (integer) or second/millisecond (float) of input timepoint

-
-
-
- -
-
-mmif.utils.video_document_helper.extract_frames_as_images(video_document: Document, framenums: List[int], as_PIL: bool = False)[source]
-

Extracts frames from a video document as a list of numpy.ndarray. -Use with sample_frames() function to get the list of frame numbers first.

-
-
Parameters:
-
    -

  • video_document – Document instance that holds a video document ("@type": ".../VideoDocument/...")

    • -

  • framenums – integers representing the frame numbers to extract

    • -

  • as_PIL – return PIL.Image.Image instead of ndarray

    • -
-
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Returns:
-

frames as a list of ndarray or Image

-
-
-
- -
-
-mmif.utils.video_document_helper.extract_mid_frame(mmif: Mmif, time_frame: Annotation, as_PIL: bool = False)[source]
-

Extracts the middle frame of a time interval annotation as a numpy ndarray.

-
-
Parameters:
-
    -

  • mmif – Mmif instance

    • -

  • time_frame – Annotation instance that holds a time interval annotation ("@type": ".../TimeFrame/...")

    • -

  • as_PIL – return Image instead of ndarray

    • -
-
-
Returns:
-

frame as a numpy.ndarray or PIL.Image.Image

-
-
-
- -
-
-mmif.utils.video_document_helper.extract_representative_frame(mmif: Mmif, time_frame: Annotation, as_PIL: bool = False)[source]
-

Extracts the representative frame of an annotation as a numpy ndarray or PIL Image.

-
-
Parameters:
-
    -

  • mmif – Mmif instance

    • -

  • time_frame – Annotation instance that holds a time interval annotation ("@type": ".../TimeFrame/...")

    • -

  • as_PIL – return Image instead of ndarray

    • -
-
-
Returns:
-

frame as a numpy.ndarray or PIL.Image.Image

-
-
-
- -
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-mmif.utils.video_document_helper.framenum_to_millisecond(video_doc: Document, frame: int)[source]
-

Converts a frame number to a millisecond value.

-
- -
-
-mmif.utils.video_document_helper.framenum_to_second(video_doc: Document, frame: int)[source]
-

Converts a frame number to a second value.

-
- -
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-mmif.utils.video_document_helper.get_annotation_property(mmif, annotation, prop_name)[source]
-
-

Deprecated since version 1.0.8: Use mmif.serialize.annotation.Annotation.get_property() method instead.

-
-

Get a property value from an annotation. If the property is not found in the annotation, it will look up the metadata of the annotation’s parent view and return the value from there. -xisting

-
- -
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-mmif.utils.video_document_helper.get_framerate(video_document: Document) → float[source]
-

Gets the frame rate of a video document. First by checking the fps property of the document, then by capturing the video.

-
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Parameters:
-

video_document – Document instance that holds a video document ("@type": ".../VideoDocument/...")

-
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Returns:
-

frames per second as a float, rounded to 2 decimal places

-
-
-
- -
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-mmif.utils.video_document_helper.get_mid_framenum(mmif: Mmif, time_frame: Annotation)[source]
-

Calculates the middle frame number of a time interval annotation.

-
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Parameters:
-
    -

  • mmif – Mmif instance

    • -

  • time_frame – Annotation instance that holds a time interval annotation ("@type": ".../TimeFrame/...")

    • -
-
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Returns:
-

middle frame number as an integer

-
-
-
- -
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-mmif.utils.video_document_helper.get_representative_framenum(mmif: Mmif, time_frame: Annotation)[source]
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Calculates the representative frame number from an annotation.

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Parameters:
-
    -

  • mmif – Mmif instance

    • -

  • time_frame – Annotation instance that holds a time interval annotation containing a representatives property ("@type": ".../TimeFrame/...")

    • -
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Returns:
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representative frame number as an integer

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-
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- -
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-mmif.utils.video_document_helper.millisecond_to_framenum(video_doc: Document, millisecond: float) → int[source]
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Converts a millisecond value to a frame number.

-
- -
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-mmif.utils.video_document_helper.sample_frames(start_frame: int, end_frame: int, sample_rate: float = 1) → List[int][source]
-

Helper function to sample frames from a time interval. -Can also be used as a “cutoff” function when used with start_frame==0 and sample_rate==1.

-
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Parameters:
-
    -

  • start_frame – start frame of the interval

    • -

  • end_frame – end frame of the interval

    • -

  • sample_rate – sampling rate (or step) to configure how often to take a frame, default is 1, meaning all consecutive frames are sampled

    • -
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-mmif.utils.video_document_helper.second_to_framenum(video_doc: Document, second) → int[source]
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Converts a second value to a frame number.

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- -
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-

mmif.utils.sequence_helper module

-

This module provides helpers for handling sequence labeling. Specifically, it provides

-
    -

  • a generalized label re-mapper for “post-binning” of labels

    • -

  • conversion from a list of CLAMS annotations (with classification props) into a list of reals (scores by labels), can be combined with the label re-mapper mentioned above

    • -

  • mmif.utils.sequence_helper.smooth_outlying_short_intervals(): a simple smoothing algorithm by trimming “short” outlier sequences

    • -
-

However, it DOES NOT provide

-
    -

  • direct conversion between CLAMS annotations. For example, it does not directly handle stitching of TimePoint into TimeFrames.

    • -

  • support for multi-class scenario, such as handling of _competing_ subsequence or overlapping labels.

    • -
-

Some functions can use optional external libraries (e.g., numpy) for better performance. -Hence, if you see a warning about missing optional packages, you might want to install them by running pip install mmif-python[seq].

-
-
-mmif.utils.sequence_helper.build_label_remapper(src_labels: List[str], dst_labels: Dict[str, str | int | float | bool | None]) → Dict[str, str | int | float | bool | None][source]
-

Build a label remapper dictionary from source and destination labels.

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-
Parameters:
-
    -

  • src_labels – a list of all labels on the source side

    • -

  • dst_labels – a dict from source labels to destination labels. -Source labels not in this dict will be remapped to a negative label (-).

    • -
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Returns:
-

a dict that exhaustively maps source labels to destination labels

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- -
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-mmif.utils.sequence_helper.build_score_lists(classifications: ~typing.List[~typing.Dict], label_remapper: ~typing.Dict, score_remap_op: ~typing.Callable[[...], float] = <built-in function max>) → Tuple[Dict[str, int], numpy.ndarray][source]
-

Build lists of scores indexed by the label names.

-
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Parameters:
-
    -

  • classifications – list of dictionaries of classification results, taken from input annotation objects

    • -

  • label_remapper – a dictionary that maps source label names to destination label names (formerly “postbin”)

    • -

  • score_remap_op – a function to remap the scores from multiple source labels binned to a destination label -common choices are max, min, or sum

    • -
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Returns:
-

    -

  1. a dictionary that maps label names to their index in the score list

    2. -

  2. 2-d numpy array of scores, of which rows are indexed by label map dict (first return value)

    3. -
-

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-mmif.utils.sequence_helper.smooth_outlying_short_intervals(scores: List[float], min_spseq_size: int, min_snseq_size: int, min_score: float = 0.5)[source]
-

Given a list of scores, a score threshold, and smoothing parameters, -identify the intervals of “positive” scores by “trimming” the short -positive sequences (“spseq”) and short negative sequences (“snseq”). To -decide the positivity, first step is binarization of the scores by the -min_score threshold. Given Sr as “raw” input real-number scores -list, and min_score=0.5,

-
-
Sr: [0.3, 0.6, 0.2, 0.8, 0.2, 0.9, 0.8, 0.5, 0.1, 0.5, 0.8, 0.3, 1.0, 0.7, 0.5, 0.5, 0.5, 0.8, 0.3, 0.6]
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the binarization is done by simply comparing each score to the -threshold to get S list of binary scores

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1.0 :                                     |                      
-0.9 :                |                    |                      
-0.8 :          |     |  |           |     |              |       
-0.7 :          |     |  |           |     |  |           |       
-0.6 :    |     |     |  |           |     |  |           |     | 
-0.5 :----+-----+-----+--+--+-----+--+-----+--+--+--+--+--+-----+-
-0.4 :    |     |     |  |  |     |  |     |  |  |  |  |  |     | 
-0.3 : |  |     |     |  |  |     |  |  |  |  |  |  |  |  |  |  | 
-0.2 : |  |  |  |  |  |  |  |     |  |  |  |  |  |  |  |  |  |  | 
-0.1 : |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | 
-0.0 +------------------------------------------------------------
-raw :.3 .6 .2 .8 .2 .9 .8 .5 .1 .5 .8 .3 1. .7 .5 .5 .5 .8 .3 .6
- S  : 0  1  0  1  0  1  1  0  0  0  1  0  1  1  0  1  1  1  0  1 
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Note that the size of a positive or negative sequence can be as small -as 1.

-

Then, here are examples of smoothing a list of binary scores into -intervals, by trimming “very short” (under thresholds) sequences of -positive or negative:

-
-

Note

-

legends:

-
    -

  • t is unit index (e.g. time index)

    • -

  • S is the list of binary scores (zeros and ones)

    • -

  • I is the list of intervals after smoothing

    • -
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    -

  1. with params min_spseq_size==1, min_snseq_size==4

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1]
-I: [0, 1--1--1--1--1--1--1--1--1--1--1--1, 0--0--0--0--0--0, 1]
-
    -
    -

    Explanation: min_snseq_size is used to smooth short sequences -of negative predictions. In this, zeros from t[7:10] are smoothed -into “one” I, while zeros from t[13:19] are kept as “zero” I. Note -that the “short” snseqs at the either ends (t[0:1]) are never -smoothed.

    -
    -
    2. -

  2. with params min_spseq_size==4, min_snseq_size==2

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1]
-I: [0, 1--1--1--1--1--1, 0--0--0--0--0--0--0--0--0--0--0--0--0]
-
    -
    -

    Explanation: min_spseq_size is used to smooth short sequences -of positive predictions. In this example, the spseqs of ones from -both t[10:13] and t[19:20] are smoothed. Note that the “short” -spseqs at the either ends (t[19:20]) are always smoothed.

    -
    -
    3. -

  3. with params min_spseq_size==4, min_snseq_size==4

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1]
-I: [0, 1--1--1--1--1--1--1--1--1--1--1--1--0--0--0--0--0--0--0]
-
    -
    -

    Explanation: When two threshold parameters are working together, -the algorithm will prioritize the smoothing of the snseqs over the -smoothing of the spseqs. Thus, in this example, the snseq t[7:10] -gets first smoothed “up” before the spseq t[10:13] is smoothed -“down”, resulting in a long final I.

    -
    -
    4. -

  4. with params min_spseq_size==4, min_snseq_size==4

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [1, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 1, 1]
-I: [1--1--1--1--1--1--1, 0--0--0--0, 1--1--1--1--1--1--1--1--1]
-
    -
    -

    Explanation: Since smoothing of snseqs is prioritized, short spseqs -at the beginning or the end can be kept.

    -
    -
    5. -

  5. with params min_spseq_size==1, min_snseq_size==1

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 1, 1]
-I: [0--0--0, 1--1--1--1, 0--0--0--0, 1--1--1--1, 0--0--0, 1--1]
-
    -
    -

    Explanation: When both width thresholds are set to 1, the algorithm -works essentially in the “stitching” only mode.

    -
    -
    6. -
-
-
Parameters:
-
    -

  • scores – SORTED list of scores to be smoothed. The score list -is assumed to be “exhaust” the entire time or space of -the underlying document segment. -(Sorted by the start, and then by the end of anchors)

    • -

  • min_score – minimum threshold to use to discard -low-scored units (strictly less than)

    • -

  • min_spseq_size – minimum size of a positive sequence not to be -smoothed (greater or equal to)

    • -

  • min_snseq_size – minimum size of a negative sequence not to be -smoothed (greater or equal to)

    • -
-
-
Returns:
-

list of tuples of start(inclusive)/end(exclusive) indices -of the “positive” sequences. Negative sequences (regardless of -their size) are not included in the output.

-
-
-
- -
-
-mmif.utils.sequence_helper.validate_labelset(annotations: Iterable[Annotation]) → List[str][source]
-

Simple check for a list of annotations to see if they have the same label set.

-
-
Raise:
-

AttributeError if an element in the input list doesn’t have the labelset property

-
-
Raise:
-

ValueError if different labelset values are found

-
-
Returns:
-

a list of the common labelset value (list of label names)

-
-
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- - -
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- - Other Versions - v: 1.0.17 - - -
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- - - \ No newline at end of file diff --git a/docs/1.0.17/autodoc/mmif.vocabulary.html b/docs/1.0.17/autodoc/mmif.vocabulary.html deleted file mode 100644 index 70439d80..00000000 --- a/docs/1.0.17/autodoc/mmif.vocabulary.html +++ /dev/null @@ -1,319 +0,0 @@ - - - - - - - - - mmif.vocabulary module — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
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- -
-

mmif.vocabulary module

-
-

mmif.vocabulary.annotation_types module

-
-
-class mmif.vocabulary.annotation_types.AnnotationTypes(type_uri, fuzzymode=True)[source]
-

Bases: AnnotationTypesBase

-

This class contains the CLAMS annotation types -defined in the spec version 1.1.0 as class variables.

-
-
-Alignment = http://mmif.clams.ai/vocabulary/Alignment/v1[source]
-
- -
-
-Annotation = http://mmif.clams.ai/vocabulary/Annotation/v6[source]
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- -
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-BoundingBox = http://mmif.clams.ai/vocabulary/BoundingBox/v5[source]
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- -
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-Chapter = http://mmif.clams.ai/vocabulary/Chapter/v6[source]
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- -
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-Interval = http://mmif.clams.ai/vocabulary/Interval/v5[source]
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- -
-
-NamedEntity = http://mmif.clams.ai/vocabulary/NamedEntity/v1[source]
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- -
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-NounChunk = http://mmif.clams.ai/vocabulary/NounChunk/v1[source]
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- -
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-Paragraph = http://mmif.clams.ai/vocabulary/Paragraph/v1[source]
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- -
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-Polygon = http://mmif.clams.ai/vocabulary/Polygon/v5[source]
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- -
-
-Region = http://mmif.clams.ai/vocabulary/Region/v5[source]
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- -
-
-Relation = http://mmif.clams.ai/vocabulary/Relation/v5[source]
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- -
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-Sentence = http://mmif.clams.ai/vocabulary/Sentence/v1[source]
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- -
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-Span = http://mmif.clams.ai/vocabulary/Span/v5[source]
-
- -
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-TimeFrame = http://mmif.clams.ai/vocabulary/TimeFrame/v6[source]
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- -
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-TimePoint = http://mmif.clams.ai/vocabulary/TimePoint/v5[source]
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- -
-
-Token = http://mmif.clams.ai/vocabulary/Token/v1[source]
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-VerbChunk = http://mmif.clams.ai/vocabulary/VerbChunk/v1[source]
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- -
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-VideoObject = http://mmif.clams.ai/vocabulary/VideoObject/v5[source]
-
- -
- -
-
-

mmif.vocabulary.document_types module

-
-
-class mmif.vocabulary.document_types.DocumentTypes(type_uri, fuzzymode=True)[source]
-

Bases: DocumentTypesBase

-

This class contains the CLAMS document types -defined in the spec version 1.1.0 as class variables.

-
-
-AudioDocument = http://mmif.clams.ai/vocabulary/AudioDocument/v1[source]
-
- -
-
-Document = http://mmif.clams.ai/vocabulary/Document/v1[source]
-
- -
-
-ImageDocument = http://mmif.clams.ai/vocabulary/ImageDocument/v1[source]
-
- -
-
-TextDocument = http://mmif.clams.ai/vocabulary/TextDocument/v1[source]
-
- -
-
-VideoDocument = http://mmif.clams.ai/vocabulary/VideoDocument/v1[source]
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- - - \ No newline at end of file diff --git a/docs/1.0.17/autodoc/mmif_docloc_http.html b/docs/1.0.17/autodoc/mmif_docloc_http.html deleted file mode 100644 index 7f78f9e3..00000000 --- a/docs/1.0.17/autodoc/mmif_docloc_http.html +++ /dev/null @@ -1,179 +0,0 @@ - - - - - - - - - mmif_docloc_http package — mmif-python documentation - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif_docloc_http package

-

MMIF document location helper module for http and https schemes. -If you want to write your own docloc scheme handler, please use the source code of this module as a reference. -See this plug-in section for more information.

-
-
-mmif_docloc_http.resolve(docloc)[source]
-
- -
- - -
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- - - \ No newline at end of file diff --git a/docs/1.0.17/consumer-tutorial.html b/docs/1.0.17/consumer-tutorial.html deleted file mode 100644 index 06c4793a..00000000 --- a/docs/1.0.17/consumer-tutorial.html +++ /dev/null @@ -1,172 +0,0 @@ - - - - - - - - - MMIF consumer — mmif-python documentation - - - - - - - - - - - - - - - -
- - -
- -
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    • -
  • MMIF consumer
    • -
  • -
    • -
-
-
-
-
- -
-

MMIF consumer

-

A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the appliance documentation to learn more about the appliance.

-

MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance.

-
    -

  1. The code must be hosted on a public git repository (e.g. Github, Gitlab, …)

    2. -

  2. Must listen to 5000 port.

    3. -

  3. Must expose /display route .

    4. -

  4. /display router should response to GET requests.

    5. -

  5. In the GET request, a public URL of the input MMIF file is passed via file URL parameter.

    6. -

  6. On the codebase root, there must be a Dockerfile that can build a docker image that runs the web app.

    7. -
-

We provide an example consumer at https://github.com/clamsproject/mmif-visualizer.

-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 1.0.17 - - -
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- - -
- -
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    -
    • -
  • Index
    • -
  • -
    • -
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Index

- -
- A - | B - | C - | D - | E - | F - | G - | H - | I - | K - | L - | M - | N - | P - | R - | S - | T - | U - | V - -
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A

- - - -
- -

B

- - - -
- -

C

- - - -
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D

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E

- - - -
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F

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K

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M

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P

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R

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S

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U

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V

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- - -
- -
-
-
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    -
    • -
  • Welcome to mmif-python’s documentation!
    • -
  • -
    • -
-
-
-
-
- -
-

Welcome to mmif-python’s documentation!

-
-

MultiMedia Interchange Format

-

MMIF is a JSON(-LD)-based data format designed for transferring annotation data between computational analysis applications in CLAMS project.

-
-
-

mmif-python

-

mmif-python is a Python implementation of the MMIF data format. -mmif-python provides various helper classes and functions to handle MMIF JSON in Python, -including ;

-
    -

  1. de-/serialization of MMIF internal data structures to/from JSON

    2. -

  2. validation of MMIF JSON

    3. -

  3. handling of CLAMS vocabulary types

    4. -

  4. navigation of MMIF object via various “search” methods (e.g. mmif.get_all_views_contain(vocab_type)))

    5. -
-
-
-

For more …

- -
-

Contents

- -
-
-

API documentation:

- -
-
-
-
-

Indices and tables

- -
- - -
-
- -
-
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-
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- - Other Versions - v: 1.0.17 - - -
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- - - \ No newline at end of file diff --git a/docs/1.0.17/introduction.html b/docs/1.0.17/introduction.html deleted file mode 100644 index 9ea38f6f..00000000 --- a/docs/1.0.17/introduction.html +++ /dev/null @@ -1,245 +0,0 @@ - - - - - - - - - Getting Started — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
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  • Getting Started
    • -
  • -
    • -
-
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- -
-

Getting Started

-
-

Overview

-

MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for reproducibility, transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF website. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects.

-
-
-

Prerequisites

-
    -

  • Python: the latest mmif-python requires Python 3.8 or newer. We have no plan to support Python 2.7.

    • -
-
-
-

Installation

-

Package mmif-python is distributed via the official PyPI. Users are supposed to pip-install to get latest release.

-
pip install mmif-python
-
-
-

This will install a package mmif to local python.

-

The MMIF format and specification is evolving over time, and mmif-python package will be updated along with the changes in MMIF format.

-
-

Note

-

MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and mmif-python versions, please take time to read our decision on the subject here. If you need to know which python SDK supports which specification version, see Target MMIF Versions page.

-
-
-
-

MMIF Serialization

-

mmif.serialize.mmif.Mmif represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of mmif.serialize.model.MmifObject, including the mmif.serialize.mmif.Mmif. To start with an existing MMIF str, simple initiate a new Mmif object with the file.

-
import mmif
-from mmif import Mmif
-
-mmif_str = """{
-"metadata": {
-  "mmif": "http://mmif.clams.ai/1.0.0"
-},
-"documents": [
-  {
-    "@type": "http://mmif.clams.ai/vocabulary/VideoDocument/v1",
-    "properties": {
-      "id": "m1",
-      "mime": "video/mp4",
-      "location": "file:///var/archive/video-0012.mp4"
-    }
-  },
-  {
-    "@type": "http://mmif.clams.ai/vocabulary/TextDocument/v1",
-    "properties": {
-      "id": "m2",
-      "mime": "text/plain",
-      "location": "file:///var/archive/video-0012-transcript.txt"
-    }
-  }
-],
-"views": []}"""
-mmif_obj = Mmif(mmif_str)
-
-
-

Few notes;

-
    -

  1. MMIF does not carry the primary source files in it.

    2. -

  2. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version mmif-python implementation of the MMIF might not be able to load an unsupported version of MMIF string.

    3. -
-

When serializing back to str, call mmif.serialize.model.MmifObject.serialize() on the object.

-

To get subcomponents, you can use various getters implemented in subclasses. For example;

-
from mmif.vocabulary.document_types import DocumentTypes
-
-for video in mmif_obj.Mmif.get_documents_by_type(DocumentTypes.VideoDocument):
-  with open(video.location_path(), 'b') as in_video:
-    # do something with the video file
-
-
-

For a full list of available helper methods, please refer to the API documentation.

-
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mmif package

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mmif_docloc_http package

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Developing plugins for MMIF Python SDK

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Overview

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As MMIF JSON files can carry information about media document files without actually carrying file contents, file accessing modules in mmif Python package (distributed as mmif-python on PyPI) are designed to be lightweight and flexible so that it can work with additional “plugin” Python packages that can handle concrete file access.

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This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF website. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects.

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Developer can write simple plugins that can provide additional functionalities to mmif-python. For example, mmif-python does not provide any file access functionality beyond a local file system (with file scheme), but it can be extended with a plugin that can handle file access over different protocols (e.g. http, s3, ftp, etc).

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This document contains information about how to write plugins for mmif-python.

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Document Location Scheme Plugins

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mmif.serialize.annotation.Document class has various methods to access parts of location property of the document. The location is in URI/IRI format (SCHEME://HOSTNAME/PATH, in a nutshell) and it has to be resolved to a local file for CLAMS Apps to process the local file to analyze and extract information about the media and its contents. The core mmif-python distribution only provides a default implementation that can handle file scheme URIs.

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To add a document location handler plugin, you need to implement a Python “package” (do not confuse with PYPI distribution), that meets these requirements;

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  1. the package must be named mmif_docloc_<SCHEME>. For example, to implement a handler for s3 scheme, the package name must be mmif_docloc_s3. The prefix is important as it’s used in the plugin discovery process from the core mmif-python modules.

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  2. the top module of the package must have a function named resolve. The function must take a single argument, which is a str of the document location URI. The function must return a str of the local file path. For example, if the document location is s3://mybucket/myfile.mp4, a Python user should be able to to something like this;

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import mmif_docloc_s3
-resolved = mmif_docloc_s3.resolve('s3://mybucket/myfile.mp4')
-# then resolved must be a local file path that can be used to open the file
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Here’s a minimal example codebase that you refer to when you develop a docloc plugin.

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(However, before you start writing your own plugin for a specific URI scheme, checking if there’s already a PyPI distribution for the scheme might be a good idea.)

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$ tree .
-.
-├── mmif_docloc_dummy
-│   └── __init__.py
-├── pyproject.toml
-└── setup.cfg
-
- $ cat pyproject.toml
-[build-system]
-requires = ["setuptools"]
-build-backend = "setuptools.build_meta"
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-$ cat setup.cfg
-[metadata]
-name = mmif_docloc_dummy  # this name is IMPORTANT
-version = 0.0.1
-description = a plugin to mmif-pyhon to handle `dummy` location scheme
-
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And the plugin code.

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# mmif_docloc_dummy/__init__.py
-doc_types = {'video': 'mp4'}
-
-def resolve(docloc):
-    scheme = 'dummy'
-    if docloc.startswith(f'{scheme}://'):
-        doc_id, doc_type = docloc.split('.')
-        return f'/path/to/{doc_id}.{doc_types[doc_type]}'
-    else:
-        raise ValueError(f'cannot handle document location scheme: {docloc}')
-
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Bulit-in Document Location Scheme Plugins

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At the moment, mmif-python PyPI distribution ships a built-in docloc plugin that support both http and https schemes. -Take a look at mmif_docloc_http module for details.

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Python Module Index

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- - - - - - - - \ No newline at end of file diff --git a/docs/1.0.17/searchindex.js b/docs/1.0.17/searchindex.js deleted file mode 100644 index 4061262c..00000000 --- a/docs/1.0.17/searchindex.js +++ /dev/null @@ -1 +0,0 @@ -Search.setIndex({"alltitles": {"API documentation:": [[5, null]], "Bulit-in Document Location Scheme Plugins": [[8, "bulit-in-document-location-scheme-plugins"]], "Contents": [[5, null]], "Developing plugins for MMIF Python SDK": [[8, null]], "Document Location Scheme Plugins": [[8, "document-location-scheme-plugins"]], "For more \u2026": [[5, "for-more"]], "Getting Started": [[6, null]], "Indices and tables": [[5, "indices-and-tables"]], "Installation": [[6, "installation"]], "MMIF Serialization": [[6, "mmif-serialization"]], "MMIF consumer": [[4, null]], "MultiMedia Interchange Format": [[5, "multimedia-interchange-format"]], "Overview": [[6, "overview"], [8, "overview"]], "Prerequisites": [[6, "prerequisites"]], "Target MMIF Versions": [[9, null]], "Target Specification Versions": [[9, "id1"]], "Welcome to mmif-python\u2019s documentation!": [[5, null]], "mmif package": [[7, null]], "mmif-python": [[5, "mmif-python"]], "mmif.serialize module": [[0, null]], "mmif.serialize.annotation module": [[0, "module-mmif.serialize.annotation"]], "mmif.serialize.mmif module": [[0, "module-mmif.serialize.mmif"]], "mmif.serialize.model module": [[0, "module-mmif.serialize.model"]], "mmif.serialize.view module": [[0, "module-mmif.serialize.view"]], "mmif.utils module": [[1, null]], "mmif.utils.sequence_helper module": [[1, "module-mmif.utils.sequence_helper"]], "mmif.utils.video_document_helper module": [[1, "module-mmif.utils.video_document_helper"]], "mmif.vocabulary module": [[2, null]], "mmif.vocabulary.annotation_types module": [[2, "module-mmif.vocabulary.annotation_types"]], "mmif.vocabulary.document_types module": [[2, "module-mmif.vocabulary.document_types"]], "mmif_docloc_http package": [[3, null], [7, "mmif-docloc-http-package"]]}, 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"would": 0, "write": [0, 3, 8], "xist": 1, "yield": 0, "you": [0, 1, 3, 6, 8], "your": [3, 8], "zero": [0, 1]}, "titles": ["mmif.serialize module", "mmif.utils module", "mmif.vocabulary module", "mmif_docloc_http package", "MMIF consumer", "Welcome to mmif-python\u2019s documentation!", "Getting Started", "mmif package", "Developing plugins for MMIF Python SDK", "Target MMIF Versions"], "titleterms": {"": 5, "For": 5, "annot": 0, "annotation_typ": 2, "api": 5, "bulit": 8, "consum": 4, "content": 5, "develop": 8, "document": [5, 8], "document_typ": 2, "format": 5, "get": 6, "indic": 5, "instal": 6, "interchang": 5, "locat": 8, "mmif": [0, 1, 2, 4, 5, 6, 7, 8, 9], "mmif_docloc_http": [3, 7], "model": 0, "modul": [0, 1, 2], "more": 5, "multimedia": 5, "overview": [6, 8], "packag": [3, 7], "plugin": 8, "prerequisit": 6, "python": [5, 8], "scheme": 8, "sdk": 8, "sequence_help": 1, "serial": [0, 6], "specif": 9, "start": 6, "tabl": 5, "target": 9, "util": 1, "version": 9, "video_document_help": 1, "view": 0, "vocabulari": 2, "welcom": 5}}) \ No newline at end of file diff --git a/docs/1.0.17/target-versions.html b/docs/1.0.17/target-versions.html deleted file mode 100644 index a7059b96..00000000 --- a/docs/1.0.17/target-versions.html +++ /dev/null @@ -1,294 +0,0 @@ - - - - - - - - - Target MMIF Versions — mmif-python documentation - - - - - - - - - - - - - - - - - -
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Target MMIF Versions

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This article provides targeting MMIF specification versions of different versions of mmif-python SDK.

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Target Specification Versions

mmif-python version

Target MMIF Specification

1.0.17

1.1.0

1.0.16

1.0.4

1.0.15

1.0.4

1.0.14

1.0.4

1.0.13

1.0.4

1.0.12

1.0.4

1.0.11

1.0.4

1.0.10

1.0.2

1.0.9

1.1.0

1.0.8

1.0.0

1.0.7

1.0.0

1.0.6

1.0.0

1.0.5

1.0.0

1.0.4

1.0.0

1.0.3

1.0.0

1.0.2

1.0.0

1.0.1

1.0.0

1.0.0

0.5.0

0.5.2

0.5.0

0.5.1

0.5.0

0.5.0

0.5.0

0.4.8

0.4.2

0.4.7

0.4.1

0.4.6

0.4.0

0.4.5

0.4.0

0.4.4

0.4.0

0.4.3

0.4.0

0.4.2

0.4.0

0.4.1

0.4.0

0.4.0

0.4.0

0.3.5

0.3.1

0.3.4

0.3.1

0.3.3

0.3.1

0.3.2

0.3.1

0.3.1

0.3.0

0.3.0

0.3.0

0.2.2

0.2.1

0.2.1

0.2.1

0.2.0

0.2.1

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0.3.0
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0.3.1
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0.3.2
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0.3.3
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0.3.4
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0.3.5
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0.4.0
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0.4.1
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0.4.2
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0.4.3
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0.4.4
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0.4.5
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0.4.6
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0.4.7
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0.4.8
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0.5.0
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0.5.1
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0.5.2
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1.0.0
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1.0.1
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1.0.10
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1.0.11
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1.0.12
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1.0.13
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1.0.14
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1.0.15
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1.0.16
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1.0.17
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1.0.18
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1.0.19
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1.0.2
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1.0.3
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1.0.4
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1.0.5
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1.0.6
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1.0.7
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1.0.8
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1.0.9
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1.1.0
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-mmif.serialize.model module ---------------------------- - -.. automodule:: mmif.serialize.model - :members: - :undoc-members: - :show-inheritance: - -mmif.serialize.mmif module --------------------------- - -.. automodule:: mmif.serialize.mmif - :members: - :undoc-members: - :show-inheritance: - -mmif.serialize.view module --------------------------- - -.. automodule:: mmif.serialize.view - :members: - :undoc-members: - :show-inheritance: - -mmif.serialize.annotation module --------------------------------- - -.. automodule:: mmif.serialize.annotation - :members: - :undoc-members: - :show-inheritance: - diff --git a/docs/1.0.18/_sources/autodoc/mmif.utils.rst.txt b/docs/1.0.18/_sources/autodoc/mmif.utils.rst.txt deleted file mode 100644 index 9a6ecc44..00000000 --- a/docs/1.0.18/_sources/autodoc/mmif.utils.rst.txt +++ /dev/null @@ -1,18 +0,0 @@ -mmif.utils module -================= - -mmif.utils.video_document_helper module ----------------------------------------- - -.. automodule:: mmif.utils.video_document_helper - :members: - :undoc-members: - :show-inheritance: - -mmif.utils.sequence_helper module ---------------------------------- - -.. automodule:: mmif.utils.sequence_helper - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/1.0.18/_sources/autodoc/mmif.vocabulary.rst.txt b/docs/1.0.18/_sources/autodoc/mmif.vocabulary.rst.txt deleted file mode 100644 index d250c6a3..00000000 --- a/docs/1.0.18/_sources/autodoc/mmif.vocabulary.rst.txt +++ /dev/null @@ -1,18 +0,0 @@ -mmif.vocabulary module -====================== - -mmif.vocabulary.annotation\_types module ----------------------------------------- - -.. automodule:: mmif.vocabulary.annotation_types - :members: - :undoc-members: - :show-inheritance: - -mmif.vocabulary.document\_types module --------------------------------------- - -.. automodule:: mmif.vocabulary.document_types - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/1.0.18/_sources/autodoc/mmif_docloc_http.rst.txt b/docs/1.0.18/_sources/autodoc/mmif_docloc_http.rst.txt deleted file mode 100644 index b76c8df5..00000000 --- a/docs/1.0.18/_sources/autodoc/mmif_docloc_http.rst.txt +++ /dev/null @@ -1,11 +0,0 @@ -mmif_docloc_http package -======================== - -MMIF document location helper module for `http` and `https` schemes. -If you want to write your own docloc scheme handler, please use the source code of this module as a reference. -See this :ref:`plug-in section ` for more information. - -.. automodule:: mmif_docloc_http - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/1.0.18/_sources/consumer-tutorial.rst.txt b/docs/1.0.18/_sources/consumer-tutorial.rst.txt deleted file mode 100644 index c54634e2..00000000 --- a/docs/1.0.18/_sources/consumer-tutorial.rst.txt +++ /dev/null @@ -1,17 +0,0 @@ -.. _consumer-tutorial: - -MMIF consumer -================================= - -A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the `appliance documentation `_ to learn more about the appliance. - -MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance. - -#. The code must be hosted on a public git repository (e.g. Github, Gitlab, ...) -#. Must listen to ``5000`` port. -#. Must expose ``/display`` route . -#. ``/display`` router should response to ``GET`` requests. -#. In the ``GET`` request, a public URL of the input MMIF file is passed via ``file`` URL parameter. -#. On the codebase root, there must be a ``Dockerfile`` that can build a `docker `_ image that runs the web app. - -We provide an example consumer at https://github.com/clamsproject/mmif-visualizer. diff --git a/docs/1.0.18/_sources/index.rst.txt b/docs/1.0.18/_sources/index.rst.txt deleted file mode 100644 index beb56aae..00000000 --- a/docs/1.0.18/_sources/index.rst.txt +++ /dev/null @@ -1,26 +0,0 @@ -Welcome to mmif-python's documentation! -======================================= - -.. mdinclude:: ../README.md - -.. toctree:: - :maxdepth: 2 - :caption: Contents - - introduction - plugins - target-versions - -.. toctree:: - :maxdepth: 2 - :caption: API documentation: - - modules - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/docs/1.0.18/_sources/introduction.rst.txt b/docs/1.0.18/_sources/introduction.rst.txt deleted file mode 100644 index cfd9eaf7..00000000 --- a/docs/1.0.18/_sources/introduction.rst.txt +++ /dev/null @@ -1,89 +0,0 @@ -.. _introduction: - -Getting Started -=============== - - -Overview ---------- - -MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for reproducibility, transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF website `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects. - -Prerequisites -------------- - -* `Python `_: the latest ``mmif-python`` requires Python 3.8 or newer. We have no plan to support `Python 2.7 `_. - -Installation ---------------- - -Package ``mmif-python`` is distributed via the official PyPI. Users are supposed to pip-install to get latest release. - -.. code-block:: bash - - pip install mmif-python - -This will install a package `mmif` to local python. - -The MMIF format and specification is evolving over time, and ``mmif-python`` package will be updated along with the changes in MMIF format. - -.. note:: MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and ``mmif-python`` versions, please take time to read our decision on the subject `here `_. If you need to know which python SDK supports which specification version, see :ref:`target-versions` page. - -MMIF Serialization ---------------------------- - -:class:`mmif.serialize.mmif.Mmif` represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of :class:`mmif.serialize.model.MmifObject`, including the :class:`mmif.serialize.mmif.Mmif`. To start with an existing MMIF :class:`str`, simple initiate a new ``Mmif`` object with the file. - -.. code-block:: python - - import mmif - from mmif import Mmif - - mmif_str = """{ - "metadata": { - "mmif": "http://mmif.clams.ai/1.0.0" - }, - "documents": [ - { - "@type": "http://mmif.clams.ai/vocabulary/VideoDocument/v1", - "properties": { - "id": "m1", - "mime": "video/mp4", - "location": "file:///var/archive/video-0012.mp4" - } - }, - { - "@type": "http://mmif.clams.ai/vocabulary/TextDocument/v1", - "properties": { - "id": "m2", - "mime": "text/plain", - "location": "file:///var/archive/video-0012-transcript.txt" - } - } - ], - "views": []}""" - mmif_obj = Mmif(mmif_str) - - -Few notes; - -#. MMIF does not carry the primary source files in it. -#. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version ``mmif-python`` implementation of the MMIF might not be able to load an unsupported version of MMIF string. - -When serializing back to :class:`str`, call :meth:`mmif.serialize.model.MmifObject.serialize` on the object. - -To get subcomponents, you can use various getters implemented in subclasses. For example; - -.. code-block:: python - - from mmif.vocabulary.document_types import DocumentTypes - - for video in mmif_obj.Mmif.get_documents_by_type(DocumentTypes.VideoDocument): - with open(video.location_path(), 'b') as in_video: - # do something with the video file - - -For a full list of available helper methods, please refer to :ref:`the API documentation `. - diff --git a/docs/1.0.18/_sources/modules.rst.txt b/docs/1.0.18/_sources/modules.rst.txt deleted file mode 100644 index 4bb9307d..00000000 --- a/docs/1.0.18/_sources/modules.rst.txt +++ /dev/null @@ -1,20 +0,0 @@ -.. _apidoc: - -mmif package -============ - -.. toctree:: - :maxdepth: 4 - - autodoc/mmif.serialize - autodoc/mmif.vocabulary - autodoc/mmif.utils - -mmif_docloc_http package -======================== - -.. toctree:: - :maxdepth: 2 - - autodoc/mmif_docloc_http - diff --git a/docs/1.0.18/_sources/plugins.rst.txt b/docs/1.0.18/_sources/plugins.rst.txt deleted file mode 100644 index 1af39426..00000000 --- a/docs/1.0.18/_sources/plugins.rst.txt +++ /dev/null @@ -1,89 +0,0 @@ -.. _plugins: - -Developing plugins for MMIF Python SDK -====================================== - - -Overview --------- - -As MMIF JSON files can carry information about media document files without actually carrying file contents, file accessing modules in ``mmif`` Python package (distributed as ``mmif-python`` on PyPI) are designed to be lightweight and flexible so that it can work with additional "plugin" Python packages that can handle concrete file access. - - -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF website `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects. - -Developer can write simple plugins that can provide additional functionalities to ``mmif-python``. For example, ``mmif-python`` does not provide any file access functionality beyond a local file system (with ``file`` scheme), but it can be extended with a plugin that can handle file access over different protocols (e.g. ``http``, ``s3``, ``ftp``, etc). - -This document contains information about how to write plugins for ``mmif-python``. - -.. _docloc_plugin: - -Document Location Scheme Plugins -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -:class:`mmif.serialize.annotation.Document` class has various methods to access parts of ``location`` property of the document. The location is in `URI/IRI format `_ (``SCHEME://HOSTNAME/PATH``, in a nutshell) and it has to be resolved to a local file for CLAMS Apps to process the local file to analyze and extract information about the media and its contents. The core ``mmif-python`` distribution only provides a default implementation that can handle ``file`` scheme URIs. - -To add a document location handler plugin, you need to implement a Python `"package" `_ (do not confuse with PYPI distribution), that meets these requirements; - -#. the package must be named ``mmif_docloc_``. For example, to implement a handler for ``s3`` scheme, the package name must be ``mmif_docloc_s3``. The prefix is important as it's used in the plugin discovery process from the core ``mmif-python`` modules. -#. the top module of the package must have a function named ``resolve``. The function must take a single argument, which is a :class:`str` of the document location URI. The function must return a :class:`str` of the local file path. For example, if the document location is ``s3://mybucket/myfile.mp4``, a Python user should be able to to something like this; -#. Optionally (but highly recommended), the top module also can provide another function named ``help``. The function must take no arguments and return a :class:`str` that explains how the input string to the ``resolve`` function should be formatted. - -.. code-block:: python - - import mmif_docloc_s3 - resolved = mmif_docloc_s3.resolve('s3://mybucket/myfile.mp4') - # then resolved must be a local file path that can be used to open the file - - -Here's a minimal example codebase that you refer to when you develop a ``docloc`` plugin. - -(However, before you start writing your own plugin for a specific URI scheme, checking `if there's already a PyPI distribution `_ for the scheme might be a good idea.) - -.. code-block:: sh - - $ tree . - . - ├── mmif_docloc_dummy - │ └── __init__.py - ├── pyproject.toml - └── setup.cfg - - $ cat pyproject.toml - [build-system] - requires = ["setuptools"] - build-backend = "setuptools.build_meta" - - $ cat setup.cfg - [metadata] - name = mmif_docloc_dummy # this name is IMPORTANT - version = 0.0.1 - description = a plugin to mmif-pyhon to handle `dummy` location scheme - - -And the plugin code. - -.. code-block:: python - - # mmif_docloc_dummy/__init__.py - doc_types = {'video': 'mp4'} - - def resolve(docloc): - scheme = 'dummy' - if docloc.startswith(f'{scheme}://'): - doc_id, doc_type = docloc.split('.') - return f'/path/to/{doc_id}.{doc_types[doc_type]}' - else: - raise ValueError(f'cannot handle document location scheme: {docloc}') - - def help(): - return "location format: `.video`" - - - -Bulit-in Document Location Scheme Plugins -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -At the moment, ``mmif-python`` PyPI distribution ships a built-in *docloc* plugin that support both ``http`` and ``https`` schemes. -Take a look at :mod:`mmif_docloc_http` module for details. diff --git a/docs/1.0.18/_sources/target-versions.rst.txt b/docs/1.0.18/_sources/target-versions.rst.txt deleted file mode 100644 index 34216d3e..00000000 --- a/docs/1.0.18/_sources/target-versions.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _target-versions: - -Target MMIF Versions -==================== - -This article provides targeting MMIF specification versions of different versions of ``mmif-python`` SDK. - -.. csv-table:: Target Specification Versions - :file: target-versions.csv - :header-rows: 1 diff --git a/docs/1.0.18/_static/_sphinx_javascript_frameworks_compat.js b/docs/1.0.18/_static/_sphinx_javascript_frameworks_compat.js deleted file mode 100644 index 81415803..00000000 --- a/docs/1.0.18/_static/_sphinx_javascript_frameworks_compat.js +++ /dev/null @@ -1,123 +0,0 @@ -/* Compatability shim for jQuery and underscores.js. - * - * Copyright Sphinx contributors - * Released under the two clause BSD licence - */ - -/** - * small helper function to urldecode strings - * - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL - */ -jQuery.urldecode = function(x) { - if (!x) { - return x - } - return decodeURIComponent(x.replace(/\+/g, ' ')); -}; - -/** - * small helper function to urlencode strings - */ -jQuery.urlencode = encodeURIComponent; - -/** - * This function returns the parsed url parameters of the - * current request. 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- -/** - * Simple result scoring code. - */ -if (typeof Scorer === "undefined") { - var Scorer = { - // Implement the following function to further tweak the score for each result - // The function takes a result array [docname, title, anchor, descr, score, filename] - // and returns the new score. - /* - score: result => { - const [docname, title, anchor, descr, score, filename, kind] = result - return score - }, - */ - - // query matches the full name of an object - objNameMatch: 11, - // or matches in the last dotted part of the object name - objPartialMatch: 6, - // Additive scores depending on the priority of the object - objPrio: { - 0: 15, // used to be importantResults - 1: 5, // used to be objectResults - 2: -5, // used to be unimportantResults - }, - // Used when the priority is not in the mapping. - objPrioDefault: 0, - - // query found in title - title: 15, - partialTitle: 7, - // query found in terms - term: 5, - partialTerm: 2, - }; -} - -// Global search result kind enum, used by themes to style search results. -class SearchResultKind { - static get index() { return "index"; } - static get object() { return "object"; } - static get text() { return "text"; } - static get title() { return "title"; } -} - -const _removeChildren = (element) => { - while (element && element.lastChild) element.removeChild(element.lastChild); -}; - -/** - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping - */ -const _escapeRegExp = (string) => - string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string - -const _displayItem = (item, searchTerms, highlightTerms) => { - const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; - const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; - const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; - const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; - const contentRoot = document.documentElement.dataset.content_root; - - const [docName, title, anchor, descr, score, _filename, kind] = item; - - let listItem = document.createElement("li"); - // Add a class representing the item's type: - // can be used by a theme's CSS selector for styling - // See SearchResultKind for the class names. - listItem.classList.add(`kind-${kind}`); - let requestUrl; - let linkUrl; - if (docBuilder === "dirhtml") { - // dirhtml builder - let dirname = docName + "/"; - if (dirname.match(/\/index\/$/)) - dirname = dirname.substring(0, dirname.length - 6); - else if (dirname === "index/") dirname = ""; - requestUrl = contentRoot + dirname; - linkUrl = requestUrl; - } else { - // normal html builders - requestUrl = contentRoot + docName + docFileSuffix; - linkUrl = docName + docLinkSuffix; - } - let linkEl = listItem.appendChild(document.createElement("a")); - linkEl.href = linkUrl + anchor; - linkEl.dataset.score = score; - linkEl.innerHTML = title; - if (descr) { - listItem.appendChild(document.createElement("span")).innerHTML = - " (" + descr + ")"; - // highlight search terms in the description - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - } - else if (showSearchSummary) - fetch(requestUrl) - .then((responseData) => responseData.text()) - .then((data) => { - if (data) - listItem.appendChild( - Search.makeSearchSummary(data, searchTerms, anchor) - ); - // highlight search terms in the summary - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - }); - Search.output.appendChild(listItem); -}; -const _finishSearch = (resultCount) => { - Search.stopPulse(); - Search.title.innerText = _("Search Results"); - if (!resultCount) - Search.status.innerText = Documentation.gettext( - "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." - ); - else - Search.status.innerText = Documentation.ngettext( - "Search finished, found one page matching the search query.", - "Search finished, found ${resultCount} pages matching the search query.", - resultCount, - ).replace('${resultCount}', resultCount); -}; -const _displayNextItem = ( - results, - resultCount, - searchTerms, - highlightTerms, -) => { - // results left, load the summary and display it - // this is intended to be dynamic (don't sub resultsCount) - if (results.length) { - _displayItem(results.pop(), searchTerms, highlightTerms); - setTimeout( - () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), - 5 - ); - } - // search finished, update title and status message - else _finishSearch(resultCount); -}; -// Helper function used by query() to order search results. -// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. -// Order the results by score (in opposite order of appearance, since the -// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. -const _orderResultsByScoreThenName = (a, b) => { - const leftScore = a[4]; - const rightScore = b[4]; - if (leftScore === rightScore) { - // same score: sort alphabetically - const leftTitle = a[1].toLowerCase(); - const rightTitle = b[1].toLowerCase(); - if (leftTitle === rightTitle) return 0; - return leftTitle > rightTitle ? -1 : 1; // inverted is intentional - } - return leftScore > rightScore ? 1 : -1; -}; - -/** - * Default splitQuery function. Can be overridden in ``sphinx.search`` with a - * custom function per language. - * - * The regular expression works by splitting the string on consecutive characters - * that are not Unicode letters, numbers, underscores, or emoji characters. - * This is the same as ``\W+`` in Python, preserving the surrogate pair area. - */ -if (typeof splitQuery === "undefined") { - var splitQuery = (query) => query - .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) - .filter(term => term) // remove remaining empty strings -} - -/** - * Search Module - */ -const Search = { - _index: null, - _queued_query: null, - _pulse_status: -1, - - htmlToText: (htmlString, anchor) => { - const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - for (const removalQuery of [".headerlink", "script", "style"]) { - htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); - } - if (anchor) { - const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); - if (anchorContent) return anchorContent.textContent; - - console.warn( - `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` - ); - } - - // if anchor not specified or not found, fall back to main content - const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent) return docContent.textContent; - - console.warn( - "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." - ); - return ""; - }, - - init: () => { - const query = new URLSearchParams(window.location.search).get("q"); - document - .querySelectorAll('input[name="q"]') - .forEach((el) => (el.value = query)); - if (query) Search.performSearch(query); - }, - - loadIndex: (url) => - (document.body.appendChild(document.createElement("script")).src = url), - - setIndex: (index) => { - Search._index = index; - if (Search._queued_query !== null) { - const query = Search._queued_query; - Search._queued_query = null; - Search.query(query); - } - }, - - hasIndex: () => Search._index !== null, - - deferQuery: (query) => (Search._queued_query = query), - - stopPulse: () => (Search._pulse_status = -1), - - startPulse: () => { - if (Search._pulse_status >= 0) return; - - const pulse = () => { - Search._pulse_status = (Search._pulse_status + 1) % 4; - Search.dots.innerText = ".".repeat(Search._pulse_status); - if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); - }; - pulse(); - }, - - /** - * perform a search for something (or wait until index is loaded) - */ - performSearch: (query) => { - // create the required interface elements - const searchText = document.createElement("h2"); - searchText.textContent = _("Searching"); - const searchSummary = document.createElement("p"); - searchSummary.classList.add("search-summary"); - searchSummary.innerText = ""; - const searchList = document.createElement("ul"); - searchList.setAttribute("role", "list"); - searchList.classList.add("search"); - - const out = document.getElementById("search-results"); - Search.title = out.appendChild(searchText); - Search.dots = Search.title.appendChild(document.createElement("span")); - Search.status = out.appendChild(searchSummary); - Search.output = out.appendChild(searchList); - - const searchProgress = document.getElementById("search-progress"); - // Some themes don't use the search progress node - if (searchProgress) { - searchProgress.innerText = _("Preparing search..."); - } - Search.startPulse(); - - // index already loaded, the browser was quick! - if (Search.hasIndex()) Search.query(query); - else Search.deferQuery(query); - }, - - _parseQuery: (query) => { - // stem the search terms and add them to the correct list - const stemmer = new Stemmer(); - const searchTerms = new Set(); - const excludedTerms = new Set(); - const highlightTerms = new Set(); - const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); - splitQuery(query.trim()).forEach((queryTerm) => { - const queryTermLower = queryTerm.toLowerCase(); - - // maybe skip this "word" - // stopwords array is from language_data.js - if ( - stopwords.indexOf(queryTermLower) !== -1 || - queryTerm.match(/^\d+$/) - ) - return; - - // stem the word - let word = stemmer.stemWord(queryTermLower); - // select the correct list - if (word[0] === "-") excludedTerms.add(word.substr(1)); - else { - searchTerms.add(word); - highlightTerms.add(queryTermLower); - } - }); - - if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js - localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) - } - - // console.debug("SEARCH: searching for:"); - // console.info("required: ", [...searchTerms]); - // console.info("excluded: ", [...excludedTerms]); - - return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; - }, - - /** - * execute search (requires search index to be loaded) - */ - _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - - // Collect multiple result groups to be sorted separately and then ordered. - // Each is an array of [docname, title, anchor, descr, score, filename, kind]. - const normalResults = []; - const nonMainIndexResults = []; - - _removeChildren(document.getElementById("search-progress")); - - const queryLower = query.toLowerCase().trim(); - for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { - for (const [file, id] of foundTitles) { - const score = Math.round(Scorer.title * queryLower.length / title.length); - const boost = titles[file] === title ? 1 : 0; // add a boost for document titles - normalResults.push([ - docNames[file], - titles[file] !== title ? `${titles[file]} > ${title}` : title, - id !== null ? "#" + id : "", - null, - score + boost, - filenames[file], - SearchResultKind.title, - ]); - } - } - } - - // search for explicit entries in index directives - for (const [entry, foundEntries] of Object.entries(indexEntries)) { - if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id, isMain] of foundEntries) { - const score = Math.round(100 * queryLower.length / entry.length); - const result = [ - docNames[file], - titles[file], - id ? "#" + id : "", - null, - score, - filenames[file], - SearchResultKind.index, - ]; - if (isMain) { - normalResults.push(result); - } else { - nonMainIndexResults.push(result); - } - } - } - } - - // lookup as object - objectTerms.forEach((term) => - normalResults.push(...Search.performObjectSearch(term, objectTerms)) - ); - - // lookup as search terms in fulltext - normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); - - // let the scorer override scores with a custom scoring function - if (Scorer.score) { - normalResults.forEach((item) => (item[4] = Scorer.score(item))); - nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); - } - - // Sort each group of results by score and then alphabetically by name. - normalResults.sort(_orderResultsByScoreThenName); - nonMainIndexResults.sort(_orderResultsByScoreThenName); - - // Combine the result groups in (reverse) order. - // Non-main index entries are typically arbitrary cross-references, - // so display them after other results. - let results = [...nonMainIndexResults, ...normalResults]; - - // remove duplicate search results - // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept - let seen = new Set(); - results = results.reverse().reduce((acc, result) => { - let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); - if (!seen.has(resultStr)) { - acc.push(result); - seen.add(resultStr); - } - return acc; - }, []); - - return results.reverse(); - }, - - query: (query) => { - const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); - const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); - - // for debugging - //Search.lastresults = results.slice(); // a copy - // console.info("search results:", Search.lastresults); - - // print the results - _displayNextItem(results, results.length, searchTerms, highlightTerms); - }, - - /** - * search for object names - */ - performObjectSearch: (object, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const objects = Search._index.objects; - const objNames = Search._index.objnames; - const titles = Search._index.titles; - - const results = []; - - const objectSearchCallback = (prefix, match) => { - const name = match[4] - const fullname = (prefix ? prefix + "." : "") + name; - const fullnameLower = fullname.toLowerCase(); - if (fullnameLower.indexOf(object) < 0) return; - - let score = 0; - const parts = fullnameLower.split("."); - - // check for different match types: exact matches of full name or - // "last name" (i.e. last dotted part) - if (fullnameLower === object || parts.slice(-1)[0] === object) - score += Scorer.objNameMatch; - else if (parts.slice(-1)[0].indexOf(object) > -1) - score += Scorer.objPartialMatch; // matches in last name - - const objName = objNames[match[1]][2]; - const title = titles[match[0]]; - - // If more than one term searched for, we require other words to be - // found in the name/title/description - const otherTerms = new Set(objectTerms); - otherTerms.delete(object); - if (otherTerms.size > 0) { - const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); - if ( - [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) - ) - return; - } - - let anchor = match[3]; - if (anchor === "") anchor = fullname; - else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; - - const descr = objName + _(", in ") + title; - - // add custom score for some objects according to scorer - if (Scorer.objPrio.hasOwnProperty(match[2])) - score += Scorer.objPrio[match[2]]; - else score += Scorer.objPrioDefault; - - results.push([ - docNames[match[0]], - fullname, - "#" + anchor, - descr, - score, - filenames[match[0]], - SearchResultKind.object, - ]); - }; - Object.keys(objects).forEach((prefix) => - objects[prefix].forEach((array) => - objectSearchCallback(prefix, array) - ) - ); - return results; - }, - - /** - * search for full-text terms in the index - */ - performTermsSearch: (searchTerms, excludedTerms) => { - // prepare search - const terms = Search._index.terms; - const titleTerms = Search._index.titleterms; - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - - const scoreMap = new Map(); - const fileMap = new Map(); - - // perform the search on the required terms - searchTerms.forEach((word) => { - const files = []; - const arr = [ - { files: terms[word], score: Scorer.term }, - { files: titleTerms[word], score: Scorer.title }, - ]; - // add support for partial matches - if (word.length > 2) { - const escapedWord = _escapeRegExp(word); - if (!terms.hasOwnProperty(word)) { - Object.keys(terms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: terms[term], score: Scorer.partialTerm }); - }); - } - if (!titleTerms.hasOwnProperty(word)) { - Object.keys(titleTerms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); - }); - } - } - - // no match but word was a required one - if (arr.every((record) => record.files === undefined)) return; - - // found search word in contents - arr.forEach((record) => { - if (record.files === undefined) return; - - let recordFiles = record.files; - if (recordFiles.length === undefined) recordFiles = [recordFiles]; - files.push(...recordFiles); - - // set score for the word in each file - recordFiles.forEach((file) => { - if (!scoreMap.has(file)) scoreMap.set(file, {}); - scoreMap.get(file)[word] = record.score; - }); - }); - - // create the mapping - files.forEach((file) => { - if (!fileMap.has(file)) fileMap.set(file, [word]); - else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); - }); - }); - - // now check if the files don't contain excluded terms - const results = []; - for (const [file, wordList] of fileMap) { - // check if all requirements are matched - - // as search terms with length < 3 are discarded - const filteredTermCount = [...searchTerms].filter( - (term) => term.length > 2 - ).length; - if ( - wordList.length !== searchTerms.size && - wordList.length !== filteredTermCount - ) - continue; - - // ensure that none of the excluded terms is in the search result - if ( - [...excludedTerms].some( - (term) => - terms[term] === file || - titleTerms[term] === file || - (terms[term] || []).includes(file) || - (titleTerms[term] || []).includes(file) - ) - ) - break; - - // select one (max) score for the file. - const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); - // add result to the result list - results.push([ - docNames[file], - titles[file], - "", - null, - score, - filenames[file], - SearchResultKind.text, - ]); - } - return results; - }, - - /** - * helper function to return a node containing the - * search summary for a given text. keywords is a list - * of stemmed words. - */ - makeSearchSummary: (htmlText, keywords, anchor) => { - const text = Search.htmlToText(htmlText, anchor); - if (text === "") return null; - - const textLower = text.toLowerCase(); - const actualStartPosition = [...keywords] - .map((k) => textLower.indexOf(k.toLowerCase())) - .filter((i) => i > -1) - .slice(-1)[0]; - const startWithContext = Math.max(actualStartPosition - 120, 0); - - const top = startWithContext === 0 ? "" : "..."; - const tail = startWithContext + 240 < text.length ? "..." : ""; - - let summary = document.createElement("p"); - summary.classList.add("context"); - summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; - - return summary; - }, -}; - -_ready(Search.init); diff --git a/docs/1.0.18/_static/sphinx_highlight.js b/docs/1.0.18/_static/sphinx_highlight.js deleted file mode 100644 index 8a96c69a..00000000 --- a/docs/1.0.18/_static/sphinx_highlight.js +++ /dev/null @@ -1,154 +0,0 @@ -/* Highlighting utilities for Sphinx HTML documentation. */ -"use strict"; - -const SPHINX_HIGHLIGHT_ENABLED = true - -/** - * highlight a given string on a node by wrapping it in - * span elements with the given class name. - */ -const _highlight = (node, addItems, text, className) => { - if (node.nodeType === Node.TEXT_NODE) { - const val = node.nodeValue; - const parent = node.parentNode; - const pos = val.toLowerCase().indexOf(text); - if ( - pos >= 0 && - !parent.classList.contains(className) && - !parent.classList.contains("nohighlight") - ) { - let span; - - const closestNode = parent.closest("body, svg, foreignObject"); - const isInSVG = closestNode && closestNode.matches("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.classList.add(className); - } - - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - const rest = document.createTextNode(val.substr(pos + text.length)); - parent.insertBefore( - span, - parent.insertBefore( - rest, - node.nextSibling - ) - ); - node.nodeValue = val.substr(0, pos); - /* There may be more occurrences of search term in this node. So call this - * function recursively on the remaining fragment. - */ - _highlight(rest, addItems, text, className); - - if (isInSVG) { - const rect = document.createElementNS( - "http://www.w3.org/2000/svg", - "rect" - ); - const bbox = parent.getBBox(); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute("class", className); - addItems.push({ parent: parent, target: rect }); - } - } - } else if (node.matches && !node.matches("button, select, textarea")) { - node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); - } -}; -const _highlightText = (thisNode, text, className) => { - let addItems = []; - _highlight(thisNode, addItems, text, className); - addItems.forEach((obj) => - obj.parent.insertAdjacentElement("beforebegin", obj.target) - ); -}; - -/** - * Small JavaScript module for the documentation. - */ -const SphinxHighlight = { - - /** - * highlight the search words provided in localstorage in the text - */ - highlightSearchWords: () => { - if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight - - // get and clear terms from localstorage - const url = new URL(window.location); - const highlight = - localStorage.getItem("sphinx_highlight_terms") - || url.searchParams.get("highlight") - || ""; - localStorage.removeItem("sphinx_highlight_terms") - url.searchParams.delete("highlight"); - window.history.replaceState({}, "", url); - - // get individual terms from highlight string - const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); - if (terms.length === 0) return; // nothing to do - - // There should never be more than one element matching "div.body" - const divBody = document.querySelectorAll("div.body"); - const body = divBody.length ? divBody[0] : document.querySelector("body"); - window.setTimeout(() => { - terms.forEach((term) => _highlightText(body, term, "highlighted")); - }, 10); - - const searchBox = document.getElementById("searchbox"); - if (searchBox === null) return; - searchBox.appendChild( - document - .createRange() - .createContextualFragment( - '

' + - '' + - _("Hide Search Matches") + - "

" - ) - ); - }, - - /** - * helper function to hide the search marks again - */ - hideSearchWords: () => { - document - .querySelectorAll("#searchbox .highlight-link") - .forEach((el) => el.remove()); - document - .querySelectorAll("span.highlighted") - .forEach((el) => el.classList.remove("highlighted")); - localStorage.removeItem("sphinx_highlight_terms") - }, - - initEscapeListener: () => { - // only install a listener if it is really needed - if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; - - document.addEventListener("keydown", (event) => { - // bail for input elements - if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; - // bail with special keys - if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; - if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { - SphinxHighlight.hideSearchWords(); - event.preventDefault(); - } - }); - }, -}; - -_ready(() => { - /* Do not call highlightSearchWords() when we are on the search page. - * It will highlight words from the *previous* search query. - */ - if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); - SphinxHighlight.initEscapeListener(); -}); diff --git a/docs/1.0.18/autodoc/mmif.serialize.html b/docs/1.0.18/autodoc/mmif.serialize.html deleted file mode 100644 index 9573f9a7..00000000 --- a/docs/1.0.18/autodoc/mmif.serialize.html +++ /dev/null @@ -1,1469 +0,0 @@ - - - - - - - - - mmif.serialize module — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
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mmif.serialize module

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mmif.serialize.model module

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The model module contains the classes used to represent an -abstract MMIF object as a live Python object.

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The MmifObject class or one of its derivatives is subclassed by -all other classes defined in this SDK, except for MmifObjectEncoder.

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These objects are generally instantiated from JSON, either as a string -or as an already-loaded Python dictionary. This base class provides the -core functionality for deserializing MMIF JSON data into live objects -and serializing live objects into MMIF JSON data. Specialized behavior -for the different components of MMIF is added in the subclasses.

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-class mmif.serialize.model.DataDict(mmif_obj: bytes | str | dict | None = None, *_)[source]
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Bases: MmifObject, Generic[T, S]

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-empty()[source]
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-get(key: T, default=None) → S | None[source]
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-items()[source]
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-keys()[source]
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-update(other, overwrite)[source]
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-values()[source]
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-class mmif.serialize.model.DataList(mmif_obj: bytes | str | list | None = None, *_)[source]
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Bases: MmifObject, Generic[T]

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The DataList class is an abstraction that represents the -various lists found in a MMIF file, such as documents, subdocuments, -views, and annotations.

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Parameters:
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mmif_obj (Union[str, list]) – the data that the list contains

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-append(value, overwrite)[source]
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-deserialize(mmif_json: str | list) → None[source]
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Passes the input data into the internal deserializer.

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-empty()[source]
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-get(key: str) → T | None[source]
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Standard dictionary-style get() method, albeit with no default -parameter. Relies on the implementation of __getitem__.

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Will return None if the key is not found.

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Parameters:
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key – the key to search for

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Returns:
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the value matching that key

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-class mmif.serialize.model.MmifObject(mmif_obj: bytes | str | dict | None = None, *_)[source]
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Bases: object

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Abstract superclass for MMIF related key-value pair objects.

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Any MMIF object can be initialized as an empty placeholder or -an actual representation with a JSON formatted string or equivalent -dict object argument.

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This superclass has four specially designed instance variables, and these -variable names cannot be used as attribute names for MMIF objects.

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  1. _unnamed_attributes: -Only can be either None or an empty dictionary. If it’s set to None, -it means the class won’t take any Additional Attributes in the -JSON schema sense. If it’s an empty dict, users can throw any k-v -pairs to the class, as long as the key is not a “reserved” name, -and those additional attributes will be stored in this dict while -in memory.

    2. -

  2. _attribute_classes: -This is a dict from a key name to a specific python class to use for -deserialize the value. Note that a key name in this dict does NOT -have to be a named attribute, but is recommended to be one.

    3. -

  3. _required_attributes: -This is a simple list of names of attributes that are required in -the object. When serialize, an object will skip its empty (e.g. -zero-length, or None) attributes unless they are in this list. -Otherwise, the serialized JSON string would have empty -representations (e.g. "", []).

    4. -

  4. _exclude_from_diff: -This is a simple list of names of attributes that should be excluded -from the diff calculation in __eq__.

    5. -
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# TODO (krim @ 8/17/20): this dict is however, a duplicate with the type hints in the class definition. -Maybe there is a better way to utilize type hints (e.g. getting them -as a programmatically), but for now developers should be careful to -add types to hints as well as to this dict.

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Also note that those special attributes MUST be set in the __init__() -before calling super method, otherwise deserialization will not work.

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And also, a subclass that has one or more named attributes, it must -set those attributes in the __init__() before calling super method. -When serializing a MmifObject, all empty attributes will be ignored, -so for optional named attributes, you must leave the values empty -(len == 0), but NOT None. Any None-valued named attributes will cause -issues with current implementation.

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Parameters:
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mmif_obj – JSON string or dict to initialize an object. -If not given, an empty object will be initialized, sometimes with -an ID value automatically generated, based on its parent object.

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-deserialize(mmif_json: str | dict) → None[source]
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Takes a JSON-formatted string or a simple dict that’s json-loaded from -such a string as an input and populates object’s fields with the values -specified in the input.

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Parameters:
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mmif_json – JSON-formatted string or dict from such a string -that represents a MMIF object

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-disallow_additional_properties() → None[source]
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Call this method in __init__() to prevent the insertion -of unnamed attributes after initialization.

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-id_delimiter: ClassVar[str] = ':'[source]
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-static is_empty(obj) → bool[source]
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return True if the obj is None or “emtpy”. The emptiness first defined as -having zero length. But for objects that lack __len__ method, we need -additional check.

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-reserved_names: Set[str] = {'_attribute_classes', '_exclude_from_diff', '_required_attributes', '_unnamed_attributes', 'reserved_names'}[source]
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-serialize(pretty: bool = False) → str[source]
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Generates JSON representation of an object.

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Parameters:
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pretty – If True, returns string representation with indentation.

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Returns:
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JSON string of the object.

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-set_additional_property(key: str, value: Any) → None[source]
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Method to set values in _unnamed_attributes.

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Parameters:
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  • key – the attribute name

    • -

  • value – the desired value

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Returns:
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None

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Raise:
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AttributeError if additional properties are disallowed by disallow_additional_properties()

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-view_prefix: ClassVar[str] = 'v_'[source]
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-class mmif.serialize.model.MmifObjectEncoder(*, skipkeys=False, ensure_ascii=True, check_circular=True, allow_nan=True, sort_keys=False, indent=None, separators=None, default=None)[source]
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Bases: JSONEncoder

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Encoder class to define behaviors of de-/serialization

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-default(obj: MmifObject)[source]
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Overrides default encoding behavior to prioritize MmifObject.serialize().

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mmif.serialize.mmif module

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The mmif module contains the classes used to represent a full MMIF -file as a live Python object.

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See the specification docs and the JSON Schema file for more information.

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-class mmif.serialize.mmif.Mmif(mmif_obj: bytes | str | dict | None = None, *, validate: bool = True)[source]
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Bases: MmifObject

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MmifObject that represents a full MMIF file.

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Parameters:
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  • mmif_obj – the JSON data

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  • validate – whether to validate the data against the MMIF JSON schema.

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-add_document(document: Document, overwrite=False) → None[source]
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Appends a Document object to the documents list.

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Fails if there is already a document with the same ID in the MMIF object.

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Parameters:
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  • document – the Document object to add

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  • overwrite – if set to True, will overwrite -an existing view with the same ID

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Returns:
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None

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-add_view(view: View, overwrite=False) → None[source]
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Appends a View object to the views list.

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Fails if there is already a view with the same ID in the MMIF object.

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Parameters:
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  • view – the Document object to add

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  • overwrite – if set to True, will overwrite -an existing view with the same ID

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Returns:
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None

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-generate_capital_annotations()[source]
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Automatically convert any “pending” temporary properties from -Document objects to Annotation objects . The generated Annotation -objects are then added to the last View in the views lists.

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See https://github.com/clamsproject/mmif-python/issues/226 for rationale -behind this behavior and discussion.

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-get_alignments(at_type1: str | TypesBase, at_type2: str | TypesBase) → Dict[str, List[Annotation]][source]
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Finds views where alignments between two given annotation types occurred.

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Returns:
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a dict that keyed by view IDs (str) and has lists of alignment Annotation objects as values.

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-get_all_views_contain(*at_types: TypesBase | str) → List[View][source]
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Returns the list of all views in the MMIF if given types -are present in that view’s ‘contains’ metadata.

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Parameters:
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at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

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Returns:
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the list of views that contain the type

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-get_all_views_with_error() → List[View][source]
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Returns the list of all views in the MMIF that have errors.

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Returns:
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the list of views that contain errors but no annotations

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-get_annotations_between_time(start: int | float, end: int | float, time_unit: str = 'ms', at_types: List[str | TypesBase] = []) → Iterator[Annotation][source]
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Finds annotations that are anchored between the given time points.

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Parameters:
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  • start – the start time point in the unit of input_unit

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  • end – the end time point in the unit of input_unit

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  • time_unit – the unit of the input time points. Default is ms.

    • -

  • at_types – a list of annotation types to filter with. Any type in this list will be included in the return.

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Returns:
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an iterator of Annotation objects that are anchored between the given time points

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-get_document_by_id(doc_id: str) → Document[source]
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Finds a Document object with the given ID.

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Parameters:
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doc_id – the ID to search for

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Returns:
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a reference to the corresponding document, if it exists

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Raises:
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KeyError – if there is no corresponding document

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-get_document_location(m_type: DocumentTypes | str, path_only=False) → str | None[source]
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Method to get the location of first document of given type.

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Parameters:
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m_type – the type to search for

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Returns:
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the value of the location field in the corresponding document

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-get_documents_by_app(app_id: str) → List[Document][source]
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Method to get all documents object queries by its originated app name.

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Parameters:
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app_id – the app name to search for

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Returns:
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a list of documents matching the requested app name, or an empty list if the app not found

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-get_documents_by_property(prop_key: str, prop_value: str) → List[Document][source]
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Method to retrieve documents by an arbitrary key-value pair in the document properties objects.

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Parameters:
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  • prop_key – the metadata key to search for

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  • prop_value – the metadata value to match

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Returns:
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a list of documents matching the requested metadata key-value pair

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-get_documents_by_type(doc_type: str | DocumentTypes) → List[Document][source]
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Method to get all documents where the type matches a particular document type, which should be one of the CLAMS document types.

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Parameters:
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doc_type – the type of documents to search for, must be one of Document type defined in the CLAMS vocabulary.

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Returns:
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a list of documents matching the requested type, or an empty list if none found.

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-get_documents_in_view(vid: str | None = None) → List[Document][source]
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Method to get all documents object queries by a view id.

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Parameters:
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vid – the source view ID to search for

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Returns:
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a list of documents matching the requested source view ID, or an empty list if the view not found

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-get_documents_locations(m_type: DocumentTypes | str, path_only=False) → List[str | None][source]
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This method returns the file paths of documents of given type. -Only top-level documents have locations, so we only check them.

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Parameters:
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m_type – the type to search for

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Returns:
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a list of the values of the location fields in the corresponding documents

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-get_end(annotation: Annotation) → int | float[source]
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An alias to get_anchor_point method with start=False.

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-get_last_error() → str | None[source]
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Returns the last error message found in the views.

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Returns:
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the error message in human-readable format, or None if no error is found

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-get_start(annotation: Annotation) → int | float[source]
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An alias to get_anchor_point method with start=True.

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-get_view_by_id(req_view_id: str) → View[source]
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Finds a View object with the given ID.

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Parameters:
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req_view_id – the ID to search for

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Returns:
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a reference to the corresponding view, if it exists

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Raises:
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Exception – if there is no corresponding view

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-get_view_contains(at_types: TypesBase | str | List[str | TypesBase]) → View | None[source]
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Returns the last view appended that contains the given -types in its ‘contains’ metadata.

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Parameters:
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at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

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Returns:
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the view, or None if the type is not found

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-get_view_with_error() → View | None[source]
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Returns the last view appended that contains an error.

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Returns:
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the view, or None if no error is found

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-get_views_contain(*at_types: TypesBase | str) → List[View][source]
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Returns the list of all views in the MMIF if given types -are present in that view’s ‘contains’ metadata.

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Parameters:
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at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

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Returns:
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the list of views that contain the type

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-get_views_for_document(doc_id: str) → List[View][source]
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Returns the list of all views that have annotations anchored on a particular document. -Note that when the document is inside a view (generated during the pipeline’s running), -doc_id must be prefixed with the view_id.

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-get_views_with_error() → List[View][source]
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Returns the list of all views in the MMIF that have errors.

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Returns:
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the list of views that contain errors but no annotations

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-new_view() → View[source]
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Creates an empty view with a new ID and appends it to the views list.

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Returns:
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a reference to the new View object

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-new_view_id() → str[source]
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Fetches an ID for a new view.

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Returns:
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the ID

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-sanitize()[source]
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Sanitizes a Mmif object by running some safeguards. -Concretely, it performs the following before returning the JSON string.

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  1. validating output using built-in MMIF jsonschema

    2. -

  2. remove non-existing annotation types from contains metadata

    3. -
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-serialize(pretty: bool = False, sanitize: bool = False, autogenerate_capital_annotations=True) → str[source]
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Serializes the MMIF object to a JSON string.

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Parameters:
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  • sanitize – If True, performs some sanitization of before returning -the JSON string. See sanitize() for details.

    • -

  • autogenerate_capital_annotations – If True, automatically convert -any “pending” temporary properties from Document objects to -Annotation objects. See generate_capital_annotations() for -details.

    • -

  • pretty – If True, returns string representation with indentation.

    • -
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Returns:
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JSON string of the MMIF object.

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-static validate(json_str: bytes | str | dict) → None[source]
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Validates a MMIF JSON object against the MMIF Schema. -Note that this method operates before processing by MmifObject._load_str, -so it expects @ and not _ for the JSON-LD @-keys.

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Raises:
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jsonschema.exceptions.ValidationError – if the input fails validation

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Parameters:
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json_str – a MMIF JSON dict or string

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Returns:
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None

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mmif.serialize.view module

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The view module contains the classes used to represent a MMIF view -as a live Python object.

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In MMIF, views are created by apps in a pipeline that are annotating -data that was previously present in the MMIF file.

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-class mmif.serialize.view.Contain(mmif_obj: bytes | str | dict | None = None, *_)[source]
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Bases: DataDict[str, str]

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Contain object that represents the metadata of a single -annotation type in the contains metadata of a MMIF view.

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-class mmif.serialize.view.View(view_obj: bytes | str | dict | None = None, parent_mmif=None, *_)[source]
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Bases: MmifObject

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View object that represents a single view in a MMIF file.

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A view is identified by an ID, and contains certain metadata, -a list of annotations, and potentially a JSON-LD @context -IRI.

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If view_obj is not provided, an empty View will be generated.

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Parameters:
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view_obj – the JSON data that defines the view

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-add_annotation(annotation: Annotation, overwrite=False) → Annotation[source]
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Adds an annotation to the current view.

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Fails if there is already an annotation with the same ID -in the view, unless overwrite is set to True.

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Parameters:
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Raises:
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KeyError – if overwrite is set to False and -an annotation with the same ID exists -in the view

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Returns:
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the same Annotation object passed in as annotation

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-add_document(document: Document, overwrite=False) → Annotation[source]
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Appends a Document object to the annotations list.

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Fails if there is already a document with the same ID in the annotations list.

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Parameters:
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  • document – the Document object to add

    • -

  • overwrite – if set to True, will overwrite -an existing view with the same ID

    • -
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Returns:
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None

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-get_annotation_by_id(ann_id) → Annotation[source]
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-get_annotations(at_type: str | TypesBase | None = None, **properties) → Generator[Annotation, None, None][source]
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Look for certain annotations in this view, specified by parameters

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Parameters:
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    -

  • at_type – @type of the annotations to look for. When this is None, any @type will match.

    • -

  • properties – properties of the annotations to look for. When given more than one property, all properties must match. Note that annotation type metadata are specified in the contains view metadata, not in individual annotation objects.

    • -
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-get_document_by_id(doc_id) → Document[source]
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-get_documents() → List[Document][source]
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-get_error() → str | None[source]
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Get the “text” representation of the error occurred during -processing. Text representation is supposed to be human-readable. -When ths view does not have any error, returns None.

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-has_error() → bool[source]
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-has_warnings()[source]
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-new_annotation(at_type: str | TypesBase, aid: str | None = None, overwrite=False, **properties) → Annotation[source]
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Generates a new mmif.serialize.annotation.Annotation -object and adds it to the current view.

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Fails if there is already an annotation with the same ID -in the view, unless overwrite is set to True.

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Parameters:
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    -

  • at_type – the desired @type of the annotation.

    • -

  • aid – the desired ID of the annotation, when not given, -the mmif SDK tries to automatically generate an ID based on -Annotation type and existing annotations in the view.

    • -

  • overwrite – if set to True, will overwrite an -existing annotation with the same ID.

    • -
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Raises:
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KeyError – if overwrite is set to False and -an annotation with the same ID exists -in the view.

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Returns:
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the generated mmif.serialize.annotation.Annotation

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-new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
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Adds a new element to the contains metadata.

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Parameters:
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    -

  • at_type – the @type of the annotation type being added

    • -

  • contains_metadata – any metadata associated with the annotation type

    • -
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Returns:
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the generated Contain object

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-new_textdocument(text: str, lang: str = 'en', did: str | None = None, overwrite=False, **properties) → Document[source]
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Generates a new mmif.serialize.annotation.Document -object, particularly typed as TextDocument and adds it to the current view.

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Fails if there is already a text document with the same ID -in the view, unless overwrite is set to True.

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Parameters:
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    -

  • text – text content of the new document

    • -

  • lang – ISO 639-1 code of the language used in the new document

    • -

  • did – the desired ID of the document, when not given, -the mmif SDK tries to automatically generate an ID based on -Annotation type and existing documents in the view.

    • -

  • overwrite – if set to True, will overwrite an -existing document with the same ID

    • -
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Raises:
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KeyError – if overwrite is set to False and -an document with the same ID exists -in the view

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Returns:
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the generated mmif.serialize.annotation.Document

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-set_error(err_message: str, err_trace: str) → None[source]
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- -
- -
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-class mmif.serialize.view.ViewMetadata(viewmetadata_obj: bytes | str | dict | None = None, *_)[source]
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Bases: MmifObject

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ViewMetadata object that represents the metadata object within a MMIF view.

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Parameters:
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viewmetadata_obj – the JSON data that defines the metadata

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-add_app_configuration(config_key: str, config_value: str | int | float | bool | None | List[str | int | float | bool | None]) → None[source]
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Add a configuration key-value pair to the app_configuration dictionary.

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- -
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-add_contain(contain: Contain, at_type: str | TypesBase) → None[source]
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- -
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-add_parameter(param_key: str, param_value: str)[source]
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Add a single runtime parameter to the view metadata. Note that parameter value must be a string.

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-add_parameters(**runtime_params: str)[source]
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Add runtime parameters as a batch (dict) to the view metadata. Note that parameter values must be strings.

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-add_warnings(*warnings: Warning)[source]
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- -
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-emtpy_warnings()[source]
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- -
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-get_app_configuration(config_key: str) → str | int | float | bool | None | List[str | int | float | bool | None][source]
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Get a configuration value from the app_configuration dictionary.

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-get_error_as_text() → str[source]
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-get_parameter(param_key: str) → str[source]
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Get a runtime parameter from the view metadata.

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-has_error() → bool[source]
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- -
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-has_warnings()[source]
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- -
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-new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
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Adds a new element to the contains dictionary.

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Parameters:
-
    -

  • at_type – the @type of the annotation type being added

    • -

  • contains_metadata – any metadata associated with the annotation type

    • -
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Returns:
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the generated Contain object

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- -
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-set_error(message: str, stack_trace: str)[source]
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- -
- -
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-

mmif.serialize.annotation module

-

The annotation module contains the classes used to represent a -MMIF annotation as a live Python object.

-

In MMIF, annotations are created by apps in a pipeline as a part -of a view. For documentation on how views are represented, see -mmif.serialize.view.

-
-
-class mmif.serialize.annotation.Annotation(anno_obj: bytes | str | dict | None = None, *_)[source]
-

Bases: MmifObject

-

MmifObject that represents an annotation in a MMIF view.

-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]]) → None[source]
-

Adds a property to the annotation’s properties.

-
-
Parameters:
-
    -

  • name – the name of the property

    • -

  • value – the property’s desired value

    • -
-
-
Returns:
-

None

-
-
-
- -
-
-aligned_to_by(alignment: Annotation) → Annotation | None[source]
-

Retrieves the other side of Alignment annotation that has this annotation on one side.

-
-
Parameters:
-

alignment – Alignment annotation that has this annotation on one side

-
-
Returns:
-

the annotation that this annotation is aligned to (other side of Alignment), -or None if this annotation is not used in the Alignment.

-
-
-
- -
-
-property at_type: TypesBase[source]
-
- -
-
-static check_prop_value_is_simple_enough(value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]]) → bool[source]
-
- -
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-get(prop_name: str) → AnnotationProperties | str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]][source]
-

A special getter for Annotation properties. This is to allow for -directly accessing properties without having to go through the -properties object, or view-level annotation properties encoded in the -view.metadata.contains dict. Note that the regular props will take -the priority over the ephemeral props when there are conflicts.

-
- -
-
-get_all_aligned() → Iterator[Annotation][source]
-

Generator to iterate through all alignments and aligned annotations. Note that this generator will yield -the Alignment annotations as well. Every odd-numbered yield will be an Alignment annotation, and every -even-numbered yield will be the aligned annotation. If there’s a specific annotation type that you’re looking -for, you need to filter the generated results outside.

-
-
Returns:
-

yields the alignment annotation and the aligned annotation. -The order is decided by the order of appearance of Alignment annotations in the MMIF

-
-
-
- -
-
-get_property(prop_name: str) → AnnotationProperties | str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]][source]
-

A special getter for Annotation properties. This is to allow for -directly accessing properties without having to go through the -properties object, or view-level annotation properties encoded in the -view.metadata.contains dict. Note that the regular props will take -the priority over the ephemeral props when there are conflicts.

-
- -
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-property id: str[source]
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- -
-
-is_document()[source]
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- -
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-is_type(at_type: str | TypesBase) → bool[source]
-

Check if the @type of this object matches.

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- -
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-property long_id: str[source]
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- -
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-property parent: str[source]
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- -
- -
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-class mmif.serialize.annotation.AnnotationProperties(mmif_obj: bytes | str | dict | None = None, *_)[source]
-

Bases: MmifObject, MutableMapping[str, T]

-

AnnotationProperties object that represents the -properties object within a MMIF annotation.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
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- -
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-class mmif.serialize.annotation.Document(doc_obj: bytes | str | dict | None = None, *_)[source]
-

Bases: Annotation

-

Document object that represents a single document in a MMIF file.

-

A document is identified by an ID, and contains certain attributes -and potentially contains the contents of the document itself, -metadata about how the document was created, and/or a list of -subdocuments grouped together logically.

-

If document_obj is not provided, an empty Document will be generated.

-
-
Parameters:
-

document_obj – the JSON data that defines the document

-
-
-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None]) → None[source]
-

Adds a property to the document’s properties.

-

Unlike the parent Annotation class, added properties of a -Document object can be lost during serialization unless it belongs -to somewhere in a Mmif object. This is because we want to keep -Document object as “read-only” as possible. Thus, if you want to add -a property to a Document object,

-
    -

  • add the document to a Mmif object (either in the documents list or -in a view from the views list), or

    • -

  • directly write to Document.properties instead of using this method -(which is not recommended).

    • -
-

With the former method, the SDK will record the added property as a -Annotation annotation object, separate from the original Document -object. See Mmif.generate_capital_annotations() for more.

-

A few notes to keep in mind:

-
    -

  1. You can’t overwrite an existing property of a Document object.

    2. -

  2. A MMIF can have multiple Annotation objects with the same -property name but different values. When this happens, the SDK will -only keep the latest value (in order of appearances in views list) of -the property, effectively overwriting the previous values.

    3. -
-
- -
-
-get(prop_name)[source]
-

A special getter for Document properties. The major difference from -the super class’s Annotation.get() method is that Document -class has one more set of “pending” properties, that are added after -the Document object is created and will be serialized as a separate -Annotation object of which @type = Annotation. The -pending properties will take the priority over the regular properties -when there are conflicts.

-
- -
-
-get_property(prop_name)[source]
-

A special getter for Document properties. The major difference from -the super class’s Annotation.get() method is that Document -class has one more set of “pending” properties, that are added after -the Document object is created and will be serialized as a separate -Annotation object of which @type = Annotation. The -pending properties will take the priority over the regular properties -when there are conflicts.

-
- -
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-property location: str | None[source]
-

location property must be a legitimate URI. That is, should the document be a local file -then the file:// scheme must be used. -Returns None when no location is set.

-
- -
-
-location_address() → str | None[source]
-

Retrieves the full address from the document location URI. -Returns None when no location is set.

-
- -
-
-location_path(nonexist_ok=True) → str | None[source]
-

Retrieves a path that’s resolved to a pathname in the local file system. -To obtain the original value of the “path” part in the location string -(before resolving), use properties.location_path_literal method. -Returns None when no location is set.

-
-
Parameters:
-

nonexist_ok – if False, raise FileNotFoundError when the resolved path doesn’t exist

-
-
-
- -
-
-location_scheme() → str | None[source]
-

Retrieves URI scheme of the document location. -Returns None when no location is set.

-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
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-class mmif.serialize.annotation.DocumentProperties(mmif_obj: bytes | str | dict | None = None, *_)[source]
-

Bases: AnnotationProperties

-

DocumentProperties object that represents the -properties object within a MMIF document.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
-
-property location: str | None[source]
-

location property must be a legitimate URI. That is, should the document be a local file -then the file:// scheme must be used. -Returns None when no location is set.

-
- -
-
-location_address() → str | None[source]
-

Retrieves the full address from the document location URI. -Returns None when no location is set.

-
- -
-
-location_path() → str | None[source]
-
- -
-
-location_path_literal() → str | None[source]
-

Retrieves only path name of the document location (hostname is ignored). -Returns None when no location is set.

-
- -
-
-location_path_resolved(nonexist_ok=True) → str | None[source]
-

Retrieves only path name of the document location (hostname is ignored), -and then try to resolve the path name in the local file system. -This method should be used when the document scheme is file or empty. -For other schemes, users should install mmif-locdoc-<scheme> plugin.

-

Returns None when no location is set. -Raise ValueError when no code found to resolve the given location scheme.

-
- -
-
-location_scheme() → str | None[source]
-

Retrieves URI scheme of the document location. -Returns None when no location is set.

-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.Text(text_obj: bytes | str | dict | None = None, *_)[source]
-

Bases: MmifObject

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-property lang: str[source]
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- -
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-property value: str[source]
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- -
- -
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- - -
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- -
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- - - \ No newline at end of file diff --git a/docs/1.0.18/autodoc/mmif.utils.html b/docs/1.0.18/autodoc/mmif.utils.html deleted file mode 100644 index 9a95b48d..00000000 --- a/docs/1.0.18/autodoc/mmif.utils.html +++ /dev/null @@ -1,615 +0,0 @@ - - - - - - - - - mmif.utils module — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
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- -
-
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-
- -
-

mmif.utils module

-
-

mmif.utils.video_document_helper module

-
-
-mmif.utils.video_document_helper.capture(video_document: Document)[source]
-

Captures a video file using OpenCV and adds fps, frame count, and duration as properties to the document.

-
-
Parameters:
-

video_document – Document instance that holds a video document ("@type": ".../VideoDocument/...")

-
-
Returns:
-

OpenCV VideoCapture object

-
-
-
- -
-
-mmif.utils.video_document_helper.convert_timeframe(mmif: Mmif, time_frame: Annotation, out_unit: str) → Tuple[int | float | str, int | float | str][source]
-

Converts start and end points in a TimeFrame annotation a different time unit.

-
-
Parameters:
-
    -

  • mmif – Mmif instance

    • -

  • time_frame – Annotation instance that holds a time interval annotation ("@type": ".../TimeFrame/...")

    • -

  • out_unit – time unit to which the point is converted

    • -
-
-
Returns:
-

tuple of frame numbers, seconds/milliseconds, or ISO notation of TimeFrame’s start and end

-
-
-
- -
-
-mmif.utils.video_document_helper.convert_timepoint(mmif: Mmif, timepoint: Annotation, out_unit: str) → int | float | str[source]
-

Converts a time point included in an annotation to a different time unit. -The input annotation must have timePoint property.

-
-
Parameters:
-
    -

  • mmif – input MMIF to obtain fps and input timeunit

    • -

  • timepoint – Annotation instance with timePoint property

    • -

  • out_unit – time unit to which the point is converted (frames, seconds, milliseconds)

    • -
-
-
Returns:
-

frame number (integer) or second/millisecond (float) of input timepoint

-
-
-
- -
-
-mmif.utils.video_document_helper.extract_frames_as_images(video_document: Document, framenums: List[int], as_PIL: bool = False)[source]
-

Extracts frames from a video document as a list of numpy.ndarray. -Use with sample_frames() function to get the list of frame numbers first.

-
-
Parameters:
-
    -

  • video_document – Document instance that holds a video document ("@type": ".../VideoDocument/...")

    • -

  • framenums – integers representing the frame numbers to extract

    • -

  • as_PIL – return PIL.Image.Image instead of ndarray

    • -
-
-
Returns:
-

frames as a list of ndarray or Image

-
-
-
- -
-
-mmif.utils.video_document_helper.extract_mid_frame(mmif: Mmif, time_frame: Annotation, as_PIL: bool = False)[source]
-

Extracts the middle frame of a time interval annotation as a numpy ndarray.

-
-
Parameters:
-
    -

  • mmif – Mmif instance

    • -

  • time_frame – Annotation instance that holds a time interval annotation ("@type": ".../TimeFrame/...")

    • -

  • as_PIL – return Image instead of ndarray

    • -
-
-
Returns:
-

frame as a numpy.ndarray or PIL.Image.Image

-
-
-
- -
-
-mmif.utils.video_document_helper.extract_representative_frame(mmif: Mmif, time_frame: Annotation, as_PIL: bool = False)[source]
-

Extracts the representative frame of an annotation as a numpy ndarray or PIL Image.

-
-
Parameters:
-
    -

  • mmif – Mmif instance

    • -

  • time_frame – Annotation instance that holds a time interval annotation ("@type": ".../TimeFrame/...")

    • -

  • as_PIL – return Image instead of ndarray

    • -
-
-
Returns:
-

frame as a numpy.ndarray or PIL.Image.Image

-
-
-
- -
-
-mmif.utils.video_document_helper.framenum_to_millisecond(video_doc: Document, frame: int)[source]
-

Converts a frame number to a millisecond value.

-
- -
-
-mmif.utils.video_document_helper.framenum_to_second(video_doc: Document, frame: int)[source]
-

Converts a frame number to a second value.

-
- -
-
-mmif.utils.video_document_helper.get_annotation_property(mmif, annotation, prop_name)[source]
-
-

Deprecated since version 1.0.8: Use mmif.serialize.annotation.Annotation.get_property() method instead.

-
-

Get a property value from an annotation. If the property is not found in the annotation, it will look up the metadata of the annotation’s parent view and return the value from there. -xisting

-
- -
-
-mmif.utils.video_document_helper.get_framerate(video_document: Document) → float[source]
-

Gets the frame rate of a video document. First by checking the fps property of the document, then by capturing the video.

-
-
Parameters:
-

video_document – Document instance that holds a video document ("@type": ".../VideoDocument/...")

-
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Returns:
-

frames per second as a float, rounded to 2 decimal places

-
-
-
- -
-
-mmif.utils.video_document_helper.get_mid_framenum(mmif: Mmif, time_frame: Annotation)[source]
-

Calculates the middle frame number of a time interval annotation.

-
-
Parameters:
-
    -

  • mmif – Mmif instance

    • -

  • time_frame – Annotation instance that holds a time interval annotation ("@type": ".../TimeFrame/...")

    • -
-
-
Returns:
-

middle frame number as an integer

-
-
-
- -
-
-mmif.utils.video_document_helper.get_representative_framenum(mmif: Mmif, time_frame: Annotation)[source]
-

Calculates the representative frame number from an annotation.

-
-
Parameters:
-
    -

  • mmif – Mmif instance

    • -

  • time_frame – Annotation instance that holds a time interval annotation containing a representatives property ("@type": ".../TimeFrame/...")

    • -
-
-
Returns:
-

representative frame number as an integer

-
-
-
- -
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-mmif.utils.video_document_helper.millisecond_to_framenum(video_doc: Document, millisecond: float) → int[source]
-

Converts a millisecond value to a frame number.

-
- -
-
-mmif.utils.video_document_helper.sample_frames(start_frame: int, end_frame: int, sample_rate: float = 1) → List[int][source]
-

Helper function to sample frames from a time interval. -Can also be used as a “cutoff” function when used with start_frame==0 and sample_rate==1.

-
-
Parameters:
-
    -

  • start_frame – start frame of the interval

    • -

  • end_frame – end frame of the interval

    • -

  • sample_rate – sampling rate (or step) to configure how often to take a frame, default is 1, meaning all consecutive frames are sampled

    • -
-
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- -
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-mmif.utils.video_document_helper.second_to_framenum(video_doc: Document, second) → int[source]
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Converts a second value to a frame number.

-
- -
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-

mmif.utils.sequence_helper module

-

This module provides helpers for handling sequence labeling. Specifically, it provides

-
    -

  • a generalized label re-mapper for “post-binning” of labels

    • -

  • conversion from a list of CLAMS annotations (with classification props) into a list of reals (scores by labels), can be combined with the label re-mapper mentioned above

    • -

  • mmif.utils.sequence_helper.smooth_outlying_short_intervals(): a simple smoothing algorithm by trimming “short” outlier sequences

    • -
-

However, it DOES NOT provide

-
    -

  • direct conversion between CLAMS annotations. For example, it does not directly handle stitching of TimePoint into TimeFrames.

    • -

  • support for multi-class scenario, such as handling of _competing_ subsequence or overlapping labels.

    • -
-

Some functions can use optional external libraries (e.g., numpy) for better performance. -Hence, if you see a warning about missing optional packages, you might want to install them by running pip install mmif-python[seq].

-
-
-mmif.utils.sequence_helper.build_label_remapper(src_labels: List[str], dst_labels: Dict[str, str | int | float | bool | None]) → Dict[str, str | int | float | bool | None][source]
-

Build a label remapper dictionary from source and destination labels.

-
-
Parameters:
-
    -

  • src_labels – a list of all labels on the source side

    • -

  • dst_labels – a dict from source labels to destination labels. -Source labels not in this dict will be remapped to a negative label (-).

    • -
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-
Returns:
-

a dict that exhaustively maps source labels to destination labels

-
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- -
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-mmif.utils.sequence_helper.build_score_lists(classifications: ~typing.List[~typing.Dict], label_remapper: ~typing.Dict, score_remap_op: ~typing.Callable[[...], float] = <built-in function max>) → Tuple[Dict[str, int], numpy.ndarray][source]
-

Build lists of scores indexed by the label names.

-
-
Parameters:
-
    -

  • classifications – list of dictionaries of classification results, taken from input annotation objects

    • -

  • label_remapper – a dictionary that maps source label names to destination label names (formerly “postbin”)

    • -

  • score_remap_op – a function to remap the scores from multiple source labels binned to a destination label -common choices are max, min, or sum

    • -
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Returns:
-

    -

  1. a dictionary that maps label names to their index in the score list

    2. -

  2. 2-d numpy array of scores, of which rows are indexed by label map dict (first return value)

    3. -
-

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- -
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-mmif.utils.sequence_helper.smooth_outlying_short_intervals(scores: List[float], min_spseq_size: int, min_snseq_size: int, min_score: float = 0.5)[source]
-

Given a list of scores, a score threshold, and smoothing parameters, -identify the intervals of “positive” scores by “trimming” the short -positive sequences (“spseq”) and short negative sequences (“snseq”). To -decide the positivity, first step is binarization of the scores by the -min_score threshold. Given Sr as “raw” input real-number scores -list, and min_score=0.5,

-
-
Sr: [0.3, 0.6, 0.2, 0.8, 0.2, 0.9, 0.8, 0.5, 0.1, 0.5, 0.8, 0.3, 1.0, 0.7, 0.5, 0.5, 0.5, 0.8, 0.3, 0.6]
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-
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the binarization is done by simply comparing each score to the -threshold to get S list of binary scores

-
-
1.0 :                                     |                      
-0.9 :                |                    |                      
-0.8 :          |     |  |           |     |              |       
-0.7 :          |     |  |           |     |  |           |       
-0.6 :    |     |     |  |           |     |  |           |     | 
-0.5 :----+-----+-----+--+--+-----+--+-----+--+--+--+--+--+-----+-
-0.4 :    |     |     |  |  |     |  |     |  |  |  |  |  |     | 
-0.3 : |  |     |     |  |  |     |  |  |  |  |  |  |  |  |  |  | 
-0.2 : |  |  |  |  |  |  |  |     |  |  |  |  |  |  |  |  |  |  | 
-0.1 : |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | 
-0.0 +------------------------------------------------------------
-raw :.3 .6 .2 .8 .2 .9 .8 .5 .1 .5 .8 .3 1. .7 .5 .5 .5 .8 .3 .6
- S  : 0  1  0  1  0  1  1  0  0  0  1  0  1  1  0  1  1  1  0  1 
-
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Note that the size of a positive or negative sequence can be as small -as 1.

-

Then, here are examples of smoothing a list of binary scores into -intervals, by trimming “very short” (under thresholds) sequences of -positive or negative:

-
-

Note

-

legends:

-
    -

  • t is unit index (e.g. time index)

    • -

  • S is the list of binary scores (zeros and ones)

    • -

  • I is the list of intervals after smoothing

    • -
-
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    -

  1. with params min_spseq_size==1, min_snseq_size==4

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1]
-I: [0, 1--1--1--1--1--1--1--1--1--1--1--1, 0--0--0--0--0--0, 1]
-
    -
    -

    Explanation: min_snseq_size is used to smooth short sequences -of negative predictions. In this, zeros from t[7:10] are smoothed -into “one” I, while zeros from t[13:19] are kept as “zero” I. Note -that the “short” snseqs at the either ends (t[0:1]) are never -smoothed.

    -
    -
    2. -

  2. with params min_spseq_size==4, min_snseq_size==2

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1]
-I: [0, 1--1--1--1--1--1, 0--0--0--0--0--0--0--0--0--0--0--0--0]
-
    -
    -

    Explanation: min_spseq_size is used to smooth short sequences -of positive predictions. In this example, the spseqs of ones from -both t[10:13] and t[19:20] are smoothed. Note that the “short” -spseqs at the either ends (t[19:20]) are always smoothed.

    -
    -
    3. -

  3. with params min_spseq_size==4, min_snseq_size==4

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1]
-I: [0, 1--1--1--1--1--1--1--1--1--1--1--1--0--0--0--0--0--0--0]
-
    -
    -

    Explanation: When two threshold parameters are working together, -the algorithm will prioritize the smoothing of the snseqs over the -smoothing of the spseqs. Thus, in this example, the snseq t[7:10] -gets first smoothed “up” before the spseq t[10:13] is smoothed -“down”, resulting in a long final I.

    -
    -
    4. -

  4. with params min_spseq_size==4, min_snseq_size==4

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [1, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 1, 1]
-I: [1--1--1--1--1--1--1, 0--0--0--0, 1--1--1--1--1--1--1--1--1]
-
    -
    -

    Explanation: Since smoothing of snseqs is prioritized, short spseqs -at the beginning or the end can be kept.

    -
    -
    5. -

  5. with params min_spseq_size==1, min_snseq_size==1

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 1, 1]
-I: [0--0--0, 1--1--1--1, 0--0--0--0, 1--1--1--1, 0--0--0, 1--1]
-
    -
    -

    Explanation: When both width thresholds are set to 1, the algorithm -works essentially in the “stitching” only mode.

    -
    -
    6. -
-
-
Parameters:
-
    -

  • scores – SORTED list of scores to be smoothed. The score list -is assumed to be “exhaust” the entire time or space of -the underlying document segment. -(Sorted by the start, and then by the end of anchors)

    • -

  • min_score – minimum threshold to use to discard -low-scored units (strictly less than)

    • -

  • min_spseq_size – minimum size of a positive sequence not to be -smoothed (greater or equal to)

    • -

  • min_snseq_size – minimum size of a negative sequence not to be -smoothed (greater or equal to)

    • -
-
-
Returns:
-

list of tuples of start(inclusive)/end(exclusive) indices -of the “positive” sequences. Negative sequences (regardless of -their size) are not included in the output.

-
-
-
- -
-
-mmif.utils.sequence_helper.validate_labelset(annotations: Iterable[Annotation]) → List[str][source]
-

Simple check for a list of annotations to see if they have the same label set.

-
-
Raise:
-

AttributeError if an element in the input list doesn’t have the labelset property

-
-
Raise:
-

ValueError if different labelset values are found

-
-
Returns:
-

a list of the common labelset value (list of label names)

-
-
-
- -
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- - -
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- - Other Versions - v: 1.0.18 - - -
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- - - \ No newline at end of file diff --git a/docs/1.0.18/autodoc/mmif.vocabulary.html b/docs/1.0.18/autodoc/mmif.vocabulary.html deleted file mode 100644 index 3fa85335..00000000 --- a/docs/1.0.18/autodoc/mmif.vocabulary.html +++ /dev/null @@ -1,319 +0,0 @@ - - - - - - - - - mmif.vocabulary module — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
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-
- -
-

mmif.vocabulary module

-
-

mmif.vocabulary.annotation_types module

-
-
-class mmif.vocabulary.annotation_types.AnnotationTypes(type_uri, fuzzymode=True)[source]
-

Bases: AnnotationTypesBase

-

This class contains the CLAMS annotation types -defined in the spec version 1.1.0 as class variables.

-
-
-Alignment = http://mmif.clams.ai/vocabulary/Alignment/v1[source]
-
- -
-
-Annotation = http://mmif.clams.ai/vocabulary/Annotation/v6[source]
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- -
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-BoundingBox = http://mmif.clams.ai/vocabulary/BoundingBox/v5[source]
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- -
-
-Chapter = http://mmif.clams.ai/vocabulary/Chapter/v6[source]
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- -
-
-Interval = http://mmif.clams.ai/vocabulary/Interval/v5[source]
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- -
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-NamedEntity = http://mmif.clams.ai/vocabulary/NamedEntity/v1[source]
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- -
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-NounChunk = http://mmif.clams.ai/vocabulary/NounChunk/v1[source]
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- -
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-Paragraph = http://mmif.clams.ai/vocabulary/Paragraph/v1[source]
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- -
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-Polygon = http://mmif.clams.ai/vocabulary/Polygon/v5[source]
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- -
-
-Region = http://mmif.clams.ai/vocabulary/Region/v5[source]
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- -
-
-Relation = http://mmif.clams.ai/vocabulary/Relation/v5[source]
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- -
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-Sentence = http://mmif.clams.ai/vocabulary/Sentence/v1[source]
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- -
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-Span = http://mmif.clams.ai/vocabulary/Span/v5[source]
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- -
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-TimeFrame = http://mmif.clams.ai/vocabulary/TimeFrame/v6[source]
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- -
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-TimePoint = http://mmif.clams.ai/vocabulary/TimePoint/v5[source]
-
- -
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-Token = http://mmif.clams.ai/vocabulary/Token/v1[source]
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-VerbChunk = http://mmif.clams.ai/vocabulary/VerbChunk/v1[source]
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- -
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-VideoObject = http://mmif.clams.ai/vocabulary/VideoObject/v5[source]
-
- -
- -
-
-

mmif.vocabulary.document_types module

-
-
-class mmif.vocabulary.document_types.DocumentTypes(type_uri, fuzzymode=True)[source]
-

Bases: DocumentTypesBase

-

This class contains the CLAMS document types -defined in the spec version 1.1.0 as class variables.

-
-
-AudioDocument = http://mmif.clams.ai/vocabulary/AudioDocument/v1[source]
-
- -
-
-Document = http://mmif.clams.ai/vocabulary/Document/v1[source]
-
- -
-
-ImageDocument = http://mmif.clams.ai/vocabulary/ImageDocument/v1[source]
-
- -
-
-TextDocument = http://mmif.clams.ai/vocabulary/TextDocument/v1[source]
-
- -
-
-VideoDocument = http://mmif.clams.ai/vocabulary/VideoDocument/v1[source]
-
- -
- -
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- - - \ No newline at end of file diff --git a/docs/1.0.18/autodoc/mmif_docloc_http.html b/docs/1.0.18/autodoc/mmif_docloc_http.html deleted file mode 100644 index 5e3cd7d3..00000000 --- a/docs/1.0.18/autodoc/mmif_docloc_http.html +++ /dev/null @@ -1,185 +0,0 @@ - - - - - - - - - mmif_docloc_http package — mmif-python documentation - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif_docloc_http package

-

MMIF document location helper module for http and https schemes. -If you want to write your own docloc scheme handler, please use the source code of this module as a reference. -See this plug-in section for more information.

-
-
-mmif_docloc_http.help()[source]
-
- -
-
-mmif_docloc_http.resolve(docloc)[source]
-
- -
- - -
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- - Other Versions - v: 1.0.18 - - -
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- - - \ No newline at end of file diff --git a/docs/1.0.18/consumer-tutorial.html b/docs/1.0.18/consumer-tutorial.html deleted file mode 100644 index d3869bda..00000000 --- a/docs/1.0.18/consumer-tutorial.html +++ /dev/null @@ -1,172 +0,0 @@ - - - - - - - - - MMIF consumer — mmif-python documentation - - - - - - - - - - - - - - - -
- - -
- -
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    • -
  • MMIF consumer
    • -
  • -
    • -
-
-
-
-
- -
-

MMIF consumer

-

A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the appliance documentation to learn more about the appliance.

-

MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance.

-
    -

  1. The code must be hosted on a public git repository (e.g. Github, Gitlab, …)

    2. -

  2. Must listen to 5000 port.

    3. -

  3. Must expose /display route .

    4. -

  4. /display router should response to GET requests.

    5. -

  5. In the GET request, a public URL of the input MMIF file is passed via file URL parameter.

    6. -

  6. On the codebase root, there must be a Dockerfile that can build a docker image that runs the web app.

    7. -
-

We provide an example consumer at https://github.com/clamsproject/mmif-visualizer.

-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 1.0.18 - - -
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- - - \ No newline at end of file diff --git a/docs/1.0.18/genindex.html b/docs/1.0.18/genindex.html deleted file mode 100644 index 56b5085e..00000000 --- a/docs/1.0.18/genindex.html +++ /dev/null @@ -1,782 +0,0 @@ - - - - - - - - Index — mmif-python documentation - - - - - - - - - - - - - - - -
- - -
- -
-
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    -
    • -
  • Index
    • -
  • -
    • -
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Index

- -
- A - | B - | C - | D - | E - | F - | G - | H - | I - | K - | L - | M - | N - | P - | R - | S - | T - | U - | V - -
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A

- - - -
- -

B

- - - -
- -

C

- - - -
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D

- - - -
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E

- - - -
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F

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G

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I

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K

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L

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M

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N

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P

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R

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S

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U

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V

- - - -
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- - -
- -
-
-
-
    -
    • -
  • Welcome to mmif-python’s documentation!
    • -
  • -
    • -
-
-
-
-
- -
-

Welcome to mmif-python’s documentation!

-
-

MultiMedia Interchange Format

-

MMIF is a JSON(-LD)-based data format designed for transferring annotation data between computational analysis applications in CLAMS project.

-
-
-

mmif-python

-

mmif-python is a Python implementation of the MMIF data format. -mmif-python provides various helper classes and functions to handle MMIF JSON in Python, -including ;

-
    -

  1. de-/serialization of MMIF internal data structures to/from JSON

    2. -

  2. validation of MMIF JSON

    3. -

  3. handling of CLAMS vocabulary types

    4. -

  4. navigation of MMIF object via various “search” methods (e.g. mmif.get_all_views_contain(vocab_type)))

    5. -
-
-
-

For more …

- -
-

Contents

- -
-
-

API documentation:

- -
-
-
-
-

Indices and tables

- -
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 1.0.18 - - -
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- - - \ No newline at end of file diff --git a/docs/1.0.18/introduction.html b/docs/1.0.18/introduction.html deleted file mode 100644 index a1ff2c32..00000000 --- a/docs/1.0.18/introduction.html +++ /dev/null @@ -1,245 +0,0 @@ - - - - - - - - - Getting Started — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
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  • Getting Started
    • -
  • -
    • -
-
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-
- -
-

Getting Started

-
-

Overview

-

MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for reproducibility, transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF website. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects.

-
-
-

Prerequisites

-
    -

  • Python: the latest mmif-python requires Python 3.8 or newer. We have no plan to support Python 2.7.

    • -
-
-
-

Installation

-

Package mmif-python is distributed via the official PyPI. Users are supposed to pip-install to get latest release.

-
pip install mmif-python
-
-
-

This will install a package mmif to local python.

-

The MMIF format and specification is evolving over time, and mmif-python package will be updated along with the changes in MMIF format.

-
-

Note

-

MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and mmif-python versions, please take time to read our decision on the subject here. If you need to know which python SDK supports which specification version, see Target MMIF Versions page.

-
-
-
-

MMIF Serialization

-

mmif.serialize.mmif.Mmif represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of mmif.serialize.model.MmifObject, including the mmif.serialize.mmif.Mmif. To start with an existing MMIF str, simple initiate a new Mmif object with the file.

-
import mmif
-from mmif import Mmif
-
-mmif_str = """{
-"metadata": {
-  "mmif": "http://mmif.clams.ai/1.0.0"
-},
-"documents": [
-  {
-    "@type": "http://mmif.clams.ai/vocabulary/VideoDocument/v1",
-    "properties": {
-      "id": "m1",
-      "mime": "video/mp4",
-      "location": "file:///var/archive/video-0012.mp4"
-    }
-  },
-  {
-    "@type": "http://mmif.clams.ai/vocabulary/TextDocument/v1",
-    "properties": {
-      "id": "m2",
-      "mime": "text/plain",
-      "location": "file:///var/archive/video-0012-transcript.txt"
-    }
-  }
-],
-"views": []}"""
-mmif_obj = Mmif(mmif_str)
-
-
-

Few notes;

-
    -

  1. MMIF does not carry the primary source files in it.

    2. -

  2. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version mmif-python implementation of the MMIF might not be able to load an unsupported version of MMIF string.

    3. -
-

When serializing back to str, call mmif.serialize.model.MmifObject.serialize() on the object.

-

To get subcomponents, you can use various getters implemented in subclasses. For example;

-
from mmif.vocabulary.document_types import DocumentTypes
-
-for video in mmif_obj.Mmif.get_documents_by_type(DocumentTypes.VideoDocument):
-  with open(video.location_path(), 'b') as in_video:
-    # do something with the video file
-
-
-

For a full list of available helper methods, please refer to the API documentation.

-
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- - Other Versions - v: 1.0.18 - - -
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mmif package

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mmif_docloc_http package

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  • Developing plugins for MMIF Python SDK
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Developing plugins for MMIF Python SDK

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Overview

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As MMIF JSON files can carry information about media document files without actually carrying file contents, file accessing modules in mmif Python package (distributed as mmif-python on PyPI) are designed to be lightweight and flexible so that it can work with additional “plugin” Python packages that can handle concrete file access.

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This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF website. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects.

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Developer can write simple plugins that can provide additional functionalities to mmif-python. For example, mmif-python does not provide any file access functionality beyond a local file system (with file scheme), but it can be extended with a plugin that can handle file access over different protocols (e.g. http, s3, ftp, etc).

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This document contains information about how to write plugins for mmif-python.

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Document Location Scheme Plugins

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mmif.serialize.annotation.Document class has various methods to access parts of location property of the document. The location is in URI/IRI format (SCHEME://HOSTNAME/PATH, in a nutshell) and it has to be resolved to a local file for CLAMS Apps to process the local file to analyze and extract information about the media and its contents. The core mmif-python distribution only provides a default implementation that can handle file scheme URIs.

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To add a document location handler plugin, you need to implement a Python “package” (do not confuse with PYPI distribution), that meets these requirements;

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  1. the package must be named mmif_docloc_<SCHEME>. For example, to implement a handler for s3 scheme, the package name must be mmif_docloc_s3. The prefix is important as it’s used in the plugin discovery process from the core mmif-python modules.

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  2. the top module of the package must have a function named resolve. The function must take a single argument, which is a str of the document location URI. The function must return a str of the local file path. For example, if the document location is s3://mybucket/myfile.mp4, a Python user should be able to to something like this;

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  3. Optionally (but highly recommended), the top module also can provide another function named help. The function must take no arguments and return a str that explains how the input string to the resolve function should be formatted.

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import mmif_docloc_s3
-resolved = mmif_docloc_s3.resolve('s3://mybucket/myfile.mp4')
-# then resolved must be a local file path that can be used to open the file
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Here’s a minimal example codebase that you refer to when you develop a docloc plugin.

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(However, before you start writing your own plugin for a specific URI scheme, checking if there’s already a PyPI distribution for the scheme might be a good idea.)

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$ tree .
-.
-├── mmif_docloc_dummy
-│   └── __init__.py
-├── pyproject.toml
-└── setup.cfg
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- $ cat pyproject.toml
-[build-system]
-requires = ["setuptools"]
-build-backend = "setuptools.build_meta"
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-$ cat setup.cfg
-[metadata]
-name = mmif_docloc_dummy  # this name is IMPORTANT
-version = 0.0.1
-description = a plugin to mmif-pyhon to handle `dummy` location scheme
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And the plugin code.

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# mmif_docloc_dummy/__init__.py
-doc_types = {'video': 'mp4'}
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-def resolve(docloc):
-    scheme = 'dummy'
-    if docloc.startswith(f'{scheme}://'):
-        doc_id, doc_type = docloc.split('.')
-        return f'/path/to/{doc_id}.{doc_types[doc_type]}'
-    else:
-        raise ValueError(f'cannot handle document location scheme: {docloc}')
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-def help():
-    return "location format: `<DOCUMENT_ID>.video`"
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Bulit-in Document Location Scheme Plugins

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At the moment, mmif-python PyPI distribution ships a built-in docloc plugin that support both http and https schemes. -Take a look at mmif_docloc_http module for details.

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Python Module Index

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    - mmif.utils.video_document_helper -
    - mmif.vocabulary.annotation_types -
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- - - - - - - - \ No newline at end of file diff --git a/docs/1.0.18/searchindex.js b/docs/1.0.18/searchindex.js deleted file mode 100644 index d0bd2dd3..00000000 --- a/docs/1.0.18/searchindex.js +++ /dev/null @@ -1 +0,0 @@ -Search.setIndex({"alltitles": {"API documentation:": [[5, null]], "Bulit-in Document Location Scheme Plugins": [[8, "bulit-in-document-location-scheme-plugins"]], "Contents": [[5, null]], "Developing plugins for MMIF Python SDK": [[8, null]], "Document Location Scheme Plugins": [[8, "document-location-scheme-plugins"]], "For more \u2026": [[5, "for-more"]], "Getting Started": [[6, null]], "Indices and tables": [[5, "indices-and-tables"]], "Installation": [[6, "installation"]], "MMIF Serialization": [[6, "mmif-serialization"]], "MMIF consumer": [[4, null]], "MultiMedia Interchange Format": [[5, "multimedia-interchange-format"]], "Overview": [[6, "overview"], [8, "overview"]], "Prerequisites": [[6, "prerequisites"]], "Target MMIF Versions": [[9, null]], "Target Specification Versions": [[9, "id1"]], "Welcome to mmif-python\u2019s documentation!": [[5, null]], "mmif package": [[7, null]], "mmif-python": [[5, "mmif-python"]], "mmif.serialize module": [[0, null]], "mmif.serialize.annotation module": [[0, "module-mmif.serialize.annotation"]], "mmif.serialize.mmif module": [[0, "module-mmif.serialize.mmif"]], "mmif.serialize.model module": [[0, "module-mmif.serialize.model"]], "mmif.serialize.view module": [[0, "module-mmif.serialize.view"]], "mmif.utils module": [[1, null]], "mmif.utils.sequence_helper module": [[1, "module-mmif.utils.sequence_helper"]], "mmif.utils.video_document_helper module": [[1, "module-mmif.utils.video_document_helper"]], "mmif.vocabulary module": [[2, null]], "mmif.vocabulary.annotation_types module": [[2, "module-mmif.vocabulary.annotation_types"]], "mmif.vocabulary.document_types module": [[2, "module-mmif.vocabulary.document_types"]], "mmif_docloc_http package": [[3, null], [7, "mmif-docloc-http-package"]]}, 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"mmif.serialize.view.ViewMetadata.add_app_configuration", false]], "add_contain() (mmif.serialize.view.viewmetadata method)": [[0, "mmif.serialize.view.ViewMetadata.add_contain", false]], "add_document() (mmif.serialize.mmif.mmif method)": [[0, "mmif.serialize.mmif.Mmif.add_document", false]], "add_document() (mmif.serialize.view.view method)": [[0, "mmif.serialize.view.View.add_document", false]], "add_parameter() (mmif.serialize.view.viewmetadata method)": [[0, "mmif.serialize.view.ViewMetadata.add_parameter", false]], "add_parameters() (mmif.serialize.view.viewmetadata method)": [[0, "mmif.serialize.view.ViewMetadata.add_parameters", false]], "add_property() (mmif.serialize.annotation.annotation method)": [[0, "mmif.serialize.annotation.Annotation.add_property", false]], "add_property() (mmif.serialize.annotation.document method)": [[0, "mmif.serialize.annotation.Document.add_property", false]], "add_view() (mmif.serialize.mmif.mmif method)": [[0, "mmif.serialize.mmif.Mmif.add_view", false]], "add_warnings() (mmif.serialize.view.viewmetadata method)": [[0, "mmif.serialize.view.ViewMetadata.add_warnings", false]], "aligned_to_by() (mmif.serialize.annotation.annotation method)": [[0, "mmif.serialize.annotation.Annotation.aligned_to_by", false]], "alignment (mmif.vocabulary.annotation_types.annotationtypes attribute)": [[2, "mmif.vocabulary.annotation_types.AnnotationTypes.Alignment", false]], "annotation (class in mmif.serialize.annotation)": [[0, "mmif.serialize.annotation.Annotation", false]], "annotation (mmif.vocabulary.annotation_types.annotationtypes attribute)": [[2, "mmif.vocabulary.annotation_types.AnnotationTypes.Annotation", false]], "annotationproperties (class in mmif.serialize.annotation)": [[0, "mmif.serialize.annotation.AnnotationProperties", false]], "annotationtypes (class in mmif.vocabulary.annotation_types)": [[2, "mmif.vocabulary.annotation_types.AnnotationTypes", false]], "append() 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"mmif.vocabulary.annotation_types.AnnotationTypes.Chapter", false]], "check_prop_value_is_simple_enough() (mmif.serialize.annotation.annotation static method)": [[0, "mmif.serialize.annotation.Annotation.check_prop_value_is_simple_enough", false]], "contain (class in mmif.serialize.view)": [[0, "mmif.serialize.view.Contain", false]], "convert_timeframe() (in module mmif.utils.video_document_helper)": [[1, "mmif.utils.video_document_helper.convert_timeframe", false]], "convert_timepoint() (in module mmif.utils.video_document_helper)": [[1, "mmif.utils.video_document_helper.convert_timepoint", false]], "datadict (class in mmif.serialize.model)": [[0, "mmif.serialize.model.DataDict", false]], "datalist (class in mmif.serialize.model)": [[0, "mmif.serialize.model.DataList", false]], "default() (mmif.serialize.model.mmifobjectencoder method)": [[0, "mmif.serialize.model.MmifObjectEncoder.default", false]], "deserialize() (mmif.serialize.model.datalist method)": [[0, "mmif.serialize.model.DataList.deserialize", false]], "deserialize() (mmif.serialize.model.mmifobject method)": [[0, "mmif.serialize.model.MmifObject.deserialize", false]], "disallow_additional_properties() (mmif.serialize.model.mmifobject method)": [[0, "mmif.serialize.model.MmifObject.disallow_additional_properties", false]], "document (class in mmif.serialize.annotation)": [[0, "mmif.serialize.annotation.Document", false]], "document (mmif.vocabulary.document_types.documenttypes attribute)": [[2, "mmif.vocabulary.document_types.DocumentTypes.Document", false]], "documentproperties (class in mmif.serialize.annotation)": [[0, "mmif.serialize.annotation.DocumentProperties", false]], "documenttypes (class in mmif.vocabulary.document_types)": [[2, "mmif.vocabulary.document_types.DocumentTypes", false]], "empty() (mmif.serialize.model.datadict method)": [[0, "mmif.serialize.model.DataDict.empty", false]], "empty() (mmif.serialize.model.datalist method)": [[0, 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6], "web": 4, "websit": [6, 8], "well": [0, 6, 8], "when": [0, 1, 6, 8], "where": 0, "whether": 0, "which": [0, 1, 6, 8], "while": [0, 1], "width": 1, "within": 0, "without": [0, 8], "won": 0, "work": [0, 1, 8], "workflow": 6, "would": 0, "write": [0, 3, 8], "xist": 1, "yield": 0, "you": [0, 1, 3, 6, 8], "your": [3, 8], "zero": [0, 1]}, "titles": ["mmif.serialize module", "mmif.utils module", "mmif.vocabulary module", "mmif_docloc_http package", "MMIF consumer", "Welcome to mmif-python\u2019s documentation!", "Getting Started", "mmif package", "Developing plugins for MMIF Python SDK", "Target MMIF Versions"], "titleterms": {"": 5, "For": 5, "annot": 0, "annotation_typ": 2, "api": 5, "bulit": 8, "consum": 4, "content": 5, "develop": 8, "document": [5, 8], "document_typ": 2, "format": 5, "get": 6, "indic": 5, "instal": 6, "interchang": 5, "locat": 8, "mmif": [0, 1, 2, 4, 5, 6, 7, 8, 9], "mmif_docloc_http": [3, 7], "model": 0, "modul": [0, 1, 2], "more": 5, "multimedia": 5, "overview": [6, 8], "packag": [3, 7], "plugin": 8, "prerequisit": 6, "python": [5, 8], "scheme": 8, "sdk": 8, "sequence_help": 1, "serial": [0, 6], "specif": 9, "start": 6, "tabl": 5, "target": 9, "util": 1, "version": 9, "video_document_help": 1, "view": 0, "vocabulari": 2, "welcom": 5}}) \ No newline at end of file diff --git a/docs/1.0.18/target-versions.html b/docs/1.0.18/target-versions.html deleted file mode 100644 index aef0bc87..00000000 --- a/docs/1.0.18/target-versions.html +++ /dev/null @@ -1,297 +0,0 @@ - - - - - - - - - Target MMIF Versions — mmif-python documentation - - - - - - - - - - - - - - - - - -
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Target MMIF Versions

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This article provides targeting MMIF specification versions of different versions of mmif-python SDK.

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Target Specification Versions

mmif-python version

Target MMIF Specification

1.0.18

1.1.0

1.0.17

1.0.5

1.0.16

1.0.4

1.0.15

1.0.4

1.0.14

1.0.4

1.0.13

1.0.4

1.0.12

1.0.4

1.0.11

1.0.4

1.0.10

1.0.2

1.0.9

1.1.0

1.0.8

1.0.0

1.0.7

1.0.0

1.0.6

1.0.0

1.0.5

1.0.0

1.0.4

1.0.0

1.0.3

1.0.0

1.0.2

1.0.0

1.0.1

1.0.0

1.0.0

0.5.0

0.5.2

0.5.0

0.5.1

0.5.0

0.5.0

0.5.0

0.4.8

0.4.2

0.4.7

0.4.1

0.4.6

0.4.0

0.4.5

0.4.0

0.4.4

0.4.0

0.4.3

0.4.0

0.4.2

0.4.0

0.4.1

0.4.0

0.4.0

0.4.0

0.3.5

0.3.1

0.3.4

0.3.1

0.3.3

0.3.1

0.3.2

0.3.1

0.3.1

0.3.0

0.3.0

0.3.0

0.2.2

0.2.1

0.2.1

0.2.1

0.2.0

0.2.1

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0.3.0
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0.3.1
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0.3.2
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0.3.3
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0.3.4
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0.3.5
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0.4.0
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0.4.1
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0.4.2
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0.4.3
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0.4.4
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0.4.5
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0.4.6
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0.4.7
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0.4.8
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0.5.0
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0.5.1
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0.5.2
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1.0.0
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1.0.1
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1.0.10
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1.0.11
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1.0.12
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1.0.13
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1.0.14
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1.0.15
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1.0.16
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1.0.17
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1.0.18
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1.0.19
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1.0.2
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1.0.3
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1.0.4
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1.0.5
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1.0.6
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1.0.7
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1.0.8
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1.0.9
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1.1.0
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-Core package to provide serialization and deserialization of MMIF format. - -``model`` module ---------------------------- - -.. automodule:: mmif.serialize.model - :members: - :undoc-members: - :show-inheritance: - -``mmif`` module --------------------------- - -.. automodule:: mmif.serialize.mmif - :members: - :undoc-members: - :show-inheritance: - -``view`` module --------------------------- - -.. automodule:: mmif.serialize.view - :members: - :undoc-members: - :show-inheritance: - -``annotation`` module --------------------------------- - -.. automodule:: mmif.serialize.annotation - :members: - :undoc-members: - :show-inheritance: - diff --git a/docs/1.0.19/_sources/autodoc/mmif.utils.rst.txt b/docs/1.0.19/_sources/autodoc/mmif.utils.rst.txt deleted file mode 100644 index a9275023..00000000 --- a/docs/1.0.19/_sources/autodoc/mmif.utils.rst.txt +++ /dev/null @@ -1,39 +0,0 @@ -mmif.utils package -================== - -Package containing utility modules for handling different types of source -documents, and general implementation of common data structures and -algorithms. - -``video_document_helper`` module ----------------------------------------- - -.. automodule:: mmif.utils.video_document_helper - :members: - :undoc-members: - :show-inheritance: - -``text_document_helper`` module ---------------------------------- - -.. automodule:: mmif.utils.sequence_helper - :members: - :undoc-members: - :show-inheritance: - -``sequence_helper`` module ---------------------------------- - -.. automodule:: mmif.utils.sequence_helper - :members: - :undoc-members: - :show-inheritance: - -``sequence_helper`` module ---------------------------------- - -.. automodule:: mmif.utils.sequence_helper - :members: - :undoc-members: - :show-inheritance: - diff --git a/docs/1.0.19/_sources/autodoc/mmif.vocabulary.rst.txt b/docs/1.0.19/_sources/autodoc/mmif.vocabulary.rst.txt deleted file mode 100644 index 17da0283..00000000 --- a/docs/1.0.19/_sources/autodoc/mmif.vocabulary.rst.txt +++ /dev/null @@ -1,28 +0,0 @@ -mmif.vocabulary module -====================== - -Module contains Enum-like classes for CLAMS vocabulary. - -.. autoclass:: mmif.vocabulary.ThingTypesBase - :show-inheritance: -.. autoclass:: mmif.vocabulary.ThingType - :members: - :undoc-members: - :show-inheritance: - -.. autoclass:: mmif.vocabulary.ClamsTypesBase - :show-inheritance: -.. autoclass:: mmif.vocabulary.AnnotationTypesBase - :show-inheritance: -.. autoclass:: mmif.vocabulary.DocumentTypesBase - :show-inheritance: - -.. autoclass:: mmif.vocabulary.AnnotationTypes - :members: - :undoc-members: - :show-inheritance: - -.. autoclass:: mmif.vocabulary.DocumentTypes - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/1.0.19/_sources/autodoc/mmif_docloc_http.rst.txt b/docs/1.0.19/_sources/autodoc/mmif_docloc_http.rst.txt deleted file mode 100644 index b76c8df5..00000000 --- a/docs/1.0.19/_sources/autodoc/mmif_docloc_http.rst.txt +++ /dev/null @@ -1,11 +0,0 @@ -mmif_docloc_http package -======================== - -MMIF document location helper module for `http` and `https` schemes. -If you want to write your own docloc scheme handler, please use the source code of this module as a reference. -See this :ref:`plug-in section ` for more information. - -.. automodule:: mmif_docloc_http - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/1.0.19/_sources/consumer-tutorial.rst.txt b/docs/1.0.19/_sources/consumer-tutorial.rst.txt deleted file mode 100644 index c54634e2..00000000 --- a/docs/1.0.19/_sources/consumer-tutorial.rst.txt +++ /dev/null @@ -1,17 +0,0 @@ -.. _consumer-tutorial: - -MMIF consumer -================================= - -A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the `appliance documentation `_ to learn more about the appliance. - -MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance. - -#. The code must be hosted on a public git repository (e.g. Github, Gitlab, ...) -#. Must listen to ``5000`` port. -#. Must expose ``/display`` route . -#. ``/display`` router should response to ``GET`` requests. -#. In the ``GET`` request, a public URL of the input MMIF file is passed via ``file`` URL parameter. -#. On the codebase root, there must be a ``Dockerfile`` that can build a `docker `_ image that runs the web app. - -We provide an example consumer at https://github.com/clamsproject/mmif-visualizer. diff --git a/docs/1.0.19/_sources/index.rst.txt b/docs/1.0.19/_sources/index.rst.txt deleted file mode 100644 index beb56aae..00000000 --- a/docs/1.0.19/_sources/index.rst.txt +++ /dev/null @@ -1,26 +0,0 @@ -Welcome to mmif-python's documentation! -======================================= - -.. mdinclude:: ../README.md - -.. toctree:: - :maxdepth: 2 - :caption: Contents - - introduction - plugins - target-versions - -.. toctree:: - :maxdepth: 2 - :caption: API documentation: - - modules - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/docs/1.0.19/_sources/introduction.rst.txt b/docs/1.0.19/_sources/introduction.rst.txt deleted file mode 100644 index cfd9eaf7..00000000 --- a/docs/1.0.19/_sources/introduction.rst.txt +++ /dev/null @@ -1,89 +0,0 @@ -.. _introduction: - -Getting Started -=============== - - -Overview ---------- - -MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for reproducibility, transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF website `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects. - -Prerequisites -------------- - -* `Python `_: the latest ``mmif-python`` requires Python 3.8 or newer. We have no plan to support `Python 2.7 `_. - -Installation ---------------- - -Package ``mmif-python`` is distributed via the official PyPI. Users are supposed to pip-install to get latest release. - -.. code-block:: bash - - pip install mmif-python - -This will install a package `mmif` to local python. - -The MMIF format and specification is evolving over time, and ``mmif-python`` package will be updated along with the changes in MMIF format. - -.. note:: MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and ``mmif-python`` versions, please take time to read our decision on the subject `here `_. If you need to know which python SDK supports which specification version, see :ref:`target-versions` page. - -MMIF Serialization ---------------------------- - -:class:`mmif.serialize.mmif.Mmif` represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of :class:`mmif.serialize.model.MmifObject`, including the :class:`mmif.serialize.mmif.Mmif`. To start with an existing MMIF :class:`str`, simple initiate a new ``Mmif`` object with the file. - -.. code-block:: python - - import mmif - from mmif import Mmif - - mmif_str = """{ - "metadata": { - "mmif": "http://mmif.clams.ai/1.0.0" - }, - "documents": [ - { - "@type": "http://mmif.clams.ai/vocabulary/VideoDocument/v1", - "properties": { - "id": "m1", - "mime": "video/mp4", - "location": "file:///var/archive/video-0012.mp4" - } - }, - { - "@type": "http://mmif.clams.ai/vocabulary/TextDocument/v1", - "properties": { - "id": "m2", - "mime": "text/plain", - "location": "file:///var/archive/video-0012-transcript.txt" - } - } - ], - "views": []}""" - mmif_obj = Mmif(mmif_str) - - -Few notes; - -#. MMIF does not carry the primary source files in it. -#. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version ``mmif-python`` implementation of the MMIF might not be able to load an unsupported version of MMIF string. - -When serializing back to :class:`str`, call :meth:`mmif.serialize.model.MmifObject.serialize` on the object. - -To get subcomponents, you can use various getters implemented in subclasses. For example; - -.. code-block:: python - - from mmif.vocabulary.document_types import DocumentTypes - - for video in mmif_obj.Mmif.get_documents_by_type(DocumentTypes.VideoDocument): - with open(video.location_path(), 'b') as in_video: - # do something with the video file - - -For a full list of available helper methods, please refer to :ref:`the API documentation `. - diff --git a/docs/1.0.19/_sources/modules.rst.txt b/docs/1.0.19/_sources/modules.rst.txt deleted file mode 100644 index 4bb9307d..00000000 --- a/docs/1.0.19/_sources/modules.rst.txt +++ /dev/null @@ -1,20 +0,0 @@ -.. _apidoc: - -mmif package -============ - -.. toctree:: - :maxdepth: 4 - - autodoc/mmif.serialize - autodoc/mmif.vocabulary - autodoc/mmif.utils - -mmif_docloc_http package -======================== - -.. toctree:: - :maxdepth: 2 - - autodoc/mmif_docloc_http - diff --git a/docs/1.0.19/_sources/plugins.rst.txt b/docs/1.0.19/_sources/plugins.rst.txt deleted file mode 100644 index 1af39426..00000000 --- a/docs/1.0.19/_sources/plugins.rst.txt +++ /dev/null @@ -1,89 +0,0 @@ -.. _plugins: - -Developing plugins for MMIF Python SDK -====================================== - - -Overview --------- - -As MMIF JSON files can carry information about media document files without actually carrying file contents, file accessing modules in ``mmif`` Python package (distributed as ``mmif-python`` on PyPI) are designed to be lightweight and flexible so that it can work with additional "plugin" Python packages that can handle concrete file access. - - -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF website `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects. - -Developer can write simple plugins that can provide additional functionalities to ``mmif-python``. For example, ``mmif-python`` does not provide any file access functionality beyond a local file system (with ``file`` scheme), but it can be extended with a plugin that can handle file access over different protocols (e.g. ``http``, ``s3``, ``ftp``, etc). - -This document contains information about how to write plugins for ``mmif-python``. - -.. _docloc_plugin: - -Document Location Scheme Plugins -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -:class:`mmif.serialize.annotation.Document` class has various methods to access parts of ``location`` property of the document. The location is in `URI/IRI format `_ (``SCHEME://HOSTNAME/PATH``, in a nutshell) and it has to be resolved to a local file for CLAMS Apps to process the local file to analyze and extract information about the media and its contents. The core ``mmif-python`` distribution only provides a default implementation that can handle ``file`` scheme URIs. - -To add a document location handler plugin, you need to implement a Python `"package" `_ (do not confuse with PYPI distribution), that meets these requirements; - -#. the package must be named ``mmif_docloc_``. For example, to implement a handler for ``s3`` scheme, the package name must be ``mmif_docloc_s3``. The prefix is important as it's used in the plugin discovery process from the core ``mmif-python`` modules. -#. the top module of the package must have a function named ``resolve``. The function must take a single argument, which is a :class:`str` of the document location URI. The function must return a :class:`str` of the local file path. For example, if the document location is ``s3://mybucket/myfile.mp4``, a Python user should be able to to something like this; -#. Optionally (but highly recommended), the top module also can provide another function named ``help``. The function must take no arguments and return a :class:`str` that explains how the input string to the ``resolve`` function should be formatted. - -.. code-block:: python - - import mmif_docloc_s3 - resolved = mmif_docloc_s3.resolve('s3://mybucket/myfile.mp4') - # then resolved must be a local file path that can be used to open the file - - -Here's a minimal example codebase that you refer to when you develop a ``docloc`` plugin. - -(However, before you start writing your own plugin for a specific URI scheme, checking `if there's already a PyPI distribution `_ for the scheme might be a good idea.) - -.. code-block:: sh - - $ tree . - . - ├── mmif_docloc_dummy - │ └── __init__.py - ├── pyproject.toml - └── setup.cfg - - $ cat pyproject.toml - [build-system] - requires = ["setuptools"] - build-backend = "setuptools.build_meta" - - $ cat setup.cfg - [metadata] - name = mmif_docloc_dummy # this name is IMPORTANT - version = 0.0.1 - description = a plugin to mmif-pyhon to handle `dummy` location scheme - - -And the plugin code. - -.. code-block:: python - - # mmif_docloc_dummy/__init__.py - doc_types = {'video': 'mp4'} - - def resolve(docloc): - scheme = 'dummy' - if docloc.startswith(f'{scheme}://'): - doc_id, doc_type = docloc.split('.') - return f'/path/to/{doc_id}.{doc_types[doc_type]}' - else: - raise ValueError(f'cannot handle document location scheme: {docloc}') - - def help(): - return "location format: `.video`" - - - -Bulit-in Document Location Scheme Plugins -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -At the moment, ``mmif-python`` PyPI distribution ships a built-in *docloc* plugin that support both ``http`` and ``https`` schemes. -Take a look at :mod:`mmif_docloc_http` module for details. diff --git a/docs/1.0.19/_sources/target-versions.rst.txt b/docs/1.0.19/_sources/target-versions.rst.txt deleted file mode 100644 index 34216d3e..00000000 --- a/docs/1.0.19/_sources/target-versions.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _target-versions: - -Target MMIF Versions -==================== - -This article provides targeting MMIF specification versions of different versions of ``mmif-python`` SDK. - -.. csv-table:: Target Specification Versions - :file: target-versions.csv - :header-rows: 1 diff --git a/docs/1.0.19/_static/_sphinx_javascript_frameworks_compat.js b/docs/1.0.19/_static/_sphinx_javascript_frameworks_compat.js deleted file mode 100644 index 81415803..00000000 --- a/docs/1.0.19/_static/_sphinx_javascript_frameworks_compat.js +++ /dev/null @@ -1,123 +0,0 @@ -/* Compatability shim for jQuery and underscores.js. - * - * Copyright Sphinx contributors - * Released under the two clause BSD licence - */ - -/** - * small helper function to urldecode strings - * - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL - */ -jQuery.urldecode = function(x) { - if (!x) { - return x - } - return decodeURIComponent(x.replace(/\+/g, ' ')); -}; - -/** - * small helper function to urlencode strings - */ -jQuery.urlencode = encodeURIComponent; - -/** - * This function returns the parsed url parameters of the - * current request. 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- -/** - * Simple result scoring code. - */ -if (typeof Scorer === "undefined") { - var Scorer = { - // Implement the following function to further tweak the score for each result - // The function takes a result array [docname, title, anchor, descr, score, filename] - // and returns the new score. - /* - score: result => { - const [docname, title, anchor, descr, score, filename, kind] = result - return score - }, - */ - - // query matches the full name of an object - objNameMatch: 11, - // or matches in the last dotted part of the object name - objPartialMatch: 6, - // Additive scores depending on the priority of the object - objPrio: { - 0: 15, // used to be importantResults - 1: 5, // used to be objectResults - 2: -5, // used to be unimportantResults - }, - // Used when the priority is not in the mapping. - objPrioDefault: 0, - - // query found in title - title: 15, - partialTitle: 7, - // query found in terms - term: 5, - partialTerm: 2, - }; -} - -// Global search result kind enum, used by themes to style search results. -class SearchResultKind { - static get index() { return "index"; } - static get object() { return "object"; } - static get text() { return "text"; } - static get title() { return "title"; } -} - -const _removeChildren = (element) => { - while (element && element.lastChild) element.removeChild(element.lastChild); -}; - -/** - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping - */ -const _escapeRegExp = (string) => - string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string - -const _displayItem = (item, searchTerms, highlightTerms) => { - const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; - const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; - const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; - const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; - const contentRoot = document.documentElement.dataset.content_root; - - const [docName, title, anchor, descr, score, _filename, kind] = item; - - let listItem = document.createElement("li"); - // Add a class representing the item's type: - // can be used by a theme's CSS selector for styling - // See SearchResultKind for the class names. - listItem.classList.add(`kind-${kind}`); - let requestUrl; - let linkUrl; - if (docBuilder === "dirhtml") { - // dirhtml builder - let dirname = docName + "/"; - if (dirname.match(/\/index\/$/)) - dirname = dirname.substring(0, dirname.length - 6); - else if (dirname === "index/") dirname = ""; - requestUrl = contentRoot + dirname; - linkUrl = requestUrl; - } else { - // normal html builders - requestUrl = contentRoot + docName + docFileSuffix; - linkUrl = docName + docLinkSuffix; - } - let linkEl = listItem.appendChild(document.createElement("a")); - linkEl.href = linkUrl + anchor; - linkEl.dataset.score = score; - linkEl.innerHTML = title; - if (descr) { - listItem.appendChild(document.createElement("span")).innerHTML = - " (" + descr + ")"; - // highlight search terms in the description - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - } - else if (showSearchSummary) - fetch(requestUrl) - .then((responseData) => responseData.text()) - .then((data) => { - if (data) - listItem.appendChild( - Search.makeSearchSummary(data, searchTerms, anchor) - ); - // highlight search terms in the summary - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - }); - Search.output.appendChild(listItem); -}; -const _finishSearch = (resultCount) => { - Search.stopPulse(); - Search.title.innerText = _("Search Results"); - if (!resultCount) - Search.status.innerText = Documentation.gettext( - "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." - ); - else - Search.status.innerText = Documentation.ngettext( - "Search finished, found one page matching the search query.", - "Search finished, found ${resultCount} pages matching the search query.", - resultCount, - ).replace('${resultCount}', resultCount); -}; -const _displayNextItem = ( - results, - resultCount, - searchTerms, - highlightTerms, -) => { - // results left, load the summary and display it - // this is intended to be dynamic (don't sub resultsCount) - if (results.length) { - _displayItem(results.pop(), searchTerms, highlightTerms); - setTimeout( - () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), - 5 - ); - } - // search finished, update title and status message - else _finishSearch(resultCount); -}; -// Helper function used by query() to order search results. -// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. -// Order the results by score (in opposite order of appearance, since the -// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. -const _orderResultsByScoreThenName = (a, b) => { - const leftScore = a[4]; - const rightScore = b[4]; - if (leftScore === rightScore) { - // same score: sort alphabetically - const leftTitle = a[1].toLowerCase(); - const rightTitle = b[1].toLowerCase(); - if (leftTitle === rightTitle) return 0; - return leftTitle > rightTitle ? -1 : 1; // inverted is intentional - } - return leftScore > rightScore ? 1 : -1; -}; - -/** - * Default splitQuery function. Can be overridden in ``sphinx.search`` with a - * custom function per language. - * - * The regular expression works by splitting the string on consecutive characters - * that are not Unicode letters, numbers, underscores, or emoji characters. - * This is the same as ``\W+`` in Python, preserving the surrogate pair area. - */ -if (typeof splitQuery === "undefined") { - var splitQuery = (query) => query - .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) - .filter(term => term) // remove remaining empty strings -} - -/** - * Search Module - */ -const Search = { - _index: null, - _queued_query: null, - _pulse_status: -1, - - htmlToText: (htmlString, anchor) => { - const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - for (const removalQuery of [".headerlink", "script", "style"]) { - htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); - } - if (anchor) { - const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); - if (anchorContent) return anchorContent.textContent; - - console.warn( - `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` - ); - } - - // if anchor not specified or not found, fall back to main content - const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent) return docContent.textContent; - - console.warn( - "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." - ); - return ""; - }, - - init: () => { - const query = new URLSearchParams(window.location.search).get("q"); - document - .querySelectorAll('input[name="q"]') - .forEach((el) => (el.value = query)); - if (query) Search.performSearch(query); - }, - - loadIndex: (url) => - (document.body.appendChild(document.createElement("script")).src = url), - - setIndex: (index) => { - Search._index = index; - if (Search._queued_query !== null) { - const query = Search._queued_query; - Search._queued_query = null; - Search.query(query); - } - }, - - hasIndex: () => Search._index !== null, - - deferQuery: (query) => (Search._queued_query = query), - - stopPulse: () => (Search._pulse_status = -1), - - startPulse: () => { - if (Search._pulse_status >= 0) return; - - const pulse = () => { - Search._pulse_status = (Search._pulse_status + 1) % 4; - Search.dots.innerText = ".".repeat(Search._pulse_status); - if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); - }; - pulse(); - }, - - /** - * perform a search for something (or wait until index is loaded) - */ - performSearch: (query) => { - // create the required interface elements - const searchText = document.createElement("h2"); - searchText.textContent = _("Searching"); - const searchSummary = document.createElement("p"); - searchSummary.classList.add("search-summary"); - searchSummary.innerText = ""; - const searchList = document.createElement("ul"); - searchList.setAttribute("role", "list"); - searchList.classList.add("search"); - - const out = document.getElementById("search-results"); - Search.title = out.appendChild(searchText); - Search.dots = Search.title.appendChild(document.createElement("span")); - Search.status = out.appendChild(searchSummary); - Search.output = out.appendChild(searchList); - - const searchProgress = document.getElementById("search-progress"); - // Some themes don't use the search progress node - if (searchProgress) { - searchProgress.innerText = _("Preparing search..."); - } - Search.startPulse(); - - // index already loaded, the browser was quick! - if (Search.hasIndex()) Search.query(query); - else Search.deferQuery(query); - }, - - _parseQuery: (query) => { - // stem the search terms and add them to the correct list - const stemmer = new Stemmer(); - const searchTerms = new Set(); - const excludedTerms = new Set(); - const highlightTerms = new Set(); - const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); - splitQuery(query.trim()).forEach((queryTerm) => { - const queryTermLower = queryTerm.toLowerCase(); - - // maybe skip this "word" - // stopwords array is from language_data.js - if ( - stopwords.indexOf(queryTermLower) !== -1 || - queryTerm.match(/^\d+$/) - ) - return; - - // stem the word - let word = stemmer.stemWord(queryTermLower); - // select the correct list - if (word[0] === "-") excludedTerms.add(word.substr(1)); - else { - searchTerms.add(word); - highlightTerms.add(queryTermLower); - } - }); - - if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js - localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) - } - - // console.debug("SEARCH: searching for:"); - // console.info("required: ", [...searchTerms]); - // console.info("excluded: ", [...excludedTerms]); - - return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; - }, - - /** - * execute search (requires search index to be loaded) - */ - _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - - // Collect multiple result groups to be sorted separately and then ordered. - // Each is an array of [docname, title, anchor, descr, score, filename, kind]. - const normalResults = []; - const nonMainIndexResults = []; - - _removeChildren(document.getElementById("search-progress")); - - const queryLower = query.toLowerCase().trim(); - for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { - for (const [file, id] of foundTitles) { - const score = Math.round(Scorer.title * queryLower.length / title.length); - const boost = titles[file] === title ? 1 : 0; // add a boost for document titles - normalResults.push([ - docNames[file], - titles[file] !== title ? `${titles[file]} > ${title}` : title, - id !== null ? "#" + id : "", - null, - score + boost, - filenames[file], - SearchResultKind.title, - ]); - } - } - } - - // search for explicit entries in index directives - for (const [entry, foundEntries] of Object.entries(indexEntries)) { - if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id, isMain] of foundEntries) { - const score = Math.round(100 * queryLower.length / entry.length); - const result = [ - docNames[file], - titles[file], - id ? "#" + id : "", - null, - score, - filenames[file], - SearchResultKind.index, - ]; - if (isMain) { - normalResults.push(result); - } else { - nonMainIndexResults.push(result); - } - } - } - } - - // lookup as object - objectTerms.forEach((term) => - normalResults.push(...Search.performObjectSearch(term, objectTerms)) - ); - - // lookup as search terms in fulltext - normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); - - // let the scorer override scores with a custom scoring function - if (Scorer.score) { - normalResults.forEach((item) => (item[4] = Scorer.score(item))); - nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); - } - - // Sort each group of results by score and then alphabetically by name. - normalResults.sort(_orderResultsByScoreThenName); - nonMainIndexResults.sort(_orderResultsByScoreThenName); - - // Combine the result groups in (reverse) order. - // Non-main index entries are typically arbitrary cross-references, - // so display them after other results. - let results = [...nonMainIndexResults, ...normalResults]; - - // remove duplicate search results - // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept - let seen = new Set(); - results = results.reverse().reduce((acc, result) => { - let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); - if (!seen.has(resultStr)) { - acc.push(result); - seen.add(resultStr); - } - return acc; - }, []); - - return results.reverse(); - }, - - query: (query) => { - const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); - const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); - - // for debugging - //Search.lastresults = results.slice(); // a copy - // console.info("search results:", Search.lastresults); - - // print the results - _displayNextItem(results, results.length, searchTerms, highlightTerms); - }, - - /** - * search for object names - */ - performObjectSearch: (object, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const objects = Search._index.objects; - const objNames = Search._index.objnames; - const titles = Search._index.titles; - - const results = []; - - const objectSearchCallback = (prefix, match) => { - const name = match[4] - const fullname = (prefix ? prefix + "." : "") + name; - const fullnameLower = fullname.toLowerCase(); - if (fullnameLower.indexOf(object) < 0) return; - - let score = 0; - const parts = fullnameLower.split("."); - - // check for different match types: exact matches of full name or - // "last name" (i.e. last dotted part) - if (fullnameLower === object || parts.slice(-1)[0] === object) - score += Scorer.objNameMatch; - else if (parts.slice(-1)[0].indexOf(object) > -1) - score += Scorer.objPartialMatch; // matches in last name - - const objName = objNames[match[1]][2]; - const title = titles[match[0]]; - - // If more than one term searched for, we require other words to be - // found in the name/title/description - const otherTerms = new Set(objectTerms); - otherTerms.delete(object); - if (otherTerms.size > 0) { - const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); - if ( - [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) - ) - return; - } - - let anchor = match[3]; - if (anchor === "") anchor = fullname; - else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; - - const descr = objName + _(", in ") + title; - - // add custom score for some objects according to scorer - if (Scorer.objPrio.hasOwnProperty(match[2])) - score += Scorer.objPrio[match[2]]; - else score += Scorer.objPrioDefault; - - results.push([ - docNames[match[0]], - fullname, - "#" + anchor, - descr, - score, - filenames[match[0]], - SearchResultKind.object, - ]); - }; - Object.keys(objects).forEach((prefix) => - objects[prefix].forEach((array) => - objectSearchCallback(prefix, array) - ) - ); - return results; - }, - - /** - * search for full-text terms in the index - */ - performTermsSearch: (searchTerms, excludedTerms) => { - // prepare search - const terms = Search._index.terms; - const titleTerms = Search._index.titleterms; - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - - const scoreMap = new Map(); - const fileMap = new Map(); - - // perform the search on the required terms - searchTerms.forEach((word) => { - const files = []; - const arr = [ - { files: terms[word], score: Scorer.term }, - { files: titleTerms[word], score: Scorer.title }, - ]; - // add support for partial matches - if (word.length > 2) { - const escapedWord = _escapeRegExp(word); - if (!terms.hasOwnProperty(word)) { - Object.keys(terms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: terms[term], score: Scorer.partialTerm }); - }); - } - if (!titleTerms.hasOwnProperty(word)) { - Object.keys(titleTerms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); - }); - } - } - - // no match but word was a required one - if (arr.every((record) => record.files === undefined)) return; - - // found search word in contents - arr.forEach((record) => { - if (record.files === undefined) return; - - let recordFiles = record.files; - if (recordFiles.length === undefined) recordFiles = [recordFiles]; - files.push(...recordFiles); - - // set score for the word in each file - recordFiles.forEach((file) => { - if (!scoreMap.has(file)) scoreMap.set(file, {}); - scoreMap.get(file)[word] = record.score; - }); - }); - - // create the mapping - files.forEach((file) => { - if (!fileMap.has(file)) fileMap.set(file, [word]); - else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); - }); - }); - - // now check if the files don't contain excluded terms - const results = []; - for (const [file, wordList] of fileMap) { - // check if all requirements are matched - - // as search terms with length < 3 are discarded - const filteredTermCount = [...searchTerms].filter( - (term) => term.length > 2 - ).length; - if ( - wordList.length !== searchTerms.size && - wordList.length !== filteredTermCount - ) - continue; - - // ensure that none of the excluded terms is in the search result - if ( - [...excludedTerms].some( - (term) => - terms[term] === file || - titleTerms[term] === file || - (terms[term] || []).includes(file) || - (titleTerms[term] || []).includes(file) - ) - ) - break; - - // select one (max) score for the file. - const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); - // add result to the result list - results.push([ - docNames[file], - titles[file], - "", - null, - score, - filenames[file], - SearchResultKind.text, - ]); - } - return results; - }, - - /** - * helper function to return a node containing the - * search summary for a given text. keywords is a list - * of stemmed words. - */ - makeSearchSummary: (htmlText, keywords, anchor) => { - const text = Search.htmlToText(htmlText, anchor); - if (text === "") return null; - - const textLower = text.toLowerCase(); - const actualStartPosition = [...keywords] - .map((k) => textLower.indexOf(k.toLowerCase())) - .filter((i) => i > -1) - .slice(-1)[0]; - const startWithContext = Math.max(actualStartPosition - 120, 0); - - const top = startWithContext === 0 ? "" : "..."; - const tail = startWithContext + 240 < text.length ? "..." : ""; - - let summary = document.createElement("p"); - summary.classList.add("context"); - summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; - - return summary; - }, -}; - -_ready(Search.init); diff --git a/docs/1.0.19/_static/sphinx_highlight.js b/docs/1.0.19/_static/sphinx_highlight.js deleted file mode 100644 index 8a96c69a..00000000 --- a/docs/1.0.19/_static/sphinx_highlight.js +++ /dev/null @@ -1,154 +0,0 @@ -/* Highlighting utilities for Sphinx HTML documentation. */ -"use strict"; - -const SPHINX_HIGHLIGHT_ENABLED = true - -/** - * highlight a given string on a node by wrapping it in - * span elements with the given class name. - */ -const _highlight = (node, addItems, text, className) => { - if (node.nodeType === Node.TEXT_NODE) { - const val = node.nodeValue; - const parent = node.parentNode; - const pos = val.toLowerCase().indexOf(text); - if ( - pos >= 0 && - !parent.classList.contains(className) && - !parent.classList.contains("nohighlight") - ) { - let span; - - const closestNode = parent.closest("body, svg, foreignObject"); - const isInSVG = closestNode && closestNode.matches("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.classList.add(className); - } - - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - const rest = document.createTextNode(val.substr(pos + text.length)); - parent.insertBefore( - span, - parent.insertBefore( - rest, - node.nextSibling - ) - ); - node.nodeValue = val.substr(0, pos); - /* There may be more occurrences of search term in this node. So call this - * function recursively on the remaining fragment. - */ - _highlight(rest, addItems, text, className); - - if (isInSVG) { - const rect = document.createElementNS( - "http://www.w3.org/2000/svg", - "rect" - ); - const bbox = parent.getBBox(); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute("class", className); - addItems.push({ parent: parent, target: rect }); - } - } - } else if (node.matches && !node.matches("button, select, textarea")) { - node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); - } -}; -const _highlightText = (thisNode, text, className) => { - let addItems = []; - _highlight(thisNode, addItems, text, className); - addItems.forEach((obj) => - obj.parent.insertAdjacentElement("beforebegin", obj.target) - ); -}; - -/** - * Small JavaScript module for the documentation. - */ -const SphinxHighlight = { - - /** - * highlight the search words provided in localstorage in the text - */ - highlightSearchWords: () => { - if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight - - // get and clear terms from localstorage - const url = new URL(window.location); - const highlight = - localStorage.getItem("sphinx_highlight_terms") - || url.searchParams.get("highlight") - || ""; - localStorage.removeItem("sphinx_highlight_terms") - url.searchParams.delete("highlight"); - window.history.replaceState({}, "", url); - - // get individual terms from highlight string - const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); - if (terms.length === 0) return; // nothing to do - - // There should never be more than one element matching "div.body" - const divBody = document.querySelectorAll("div.body"); - const body = divBody.length ? divBody[0] : document.querySelector("body"); - window.setTimeout(() => { - terms.forEach((term) => _highlightText(body, term, "highlighted")); - }, 10); - - const searchBox = document.getElementById("searchbox"); - if (searchBox === null) return; - searchBox.appendChild( - document - .createRange() - .createContextualFragment( - '

' + - '' + - _("Hide Search Matches") + - "

" - ) - ); - }, - - /** - * helper function to hide the search marks again - */ - hideSearchWords: () => { - document - .querySelectorAll("#searchbox .highlight-link") - .forEach((el) => el.remove()); - document - .querySelectorAll("span.highlighted") - .forEach((el) => el.classList.remove("highlighted")); - localStorage.removeItem("sphinx_highlight_terms") - }, - - initEscapeListener: () => { - // only install a listener if it is really needed - if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; - - document.addEventListener("keydown", (event) => { - // bail for input elements - if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; - // bail with special keys - if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; - if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { - SphinxHighlight.hideSearchWords(); - event.preventDefault(); - } - }); - }, -}; - -_ready(() => { - /* Do not call highlightSearchWords() when we are on the search page. - * It will highlight words from the *previous* search query. - */ - if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); - SphinxHighlight.initEscapeListener(); -}); diff --git a/docs/1.0.19/autodoc/mmif.serialize.html b/docs/1.0.19/autodoc/mmif.serialize.html deleted file mode 100644 index 97fed156..00000000 --- a/docs/1.0.19/autodoc/mmif.serialize.html +++ /dev/null @@ -1,1470 +0,0 @@ - - - - - - - - - mmif.serialize package — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
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mmif.serialize package

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Core package to provide serialization and deserialization of MMIF format.

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model module

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The model module contains the classes used to represent an -abstract MMIF object as a live Python object.

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The MmifObject class or one of its derivatives is subclassed by -all other classes defined in this SDK, except for MmifObjectEncoder.

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These objects are generally instantiated from JSON, either as a string -or as an already-loaded Python dictionary. This base class provides the -core functionality for deserializing MMIF JSON data into live objects -and serializing live objects into MMIF JSON data. Specialized behavior -for the different components of MMIF is added in the subclasses.

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-class mmif.serialize.model.DataDict(mmif_obj: bytes | str | dict | None = None, *_)[source]
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Bases: MmifObject, Generic[T, S]

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-empty()[source]
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-get(key: T, default=None) → S | None[source]
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-items()[source]
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-keys()[source]
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-update(other, overwrite)[source]
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-values()[source]
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-class mmif.serialize.model.DataList(mmif_obj: bytes | str | list | None = None, *_)[source]
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Bases: MmifObject, Generic[T]

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The DataList class is an abstraction that represents the -various lists found in a MMIF file, such as documents, subdocuments, -views, and annotations.

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Parameters:
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mmif_obj (Union[str, list]) – the data that the list contains

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-append(value, overwrite)[source]
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-deserialize(mmif_json: str | list) → None[source]
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Passes the input data into the internal deserializer.

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-empty()[source]
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-get(key: str) → T | None[source]
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Standard dictionary-style get() method, albeit with no default -parameter. Relies on the implementation of __getitem__.

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Will return None if the key is not found.

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Parameters:
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key – the key to search for

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Returns:
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the value matching that key

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-class mmif.serialize.model.MmifObject(mmif_obj: bytes | str | dict | None = None, *_)[source]
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Bases: object

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Abstract superclass for MMIF related key-value pair objects.

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Any MMIF object can be initialized as an empty placeholder or -an actual representation with a JSON formatted string or equivalent -dict object argument.

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This superclass has four specially designed instance variables, and these -variable names cannot be used as attribute names for MMIF objects.

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  1. _unnamed_attributes: -Only can be either None or an empty dictionary. If it’s set to None, -it means the class won’t take any Additional Attributes in the -JSON schema sense. If it’s an empty dict, users can throw any k-v -pairs to the class, as long as the key is not a “reserved” name, -and those additional attributes will be stored in this dict while -in memory.

    2. -

  2. _attribute_classes: -This is a dict from a key name to a specific python class to use for -deserialize the value. Note that a key name in this dict does NOT -have to be a named attribute, but is recommended to be one.

    3. -

  3. _required_attributes: -This is a simple list of names of attributes that are required in -the object. When serialize, an object will skip its empty (e.g. -zero-length, or None) attributes unless they are in this list. -Otherwise, the serialized JSON string would have empty -representations (e.g. "", []).

    4. -

  4. _exclude_from_diff: -This is a simple list of names of attributes that should be excluded -from the diff calculation in __eq__.

    5. -
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# TODO (krim @ 8/17/20): this dict is however, a duplicate with the type hints in the class definition. -Maybe there is a better way to utilize type hints (e.g. getting them -as a programmatically), but for now developers should be careful to -add types to hints as well as to this dict.

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Also note that those special attributes MUST be set in the __init__() -before calling super method, otherwise deserialization will not work.

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And also, a subclass that has one or more named attributes, it must -set those attributes in the __init__() before calling super method. -When serializing a MmifObject, all empty attributes will be ignored, -so for optional named attributes, you must leave the values empty -(len == 0), but NOT None. Any None-valued named attributes will cause -issues with current implementation.

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Parameters:
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mmif_obj – JSON string or dict to initialize an object. -If not given, an empty object will be initialized, sometimes with -an ID value automatically generated, based on its parent object.

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-deserialize(mmif_json: str | dict) → None[source]
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Takes a JSON-formatted string or a simple dict that’s json-loaded from -such a string as an input and populates object’s fields with the values -specified in the input.

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Parameters:
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mmif_json – JSON-formatted string or dict from such a string -that represents a MMIF object

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-disallow_additional_properties() → None[source]
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Call this method in __init__() to prevent the insertion -of unnamed attributes after initialization.

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-id_delimiter: ClassVar[str] = ':'[source]
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-static is_empty(obj) → bool[source]
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return True if the obj is None or “emtpy”. The emptiness first defined as -having zero length. But for objects that lack __len__ method, we need -additional check.

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-reserved_names: Set[str] = {'_attribute_classes', '_exclude_from_diff', '_required_attributes', '_unnamed_attributes', 'reserved_names'}[source]
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-serialize(pretty: bool = False) → str[source]
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Generates JSON representation of an object.

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Parameters:
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pretty – If True, returns string representation with indentation.

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Returns:
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JSON string of the object.

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-set_additional_property(key: str, value: Any) → None[source]
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Method to set values in _unnamed_attributes.

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Parameters:
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  • key – the attribute name

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  • value – the desired value

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Returns:
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None

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Raise:
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AttributeError if additional properties are disallowed by disallow_additional_properties()

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-view_prefix: ClassVar[str] = 'v_'[source]
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-class mmif.serialize.model.MmifObjectEncoder(*, skipkeys=False, ensure_ascii=True, check_circular=True, allow_nan=True, sort_keys=False, indent=None, separators=None, default=None)[source]
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Bases: JSONEncoder

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Encoder class to define behaviors of de-/serialization

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-default(obj: MmifObject)[source]
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Overrides default encoding behavior to prioritize MmifObject.serialize().

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mmif module

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The mmif module contains the classes used to represent a full MMIF -file as a live Python object.

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See the specification docs and the JSON Schema file for more information.

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-class mmif.serialize.mmif.Mmif(mmif_obj: bytes | str | dict | None = None, *, validate: bool = True)[source]
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Bases: MmifObject

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MmifObject that represents a full MMIF file.

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Parameters:
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  • mmif_obj – the JSON data

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  • validate – whether to validate the data against the MMIF JSON schema.

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-add_document(document: Document, overwrite=False) → None[source]
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Appends a Document object to the documents list.

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Fails if there is already a document with the same ID in the MMIF object.

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Parameters:
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  • document – the Document object to add

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  • overwrite – if set to True, will overwrite -an existing view with the same ID

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Returns:
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None

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-add_view(view: View, overwrite=False) → None[source]
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Appends a View object to the views list.

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Fails if there is already a view with the same ID in the MMIF object.

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Parameters:
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  • view – the Document object to add

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  • overwrite – if set to True, will overwrite -an existing view with the same ID

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Returns:
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None

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-generate_capital_annotations()[source]
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Automatically convert any “pending” temporary properties from -Document objects to Annotation objects . The generated Annotation -objects are then added to the last View in the views lists.

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See https://github.com/clamsproject/mmif-python/issues/226 for rationale -behind this behavior and discussion.

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-get_alignments(at_type1: str | TypesBase, at_type2: str | TypesBase) → Dict[str, List[Annotation]][source]
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Finds views where alignments between two given annotation types occurred.

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Returns:
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a dict that keyed by view IDs (str) and has lists of alignment Annotation objects as values.

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-get_all_views_contain(*at_types: TypesBase | str) → List[View][source]
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Returns the list of all views in the MMIF if given types -are present in that view’s ‘contains’ metadata.

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Parameters:
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at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

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Returns:
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the list of views that contain the type

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-get_all_views_with_error() → List[View][source]
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Returns the list of all views in the MMIF that have errors.

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Returns:
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the list of views that contain errors but no annotations

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-get_annotations_between_time(start: int | float, end: int | float, time_unit: str = 'ms', at_types: List[str | TypesBase] = []) → Iterator[Annotation][source]
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Finds annotations that are anchored between the given time points.

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Parameters:
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  • start – the start time point in the unit of input_unit

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  • end – the end time point in the unit of input_unit

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  • time_unit – the unit of the input time points. Default is ms.

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  • at_types – a list of annotation types to filter with. Any type in this list will be included in the return.

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Returns:
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an iterator of Annotation objects that are anchored between the given time points

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-get_document_by_id(doc_id: str) → Document[source]
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Finds a Document object with the given ID.

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Parameters:
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doc_id – the ID to search for

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Returns:
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a reference to the corresponding document, if it exists

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Raises:
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KeyError – if there is no corresponding document

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-get_document_location(m_type: DocumentTypes | str, path_only=False) → str | None[source]
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Method to get the location of first document of given type.

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Parameters:
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m_type – the type to search for

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Returns:
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the value of the location field in the corresponding document

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-get_documents_by_app(app_id: str) → List[Document][source]
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Method to get all documents object queries by its originated app name.

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Parameters:
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app_id – the app name to search for

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Returns:
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a list of documents matching the requested app name, or an empty list if the app not found

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-get_documents_by_property(prop_key: str, prop_value: str) → List[Document][source]
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Method to retrieve documents by an arbitrary key-value pair in the document properties objects.

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Parameters:
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  • prop_key – the metadata key to search for

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  • prop_value – the metadata value to match

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Returns:
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a list of documents matching the requested metadata key-value pair

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-get_documents_by_type(doc_type: str | DocumentTypes) → List[Document][source]
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Method to get all documents where the type matches a particular document type, which should be one of the CLAMS document types.

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Parameters:
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doc_type – the type of documents to search for, must be one of Document type defined in the CLAMS vocabulary.

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Returns:
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a list of documents matching the requested type, or an empty list if none found.

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-get_documents_in_view(vid: str | None = None) → List[Document][source]
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Method to get all documents object queries by a view id.

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Parameters:
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vid – the source view ID to search for

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Returns:
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a list of documents matching the requested source view ID, or an empty list if the view not found

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-get_documents_locations(m_type: DocumentTypes | str, path_only=False) → List[str | None][source]
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This method returns the file paths of documents of given type. -Only top-level documents have locations, so we only check them.

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Parameters:
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m_type – the type to search for

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Returns:
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a list of the values of the location fields in the corresponding documents

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-get_end(annotation: Annotation) → int | float[source]
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An alias to get_anchor_point method with start=False.

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-get_last_error() → str | None[source]
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Returns the last error message found in the views.

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Returns:
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the error message in human-readable format, or None if no error is found

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-get_start(annotation: Annotation) → int | float[source]
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An alias to get_anchor_point method with start=True.

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-get_view_by_id(req_view_id: str) → View[source]
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Finds a View object with the given ID.

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Parameters:
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req_view_id – the ID to search for

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Returns:
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a reference to the corresponding view, if it exists

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Raises:
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Exception – if there is no corresponding view

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-get_view_contains(at_types: TypesBase | str | List[str | TypesBase]) → View | None[source]
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Returns the last view appended that contains the given -types in its ‘contains’ metadata.

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Parameters:
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at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

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Returns:
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the view, or None if the type is not found

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-get_view_with_error() → View | None[source]
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Returns the last view appended that contains an error.

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Returns:
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the view, or None if no error is found

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-get_views_contain(*at_types: TypesBase | str) → List[View][source]
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Returns the list of all views in the MMIF if given types -are present in that view’s ‘contains’ metadata.

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Parameters:
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at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

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Returns:
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the list of views that contain the type

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-get_views_for_document(doc_id: str) → List[View][source]
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Returns the list of all views that have annotations anchored on a particular document. -Note that when the document is inside a view (generated during the pipeline’s running), -doc_id must be prefixed with the view_id.

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-get_views_with_error() → List[View][source]
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Returns the list of all views in the MMIF that have errors.

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Returns:
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the list of views that contain errors but no annotations

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-new_view() → View[source]
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Creates an empty view with a new ID and appends it to the views list.

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Returns:
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a reference to the new View object

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-new_view_id() → str[source]
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Fetches an ID for a new view.

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Returns:
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the ID

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-sanitize()[source]
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Sanitizes a Mmif object by running some safeguards. -Concretely, it performs the following before returning the JSON string.

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  1. validating output using built-in MMIF jsonschema

    2. -

  2. remove non-existing annotation types from contains metadata

    3. -
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-serialize(pretty: bool = False, sanitize: bool = False, autogenerate_capital_annotations=True) → str[source]
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Serializes the MMIF object to a JSON string.

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Parameters:
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  • sanitize – If True, performs some sanitization of before returning -the JSON string. See sanitize() for details.

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  • autogenerate_capital_annotations – If True, automatically convert -any “pending” temporary properties from Document objects to -Annotation objects. See generate_capital_annotations() for -details.

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  • pretty – If True, returns string representation with indentation.

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Returns:
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JSON string of the MMIF object.

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-static validate(json_str: bytes | str | dict) → None[source]
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Validates a MMIF JSON object against the MMIF Schema. -Note that this method operates before processing by MmifObject._load_str, -so it expects @ and not _ for the JSON-LD @-keys.

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Raises:
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jsonschema.exceptions.ValidationError – if the input fails validation

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Parameters:
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json_str – a MMIF JSON dict or string

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Returns:
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None

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view module

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The view module contains the classes used to represent a MMIF view -as a live Python object.

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In MMIF, views are created by apps in a pipeline that are annotating -data that was previously present in the MMIF file.

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-class mmif.serialize.view.Contain(mmif_obj: bytes | str | dict | None = None, *_)[source]
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Bases: DataDict[str, str]

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Contain object that represents the metadata of a single -annotation type in the contains metadata of a MMIF view.

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-class mmif.serialize.view.View(view_obj: bytes | str | dict | None = None, parent_mmif=None, *_)[source]
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Bases: MmifObject

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View object that represents a single view in a MMIF file.

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A view is identified by an ID, and contains certain metadata, -a list of annotations, and potentially a JSON-LD @context -IRI.

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If view_obj is not provided, an empty View will be generated.

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Parameters:
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view_obj – the JSON data that defines the view

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-add_annotation(annotation: Annotation, overwrite=False) → Annotation[source]
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Adds an annotation to the current view.

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Fails if there is already an annotation with the same ID -in the view, unless overwrite is set to True.

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Parameters:
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Raises:
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KeyError – if overwrite is set to False and -an annotation with the same ID exists -in the view

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Returns:
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the same Annotation object passed in as annotation

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-add_document(document: Document, overwrite=False) → Annotation[source]
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Appends a Document object to the annotations list.

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Fails if there is already a document with the same ID in the annotations list.

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Parameters:
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  • document – the Document object to add

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  • overwrite – if set to True, will overwrite -an existing view with the same ID

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Returns:
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None

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-get_annotation_by_id(ann_id) → Annotation[source]
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-get_annotations(at_type: str | TypesBase | None = None, **properties) → Generator[Annotation, None, None][source]
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Look for certain annotations in this view, specified by parameters

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Parameters:
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  • at_type – @type of the annotations to look for. When this is None, any @type will match.

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  • properties – properties of the annotations to look for. When given more than one property, all properties must match. Note that annotation type metadata are specified in the contains view metadata, not in individual annotation objects.

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-get_document_by_id(doc_id) → Document[source]
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-get_documents() → List[Document][source]
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-get_error() → str | None[source]
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Get the “text” representation of the error occurred during -processing. Text representation is supposed to be human-readable. -When ths view does not have any error, returns None.

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-has_error() → bool[source]
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-has_warnings()[source]
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-new_annotation(at_type: str | TypesBase, aid: str | None = None, overwrite=False, **properties) → Annotation[source]
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Generates a new mmif.serialize.annotation.Annotation -object and adds it to the current view.

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Fails if there is already an annotation with the same ID -in the view, unless overwrite is set to True.

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Parameters:
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  • at_type – the desired @type of the annotation.

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  • aid – the desired ID of the annotation, when not given, -the mmif SDK tries to automatically generate an ID based on -Annotation type and existing annotations in the view.

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  • overwrite – if set to True, will overwrite an -existing annotation with the same ID.

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Raises:
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KeyError – if overwrite is set to False and -an annotation with the same ID exists -in the view.

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Returns:
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the generated mmif.serialize.annotation.Annotation

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-new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
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Adds a new element to the contains metadata.

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Parameters:
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  • at_type – the @type of the annotation type being added

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  • contains_metadata – any metadata associated with the annotation type

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Returns:
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the generated Contain object

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-new_textdocument(text: str, lang: str = 'en', did: str | None = None, overwrite=False, **properties) → Document[source]
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Generates a new mmif.serialize.annotation.Document -object, particularly typed as TextDocument and adds it to the current view.

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Fails if there is already a text document with the same ID -in the view, unless overwrite is set to True.

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Parameters:
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  • text – text content of the new document

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  • lang – ISO 639-1 code of the language used in the new document

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  • did – the desired ID of the document, when not given, -the mmif SDK tries to automatically generate an ID based on -Annotation type and existing documents in the view.

    • -

  • overwrite – if set to True, will overwrite an -existing document with the same ID

    • -
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Raises:
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KeyError – if overwrite is set to False and -an document with the same ID exists -in the view

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Returns:
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the generated mmif.serialize.annotation.Document

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-set_error(err_message: str, err_trace: str) → None[source]
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-class mmif.serialize.view.ViewMetadata(viewmetadata_obj: bytes | str | dict | None = None, *_)[source]
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Bases: MmifObject

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ViewMetadata object that represents the metadata object within a MMIF view.

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Parameters:
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viewmetadata_obj – the JSON data that defines the metadata

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-add_app_configuration(config_key: str, config_value: str | int | float | bool | None | List[str | int | float | bool | None]) → None[source]
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Add a configuration key-value pair to the app_configuration dictionary.

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-add_contain(contain: Contain, at_type: str | TypesBase) → None[source]
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-add_parameter(param_key: str, param_value: str)[source]
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Add a single runtime parameter to the view metadata. Note that parameter value must be a string.

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-add_parameters(**runtime_params: str)[source]
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Add runtime parameters as a batch (dict) to the view metadata. Note that parameter values must be strings.

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-add_warnings(*warnings: Warning)[source]
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-emtpy_warnings()[source]
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-get_app_configuration(config_key: str) → str | int | float | bool | None | List[str | int | float | bool | None][source]
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Get a configuration value from the app_configuration dictionary.

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-get_error_as_text() → str[source]
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-get_parameter(param_key: str) → str[source]
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Get a runtime parameter from the view metadata.

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-has_error() → bool[source]
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-has_warnings()[source]
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-new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
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Adds a new element to the contains dictionary.

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Parameters:
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    -

  • at_type – the @type of the annotation type being added

    • -

  • contains_metadata – any metadata associated with the annotation type

    • -
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Returns:
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the generated Contain object

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-set_error(message: str, stack_trace: str)[source]
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annotation module

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The annotation module contains the classes used to represent a -MMIF annotation as a live Python object.

-

In MMIF, annotations are created by apps in a pipeline as a part -of a view. For documentation on how views are represented, see -mmif.serialize.view.

-
-
-class mmif.serialize.annotation.Annotation(anno_obj: bytes | str | dict | None = None, *_)[source]
-

Bases: MmifObject

-

MmifObject that represents an annotation in a MMIF view.

-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]]) → None[source]
-

Adds a property to the annotation’s properties.

-
-
Parameters:
-
    -

  • name – the name of the property

    • -

  • value – the property’s desired value

    • -
-
-
Returns:
-

None

-
-
-
- -
-
-aligned_to_by(alignment: Annotation) → Annotation | None[source]
-

Retrieves the other side of Alignment annotation that has this annotation on one side.

-
-
Parameters:
-

alignment – Alignment annotation that has this annotation on one side

-
-
Returns:
-

the annotation that this annotation is aligned to (other side of Alignment), -or None if this annotation is not used in the Alignment.

-
-
-
- -
-
-property at_type: TypesBase[source]
-
- -
-
-static check_prop_value_is_simple_enough(value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]]) → bool[source]
-
- -
-
-get(prop_name: str) → AnnotationProperties | str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]][source]
-

A special getter for Annotation properties. This is to allow for -directly accessing properties without having to go through the -properties object, or view-level annotation properties encoded in the -view.metadata.contains dict. Note that the regular props will take -the priority over the ephemeral props when there are conflicts.

-
- -
-
-get_all_aligned() → Iterator[Annotation][source]
-

Generator to iterate through all alignments and aligned annotations. Note that this generator will yield -the Alignment annotations as well. Every odd-numbered yield will be an Alignment annotation, and every -even-numbered yield will be the aligned annotation. If there’s a specific annotation type that you’re looking -for, you need to filter the generated results outside.

-
-
Returns:
-

yields the alignment annotation and the aligned annotation. -The order is decided by the order of appearance of Alignment annotations in the MMIF

-
-
-
- -
-
-get_property(prop_name: str) → AnnotationProperties | str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]] | Dict[str, str | int | float | bool | None] | Dict[str, List[str | int | float | bool | None]][source]
-

A special getter for Annotation properties. This is to allow for -directly accessing properties without having to go through the -properties object, or view-level annotation properties encoded in the -view.metadata.contains dict. Note that the regular props will take -the priority over the ephemeral props when there are conflicts.

-
- -
-
-property id: str[source]
-
- -
-
-is_document()[source]
-
- -
-
-is_type(at_type: str | TypesBase) → bool[source]
-

Check if the @type of this object matches.

-
- -
-
-property long_id: str[source]
-
- -
-
-property parent: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.AnnotationProperties(mmif_obj: bytes | str | dict | None = None, *_)[source]
-

Bases: MmifObject, MutableMapping[str, T]

-

AnnotationProperties object that represents the -properties object within a MMIF annotation.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
- -
-
-class mmif.serialize.annotation.Document(doc_obj: bytes | str | dict | None = None, *_)[source]
-

Bases: Annotation

-

Document object that represents a single document in a MMIF file.

-

A document is identified by an ID, and contains certain attributes -and potentially contains the contents of the document itself, -metadata about how the document was created, and/or a list of -subdocuments grouped together logically.

-

If document_obj is not provided, an empty Document will be generated.

-
-
Parameters:
-

document_obj – the JSON data that defines the document

-
-
-
-
-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None]) → None[source]
-

Adds a property to the document’s properties.

-

Unlike the parent Annotation class, added properties of a -Document object can be lost during serialization unless it belongs -to somewhere in a Mmif object. This is because we want to keep -Document object as “read-only” as possible. Thus, if you want to add -a property to a Document object,

-
    -

  • add the document to a Mmif object (either in the documents list or -in a view from the views list), or

    • -

  • directly write to Document.properties instead of using this method -(which is not recommended).

    • -
-

With the former method, the SDK will record the added property as a -Annotation annotation object, separate from the original Document -object. See Mmif.generate_capital_annotations() for more.

-

A few notes to keep in mind:

-
    -

  1. You can’t overwrite an existing property of a Document object.

    2. -

  2. A MMIF can have multiple Annotation objects with the same -property name but different values. When this happens, the SDK will -only keep the latest value (in order of appearances in views list) of -the property, effectively overwriting the previous values.

    3. -
-
- -
-
-get(prop_name)[source]
-

A special getter for Document properties. The major difference from -the super class’s Annotation.get() method is that Document -class has one more set of “pending” properties, that are added after -the Document object is created and will be serialized as a separate -Annotation object of which @type = Annotation. The -pending properties will take the priority over the regular properties -when there are conflicts.

-
- -
-
-get_property(prop_name)[source]
-

A special getter for Document properties. The major difference from -the super class’s Annotation.get() method is that Document -class has one more set of “pending” properties, that are added after -the Document object is created and will be serialized as a separate -Annotation object of which @type = Annotation. The -pending properties will take the priority over the regular properties -when there are conflicts.

-
- -
-
-property location: str | None[source]
-

location property must be a legitimate URI. That is, should the document be a local file -then the file:// scheme must be used. -Returns None when no location is set.

-
- -
-
-location_address() → str | None[source]
-

Retrieves the full address from the document location URI. -Returns None when no location is set.

-
- -
-
-location_path(nonexist_ok=True) → str | None[source]
-

Retrieves a path that’s resolved to a pathname in the local file system. -To obtain the original value of the “path” part in the location string -(before resolving), use properties.location_path_literal method. -Returns None when no location is set.

-
-
Parameters:
-

nonexist_ok – if False, raise FileNotFoundError when the resolved path doesn’t exist

-
-
-
- -
-
-location_scheme() → str | None[source]
-

Retrieves URI scheme of the document location. -Returns None when no location is set.

-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.DocumentProperties(mmif_obj: bytes | str | dict | None = None, *_)[source]
-

Bases: AnnotationProperties

-

DocumentProperties object that represents the -properties object within a MMIF document.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
-
-property location: str | None[source]
-

location property must be a legitimate URI. That is, should the document be a local file -then the file:// scheme must be used. -Returns None when no location is set.

-
- -
-
-location_address() → str | None[source]
-

Retrieves the full address from the document location URI. -Returns None when no location is set.

-
- -
-
-location_path() → str | None[source]
-
- -
-
-location_path_literal() → str | None[source]
-

Retrieves only path name of the document location (hostname is ignored). -Returns None when no location is set.

-
- -
-
-location_path_resolved(nonexist_ok=True) → str | None[source]
-

Retrieves only path name of the document location (hostname is ignored), -and then try to resolve the path name in the local file system. -This method should be used when the document scheme is file or empty. -For other schemes, users should install mmif-locdoc-<scheme> plugin.

-

Returns None when no location is set. -Raise ValueError when no code found to resolve the given location scheme.

-
- -
-
-location_scheme() → str | None[source]
-

Retrieves URI scheme of the document location. -Returns None when no location is set.

-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.Text(text_obj: bytes | str | dict | None = None, *_)[source]
-

Bases: MmifObject

-
-
-property lang: str[source]
-
- -
-
-property value: str[source]
-
- -
- -
-
- - -
-
- -
-
-
-
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- - - \ No newline at end of file diff --git a/docs/1.0.19/autodoc/mmif.utils.html b/docs/1.0.19/autodoc/mmif.utils.html deleted file mode 100644 index 1056dab8..00000000 --- a/docs/1.0.19/autodoc/mmif.utils.html +++ /dev/null @@ -1,1050 +0,0 @@ - - - - - - - - - mmif.utils package — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.utils package

-

Package containing utility modules for handling different types of source -documents, and general implementation of common data structures and -algorithms.

-
-

video_document_helper module

-
-
-mmif.utils.video_document_helper.capture(video_document: Document)[source]
-

Captures a video file using OpenCV and adds fps, frame count, and duration as properties to the document.

-
-
Parameters:
-

video_document – Document instance that holds a video document ("@type": ".../VideoDocument/...")

-
-
Returns:
-

OpenCV VideoCapture object

-
-
-
- -
-
-mmif.utils.video_document_helper.convert_timeframe(mmif: Mmif, time_frame: Annotation, out_unit: str) → Tuple[int | float | str, int | float | str][source]
-

Converts start and end points in a TimeFrame annotation a different time unit.

-
-
Parameters:
-
    -

  • mmif – Mmif instance

    • -

  • time_frame – Annotation instance that holds a time interval annotation ("@type": ".../TimeFrame/...")

    • -

  • out_unit – time unit to which the point is converted

    • -
-
-
Returns:
-

tuple of frame numbers, seconds/milliseconds, or ISO notation of TimeFrame’s start and end

-
-
-
- -
-
-mmif.utils.video_document_helper.convert_timepoint(mmif: Mmif, timepoint: Annotation, out_unit: str) → int | float | str[source]
-

Converts a time point included in an annotation to a different time unit. -The input annotation must have timePoint property.

-
-
Parameters:
-
    -

  • mmif – input MMIF to obtain fps and input timeunit

    • -

  • timepoint – Annotation instance with timePoint property

    • -

  • out_unit – time unit to which the point is converted (frames, seconds, milliseconds)

    • -
-
-
Returns:
-

frame number (integer) or second/millisecond (float) of input timepoint

-
-
-
- -
-
-mmif.utils.video_document_helper.extract_frames_as_images(video_document: Document, framenums: List[int], as_PIL: bool = False)[source]
-

Extracts frames from a video document as a list of numpy.ndarray. -Use with sample_frames() function to get the list of frame numbers first.

-
-
Parameters:
-
    -

  • video_document – Document instance that holds a video document ("@type": ".../VideoDocument/...")

    • -

  • framenums – integers representing the frame numbers to extract

    • -

  • as_PIL – return PIL.Image.Image instead of ndarray

    • -
-
-
Returns:
-

frames as a list of ndarray or Image

-
-
-
- -
-
-mmif.utils.video_document_helper.extract_mid_frame(mmif: Mmif, time_frame: Annotation, as_PIL: bool = False)[source]
-

Extracts the middle frame of a time interval annotation as a numpy ndarray.

-
-
Parameters:
-
    -

  • mmif – Mmif instance

    • -

  • time_frame – Annotation instance that holds a time interval annotation ("@type": ".../TimeFrame/...")

    • -

  • as_PIL – return Image instead of ndarray

    • -
-
-
Returns:
-

frame as a numpy.ndarray or PIL.Image.Image

-
-
-
- -
-
-mmif.utils.video_document_helper.extract_representative_frame(mmif: Mmif, time_frame: Annotation, as_PIL: bool = False)[source]
-

Extracts the representative frame of an annotation as a numpy ndarray or PIL Image.

-
-
Parameters:
-
    -

  • mmif – Mmif instance

    • -

  • time_frame – Annotation instance that holds a time interval annotation ("@type": ".../TimeFrame/...")

    • -

  • as_PIL – return Image instead of ndarray

    • -
-
-
Returns:
-

frame as a numpy.ndarray or PIL.Image.Image

-
-
-
- -
-
-mmif.utils.video_document_helper.framenum_to_millisecond(video_doc: Document, frame: int)[source]
-

Converts a frame number to a millisecond value.

-
- -
-
-mmif.utils.video_document_helper.framenum_to_second(video_doc: Document, frame: int)[source]
-

Converts a frame number to a second value.

-
- -
-
-mmif.utils.video_document_helper.get_annotation_property(mmif, annotation, prop_name)[source]
-
-

Deprecated since version 1.0.8: Use mmif.serialize.annotation.Annotation.get_property() method instead.

-
-

Get a property value from an annotation. If the property is not found in the annotation, it will look up the metadata of the annotation’s parent view and return the value from there. -xisting

-
- -
-
-mmif.utils.video_document_helper.get_framerate(video_document: Document) → float[source]
-

Gets the frame rate of a video document. First by checking the fps property of the document, then by capturing the video.

-
-
Parameters:
-

video_document – Document instance that holds a video document ("@type": ".../VideoDocument/...")

-
-
Returns:
-

frames per second as a float, rounded to 2 decimal places

-
-
-
- -
-
-mmif.utils.video_document_helper.get_mid_framenum(mmif: Mmif, time_frame: Annotation)[source]
-

Calculates the middle frame number of a time interval annotation.

-
-
Parameters:
-
    -

  • mmif – Mmif instance

    • -

  • time_frame – Annotation instance that holds a time interval annotation ("@type": ".../TimeFrame/...")

    • -
-
-
Returns:
-

middle frame number as an integer

-
-
-
- -
-
-mmif.utils.video_document_helper.get_representative_framenum(mmif: Mmif, time_frame: Annotation)[source]
-

Calculates the representative frame number from an annotation.

-
-
Parameters:
-
    -

  • mmif – Mmif instance

    • -

  • time_frame – Annotation instance that holds a time interval annotation containing a representatives property ("@type": ".../TimeFrame/...")

    • -
-
-
Returns:
-

representative frame number as an integer

-
-
-
- -
-
-mmif.utils.video_document_helper.millisecond_to_framenum(video_doc: Document, millisecond: float) → int[source]
-

Converts a millisecond value to a frame number.

-
- -
-
-mmif.utils.video_document_helper.sample_frames(start_frame: int, end_frame: int, sample_rate: float = 1) → List[int][source]
-

Helper function to sample frames from a time interval. -Can also be used as a “cutoff” function when used with start_frame==0 and sample_rate==1.

-
-
Parameters:
-
    -

  • start_frame – start frame of the interval

    • -

  • end_frame – end frame of the interval

    • -

  • sample_rate – sampling rate (or step) to configure how often to take a frame, default is 1, meaning all consecutive frames are sampled

    • -
-
-
-
- -
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-mmif.utils.video_document_helper.second_to_framenum(video_doc: Document, second) → int[source]
-

Converts a second value to a frame number.

-
- -
-
-

text_document_helper module

-

This module provides helpers for handling sequence labeling. Specifically, it provides

-
    -

  • a generalized label re-mapper for “post-binning” of labels

    • -

  • conversion from a list of CLAMS annotations (with classification props) into a list of reals (scores by labels), can be combined with the label re-mapper mentioned above

    • -

  • mmif.utils.sequence_helper.smooth_outlying_short_intervals(): a simple smoothing algorithm by trimming “short” outlier sequences

    • -
-

However, it DOES NOT provide

-
    -

  • direct conversion between CLAMS annotations. For example, it does not directly handle stitching of TimePoint into TimeFrames.

    • -

  • support for multi-class scenario, such as handling of _competing_ subsequence or overlapping labels.

    • -
-

Some functions can use optional external libraries (e.g., numpy) for better performance. -Hence, if you see a warning about missing optional packages, you might want to install them by running pip install mmif-python[seq].

-
-
-mmif.utils.sequence_helper.build_label_remapper(src_labels: List[str], dst_labels: Dict[str, str | int | float | bool | None]) → Dict[str, str | int | float | bool | None][source]
-

Build a label remapper dictionary from source and destination labels.

-
-
Parameters:
-
    -

  • src_labels – a list of all labels on the source side

    • -

  • dst_labels – a dict from source labels to destination labels. -Source labels not in this dict will be remapped to a negative label (-).

    • -
-
-
Returns:
-

a dict that exhaustively maps source labels to destination labels

-
-
-
- -
-
-mmif.utils.sequence_helper.build_score_lists(classifications: ~typing.List[~typing.Dict], label_remapper: ~typing.Dict, score_remap_op: ~typing.Callable[[...], float] = <built-in function max>) → Tuple[Dict[str, int], numpy.ndarray][source]
-

Build lists of scores indexed by the label names.

-
-
Parameters:
-
    -

  • classifications – list of dictionaries of classification results, taken from input annotation objects

    • -

  • label_remapper – a dictionary that maps source label names to destination label names (formerly “postbin”)

    • -

  • score_remap_op – a function to remap the scores from multiple source labels binned to a destination label -common choices are max, min, or sum

    • -
-
-
Returns:
-

    -

  1. a dictionary that maps label names to their index in the score list

    2. -

  2. 2-d numpy array of scores, of which rows are indexed by label map dict (first return value)

    3. -
-

-
-
-
- -
-
-mmif.utils.sequence_helper.smooth_outlying_short_intervals(scores: List[float], min_spseq_size: int, min_snseq_size: int, min_score: float = 0.5)[source]
-

Given a list of scores, a score threshold, and smoothing parameters, -identify the intervals of “positive” scores by “trimming” the short -positive sequences (“spseq”) and short negative sequences (“snseq”). To -decide the positivity, first step is binarization of the scores by the -min_score threshold. Given Sr as “raw” input real-number scores -list, and min_score=0.5,

-
-
Sr: [0.3, 0.6, 0.2, 0.8, 0.2, 0.9, 0.8, 0.5, 0.1, 0.5, 0.8, 0.3, 1.0, 0.7, 0.5, 0.5, 0.5, 0.8, 0.3, 0.6]
-
-
-
-

the binarization is done by simply comparing each score to the -threshold to get S list of binary scores

-
-
1.0 :                                     |                      
-0.9 :                |                    |                      
-0.8 :          |     |  |           |     |              |       
-0.7 :          |     |  |           |     |  |           |       
-0.6 :    |     |     |  |           |     |  |           |     | 
-0.5 :----+-----+-----+--+--+-----+--+-----+--+--+--+--+--+-----+-
-0.4 :    |     |     |  |  |     |  |     |  |  |  |  |  |     | 
-0.3 : |  |     |     |  |  |     |  |  |  |  |  |  |  |  |  |  | 
-0.2 : |  |  |  |  |  |  |  |     |  |  |  |  |  |  |  |  |  |  | 
-0.1 : |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | 
-0.0 +------------------------------------------------------------
-raw :.3 .6 .2 .8 .2 .9 .8 .5 .1 .5 .8 .3 1. .7 .5 .5 .5 .8 .3 .6
- S  : 0  1  0  1  0  1  1  0  0  0  1  0  1  1  0  1  1  1  0  1 
-
-
-
-

Note that the size of a positive or negative sequence can be as small -as 1.

-

Then, here are examples of smoothing a list of binary scores into -intervals, by trimming “very short” (under thresholds) sequences of -positive or negative:

-
-

Note

-

legends:

-
    -

  • t is unit index (e.g. time index)

    • -

  • S is the list of binary scores (zeros and ones)

    • -

  • I is the list of intervals after smoothing

    • -
-
-
    -

  1. with params min_spseq_size==1, min_snseq_size==4

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1]
-I: [0, 1--1--1--1--1--1--1--1--1--1--1--1, 0--0--0--0--0--0, 1]
-
    -
    -

    Explanation: min_snseq_size is used to smooth short sequences -of negative predictions. In this, zeros from t[7:10] are smoothed -into “one” I, while zeros from t[13:19] are kept as “zero” I. Note -that the “short” snseqs at the either ends (t[0:1]) are never -smoothed.

    -
    -
    2. -

  2. with params min_spseq_size==4, min_snseq_size==2

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1]
-I: [0, 1--1--1--1--1--1, 0--0--0--0--0--0--0--0--0--0--0--0--0]
-
    -
    -

    Explanation: min_spseq_size is used to smooth short sequences -of positive predictions. In this example, the spseqs of ones from -both t[10:13] and t[19:20] are smoothed. Note that the “short” -spseqs at the either ends (t[19:20]) are always smoothed.

    -
    -
    3. -

  3. with params min_spseq_size==4, min_snseq_size==4

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1]
-I: [0, 1--1--1--1--1--1--1--1--1--1--1--1--0--0--0--0--0--0--0]
-
    -
    -

    Explanation: When two threshold parameters are working together, -the algorithm will prioritize the smoothing of the snseqs over the -smoothing of the spseqs. Thus, in this example, the snseq t[7:10] -gets first smoothed “up” before the spseq t[10:13] is smoothed -“down”, resulting in a long final I.

    -
    -
    4. -

  4. with params min_spseq_size==4, min_snseq_size==4

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [1, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 1, 1]
-I: [1--1--1--1--1--1--1, 0--0--0--0, 1--1--1--1--1--1--1--1--1]
-
    -
    -

    Explanation: Since smoothing of snseqs is prioritized, short spseqs -at the beginning or the end can be kept.

    -
    -
    5. -

  5. with params min_spseq_size==1, min_snseq_size==1

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 1, 1]
-I: [0--0--0, 1--1--1--1, 0--0--0--0, 1--1--1--1, 0--0--0, 1--1]
-
    -
    -

    Explanation: When both width thresholds are set to 1, the algorithm -works essentially in the “stitching” only mode.

    -
    -
    6. -
-
-
Parameters:
-
    -

  • scores – SORTED list of scores to be smoothed. The score list -is assumed to be “exhaust” the entire time or space of -the underlying document segment. -(Sorted by the start, and then by the end of anchors)

    • -

  • min_score – minimum threshold to use to discard -low-scored units (strictly less than)

    • -

  • min_spseq_size – minimum size of a positive sequence not to be -smoothed (greater or equal to)

    • -

  • min_snseq_size – minimum size of a negative sequence not to be -smoothed (greater or equal to)

    • -
-
-
Returns:
-

list of tuples of start(inclusive)/end(exclusive) indices -of the “positive” sequences. Negative sequences (regardless of -their size) are not included in the output.

-
-
-
- -
-
-mmif.utils.sequence_helper.validate_labelset(annotations: Iterable[Annotation]) → List[str][source]
-

Simple check for a list of annotations to see if they have the same label set.

-
-
Raise:
-

AttributeError if an element in the input list doesn’t have the labelset property

-
-
Raise:
-

ValueError if different labelset values are found

-
-
Returns:
-

a list of the common labelset value (list of label names)

-
-
-
- -
-
-

sequence_helper module

-

This module provides helpers for handling sequence labeling. Specifically, it provides

-
    -

  • a generalized label re-mapper for “post-binning” of labels

    • -

  • conversion from a list of CLAMS annotations (with classification props) into a list of reals (scores by labels), can be combined with the label re-mapper mentioned above

    • -

  • mmif.utils.sequence_helper.smooth_outlying_short_intervals(): a simple smoothing algorithm by trimming “short” outlier sequences

    • -
-

However, it DOES NOT provide

-
    -

  • direct conversion between CLAMS annotations. For example, it does not directly handle stitching of TimePoint into TimeFrames.

    • -

  • support for multi-class scenario, such as handling of _competing_ subsequence or overlapping labels.

    • -
-

Some functions can use optional external libraries (e.g., numpy) for better performance. -Hence, if you see a warning about missing optional packages, you might want to install them by running pip install mmif-python[seq].

-
-
-mmif.utils.sequence_helper.build_label_remapper(src_labels: List[str], dst_labels: Dict[str, str | int | float | bool | None]) → Dict[str, str | int | float | bool | None][source]
-

Build a label remapper dictionary from source and destination labels.

-
-
Parameters:
-
    -

  • src_labels – a list of all labels on the source side

    • -

  • dst_labels – a dict from source labels to destination labels. -Source labels not in this dict will be remapped to a negative label (-).

    • -
-
-
Returns:
-

a dict that exhaustively maps source labels to destination labels

-
-
-
- -
-
-mmif.utils.sequence_helper.build_score_lists(classifications: ~typing.List[~typing.Dict], label_remapper: ~typing.Dict, score_remap_op: ~typing.Callable[[...], float] = <built-in function max>) → Tuple[Dict[str, int], numpy.ndarray][source]
-

Build lists of scores indexed by the label names.

-
-
Parameters:
-
    -

  • classifications – list of dictionaries of classification results, taken from input annotation objects

    • -

  • label_remapper – a dictionary that maps source label names to destination label names (formerly “postbin”)

    • -

  • score_remap_op – a function to remap the scores from multiple source labels binned to a destination label -common choices are max, min, or sum

    • -
-
-
Returns:
-

    -

  1. a dictionary that maps label names to their index in the score list

    2. -

  2. 2-d numpy array of scores, of which rows are indexed by label map dict (first return value)

    3. -
-

-
-
-
- -
-
-mmif.utils.sequence_helper.smooth_outlying_short_intervals(scores: List[float], min_spseq_size: int, min_snseq_size: int, min_score: float = 0.5)[source]
-

Given a list of scores, a score threshold, and smoothing parameters, -identify the intervals of “positive” scores by “trimming” the short -positive sequences (“spseq”) and short negative sequences (“snseq”). To -decide the positivity, first step is binarization of the scores by the -min_score threshold. Given Sr as “raw” input real-number scores -list, and min_score=0.5,

-
-
Sr: [0.3, 0.6, 0.2, 0.8, 0.2, 0.9, 0.8, 0.5, 0.1, 0.5, 0.8, 0.3, 1.0, 0.7, 0.5, 0.5, 0.5, 0.8, 0.3, 0.6]
-
-
-
-

the binarization is done by simply comparing each score to the -threshold to get S list of binary scores

-
-
1.0 :                                     |                      
-0.9 :                |                    |                      
-0.8 :          |     |  |           |     |              |       
-0.7 :          |     |  |           |     |  |           |       
-0.6 :    |     |     |  |           |     |  |           |     | 
-0.5 :----+-----+-----+--+--+-----+--+-----+--+--+--+--+--+-----+-
-0.4 :    |     |     |  |  |     |  |     |  |  |  |  |  |     | 
-0.3 : |  |     |     |  |  |     |  |  |  |  |  |  |  |  |  |  | 
-0.2 : |  |  |  |  |  |  |  |     |  |  |  |  |  |  |  |  |  |  | 
-0.1 : |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | 
-0.0 +------------------------------------------------------------
-raw :.3 .6 .2 .8 .2 .9 .8 .5 .1 .5 .8 .3 1. .7 .5 .5 .5 .8 .3 .6
- S  : 0  1  0  1  0  1  1  0  0  0  1  0  1  1  0  1  1  1  0  1 
-
-
-
-

Note that the size of a positive or negative sequence can be as small -as 1.

-

Then, here are examples of smoothing a list of binary scores into -intervals, by trimming “very short” (under thresholds) sequences of -positive or negative:

-
-

Note

-

legends:

-
    -

  • t is unit index (e.g. time index)

    • -

  • S is the list of binary scores (zeros and ones)

    • -

  • I is the list of intervals after smoothing

    • -
-
-
    -

  1. with params min_spseq_size==1, min_snseq_size==4

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1]
-I: [0, 1--1--1--1--1--1--1--1--1--1--1--1, 0--0--0--0--0--0, 1]
-
    -
    -

    Explanation: min_snseq_size is used to smooth short sequences -of negative predictions. In this, zeros from t[7:10] are smoothed -into “one” I, while zeros from t[13:19] are kept as “zero” I. Note -that the “short” snseqs at the either ends (t[0:1]) are never -smoothed.

    -
    -
    2. -

  2. with params min_spseq_size==4, min_snseq_size==2

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1]
-I: [0, 1--1--1--1--1--1, 0--0--0--0--0--0--0--0--0--0--0--0--0]
-
    -
    -

    Explanation: min_spseq_size is used to smooth short sequences -of positive predictions. In this example, the spseqs of ones from -both t[10:13] and t[19:20] are smoothed. Note that the “short” -spseqs at the either ends (t[19:20]) are always smoothed.

    -
    -
    3. -

  3. with params min_spseq_size==4, min_snseq_size==4

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1]
-I: [0, 1--1--1--1--1--1--1--1--1--1--1--1--0--0--0--0--0--0--0]
-
    -
    -

    Explanation: When two threshold parameters are working together, -the algorithm will prioritize the smoothing of the snseqs over the -smoothing of the spseqs. Thus, in this example, the snseq t[7:10] -gets first smoothed “up” before the spseq t[10:13] is smoothed -“down”, resulting in a long final I.

    -
    -
    4. -

  4. with params min_spseq_size==4, min_snseq_size==4

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [1, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 1, 1]
-I: [1--1--1--1--1--1--1, 0--0--0--0, 1--1--1--1--1--1--1--1--1]
-
    -
    -

    Explanation: Since smoothing of snseqs is prioritized, short spseqs -at the beginning or the end can be kept.

    -
    -
    5. -

  5. with params min_spseq_size==1, min_snseq_size==1

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 1, 1]
-I: [0--0--0, 1--1--1--1, 0--0--0--0, 1--1--1--1, 0--0--0, 1--1]
-
    -
    -

    Explanation: When both width thresholds are set to 1, the algorithm -works essentially in the “stitching” only mode.

    -
    -
    6. -
-
-
Parameters:
-
    -

  • scores – SORTED list of scores to be smoothed. The score list -is assumed to be “exhaust” the entire time or space of -the underlying document segment. -(Sorted by the start, and then by the end of anchors)

    • -

  • min_score – minimum threshold to use to discard -low-scored units (strictly less than)

    • -

  • min_spseq_size – minimum size of a positive sequence not to be -smoothed (greater or equal to)

    • -

  • min_snseq_size – minimum size of a negative sequence not to be -smoothed (greater or equal to)

    • -
-
-
Returns:
-

list of tuples of start(inclusive)/end(exclusive) indices -of the “positive” sequences. Negative sequences (regardless of -their size) are not included in the output.

-
-
-
- -
-
-mmif.utils.sequence_helper.validate_labelset(annotations: Iterable[Annotation]) → List[str][source]
-

Simple check for a list of annotations to see if they have the same label set.

-
-
Raise:
-

AttributeError if an element in the input list doesn’t have the labelset property

-
-
Raise:
-

ValueError if different labelset values are found

-
-
Returns:
-

a list of the common labelset value (list of label names)

-
-
-
- -
-
-

sequence_helper module

-

This module provides helpers for handling sequence labeling. Specifically, it provides

-
    -

  • a generalized label re-mapper for “post-binning” of labels

    • -

  • conversion from a list of CLAMS annotations (with classification props) into a list of reals (scores by labels), can be combined with the label re-mapper mentioned above

    • -

  • mmif.utils.sequence_helper.smooth_outlying_short_intervals(): a simple smoothing algorithm by trimming “short” outlier sequences

    • -
-

However, it DOES NOT provide

-
    -

  • direct conversion between CLAMS annotations. For example, it does not directly handle stitching of TimePoint into TimeFrames.

    • -

  • support for multi-class scenario, such as handling of _competing_ subsequence or overlapping labels.

    • -
-

Some functions can use optional external libraries (e.g., numpy) for better performance. -Hence, if you see a warning about missing optional packages, you might want to install them by running pip install mmif-python[seq].

-
-
-mmif.utils.sequence_helper.build_label_remapper(src_labels: List[str], dst_labels: Dict[str, str | int | float | bool | None]) → Dict[str, str | int | float | bool | None][source]
-

Build a label remapper dictionary from source and destination labels.

-
-
Parameters:
-
    -

  • src_labels – a list of all labels on the source side

    • -

  • dst_labels – a dict from source labels to destination labels. -Source labels not in this dict will be remapped to a negative label (-).

    • -
-
-
Returns:
-

a dict that exhaustively maps source labels to destination labels

-
-
-
- -
-
-mmif.utils.sequence_helper.build_score_lists(classifications: ~typing.List[~typing.Dict], label_remapper: ~typing.Dict, score_remap_op: ~typing.Callable[[...], float] = <built-in function max>) → Tuple[Dict[str, int], numpy.ndarray][source]
-

Build lists of scores indexed by the label names.

-
-
Parameters:
-
    -

  • classifications – list of dictionaries of classification results, taken from input annotation objects

    • -

  • label_remapper – a dictionary that maps source label names to destination label names (formerly “postbin”)

    • -

  • score_remap_op – a function to remap the scores from multiple source labels binned to a destination label -common choices are max, min, or sum

    • -
-
-
Returns:
-

    -

  1. a dictionary that maps label names to their index in the score list

    2. -

  2. 2-d numpy array of scores, of which rows are indexed by label map dict (first return value)

    3. -
-

-
-
-
- -
-
-mmif.utils.sequence_helper.smooth_outlying_short_intervals(scores: List[float], min_spseq_size: int, min_snseq_size: int, min_score: float = 0.5)[source]
-

Given a list of scores, a score threshold, and smoothing parameters, -identify the intervals of “positive” scores by “trimming” the short -positive sequences (“spseq”) and short negative sequences (“snseq”). To -decide the positivity, first step is binarization of the scores by the -min_score threshold. Given Sr as “raw” input real-number scores -list, and min_score=0.5,

-
-
Sr: [0.3, 0.6, 0.2, 0.8, 0.2, 0.9, 0.8, 0.5, 0.1, 0.5, 0.8, 0.3, 1.0, 0.7, 0.5, 0.5, 0.5, 0.8, 0.3, 0.6]
-
-
-
-

the binarization is done by simply comparing each score to the -threshold to get S list of binary scores

-
-
1.0 :                                     |                      
-0.9 :                |                    |                      
-0.8 :          |     |  |           |     |              |       
-0.7 :          |     |  |           |     |  |           |       
-0.6 :    |     |     |  |           |     |  |           |     | 
-0.5 :----+-----+-----+--+--+-----+--+-----+--+--+--+--+--+-----+-
-0.4 :    |     |     |  |  |     |  |     |  |  |  |  |  |     | 
-0.3 : |  |     |     |  |  |     |  |  |  |  |  |  |  |  |  |  | 
-0.2 : |  |  |  |  |  |  |  |     |  |  |  |  |  |  |  |  |  |  | 
-0.1 : |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | 
-0.0 +------------------------------------------------------------
-raw :.3 .6 .2 .8 .2 .9 .8 .5 .1 .5 .8 .3 1. .7 .5 .5 .5 .8 .3 .6
- S  : 0  1  0  1  0  1  1  0  0  0  1  0  1  1  0  1  1  1  0  1 
-
-
-
-

Note that the size of a positive or negative sequence can be as small -as 1.

-

Then, here are examples of smoothing a list of binary scores into -intervals, by trimming “very short” (under thresholds) sequences of -positive or negative:

-
-

Note

-

legends:

-
    -

  • t is unit index (e.g. time index)

    • -

  • S is the list of binary scores (zeros and ones)

    • -

  • I is the list of intervals after smoothing

    • -
-
-
    -

  1. with params min_spseq_size==1, min_snseq_size==4

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1]
-I: [0, 1--1--1--1--1--1--1--1--1--1--1--1, 0--0--0--0--0--0, 1]
-
    -
    -

    Explanation: min_snseq_size is used to smooth short sequences -of negative predictions. In this, zeros from t[7:10] are smoothed -into “one” I, while zeros from t[13:19] are kept as “zero” I. Note -that the “short” snseqs at the either ends (t[0:1]) are never -smoothed.

    -
    -
    2. -

  2. with params min_spseq_size==4, min_snseq_size==2

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1]
-I: [0, 1--1--1--1--1--1, 0--0--0--0--0--0--0--0--0--0--0--0--0]
-
    -
    -

    Explanation: min_spseq_size is used to smooth short sequences -of positive predictions. In this example, the spseqs of ones from -both t[10:13] and t[19:20] are smoothed. Note that the “short” -spseqs at the either ends (t[19:20]) are always smoothed.

    -
    -
    3. -

  3. with params min_spseq_size==4, min_snseq_size==4

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1]
-I: [0, 1--1--1--1--1--1--1--1--1--1--1--1--0--0--0--0--0--0--0]
-
    -
    -

    Explanation: When two threshold parameters are working together, -the algorithm will prioritize the smoothing of the snseqs over the -smoothing of the spseqs. Thus, in this example, the snseq t[7:10] -gets first smoothed “up” before the spseq t[10:13] is smoothed -“down”, resulting in a long final I.

    -
    -
    4. -

  4. with params min_spseq_size==4, min_snseq_size==4

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [1, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 1, 1]
-I: [1--1--1--1--1--1--1, 0--0--0--0, 1--1--1--1--1--1--1--1--1]
-
    -
    -

    Explanation: Since smoothing of snseqs is prioritized, short spseqs -at the beginning or the end can be kept.

    -
    -
    5. -

  5. with params min_spseq_size==1, min_snseq_size==1

    -
    -
    t: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
-S: [0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 1, 1]
-I: [0--0--0, 1--1--1--1, 0--0--0--0, 1--1--1--1, 0--0--0, 1--1]
-
    -
    -

    Explanation: When both width thresholds are set to 1, the algorithm -works essentially in the “stitching” only mode.

    -
    -
    6. -
-
-
Parameters:
-
    -

  • scores – SORTED list of scores to be smoothed. The score list -is assumed to be “exhaust” the entire time or space of -the underlying document segment. -(Sorted by the start, and then by the end of anchors)

    • -

  • min_score – minimum threshold to use to discard -low-scored units (strictly less than)

    • -

  • min_spseq_size – minimum size of a positive sequence not to be -smoothed (greater or equal to)

    • -

  • min_snseq_size – minimum size of a negative sequence not to be -smoothed (greater or equal to)

    • -
-
-
Returns:
-

list of tuples of start(inclusive)/end(exclusive) indices -of the “positive” sequences. Negative sequences (regardless of -their size) are not included in the output.

-
-
-
- -
-
-mmif.utils.sequence_helper.validate_labelset(annotations: Iterable[Annotation]) → List[str][source]
-

Simple check for a list of annotations to see if they have the same label set.

-
-
Raise:
-

AttributeError if an element in the input list doesn’t have the labelset property

-
-
Raise:
-

ValueError if different labelset values are found

-
-
Returns:
-

a list of the common labelset value (list of label names)

-
-
-
- -
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 1.0.19 - - -
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- - -
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mmif.vocabulary module

-

Module contains Enum-like classes for CLAMS vocabulary.

-
-
-mmif.vocabulary.ThingTypesBase[source]
-

alias of TypesBase

-
- -
-
-class mmif.vocabulary.ThingType(type_uri: str)[source]
-

Bases: TypesBase

-

This class contains the topmost CLAMS thing type -defined in the spec version 1.1.0 as a class variable.

-
-
-Thing = http://mmif.clams.ai/vocabulary/Thing/v1[source]
-
- -
- -
-
-class mmif.vocabulary.ClamsTypesBase(type_uri, fuzzymode=True)[source]
-

Bases: TypesBase

-

Base class for CLAMS vocabulary types. Main -This class adds handling of MMIF specification versions -in initializer and comparators.

-
- -
-
-class mmif.vocabulary.AnnotationTypesBase(type_uri, fuzzymode=True)[source]
-

Bases: ClamsTypesBase

-

Inherit from this class to build your own custom annotation -vocabularies.

-
- -
-
-class mmif.vocabulary.DocumentTypesBase(type_uri, fuzzymode=True)[source]
-

Bases: ClamsTypesBase

-

Inherit from this class to build your own custom document -vocabularies.

-
- -
-
-class mmif.vocabulary.AnnotationTypes(type_uri, fuzzymode=True)[source]
-

Bases: AnnotationTypesBase

-

This class contains the CLAMS annotation types -defined in the spec version 1.1.0 as class variables.

-
-
-Alignment = http://mmif.clams.ai/vocabulary/Alignment/v1[source]
-
- -
-
-Annotation = http://mmif.clams.ai/vocabulary/Annotation/v6[source]
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- -
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-BoundingBox = http://mmif.clams.ai/vocabulary/BoundingBox/v5[source]
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- -
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-Chapter = http://mmif.clams.ai/vocabulary/Chapter/v6[source]
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- -
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-Interval = http://mmif.clams.ai/vocabulary/Interval/v5[source]
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- -
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-NamedEntity = http://mmif.clams.ai/vocabulary/NamedEntity/v1[source]
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- -
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-NounChunk = http://mmif.clams.ai/vocabulary/NounChunk/v1[source]
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- -
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-Paragraph = http://mmif.clams.ai/vocabulary/Paragraph/v1[source]
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-Polygon = http://mmif.clams.ai/vocabulary/Polygon/v5[source]
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-Region = http://mmif.clams.ai/vocabulary/Region/v5[source]
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- -
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-Relation = http://mmif.clams.ai/vocabulary/Relation/v5[source]
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- -
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-Sentence = http://mmif.clams.ai/vocabulary/Sentence/v1[source]
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-Span = http://mmif.clams.ai/vocabulary/Span/v5[source]
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-TimeFrame = http://mmif.clams.ai/vocabulary/TimeFrame/v6[source]
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-TimePoint = http://mmif.clams.ai/vocabulary/TimePoint/v5[source]
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-Token = http://mmif.clams.ai/vocabulary/Token/v1[source]
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-VerbChunk = http://mmif.clams.ai/vocabulary/VerbChunk/v1[source]
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- -
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-VideoObject = http://mmif.clams.ai/vocabulary/VideoObject/v5[source]
-
- -
- -
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-class mmif.vocabulary.DocumentTypes(type_uri, fuzzymode=True)[source]
-

Bases: DocumentTypesBase

-

This class contains the CLAMS document types -defined in the spec version 1.1.0 as class variables.

-
-
-AudioDocument = http://mmif.clams.ai/vocabulary/AudioDocument/v1[source]
-
- -
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-Document = http://mmif.clams.ai/vocabulary/Document/v1[source]
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- -
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-ImageDocument = http://mmif.clams.ai/vocabulary/ImageDocument/v1[source]
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-TextDocument = http://mmif.clams.ai/vocabulary/TextDocument/v1[source]
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-VideoDocument = http://mmif.clams.ai/vocabulary/VideoDocument/v1[source]
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- - - \ No newline at end of file diff --git a/docs/1.0.19/autodoc/mmif_docloc_http.html b/docs/1.0.19/autodoc/mmif_docloc_http.html deleted file mode 100644 index 4ba13e89..00000000 --- a/docs/1.0.19/autodoc/mmif_docloc_http.html +++ /dev/null @@ -1,185 +0,0 @@ - - - - - - - - - mmif_docloc_http package — mmif-python documentation - - - - - - - - - - - - - - - - -
- - -
- -
-
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- -
-
-
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- -
-

mmif_docloc_http package

-

MMIF document location helper module for http and https schemes. -If you want to write your own docloc scheme handler, please use the source code of this module as a reference. -See this plug-in section for more information.

-
-
-mmif_docloc_http.help()[source]
-
- -
-
-mmif_docloc_http.resolve(docloc)[source]
-
- -
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- - Other Versions - v: 1.0.19 - - -
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- - - \ No newline at end of file diff --git a/docs/1.0.19/consumer-tutorial.html b/docs/1.0.19/consumer-tutorial.html deleted file mode 100644 index 53f74b92..00000000 --- a/docs/1.0.19/consumer-tutorial.html +++ /dev/null @@ -1,172 +0,0 @@ - - - - - - - - - MMIF consumer — mmif-python documentation - - - - - - - - - - - - - - - -
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  • MMIF consumer
    • -
  • -
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MMIF consumer

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A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the appliance documentation to learn more about the appliance.

-

MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance.

-
    -

  1. The code must be hosted on a public git repository (e.g. Github, Gitlab, …)

    2. -

  2. Must listen to 5000 port.

    3. -

  3. Must expose /display route .

    4. -

  4. /display router should response to GET requests.

    5. -

  5. In the GET request, a public URL of the input MMIF file is passed via file URL parameter.

    6. -

  6. On the codebase root, there must be a Dockerfile that can build a docker image that runs the web app.

    7. -
-

We provide an example consumer at https://github.com/clamsproject/mmif-visualizer.

-
- - -
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- -
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- - Other Versions - v: 1.0.19 - - -
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  • Index
    • -
  • -
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Index

- -
- A - | B - | C - | D - | E - | F - | G - | H - | I - | K - | L - | M - | N - | P - | R - | S - | T - | U - | V - -
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A

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B

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D

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E

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- - -
- -
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    • -
  • Welcome to mmif-python’s documentation!
    • -
  • -
    • -
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- -
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Welcome to mmif-python’s documentation!

-
-

MultiMedia Interchange Format

-

MMIF is a JSON(-LD)-based data format designed for transferring annotation data between computational analysis applications in CLAMS project.

-
-
-

mmif-python

-

mmif-python is a Python implementation of the MMIF data format. -mmif-python provides various helper classes and functions to handle MMIF JSON in Python, -including ;

-
    -

  1. de-/serialization of MMIF internal data structures to/from JSON

    2. -

  2. validation of MMIF JSON

    3. -

  3. handling of CLAMS vocabulary types

    4. -

  4. navigation of MMIF object via various “search” methods (e.g. mmif.get_all_views_contain(vocab_type)))

    5. -
-
-
-

For more …

- -
-

Contents

- -
-
-

API documentation:

- -
-
-
-
-

Indices and tables

- -
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  • Getting Started
    • -
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Getting Started

-
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Overview

-

MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for reproducibility, transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF website. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects.

-
-
-

Prerequisites

-
    -

  • Python: the latest mmif-python requires Python 3.8 or newer. We have no plan to support Python 2.7.

    • -
-
-
-

Installation

-

Package mmif-python is distributed via the official PyPI. Users are supposed to pip-install to get latest release.

-
pip install mmif-python
-
-
-

This will install a package mmif to local python.

-

The MMIF format and specification is evolving over time, and mmif-python package will be updated along with the changes in MMIF format.

-
-

Note

-

MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and mmif-python versions, please take time to read our decision on the subject here. If you need to know which python SDK supports which specification version, see Target MMIF Versions page.

-
-
-
-

MMIF Serialization

-

mmif.serialize.mmif.Mmif represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of mmif.serialize.model.MmifObject, including the mmif.serialize.mmif.Mmif. To start with an existing MMIF str, simple initiate a new Mmif object with the file.

-
import mmif
-from mmif import Mmif
-
-mmif_str = """{
-"metadata": {
-  "mmif": "http://mmif.clams.ai/1.0.0"
-},
-"documents": [
-  {
-    "@type": "http://mmif.clams.ai/vocabulary/VideoDocument/v1",
-    "properties": {
-      "id": "m1",
-      "mime": "video/mp4",
-      "location": "file:///var/archive/video-0012.mp4"
-    }
-  },
-  {
-    "@type": "http://mmif.clams.ai/vocabulary/TextDocument/v1",
-    "properties": {
-      "id": "m2",
-      "mime": "text/plain",
-      "location": "file:///var/archive/video-0012-transcript.txt"
-    }
-  }
-],
-"views": []}"""
-mmif_obj = Mmif(mmif_str)
-
-
-

Few notes;

-
    -

  1. MMIF does not carry the primary source files in it.

    2. -

  2. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version mmif-python implementation of the MMIF might not be able to load an unsupported version of MMIF string.

    3. -
-

When serializing back to str, call mmif.serialize.model.MmifObject.serialize() on the object.

-

To get subcomponents, you can use various getters implemented in subclasses. For example;

-
from mmif.vocabulary.document_types import DocumentTypes
-
-for video in mmif_obj.Mmif.get_documents_by_type(DocumentTypes.VideoDocument):
-  with open(video.location_path(), 'b') as in_video:
-    # do something with the video file
-
-
-

For a full list of available helper methods, please refer to the API documentation.

-
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mmif package

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mmif_docloc_http package

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- - - \ No newline at end of file diff --git a/docs/1.0.19/objects.inv b/docs/1.0.19/objects.inv deleted file mode 100644 index 7157fff9..00000000 Binary files a/docs/1.0.19/objects.inv and /dev/null differ diff --git a/docs/1.0.19/plugins.html b/docs/1.0.19/plugins.html deleted file mode 100644 index 62ea9651..00000000 --- a/docs/1.0.19/plugins.html +++ /dev/null @@ -1,238 +0,0 @@ - - - - - - - - - Developing plugins for MMIF Python SDK — mmif-python documentation - - - - - - - - - - - - - - - - - -
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  • Developing plugins for MMIF Python SDK
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Developing plugins for MMIF Python SDK

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Overview

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As MMIF JSON files can carry information about media document files without actually carrying file contents, file accessing modules in mmif Python package (distributed as mmif-python on PyPI) are designed to be lightweight and flexible so that it can work with additional “plugin” Python packages that can handle concrete file access.

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This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF website. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects.

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Developer can write simple plugins that can provide additional functionalities to mmif-python. For example, mmif-python does not provide any file access functionality beyond a local file system (with file scheme), but it can be extended with a plugin that can handle file access over different protocols (e.g. http, s3, ftp, etc).

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This document contains information about how to write plugins for mmif-python.

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Document Location Scheme Plugins

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mmif.serialize.annotation.Document class has various methods to access parts of location property of the document. The location is in URI/IRI format (SCHEME://HOSTNAME/PATH, in a nutshell) and it has to be resolved to a local file for CLAMS Apps to process the local file to analyze and extract information about the media and its contents. The core mmif-python distribution only provides a default implementation that can handle file scheme URIs.

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To add a document location handler plugin, you need to implement a Python “package” (do not confuse with PYPI distribution), that meets these requirements;

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  1. the package must be named mmif_docloc_<SCHEME>. For example, to implement a handler for s3 scheme, the package name must be mmif_docloc_s3. The prefix is important as it’s used in the plugin discovery process from the core mmif-python modules.

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  2. the top module of the package must have a function named resolve. The function must take a single argument, which is a str of the document location URI. The function must return a str of the local file path. For example, if the document location is s3://mybucket/myfile.mp4, a Python user should be able to to something like this;

    3. -

  3. Optionally (but highly recommended), the top module also can provide another function named help. The function must take no arguments and return a str that explains how the input string to the resolve function should be formatted.

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import mmif_docloc_s3
-resolved = mmif_docloc_s3.resolve('s3://mybucket/myfile.mp4')
-# then resolved must be a local file path that can be used to open the file
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Here’s a minimal example codebase that you refer to when you develop a docloc plugin.

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(However, before you start writing your own plugin for a specific URI scheme, checking if there’s already a PyPI distribution for the scheme might be a good idea.)

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$ tree .
-.
-├── mmif_docloc_dummy
-│   └── __init__.py
-├── pyproject.toml
-└── setup.cfg
-
- $ cat pyproject.toml
-[build-system]
-requires = ["setuptools"]
-build-backend = "setuptools.build_meta"
-
-$ cat setup.cfg
-[metadata]
-name = mmif_docloc_dummy  # this name is IMPORTANT
-version = 0.0.1
-description = a plugin to mmif-pyhon to handle `dummy` location scheme
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And the plugin code.

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# mmif_docloc_dummy/__init__.py
-doc_types = {'video': 'mp4'}
-
-def resolve(docloc):
-    scheme = 'dummy'
-    if docloc.startswith(f'{scheme}://'):
-        doc_id, doc_type = docloc.split('.')
-        return f'/path/to/{doc_id}.{doc_types[doc_type]}'
-    else:
-        raise ValueError(f'cannot handle document location scheme: {docloc}')
-
-def help():
-    return "location format: `<DOCUMENT_ID>.video`"
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Bulit-in Document Location Scheme Plugins

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At the moment, mmif-python PyPI distribution ships a built-in docloc plugin that support both http and https schemes. -Take a look at mmif_docloc_http module for details.

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- - - - - - - - \ No newline at end of file diff --git a/docs/1.0.19/searchindex.js b/docs/1.0.19/searchindex.js deleted file mode 100644 index ce45dbe0..00000000 --- a/docs/1.0.19/searchindex.js +++ /dev/null @@ -1 +0,0 @@ -Search.setIndex({"alltitles": {"API documentation:": [[5, null]], "Bulit-in Document Location Scheme Plugins": [[8, "bulit-in-document-location-scheme-plugins"]], "Contents": [[5, null]], "Developing plugins for MMIF Python SDK": [[8, null]], "Document Location Scheme Plugins": [[8, "document-location-scheme-plugins"]], "For more \u2026": [[5, "for-more"]], "Getting Started": [[6, null]], "Indices and tables": [[5, "indices-and-tables"]], "Installation": [[6, "installation"]], "MMIF Serialization": [[6, "mmif-serialization"]], "MMIF consumer": [[4, null]], "MultiMedia Interchange Format": [[5, "multimedia-interchange-format"]], "Overview": [[6, "overview"], [8, "overview"]], "Prerequisites": [[6, "prerequisites"]], "Target MMIF Versions": [[9, null]], "Target 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package", "MMIF consumer", "Welcome to mmif-python\u2019s documentation!", "Getting Started", "mmif package", "Developing plugins for MMIF Python SDK", "Target MMIF Versions"], "titleterms": {"": 5, "For": 5, "annot": 0, "api": 5, "bulit": 8, "consum": 4, "content": 5, "develop": 8, "document": [5, 8], "format": 5, "get": 6, "indic": 5, "instal": 6, "interchang": 5, "locat": 8, "mmif": [0, 1, 2, 4, 5, 6, 7, 8, 9], "mmif_docloc_http": [3, 7], "model": 0, "modul": [0, 1, 2], "more": 5, "multimedia": 5, "overview": [6, 8], "packag": [0, 1, 3, 7], "plugin": 8, "prerequisit": 6, "python": [5, 8], "scheme": 8, "sdk": 8, "sequence_help": 1, "serial": [0, 6], "specif": 9, "start": 6, "tabl": 5, "target": 9, "text_document_help": 1, "util": 1, "version": 9, "video_document_help": 1, "view": 0, "vocabulari": 2, "welcom": 5}}) \ No newline at end of file diff --git a/docs/1.0.19/target-versions.html b/docs/1.0.19/target-versions.html deleted file mode 100644 index e5577635..00000000 --- a/docs/1.0.19/target-versions.html +++ /dev/null @@ -1,300 +0,0 @@ - - - - - - - - - Target MMIF Versions — mmif-python documentation - - - - - - - - - - - - - - - - - -
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Target MMIF Versions

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This article provides targeting MMIF specification versions of different versions of mmif-python SDK.

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Target Specification Versions

mmif-python version

Target MMIF Specification

1.0.19

1.1.0

1.0.18

1.0.5

1.0.17

1.0.5

1.0.16

1.0.4

1.0.15

1.0.4

1.0.14

1.0.4

1.0.13

1.0.4

1.0.12

1.0.4

1.0.11

1.0.4

1.0.10

1.0.2

1.0.9

1.1.0

1.0.8

1.0.0

1.0.7

1.0.0

1.0.6

1.0.0

1.0.5

1.0.0

1.0.4

1.0.0

1.0.3

1.0.0

1.0.2

1.0.0

1.0.1

1.0.0

1.0.0

0.5.0

0.5.2

0.5.0

0.5.1

0.5.0

0.5.0

0.5.0

0.4.8

0.4.2

0.4.7

0.4.1

0.4.6

0.4.0

0.4.5

0.4.0

0.4.4

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The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the `appliance documentation `_ to learn more about the appliance. - -MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance. - -#. The code must be hosted on a public git repository (e.g. Github, Gitlab, ...) -#. Must listen to ``5000`` port. -#. Must expose ``/display`` route . -#. ``/display`` router should response to ``GET`` requests. -#. In the ``GET`` request, a public URL of the input MMIF file is passed via ``file`` URL parameter. -#. On the codebase root, there must be a ``Dockerfile`` that can build a `docker `_ image that runs the web app. - -We provide an example consumer at https://github.com/clamsproject/mmif-visualizer. diff --git a/docs/1.0.2/_sources/index.rst.txt b/docs/1.0.2/_sources/index.rst.txt deleted file mode 100644 index beb56aae..00000000 --- a/docs/1.0.2/_sources/index.rst.txt +++ /dev/null @@ -1,26 +0,0 @@ -Welcome to mmif-python's documentation! -======================================= - -.. mdinclude:: ../README.md - -.. toctree:: - :maxdepth: 2 - :caption: Contents - - introduction - plugins - target-versions - -.. toctree:: - :maxdepth: 2 - :caption: API documentation: - - modules - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/docs/1.0.2/_sources/introduction.rst.txt b/docs/1.0.2/_sources/introduction.rst.txt deleted file mode 100644 index cfd9eaf7..00000000 --- a/docs/1.0.2/_sources/introduction.rst.txt +++ /dev/null @@ -1,89 +0,0 @@ -.. _introduction: - -Getting Started -=============== - - -Overview ---------- - -MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for reproducibility, transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF website `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects. - -Prerequisites -------------- - -* `Python `_: the latest ``mmif-python`` requires Python 3.8 or newer. We have no plan to support `Python 2.7 `_. - -Installation ---------------- - -Package ``mmif-python`` is distributed via the official PyPI. Users are supposed to pip-install to get latest release. - -.. code-block:: bash - - pip install mmif-python - -This will install a package `mmif` to local python. - -The MMIF format and specification is evolving over time, and ``mmif-python`` package will be updated along with the changes in MMIF format. - -.. note:: MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and ``mmif-python`` versions, please take time to read our decision on the subject `here `_. If you need to know which python SDK supports which specification version, see :ref:`target-versions` page. - -MMIF Serialization ---------------------------- - -:class:`mmif.serialize.mmif.Mmif` represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of :class:`mmif.serialize.model.MmifObject`, including the :class:`mmif.serialize.mmif.Mmif`. To start with an existing MMIF :class:`str`, simple initiate a new ``Mmif`` object with the file. - -.. code-block:: python - - import mmif - from mmif import Mmif - - mmif_str = """{ - "metadata": { - "mmif": "http://mmif.clams.ai/1.0.0" - }, - "documents": [ - { - "@type": "http://mmif.clams.ai/vocabulary/VideoDocument/v1", - "properties": { - "id": "m1", - "mime": "video/mp4", - "location": "file:///var/archive/video-0012.mp4" - } - }, - { - "@type": "http://mmif.clams.ai/vocabulary/TextDocument/v1", - "properties": { - "id": "m2", - "mime": "text/plain", - "location": "file:///var/archive/video-0012-transcript.txt" - } - } - ], - "views": []}""" - mmif_obj = Mmif(mmif_str) - - -Few notes; - -#. MMIF does not carry the primary source files in it. -#. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version ``mmif-python`` implementation of the MMIF might not be able to load an unsupported version of MMIF string. - -When serializing back to :class:`str`, call :meth:`mmif.serialize.model.MmifObject.serialize` on the object. - -To get subcomponents, you can use various getters implemented in subclasses. For example; - -.. code-block:: python - - from mmif.vocabulary.document_types import DocumentTypes - - for video in mmif_obj.Mmif.get_documents_by_type(DocumentTypes.VideoDocument): - with open(video.location_path(), 'b') as in_video: - # do something with the video file - - -For a full list of available helper methods, please refer to :ref:`the API documentation `. - diff --git a/docs/1.0.2/_sources/modules.rst.txt b/docs/1.0.2/_sources/modules.rst.txt deleted file mode 100644 index e4269c6d..00000000 --- a/docs/1.0.2/_sources/modules.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _apidoc: - -mmif package -============ - -.. toctree:: - :maxdepth: 4 - - autodoc/mmif.serialize - autodoc/mmif.vocabulary diff --git a/docs/1.0.2/_sources/plugins.rst.txt b/docs/1.0.2/_sources/plugins.rst.txt deleted file mode 100644 index ae33a40e..00000000 --- a/docs/1.0.2/_sources/plugins.rst.txt +++ /dev/null @@ -1,122 +0,0 @@ -.. _plugins: - -Developing plugins for MMIF Python SDK -====================================== - - -Overview --------- - -As MMIF JSON files can carry information about media document files without actually carrying file contents, file accessing modules in ``mmif`` Python package (distributed as ``mmif-python`` on PyPI) are designed to be lightweight and flexible so that it can work with additional "plugin" Python packages that can handle concrete file access. - - -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF website `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects. - -Developer can write simple plugins that can provide additional functionalities to ``mmif-python``. For example, ``mmif-python`` does not provide any file access functionality beyond a local file system (with ``file`` scheme), but it can be extended with a plugin that can handle file access over different protocols (e.g. ``http``, ``s3``, ``ftp``, etc). - -This document contains information about how to write plugins for ``mmif-python``. - -Document Location Scheme Plugins -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -:class:`mmif.serialize.annotation.Document` class has various methods to access parts of ``location`` property of the document. The location is in `URI/IRI format `_ (``SCHEME://HOSTNAME/PATH``, in a nutshell) and it has to be resolved to a local file for CLAMS Apps to process the local file to analyze and extract information about the media and its contents. The core ``mmif-python`` distribution only provides a default implementation that can handle ``file`` scheme URIs. - -To add a document location handler plugin, you need to implement a Python `"package" `_ (do not confuse with PYPI distribution), that meets these requirements; - -#. the package must be named ``mmif_docloc_``. For example, to implement a handler for ``s3`` scheme, the package name must be ``mmif_docloc_s3``. The prefix is important as it's used in the plugin discovery process from the core ``mmif-python`` modules. -#. the top module of the package must have a function named ``resolve``. The function must take a single argument, which is a :class:`str` of the document location URI. The function must return a :class:`str` of the local file path. For example, if the document location is ``s3://mybucket/myfile.mp4``, a Python user should be able to to something like this; - -.. code-block:: python - - import mmif_docloc_s3 - resolved = mmif_docloc_s3.resolve('s3://mybucket/myfile.mp4') - # then resolved must be a local file path that can be used to open the file - - -Here's a minimal example codebase that you refer to when you develop a ``docloc`` plugin. - -(However, before you start writing your own plugin for a specific URI scheme, checking `if there's already a PyPI distribution `_ for the scheme might be a good idea.) - -.. code-block:: sh - - $ tree . - . - ├── mmif_docloc_dummy - │ └── __init__.py - ├── pyproject.toml - └── setup.cfg - - $ cat pyproject.toml - [build-system] - requires = ["setuptools"] - build-backend = "setuptools.build_meta" - - $ cat setup.cfg - [metadata] - name = mmif_docloc_dummy # this name is IMPORTANT - version = 0.0.1 - description = a plugin to mmif-pyhon to handle `dummy` location scheme - - -And the plugin code. - -.. code-block:: python - - # mmif_docloc_dummy/__init__.py - doc_types = {'video': 'mp4'} - - def resolve(docloc): - scheme = 'dummy' - if docloc.startswith(f'{scheme}://'): - doc_id, doc_type = docloc.split('.') - return f'/path/to/{doc_id}.{doc_types[doc_type]}' - else: - raise ValueError(f'cannot handle document location scheme: {docloc}') - -Utility Plugins -^^^^^^^^^^^^^^^ - -.. warning:: - - This feature is experimental and subject to change in the future. - See `this issue `_ for limitations and known issues. - -Utility plugins, or ``mmif-utils-`` plugins are used to provide monkeypatch functions to ``mmif-python``. -Currently :class:`mmif.serialize.model.MmifObject` and its subclasses are the only classes that are under the scope of monkeypatching supported by the `mmif-python` core SDK. -(Of course any Python developer can come up with other ways to custom patch any parts of the SDK, it's just not supported by the method described here.) - -For writing pluggable monkeypatches for MMIF serialization classes, you need to implement a Python `"package" `_ (do not confuse with PYPI distribution), that meets these requirements; - -#. the package must be named ``mmif_utils_``. The prefix is important as it's used in the plugin discovery process from the core ``mmif-python`` modules. ```` can be any string, but it's recommended to use a name that describes the functionality of the plugin. -#. the top module of the package must have a dictionary named ``patches``. - #. The dictionary must be keyed with each class that you want to monkeypatch. The value of the key must be an iterable of functions that will be monkeypatched to the class. - #. The function must be a callable, and it must take the class instance as the first argument, so that when monkeypatched to a class, it can be called as a method of the class instance. - -Here's a minimal example code snippet of a ``mmif-utils-`` plugin. - -.. code-block:: python - - import cv2 - from mmif.serialize import Mmif - from mmif.vocabulary import AnnotationTypes, DocumentTypes - - - def get_framerate(mmif: Mmif, video_doc_id: str): # first argument must be the class instance - video_doc = mmif.get_document_by_id(video_doc_id) - if video_doc is None or video_doc.at_type != DocumentTypes.VideoDocument: - raise ValueError(f'Video document with id "{video_doc_id}" does not exist.') - for v in mmif.get_views_for_document(video_doc_id): - for a in v.get_annotations(AnnotationTypes.Annotation): - framerate_keys = ('fps', 'framerate') - for k, v in a.properties.items(): - if k.lower() in framerate_keys: - return v - cap = cv2.VideoCapture(video_doc.location_path()) - return cap.get(cv2.CAP_PROP_FPS) - - patches = {Mmif: [get_framerate]} # all callables in the list must have `Mmif` instance as the first argument - -Then when this code is loaded as a ``mmif-utils-`` plugin, the ``get_framerate`` function will be monkeypatched to the :class:`mmif.serialize.mmif.Mmif` class, and it can be called as a method of the class instance. -NOTE that a monkeypatch will "overwrite" the original method of the class, so it's important to make sure that the monkeypatched method has the same signature as the original method. -Also if there's no original method, the method from a plugin will be simply added to the class, not altering any existing code. diff --git a/docs/1.0.2/_sources/target-versions.rst.txt b/docs/1.0.2/_sources/target-versions.rst.txt deleted file mode 100644 index 34216d3e..00000000 --- a/docs/1.0.2/_sources/target-versions.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _target-versions: - -Target MMIF Versions -==================== - -This article provides targeting MMIF specification versions of different versions of ``mmif-python`` SDK. - -.. csv-table:: Target Specification Versions - :file: target-versions.csv - :header-rows: 1 diff --git a/docs/1.0.2/_static/_sphinx_javascript_frameworks_compat.js b/docs/1.0.2/_static/_sphinx_javascript_frameworks_compat.js deleted file mode 100644 index 81415803..00000000 --- a/docs/1.0.2/_static/_sphinx_javascript_frameworks_compat.js +++ /dev/null @@ -1,123 +0,0 @@ -/* Compatability shim for jQuery and underscores.js. - * - * Copyright Sphinx contributors - * Released under the two clause BSD licence - */ - -/** - * small helper function to urldecode strings - * - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL - */ -jQuery.urldecode = function(x) { - if (!x) { - return x - } - return decodeURIComponent(x.replace(/\+/g, ' ')); -}; - -/** - * small helper function to urlencode strings - */ -jQuery.urlencode = encodeURIComponent; - -/** - * This function returns the parsed url parameters of the - * current request. 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- -/** - * Simple result scoring code. - */ -if (typeof Scorer === "undefined") { - var Scorer = { - // Implement the following function to further tweak the score for each result - // The function takes a result array [docname, title, anchor, descr, score, filename] - // and returns the new score. - /* - score: result => { - const [docname, title, anchor, descr, score, filename, kind] = result - return score - }, - */ - - // query matches the full name of an object - objNameMatch: 11, - // or matches in the last dotted part of the object name - objPartialMatch: 6, - // Additive scores depending on the priority of the object - objPrio: { - 0: 15, // used to be importantResults - 1: 5, // used to be objectResults - 2: -5, // used to be unimportantResults - }, - // Used when the priority is not in the mapping. - objPrioDefault: 0, - - // query found in title - title: 15, - partialTitle: 7, - // query found in terms - term: 5, - partialTerm: 2, - }; -} - -// Global search result kind enum, used by themes to style search results. -class SearchResultKind { - static get index() { return "index"; } - static get object() { return "object"; } - static get text() { return "text"; } - static get title() { return "title"; } -} - -const _removeChildren = (element) => { - while (element && element.lastChild) element.removeChild(element.lastChild); -}; - -/** - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping - */ -const _escapeRegExp = (string) => - string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string - -const _displayItem = (item, searchTerms, highlightTerms) => { - const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; - const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; - const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; - const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; - const contentRoot = document.documentElement.dataset.content_root; - - const [docName, title, anchor, descr, score, _filename, kind] = item; - - let listItem = document.createElement("li"); - // Add a class representing the item's type: - // can be used by a theme's CSS selector for styling - // See SearchResultKind for the class names. - listItem.classList.add(`kind-${kind}`); - let requestUrl; - let linkUrl; - if (docBuilder === "dirhtml") { - // dirhtml builder - let dirname = docName + "/"; - if (dirname.match(/\/index\/$/)) - dirname = dirname.substring(0, dirname.length - 6); - else if (dirname === "index/") dirname = ""; - requestUrl = contentRoot + dirname; - linkUrl = requestUrl; - } else { - // normal html builders - requestUrl = contentRoot + docName + docFileSuffix; - linkUrl = docName + docLinkSuffix; - } - let linkEl = listItem.appendChild(document.createElement("a")); - linkEl.href = linkUrl + anchor; - linkEl.dataset.score = score; - linkEl.innerHTML = title; - if (descr) { - listItem.appendChild(document.createElement("span")).innerHTML = - " (" + descr + ")"; - // highlight search terms in the description - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - } - else if (showSearchSummary) - fetch(requestUrl) - .then((responseData) => responseData.text()) - .then((data) => { - if (data) - listItem.appendChild( - Search.makeSearchSummary(data, searchTerms, anchor) - ); - // highlight search terms in the summary - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - }); - Search.output.appendChild(listItem); -}; -const _finishSearch = (resultCount) => { - Search.stopPulse(); - Search.title.innerText = _("Search Results"); - if (!resultCount) - Search.status.innerText = Documentation.gettext( - "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." - ); - else - Search.status.innerText = Documentation.ngettext( - "Search finished, found one page matching the search query.", - "Search finished, found ${resultCount} pages matching the search query.", - resultCount, - ).replace('${resultCount}', resultCount); -}; -const _displayNextItem = ( - results, - resultCount, - searchTerms, - highlightTerms, -) => { - // results left, load the summary and display it - // this is intended to be dynamic (don't sub resultsCount) - if (results.length) { - _displayItem(results.pop(), searchTerms, highlightTerms); - setTimeout( - () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), - 5 - ); - } - // search finished, update title and status message - else _finishSearch(resultCount); -}; -// Helper function used by query() to order search results. -// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. -// Order the results by score (in opposite order of appearance, since the -// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. -const _orderResultsByScoreThenName = (a, b) => { - const leftScore = a[4]; - const rightScore = b[4]; - if (leftScore === rightScore) { - // same score: sort alphabetically - const leftTitle = a[1].toLowerCase(); - const rightTitle = b[1].toLowerCase(); - if (leftTitle === rightTitle) return 0; - return leftTitle > rightTitle ? -1 : 1; // inverted is intentional - } - return leftScore > rightScore ? 1 : -1; -}; - -/** - * Default splitQuery function. Can be overridden in ``sphinx.search`` with a - * custom function per language. - * - * The regular expression works by splitting the string on consecutive characters - * that are not Unicode letters, numbers, underscores, or emoji characters. - * This is the same as ``\W+`` in Python, preserving the surrogate pair area. - */ -if (typeof splitQuery === "undefined") { - var splitQuery = (query) => query - .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) - .filter(term => term) // remove remaining empty strings -} - -/** - * Search Module - */ -const Search = { - _index: null, - _queued_query: null, - _pulse_status: -1, - - htmlToText: (htmlString, anchor) => { - const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - for (const removalQuery of [".headerlink", "script", "style"]) { - htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); - } - if (anchor) { - const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); - if (anchorContent) return anchorContent.textContent; - - console.warn( - `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` - ); - } - - // if anchor not specified or not found, fall back to main content - const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent) return docContent.textContent; - - console.warn( - "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." - ); - return ""; - }, - - init: () => { - const query = new URLSearchParams(window.location.search).get("q"); - document - .querySelectorAll('input[name="q"]') - .forEach((el) => (el.value = query)); - if (query) Search.performSearch(query); - }, - - loadIndex: (url) => - (document.body.appendChild(document.createElement("script")).src = url), - - setIndex: (index) => { - Search._index = index; - if (Search._queued_query !== null) { - const query = Search._queued_query; - Search._queued_query = null; - Search.query(query); - } - }, - - hasIndex: () => Search._index !== null, - - deferQuery: (query) => (Search._queued_query = query), - - stopPulse: () => (Search._pulse_status = -1), - - startPulse: () => { - if (Search._pulse_status >= 0) return; - - const pulse = () => { - Search._pulse_status = (Search._pulse_status + 1) % 4; - Search.dots.innerText = ".".repeat(Search._pulse_status); - if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); - }; - pulse(); - }, - - /** - * perform a search for something (or wait until index is loaded) - */ - performSearch: (query) => { - // create the required interface elements - const searchText = document.createElement("h2"); - searchText.textContent = _("Searching"); - const searchSummary = document.createElement("p"); - searchSummary.classList.add("search-summary"); - searchSummary.innerText = ""; - const searchList = document.createElement("ul"); - searchList.setAttribute("role", "list"); - searchList.classList.add("search"); - - const out = document.getElementById("search-results"); - Search.title = out.appendChild(searchText); - Search.dots = Search.title.appendChild(document.createElement("span")); - Search.status = out.appendChild(searchSummary); - Search.output = out.appendChild(searchList); - - const searchProgress = document.getElementById("search-progress"); - // Some themes don't use the search progress node - if (searchProgress) { - searchProgress.innerText = _("Preparing search..."); - } - Search.startPulse(); - - // index already loaded, the browser was quick! - if (Search.hasIndex()) Search.query(query); - else Search.deferQuery(query); - }, - - _parseQuery: (query) => { - // stem the search terms and add them to the correct list - const stemmer = new Stemmer(); - const searchTerms = new Set(); - const excludedTerms = new Set(); - const highlightTerms = new Set(); - const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); - splitQuery(query.trim()).forEach((queryTerm) => { - const queryTermLower = queryTerm.toLowerCase(); - - // maybe skip this "word" - // stopwords array is from language_data.js - if ( - stopwords.indexOf(queryTermLower) !== -1 || - queryTerm.match(/^\d+$/) - ) - return; - - // stem the word - let word = stemmer.stemWord(queryTermLower); - // select the correct list - if (word[0] === "-") excludedTerms.add(word.substr(1)); - else { - searchTerms.add(word); - highlightTerms.add(queryTermLower); - } - }); - - if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js - localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) - } - - // console.debug("SEARCH: searching for:"); - // console.info("required: ", [...searchTerms]); - // console.info("excluded: ", [...excludedTerms]); - - return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; - }, - - /** - * execute search (requires search index to be loaded) - */ - _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - - // Collect multiple result groups to be sorted separately and then ordered. - // Each is an array of [docname, title, anchor, descr, score, filename, kind]. - const normalResults = []; - const nonMainIndexResults = []; - - _removeChildren(document.getElementById("search-progress")); - - const queryLower = query.toLowerCase().trim(); - for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { - for (const [file, id] of foundTitles) { - const score = Math.round(Scorer.title * queryLower.length / title.length); - const boost = titles[file] === title ? 1 : 0; // add a boost for document titles - normalResults.push([ - docNames[file], - titles[file] !== title ? `${titles[file]} > ${title}` : title, - id !== null ? "#" + id : "", - null, - score + boost, - filenames[file], - SearchResultKind.title, - ]); - } - } - } - - // search for explicit entries in index directives - for (const [entry, foundEntries] of Object.entries(indexEntries)) { - if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id, isMain] of foundEntries) { - const score = Math.round(100 * queryLower.length / entry.length); - const result = [ - docNames[file], - titles[file], - id ? "#" + id : "", - null, - score, - filenames[file], - SearchResultKind.index, - ]; - if (isMain) { - normalResults.push(result); - } else { - nonMainIndexResults.push(result); - } - } - } - } - - // lookup as object - objectTerms.forEach((term) => - normalResults.push(...Search.performObjectSearch(term, objectTerms)) - ); - - // lookup as search terms in fulltext - normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); - - // let the scorer override scores with a custom scoring function - if (Scorer.score) { - normalResults.forEach((item) => (item[4] = Scorer.score(item))); - nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); - } - - // Sort each group of results by score and then alphabetically by name. - normalResults.sort(_orderResultsByScoreThenName); - nonMainIndexResults.sort(_orderResultsByScoreThenName); - - // Combine the result groups in (reverse) order. - // Non-main index entries are typically arbitrary cross-references, - // so display them after other results. - let results = [...nonMainIndexResults, ...normalResults]; - - // remove duplicate search results - // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept - let seen = new Set(); - results = results.reverse().reduce((acc, result) => { - let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); - if (!seen.has(resultStr)) { - acc.push(result); - seen.add(resultStr); - } - return acc; - }, []); - - return results.reverse(); - }, - - query: (query) => { - const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); - const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); - - // for debugging - //Search.lastresults = results.slice(); // a copy - // console.info("search results:", Search.lastresults); - - // print the results - _displayNextItem(results, results.length, searchTerms, highlightTerms); - }, - - /** - * search for object names - */ - performObjectSearch: (object, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const objects = Search._index.objects; - const objNames = Search._index.objnames; - const titles = Search._index.titles; - - const results = []; - - const objectSearchCallback = (prefix, match) => { - const name = match[4] - const fullname = (prefix ? prefix + "." : "") + name; - const fullnameLower = fullname.toLowerCase(); - if (fullnameLower.indexOf(object) < 0) return; - - let score = 0; - const parts = fullnameLower.split("."); - - // check for different match types: exact matches of full name or - // "last name" (i.e. last dotted part) - if (fullnameLower === object || parts.slice(-1)[0] === object) - score += Scorer.objNameMatch; - else if (parts.slice(-1)[0].indexOf(object) > -1) - score += Scorer.objPartialMatch; // matches in last name - - const objName = objNames[match[1]][2]; - const title = titles[match[0]]; - - // If more than one term searched for, we require other words to be - // found in the name/title/description - const otherTerms = new Set(objectTerms); - otherTerms.delete(object); - if (otherTerms.size > 0) { - const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); - if ( - [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) - ) - return; - } - - let anchor = match[3]; - if (anchor === "") anchor = fullname; - else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; - - const descr = objName + _(", in ") + title; - - // add custom score for some objects according to scorer - if (Scorer.objPrio.hasOwnProperty(match[2])) - score += Scorer.objPrio[match[2]]; - else score += Scorer.objPrioDefault; - - results.push([ - docNames[match[0]], - fullname, - "#" + anchor, - descr, - score, - filenames[match[0]], - SearchResultKind.object, - ]); - }; - Object.keys(objects).forEach((prefix) => - objects[prefix].forEach((array) => - objectSearchCallback(prefix, array) - ) - ); - return results; - }, - - /** - * search for full-text terms in the index - */ - performTermsSearch: (searchTerms, excludedTerms) => { - // prepare search - const terms = Search._index.terms; - const titleTerms = Search._index.titleterms; - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - - const scoreMap = new Map(); - const fileMap = new Map(); - - // perform the search on the required terms - searchTerms.forEach((word) => { - const files = []; - const arr = [ - { files: terms[word], score: Scorer.term }, - { files: titleTerms[word], score: Scorer.title }, - ]; - // add support for partial matches - if (word.length > 2) { - const escapedWord = _escapeRegExp(word); - if (!terms.hasOwnProperty(word)) { - Object.keys(terms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: terms[term], score: Scorer.partialTerm }); - }); - } - if (!titleTerms.hasOwnProperty(word)) { - Object.keys(titleTerms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); - }); - } - } - - // no match but word was a required one - if (arr.every((record) => record.files === undefined)) return; - - // found search word in contents - arr.forEach((record) => { - if (record.files === undefined) return; - - let recordFiles = record.files; - if (recordFiles.length === undefined) recordFiles = [recordFiles]; - files.push(...recordFiles); - - // set score for the word in each file - recordFiles.forEach((file) => { - if (!scoreMap.has(file)) scoreMap.set(file, {}); - scoreMap.get(file)[word] = record.score; - }); - }); - - // create the mapping - files.forEach((file) => { - if (!fileMap.has(file)) fileMap.set(file, [word]); - else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); - }); - }); - - // now check if the files don't contain excluded terms - const results = []; - for (const [file, wordList] of fileMap) { - // check if all requirements are matched - - // as search terms with length < 3 are discarded - const filteredTermCount = [...searchTerms].filter( - (term) => term.length > 2 - ).length; - if ( - wordList.length !== searchTerms.size && - wordList.length !== filteredTermCount - ) - continue; - - // ensure that none of the excluded terms is in the search result - if ( - [...excludedTerms].some( - (term) => - terms[term] === file || - titleTerms[term] === file || - (terms[term] || []).includes(file) || - (titleTerms[term] || []).includes(file) - ) - ) - break; - - // select one (max) score for the file. - const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); - // add result to the result list - results.push([ - docNames[file], - titles[file], - "", - null, - score, - filenames[file], - SearchResultKind.text, - ]); - } - return results; - }, - - /** - * helper function to return a node containing the - * search summary for a given text. keywords is a list - * of stemmed words. - */ - makeSearchSummary: (htmlText, keywords, anchor) => { - const text = Search.htmlToText(htmlText, anchor); - if (text === "") return null; - - const textLower = text.toLowerCase(); - const actualStartPosition = [...keywords] - .map((k) => textLower.indexOf(k.toLowerCase())) - .filter((i) => i > -1) - .slice(-1)[0]; - const startWithContext = Math.max(actualStartPosition - 120, 0); - - const top = startWithContext === 0 ? "" : "..."; - const tail = startWithContext + 240 < text.length ? "..." : ""; - - let summary = document.createElement("p"); - summary.classList.add("context"); - summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; - - return summary; - }, -}; - -_ready(Search.init); diff --git a/docs/1.0.2/_static/sphinx_highlight.js b/docs/1.0.2/_static/sphinx_highlight.js deleted file mode 100644 index 8a96c69a..00000000 --- a/docs/1.0.2/_static/sphinx_highlight.js +++ /dev/null @@ -1,154 +0,0 @@ -/* Highlighting utilities for Sphinx HTML documentation. */ -"use strict"; - -const SPHINX_HIGHLIGHT_ENABLED = true - -/** - * highlight a given string on a node by wrapping it in - * span elements with the given class name. - */ -const _highlight = (node, addItems, text, className) => { - if (node.nodeType === Node.TEXT_NODE) { - const val = node.nodeValue; - const parent = node.parentNode; - const pos = val.toLowerCase().indexOf(text); - if ( - pos >= 0 && - !parent.classList.contains(className) && - !parent.classList.contains("nohighlight") - ) { - let span; - - const closestNode = parent.closest("body, svg, foreignObject"); - const isInSVG = closestNode && closestNode.matches("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.classList.add(className); - } - - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - const rest = document.createTextNode(val.substr(pos + text.length)); - parent.insertBefore( - span, - parent.insertBefore( - rest, - node.nextSibling - ) - ); - node.nodeValue = val.substr(0, pos); - /* There may be more occurrences of search term in this node. So call this - * function recursively on the remaining fragment. - */ - _highlight(rest, addItems, text, className); - - if (isInSVG) { - const rect = document.createElementNS( - "http://www.w3.org/2000/svg", - "rect" - ); - const bbox = parent.getBBox(); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute("class", className); - addItems.push({ parent: parent, target: rect }); - } - } - } else if (node.matches && !node.matches("button, select, textarea")) { - node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); - } -}; -const _highlightText = (thisNode, text, className) => { - let addItems = []; - _highlight(thisNode, addItems, text, className); - addItems.forEach((obj) => - obj.parent.insertAdjacentElement("beforebegin", obj.target) - ); -}; - -/** - * Small JavaScript module for the documentation. - */ -const SphinxHighlight = { - - /** - * highlight the search words provided in localstorage in the text - */ - highlightSearchWords: () => { - if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight - - // get and clear terms from localstorage - const url = new URL(window.location); - const highlight = - localStorage.getItem("sphinx_highlight_terms") - || url.searchParams.get("highlight") - || ""; - localStorage.removeItem("sphinx_highlight_terms") - url.searchParams.delete("highlight"); - window.history.replaceState({}, "", url); - - // get individual terms from highlight string - const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); - if (terms.length === 0) return; // nothing to do - - // There should never be more than one element matching "div.body" - const divBody = document.querySelectorAll("div.body"); - const body = divBody.length ? divBody[0] : document.querySelector("body"); - window.setTimeout(() => { - terms.forEach((term) => _highlightText(body, term, "highlighted")); - }, 10); - - const searchBox = document.getElementById("searchbox"); - if (searchBox === null) return; - searchBox.appendChild( - document - .createRange() - .createContextualFragment( - '

' + - '' + - _("Hide Search Matches") + - "

" - ) - ); - }, - - /** - * helper function to hide the search marks again - */ - hideSearchWords: () => { - document - .querySelectorAll("#searchbox .highlight-link") - .forEach((el) => el.remove()); - document - .querySelectorAll("span.highlighted") - .forEach((el) => el.classList.remove("highlighted")); - localStorage.removeItem("sphinx_highlight_terms") - }, - - initEscapeListener: () => { - // only install a listener if it is really needed - if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; - - document.addEventListener("keydown", (event) => { - // bail for input elements - if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; - // bail with special keys - if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; - if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { - SphinxHighlight.hideSearchWords(); - event.preventDefault(); - } - }); - }, -}; - -_ready(() => { - /* Do not call highlightSearchWords() when we are on the search page. - * It will highlight words from the *previous* search query. - */ - if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); - SphinxHighlight.initEscapeListener(); -}); diff --git a/docs/1.0.2/autodoc/mmif.serialize.html b/docs/1.0.2/autodoc/mmif.serialize.html deleted file mode 100644 index 25e79580..00000000 --- a/docs/1.0.2/autodoc/mmif.serialize.html +++ /dev/null @@ -1,1271 +0,0 @@ - - - - - - - - - mmif.serialize module — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
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mmif.serialize module

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mmif.serialize.model module

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The model module contains the classes used to represent an -abstract MMIF object as a live Python object.

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The MmifObject class or one of its derivatives is subclassed by -all other classes defined in this SDK, except for MmifObjectEncoder.

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These objects are generally instantiated from JSON, either as a string -or as an already-loaded Python dictionary. This base class provides the -core functionality for deserializing MMIF JSON data into live objects -and serializing live objects into MMIF JSON data. Specialized behavior -for the different components of MMIF is added in the subclasses.

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-class mmif.serialize.model.DataDict(mmif_obj: bytes | str | dict | None = None)[source]
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Bases: MmifObject, Generic[T, S]

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-empty()[source]
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-get(key: T, default=None) → S | None[source]
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-items()[source]
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-keys()[source]
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-update(other, overwrite)[source]
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-values()[source]
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-class mmif.serialize.model.DataList(mmif_obj: bytes | str | list | None = None)[source]
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Bases: MmifObject, Generic[T]

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The DataList class is an abstraction that represents the -various lists found in a MMIF file, such as documents, subdocuments, -views, and annotations.

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Parameters:
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mmif_obj (Union[str, list]) – the data that the list contains

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-append(value, overwrite)[source]
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-deserialize(mmif_json: str | list) → None[source]
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Passes the input data into the internal deserializer.

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-empty()[source]
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-get(key: str) → T | None[source]
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Standard dictionary-style get() method, albeit with no default -parameter. Relies on the implementation of __getitem__.

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Will return None if the key is not found.

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Parameters:
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key – the key to search for

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Returns:
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the value matching that key

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-class mmif.serialize.model.MmifObject(mmif_obj: bytes | str | dict | None = None)[source]
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Bases: object

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Abstract superclass for MMIF related key-value pair objects.

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Any MMIF object can be initialized as an empty placeholder or -an actual representation with a JSON formatted string or equivalent -dict object argument.

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This superclass has four specially designed instance variables, and these -variable names cannot be used as attribute names for MMIF objects.

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  1. _unnamed_attributes: -Only can be either None or an empty dictionary. If it’s set to None, -it means the class won’t take any Additional Attributes in the JSON -schema sense. If it’s a dict, users can throw any k-v pairs to the -class, EXCEPT for the reserved two key names.

    2. -

  2. _attribute_classes: -This is a dict from a key name to a specific python class to use for -deserialize the value. Note that a key name in this dict does NOT -have to be a named attribute, but is recommended to be one.

    3. -

  3. _required_attributes: -This is a simple list of names of attributes that are required in the object. -When serialize, an object will skip its empty (e.g. zero-length, or None) -attributes unless they are in this list. Otherwise, the serialized JSON -string would have empty representations (e.g. "", []).

    4. -

  4. _exclude_from_diff: -This is a simple list of names of attributes that should be excluded from -the diff calculation in __eq__.

    5. -
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# TODO (krim @ 8/17/20): this dict is however, a duplicate with the type hints in the class definition. -Maybe there is a better way to utilize type hints (e.g. getting them as a programmatically), but for now -developers should be careful to add types to hints as well as to this dict.

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Also note that those special attributes MUST be set in the __init__() -before calling super method, otherwise deserialization will not work.

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And also, a subclass that has one or more named attributes, it must -set those attributes in the __init__() before calling super method. When -serializing a MmifObject, all empty attributes will be ignored, so for -optional named attributes, you must leave the values empty (len == 0), but -NOT None. Any None-valued named attributes will cause issues with current -implementation.

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Parameters:
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mmif_obj – JSON string or dict to initialize an object. -If not given, an empty object will be initialized, sometimes with -an ID value automatically generated, based on its parent object.

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-deserialize(mmif_json: str | dict) → None[source]
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Takes a JSON-formatted string or a simple dict that’s json-loaded from -such a string as an input and populates object’s fields with the values -specified in the input.

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Parameters:
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mmif_json – JSON-formatted string or dict from such a string -that represents a MMIF object

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-disallow_additional_properties() → None[source]
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Call this method in __init__() to prevent the insertion -of unnamed attributes after initialization.

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-static is_empty(obj) → bool[source]
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return True if the obj is None or “emtpy”. The emptiness first defined as -having zero length. But for objects that lack __len__ method, we need -additional check.

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-reserved_names: Set[str] = {'_attribute_classes', '_exclude_from_diff', '_required_attributes', '_unnamed_attributes', 'reserved_names'}[source]
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-serialize(pretty: bool = False) → str[source]
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Generates JSON representation of an object.

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Parameters:
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pretty – If True, returns string representation with indentation.

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Returns:
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JSON string of the object.

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-set_additional_property(key: str, value: Any) → None[source]
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Method to set values in _unnamed_attributes.

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Parameters:
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  • key – the attribute name

    • -

  • value – the desired value

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Returns:
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None

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Raise:
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AttributeError if additional properties are disallowed by disallow_additional_properties()

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-class mmif.serialize.model.MmifObjectEncoder(*, skipkeys=False, ensure_ascii=True, check_circular=True, allow_nan=True, sort_keys=False, indent=None, separators=None, default=None)[source]
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Bases: JSONEncoder

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Encoder class to define behaviors of de-/serialization

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-default(obj: MmifObject)[source]
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Overrides default encoding behavior to prioritize MmifObject.serialize().

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mmif.serialize.mmif module

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The mmif module contains the classes used to represent a full MMIF -file as a live Python object.

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See the specification docs and the JSON Schema file for more information.

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-class mmif.serialize.mmif.Mmif(mmif_obj: bytes | str | dict | None = None, *, validate: bool = True)[source]
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Bases: MmifObject

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MmifObject that represents a full MMIF file.

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Parameters:
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  • mmif_obj – the JSON data

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  • validate – whether to validate the data against the MMIF JSON schema.

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-add_document(document: Document, overwrite=False) → None[source]
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Appends a Document object to the documents list.

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Fails if there is already a document with the same ID in the MMIF object.

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Parameters:
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  • document – the Document object to add

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  • overwrite – if set to True, will overwrite -an existing view with the same ID

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Returns:
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None

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-add_view(view: View, overwrite=False) → None[source]
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Appends a View object to the views list.

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Fails if there is already a view with the same ID in the MMIF object.

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Parameters:
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  • view – the Document object to add

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  • overwrite – if set to True, will overwrite -an existing view with the same ID

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Returns:
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None

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-generate_capital_annotations()[source]
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Automatically convert any “pending” temporary properties from -Document objects to Annotation objects . The generated Annotation -objects are then added to the last View in the views lists.

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See https://github.com/clamsproject/mmif-python/issues/226 for rationale -behind this behavior and discussion.

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-get_alignments(at_type1: str | TypesBase, at_type2: str | TypesBase) → Dict[str, List[Annotation]][source]
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Finds views where alignments between two given annotation types occurred.

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Returns:
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a dict that keyed by view IDs (str) and has lists of alignment Annotation objects as values.

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-get_all_views_contain(at_types: TypesBase | str | List[str | TypesBase]) → List[View][source]
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Returns the list of all views in the MMIF if given types -are present in that view’s ‘contains’ metadata.

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Parameters:
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at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

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Returns:
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the list of views that contain the type

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-get_document_by_id(doc_id: str) → Document[source]
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Finds a Document object with the given ID.

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Parameters:
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doc_id – the ID to search for

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Returns:
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a reference to the corresponding document, if it exists

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Raises:
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KeyError – if there is no corresponding document

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-get_document_location(m_type: DocumentTypes | str, path_only=False) → str | None[source]
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Method to get the location of first document of given type.

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Parameters:
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m_type – the type to search for

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Returns:
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the value of the location field in the corresponding document

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-get_documents_by_app(app_id: str) → List[Document][source]
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Method to get all documents object queries by its originated app name.

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Parameters:
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app_id – the app name to search for

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Returns:
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a list of documents matching the requested app name, or an empty list if the app not found

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-get_documents_by_property(prop_key: str, prop_value: str) → List[Document][source]
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Method to retrieve documents by an arbitrary key-value pair in the document properties objects.

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Parameters:
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  • prop_key – the metadata key to search for

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  • prop_value – the metadata value to match

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Returns:
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a list of documents matching the requested metadata key-value pair

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-get_documents_by_type(doc_type: str | DocumentTypes) → List[Document][source]
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Method to get all documents where the type matches a particular document type, which should be one of the CLAMS document types.

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Parameters:
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doc_type – the type of documents to search for, must be one of Document type defined in the CLAMS vocabulary.

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Returns:
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a list of documents matching the requested type, or an empty list if none found.

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-get_documents_in_view(vid: str | None = None) → List[Document][source]
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Method to get all documents object queries by a view id.

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Parameters:
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vid – the source view ID to search for

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Returns:
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a list of documents matching the requested source view ID, or an empty list if the view not found

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-get_documents_locations(m_type: DocumentTypes | str, path_only=False) → List[str | None][source]
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This method returns the file paths of documents of given type. -Only top-level documents have locations, so we only check them.

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Parameters:
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m_type – the type to search for

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Returns:
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a list of the values of the location fields in the corresponding documents

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-get_view_by_id(req_view_id: str) → View[source]
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Finds a View object with the given ID.

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Parameters:
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req_view_id – the ID to search for

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Returns:
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a reference to the corresponding view, if it exists

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Raises:
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Exception – if there is no corresponding view

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-get_view_contains(at_types: TypesBase | str | List[str | TypesBase]) → View | None[source]
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Returns the last view appended that contains the given -types in its ‘contains’ metadata.

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Parameters:
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at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

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Returns:
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the view, or None if the type is not found

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-get_views_contain(at_types: TypesBase | str | List[str | TypesBase]) → List[View][source]
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An alias to get_all_views_contain method.

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-get_views_for_document(doc_id: str) → List[View][source]
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Returns the list of all views that have annotations anchored on a particular document. -Note that when the document is inside a view (generated during the pipeline’s running), -doc_id must be prefixed with the view_id.

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-id_delimiter: ClassVar[str] = ':'[source]
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-new_view() → View[source]
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Creates an empty view with a new ID and appends it to the views list.

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Returns:
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a reference to the new View object

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-new_view_id() → str[source]
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Fetches an ID for a new view.

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Returns:
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the ID

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-sanitize()[source]
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Sanitizes a Mmif object by running some safeguards. -Concretely, it performs the following before returning the JSON string.

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  1. validating output using built-in MMIF jsonschema

    2. -

  2. remove non-existing annotation types from contains metadata

    3. -
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-serialize(pretty: bool = False, sanitize: bool = False, autogenerate_capital_annotations=True) → str[source]
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Serializes the MMIF object to a JSON string.

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Parameters:
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  • sanitize – If True, performs some sanitization of before returning -the JSON string. See sanitize() for details.

    • -

  • autogenerate_capital_annotations – If True, automatically convert -any “pending” temporary properties from Document objects to -Annotation objects. See generate_capital_annotations() for -details.

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  • pretty – If True, returns string representation with indentation.

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Returns:
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JSON string of the MMIF object.

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-static validate(json_str: bytes | str | dict) → None[source]
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Validates a MMIF JSON object against the MMIF Schema. -Note that this method operates before processing by MmifObject._load_str, -so it expects @ and not _ for the JSON-LD @-keys.

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Raises:
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jsonschema.exceptions.ValidationError – if the input fails validation

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Parameters:
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json_str – a MMIF JSON dict or string

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Returns:
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None

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-view_prefix: ClassVar[str] = 'v_'[source]
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mmif.serialize.view module

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The view module contains the classes used to represent a MMIF view -as a live Python object.

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In MMIF, views are created by apps in a pipeline that are annotating -data that was previously present in the MMIF file.

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-class mmif.serialize.view.Contain(mmif_obj: bytes | str | dict | None = None)[source]
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Bases: DataDict[str, str]

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Contain object that represents the metadata of a single -annotation type in the contains metadata of a MMIF view.

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-class mmif.serialize.view.View(view_obj: bytes | str | dict | None = None)[source]
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Bases: MmifObject

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View object that represents a single view in a MMIF file.

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A view is identified by an ID, and contains certain metadata, -a list of annotations, and potentially a JSON-LD @context -IRI.

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If view_obj is not provided, an empty View will be generated.

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Parameters:
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view_obj – the JSON data that defines the view

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-add_annotation(annotation: Annotation, overwrite=False) → Annotation[source]
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Adds an annotation to the current view.

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Fails if there is already an annotation with the same ID -in the view, unless overwrite is set to True.

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Parameters:
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Raises:
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KeyError – if overwrite is set to False and -an annotation with the same ID exists -in the view

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Returns:
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the same Annotation object passed in as annotation

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-add_document(document: Document, overwrite=False) → Annotation[source]
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Appends a Document object to the annotations list.

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Fails if there is already a document with the same ID in the annotations list.

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Parameters:
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  • document – the Document object to add

    • -

  • overwrite – if set to True, will overwrite -an existing view with the same ID

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Returns:
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None

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-get_annotation_by_id(ann_id)[source]
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-get_annotations(at_type: str | TypesBase | None = None, **properties) → Generator[Annotation, None, None][source]
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Look for certain annotations in this view, specified by parameters

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Parameters:
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  • at_type – @type of the annotations to look for. When this is None, any @type will match.

    • -

  • properties – properties of the annotations to look for. When given more than one property, all properties must match. Note that annotation type metadata are specified in the contains view metadata, not in individual annotation objects.

    • -
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-get_document_by_id(doc_id) → Document[source]
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-get_documents() → List[Document][source]
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-new_annotation(at_type: str | TypesBase, aid: str | None = None, overwrite=False, **properties) → Annotation[source]
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Generates a new mmif.serialize.annotation.Annotation -object and adds it to the current view.

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Fails if there is already an annotation with the same ID -in the view, unless overwrite is set to True.

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Parameters:
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  • at_type – the desired @type of the annotation.

    • -

  • aid – the desired ID of the annotation, when not given, -the mmif SDK tries to automatically generate an ID based on -Annotation type and existing annotations in the view.

    • -

  • overwrite – if set to True, will overwrite an -existing annotation with the same ID.

    • -
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Raises:
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KeyError – if overwrite is set to False and -an annotation with the same ID exists -in the view.

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Returns:
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the generated mmif.serialize.annotation.Annotation

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-new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
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Adds a new element to the contains metadata.

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Parameters:
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  • at_type – the @type of the annotation type being added

    • -

  • contains_metadata – any metadata associated with the annotation type

    • -
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Returns:
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the generated Contain object

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-new_textdocument(text: str, lang: str = 'en', did: str | None = None, overwrite=False, **properties) → Document[source]
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Generates a new mmif.serialize.annotation.Document -object, particularly typed as TextDocument and adds it to the current view.

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Fails if there is already a text document with the same ID -in the view, unless overwrite is set to True.

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Parameters:
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  • text – text content of the new document

    • -

  • lang – ISO 639-1 code of the language used in the new document

    • -

  • did – the desired ID of the document, when not given, -the mmif SDK tries to automatically generate an ID based on -Annotation type and existing documents in the view.

    • -

  • overwrite – if set to True, will overwrite an -existing document with the same ID

    • -
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Raises:
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KeyError – if overwrite is set to False and -an document with the same ID exists -in the view

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Returns:
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the generated mmif.serialize.annotation.Document

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-set_error(err_message: str, err_trace: str) → None[source]
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-class mmif.serialize.view.ViewMetadata(viewmetadata_obj: bytes | str | dict | None = None)[source]
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Bases: MmifObject

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ViewMetadata object that represents the metadata object within a MMIF view.

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Parameters:
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viewmetadata_obj – the JSON data that defines the metadata

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-add_contain(contain: Contain, at_type: str | TypesBase)[source]
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-add_parameter(param_key, param_value)[source]
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-add_parameters(**runtime_params)[source]
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-add_warnings(*warnings: Warning)[source]
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-emtpy_warnings()[source]
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-get_parameter(param_key)[source]
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-new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
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Adds a new element to the contains dictionary.

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Parameters:
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    -

  • at_type – the @type of the annotation type being added

    • -

  • contains_metadata – any metadata associated with the annotation type

    • -
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Returns:
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the generated Contain object

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-set_error(message: str, stack_trace: str)[source]
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mmif.serialize.annotation module

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The annotation module contains the classes used to represent a -MMIF annotation as a live Python object.

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In MMIF, annotations are created by apps in a pipeline as a part -of a view. For documentation on how views are represented, see -mmif.serialize.view.

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-class mmif.serialize.annotation.Annotation(anno_obj: bytes | str | dict | None = None)[source]
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Bases: MmifObject

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MmifObject that represents an annotation in a MMIF view.

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-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]]) → None[source]
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Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

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- -
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-property at_type: TypesBase[source]
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- -
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-static check_prop_value_is_simple_enough(value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]])[source]
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- -
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-get(prop_name: str) → AnnotationProperties | str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]][source]
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A special getter for Annotation properties. This is to allow for -directly accessing properties without having to go through the -properties object.

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- -
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-get_property(prop_name: str) → AnnotationProperties | str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]][source]
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A special getter for Annotation properties. This is to allow for -directly accessing properties without having to go through the -properties object.

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- -
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-property id: str[source]
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- -
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-is_document()[source]
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- -
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-is_type(at_type: str | TypesBase) → bool[source]
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Check if the @type of this object matches.

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- -
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-property parent: str[source]
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- -
- -
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-class mmif.serialize.annotation.AnnotationProperties(mmif_obj: bytes | str | dict | None = None)[source]
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Bases: MmifObject, MutableMapping[str, T]

-

AnnotationProperties object that represents the -properties object within a MMIF annotation.

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Parameters:
-

mmif_obj – the JSON data that defines the properties

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- -
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-class mmif.serialize.annotation.Document(doc_obj: bytes | str | dict | None = None)[source]
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Bases: Annotation

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Document object that represents a single document in a MMIF file.

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A document is identified by an ID, and contains certain attributes -and potentially contains the contents of the document itself, -metadata about how the document was created, and/or a list of -subdocuments grouped together logically.

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If document_obj is not provided, an empty Document will be generated.

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Parameters:
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document_obj – the JSON data that defines the document

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-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None]) → None[source]
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Adds a property to the document’s properties.

-

Unlike the parent Annotation class, added properties of a -Document object can be lost during serialization unless it belongs -to somewhere in a Mmif object. This is because we want to keep -Document object as “read-only” as possible. Thus, if you want to add -a property to a Document object,

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    -

  • add the document to a Mmif object (either in the documents list or -in a view from the views list), or

    • -

  • directly write to Document.properties instead of using this method -(which is not recommended).

    • -
-

With the former method, the SDK will record the added property as a -Annotation annotation object, separate from the original Document -object. See Mmif.generate_capital_annotations() for more.

-

A few notes to keep in mind:

-
    -

  1. You can’t overwrite an existing property of a Document object.

    2. -

  2. A MMIF can have multiple Annotation objects with the same -property name but different values. When this happens, the SDK will -only keep the latest value (in order of appearances in views list) of -the property, effectively overwriting the previous values.

    3. -
-
- -
-
-get(prop_name)[source]
-

A special getter for Document properties. This is to allow for reading -the three properties in a specific order so that the latest value is -returned, in case there are multiple values for the same key.

-
- -
-
-get_property(prop_name)[source]
-

A special getter for Document properties. This is to allow for reading -the three properties in a specific order so that the latest value is -returned, in case there are multiple values for the same key.

-
- -
-
-property location: str | None[source]
-

location property must be a legitimate URI. That is, should the document be a local file -then the file:// scheme must be used. -Returns None when no location is set.

-
- -
-
-location_address() → str | None[source]
-

Retrieves the full address from the document location URI. -Returns None when no location is set.

-
- -
-
-location_path() → str | None[source]
-

Retrieves a path that’s resolved to a pathname in the local file system. -To obtain the original value of the “path” part in the location string -(before resolving), use properties.location_path_literal method. -Returns None when no location is set.

-
- -
-
-location_scheme() → str | None[source]
-

Retrieves URI scheme of the document location. -Returns None when no location is set.

-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.DocumentProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: AnnotationProperties

-

DocumentProperties object that represents the -properties object within a MMIF document.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
-
-property location: str | None[source]
-

location property must be a legitimate URI. That is, should the document be a local file -then the file:// scheme must be used. -Returns None when no location is set.

-
- -
-
-location_address() → str | None[source]
-

Retrieves the full address from the document location URI. -Returns None when no location is set.

-
- -
-
-location_path() → str | None[source]
-
- -
-
-location_path_literal() → str | None[source]
-

Retrieves only path name of the document location (hostname is ignored). -Returns None when no location is set.

-
- -
-
-location_path_resolved() → str | None[source]
-

Retrieves only path name of the document location (hostname is ignored), -and then try to resolve the path name in the local file system. -This method should be used when the document scheme is file or empty. -For other schemes, users should install mmif-locdoc-<scheme> plugin.

-

Returns None when no location is set. -Raise ValueError when no code found to resolve the given location scheme.

-
- -
-
-location_scheme() → str | None[source]
-

Retrieves URI scheme of the document location. -Returns None when no location is set.

-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.Text(text_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-
-
-property lang: str[source]
-
- -
-
-property value: str[source]
-
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- - - \ No newline at end of file diff --git a/docs/1.0.2/autodoc/mmif.vocabulary.html b/docs/1.0.2/autodoc/mmif.vocabulary.html deleted file mode 100644 index 24c105d7..00000000 --- a/docs/1.0.2/autodoc/mmif.vocabulary.html +++ /dev/null @@ -1,325 +0,0 @@ - - - - - - - - - mmif.vocabulary module — mmif-python documentation - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.vocabulary module

-
-

mmif.vocabulary.annotation_types module

-
-
-class mmif.vocabulary.annotation_types.AnnotationTypes(type_uri, fuzzymode=True)[source]
-

Bases: AnnotationTypesBase

-

This class contains the CLAMS annotation types -defined in the spec version 1.1.0 as class variables.

-
-
-Alignment = http://mmif.clams.ai/vocabulary/Alignment/v1[source]
-
- -
-
-Annotation = http://mmif.clams.ai/vocabulary/Annotation/v6[source]
-
- -
-
-BoundingBox = http://mmif.clams.ai/vocabulary/BoundingBox/v5[source]
-
- -
-
-Chapter = http://mmif.clams.ai/vocabulary/Chapter/v6[source]
-
- -
-
-Interval = http://mmif.clams.ai/vocabulary/Interval/v5[source]
-
- -
-
-NamedEntity = http://mmif.clams.ai/vocabulary/NamedEntity/v1[source]
-
- -
-
-NounChunk = http://mmif.clams.ai/vocabulary/NounChunk/v1[source]
-
- -
-
-Paragraph = http://mmif.clams.ai/vocabulary/Paragraph/v1[source]
-
- -
-
-Polygon = http://mmif.clams.ai/vocabulary/Polygon/v5[source]
-
- -
-
-Region = http://mmif.clams.ai/vocabulary/Region/v5[source]
-
- -
-
-Relation = http://mmif.clams.ai/vocabulary/Relation/v5[source]
-
- -
-
-Sentence = http://mmif.clams.ai/vocabulary/Sentence/v1[source]
-
- -
-
-Span = http://mmif.clams.ai/vocabulary/Span/v5[source]
-
- -
-
-TimeFrame = http://mmif.clams.ai/vocabulary/TimeFrame/v6[source]
-
- -
-
-TimePoint = http://mmif.clams.ai/vocabulary/TimePoint/v5[source]
-
- -
-
-Token = http://mmif.clams.ai/vocabulary/Token/v1[source]
-
- -
-
-VerbChunk = http://mmif.clams.ai/vocabulary/VerbChunk/v1[source]
-
- -
-
-VideoObject = http://mmif.clams.ai/vocabulary/VideoObject/v5[source]
-
- -
-
-typevers = {'Alignment': 'v1', 'Annotation': 'v6', 'BoundingBox': 'v5', 'Chapter': 'v6', 'Interval': 'v5', 'NamedEntity': 'v1', 'NounChunk': 'v1', 'Paragraph': 'v1', 'Polygon': 'v5', 'Region': 'v5', 'Relation': 'v5', 'Sentence': 'v1', 'Span': 'v5', 'TimeFrame': 'v6', 'TimePoint': 'v5', 'Token': 'v1', 'VerbChunk': 'v1', 'VideoObject': 'v5'}[source]
-
- -
- -
-
-

mmif.vocabulary.document_types module

-
-
-class mmif.vocabulary.document_types.DocumentTypes(type_uri, fuzzymode=True)[source]
-

Bases: DocumentTypesBase

-

This class contains the CLAMS document types -defined in the spec version 1.1.0 as class variables.

-
-
-AudioDocument = http://mmif.clams.ai/vocabulary/AudioDocument/v1[source]
-
- -
-
-Document = http://mmif.clams.ai/vocabulary/Document/v1[source]
-
- -
-
-ImageDocument = http://mmif.clams.ai/vocabulary/ImageDocument/v1[source]
-
- -
-
-TextDocument = http://mmif.clams.ai/vocabulary/TextDocument/v1[source]
-
- -
-
-VideoDocument = http://mmif.clams.ai/vocabulary/VideoDocument/v1[source]
-
- -
-
-typevers = {'AudioDocument': 'v1', 'Document': 'v1', 'ImageDocument': 'v1', 'TextDocument': 'v1', 'VideoDocument': 'v1'}[source]
-
- -
- -
-
- - -
-
- -
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- -
- - Other Versions - v: 1.0.2 - - -
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- - - \ No newline at end of file diff --git a/docs/1.0.2/consumer-tutorial.html b/docs/1.0.2/consumer-tutorial.html deleted file mode 100644 index 1e1d2782..00000000 --- a/docs/1.0.2/consumer-tutorial.html +++ /dev/null @@ -1,171 +0,0 @@ - - - - - - - - - MMIF consumer — mmif-python documentation - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • MMIF consumer
    • -
  • -
    • -
-
-
-
-
- -
-

MMIF consumer

-

A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the appliance documentation to learn more about the appliance.

-

MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance.

-
    -

  1. The code must be hosted on a public git repository (e.g. Github, Gitlab, …)

    2. -

  2. Must listen to 5000 port.

    3. -

  3. Must expose /display route .

    4. -

  4. /display router should response to GET requests.

    5. -

  5. In the GET request, a public URL of the input MMIF file is passed via file URL parameter.

    6. -

  6. On the codebase root, there must be a Dockerfile that can build a docker image that runs the web app.

    7. -
-

We provide an example consumer at https://github.com/clamsproject/mmif-visualizer.

-
- - -
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- -
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- -
- - Other Versions - v: 1.0.2 - - -
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- - -
- -
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    -
    • -
  • Index
    • -
  • -
    • -
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Index

- -
- A - | B - | C - | D - | E - | G - | I - | K - | L - | M - | N - | P - | R - | S - | T - | U - | V - -
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A

- - - -
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- - -
- -
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  • Welcome to mmif-python’s documentation!
    • -
  • -
    • -
-
-
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- -
-

Welcome to mmif-python’s documentation!

-
-

MultiMedia Interchange Format

-

MMIF is a JSON(-LD)-based data format designed for transferring annotation data between computational analysis applications in CLAMS project.

-
-

Contents

- -
-
-

API documentation:

- -
-
-
-
-

Indices and tables

- -
- - -
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- - -
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  • Getting Started
    • -
  • -
    • -
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- -
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Getting Started

-
-

Overview

-

MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for reproducibility, transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF website. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects.

-
-
-

Prerequisites

-
    -

  • Python: the latest mmif-python requires Python 3.8 or newer. We have no plan to support Python 2.7.

    • -
-
-
-

Installation

-

Package mmif-python is distributed via the official PyPI. Users are supposed to pip-install to get latest release.

-
pip install mmif-python
-
-
-

This will install a package mmif to local python.

-

The MMIF format and specification is evolving over time, and mmif-python package will be updated along with the changes in MMIF format.

-
-

Note

-

MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and mmif-python versions, please take time to read our decision on the subject here. If you need to know which python SDK supports which specification version, see Target MMIF Versions page.

-
-
-
-

MMIF Serialization

-

mmif.serialize.mmif.Mmif represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of mmif.serialize.model.MmifObject, including the mmif.serialize.mmif.Mmif. To start with an existing MMIF str, simple initiate a new Mmif object with the file.

-
import mmif
-from mmif import Mmif
-
-mmif_str = """{
-"metadata": {
-  "mmif": "http://mmif.clams.ai/1.0.0"
-},
-"documents": [
-  {
-    "@type": "http://mmif.clams.ai/vocabulary/VideoDocument/v1",
-    "properties": {
-      "id": "m1",
-      "mime": "video/mp4",
-      "location": "file:///var/archive/video-0012.mp4"
-    }
-  },
-  {
-    "@type": "http://mmif.clams.ai/vocabulary/TextDocument/v1",
-    "properties": {
-      "id": "m2",
-      "mime": "text/plain",
-      "location": "file:///var/archive/video-0012-transcript.txt"
-    }
-  }
-],
-"views": []}"""
-mmif_obj = Mmif(mmif_str)
-
-
-

Few notes;

-
    -

  1. MMIF does not carry the primary source files in it.

    2. -

  2. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version mmif-python implementation of the MMIF might not be able to load an unsupported version of MMIF string.

    3. -
-

When serializing back to str, call mmif.serialize.model.MmifObject.serialize() on the object.

-

To get subcomponents, you can use various getters implemented in subclasses. For example;

-
from mmif.vocabulary.document_types import DocumentTypes
-
-for video in mmif_obj.Mmif.get_documents_by_type(DocumentTypes.VideoDocument):
-  with open(video.location_path(), 'b') as in_video:
-    # do something with the video file
-
-
-

For a full list of available helper methods, please refer to the API documentation.

-
-
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- -
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- - Other Versions - v: 1.0.2 - - -
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- - - \ No newline at end of file diff --git a/docs/1.0.2/modules.html b/docs/1.0.2/modules.html deleted file mode 100644 index bd920618..00000000 --- a/docs/1.0.2/modules.html +++ /dev/null @@ -1,349 +0,0 @@ - - - - - - - - - mmif package — mmif-python documentation - - - - - - - - - - - - - - - - - -
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  • mmif package
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mmif package

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- - - \ No newline at end of file diff --git a/docs/1.0.2/objects.inv b/docs/1.0.2/objects.inv deleted file mode 100644 index c450fb0f..00000000 Binary files a/docs/1.0.2/objects.inv and /dev/null differ diff --git a/docs/1.0.2/plugins.html b/docs/1.0.2/plugins.html deleted file mode 100644 index 94db9e86..00000000 --- a/docs/1.0.2/plugins.html +++ /dev/null @@ -1,275 +0,0 @@ - - - - - - - - - Developing plugins for MMIF Python SDK — mmif-python documentation - - - - - - - - - - - - - - - - - -
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  • Developing plugins for MMIF Python SDK
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Developing plugins for MMIF Python SDK

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Overview

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As MMIF JSON files can carry information about media document files without actually carrying file contents, file accessing modules in mmif Python package (distributed as mmif-python on PyPI) are designed to be lightweight and flexible so that it can work with additional “plugin” Python packages that can handle concrete file access.

-

This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF website. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects.

-

Developer can write simple plugins that can provide additional functionalities to mmif-python. For example, mmif-python does not provide any file access functionality beyond a local file system (with file scheme), but it can be extended with a plugin that can handle file access over different protocols (e.g. http, s3, ftp, etc).

-

This document contains information about how to write plugins for mmif-python.

-
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Document Location Scheme Plugins

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mmif.serialize.annotation.Document class has various methods to access parts of location property of the document. The location is in URI/IRI format (SCHEME://HOSTNAME/PATH, in a nutshell) and it has to be resolved to a local file for CLAMS Apps to process the local file to analyze and extract information about the media and its contents. The core mmif-python distribution only provides a default implementation that can handle file scheme URIs.

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To add a document location handler plugin, you need to implement a Python “package” (do not confuse with PYPI distribution), that meets these requirements;

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  1. the package must be named mmif_docloc_<SCHEME>. For example, to implement a handler for s3 scheme, the package name must be mmif_docloc_s3. The prefix is important as it’s used in the plugin discovery process from the core mmif-python modules.

    2. -

  2. the top module of the package must have a function named resolve. The function must take a single argument, which is a str of the document location URI. The function must return a str of the local file path. For example, if the document location is s3://mybucket/myfile.mp4, a Python user should be able to to something like this;

    3. -
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import mmif_docloc_s3
-resolved = mmif_docloc_s3.resolve('s3://mybucket/myfile.mp4')
-# then resolved must be a local file path that can be used to open the file
-
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Here’s a minimal example codebase that you refer to when you develop a docloc plugin.

-

(However, before you start writing your own plugin for a specific URI scheme, checking if there’s already a PyPI distribution for the scheme might be a good idea.)

-
$ tree .
-.
-├── mmif_docloc_dummy
-│   └── __init__.py
-├── pyproject.toml
-└── setup.cfg
-
- $ cat pyproject.toml
-[build-system]
-requires = ["setuptools"]
-build-backend = "setuptools.build_meta"
-
-$ cat setup.cfg
-[metadata]
-name = mmif_docloc_dummy  # this name is IMPORTANT
-version = 0.0.1
-description = a plugin to mmif-pyhon to handle `dummy` location scheme
-
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And the plugin code.

-
# mmif_docloc_dummy/__init__.py
-doc_types = {'video': 'mp4'}
-
-def resolve(docloc):
-    scheme = 'dummy'
-    if docloc.startswith(f'{scheme}://'):
-        doc_id, doc_type = docloc.split('.')
-        return f'/path/to/{doc_id}.{doc_types[doc_type]}'
-    else:
-        raise ValueError(f'cannot handle document location scheme: {docloc}')
-
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-

Utility Plugins

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-

Warning

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This feature is experimental and subject to change in the future. -See this issue for limitations and known issues.

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Utility plugins, or mmif-utils- plugins are used to provide monkeypatch functions to mmif-python. -Currently mmif.serialize.model.MmifObject and its subclasses are the only classes that are under the scope of monkeypatching supported by the mmif-python core SDK. -(Of course any Python developer can come up with other ways to custom patch any parts of the SDK, it’s just not supported by the method described here.)

-

For writing pluggable monkeypatches for MMIF serialization classes, you need to implement a Python “package” (do not confuse with PYPI distribution), that meets these requirements;

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    -

  1. the package must be named mmif_utils_<NAME>. The prefix is important as it’s used in the plugin discovery process from the core mmif-python modules. <NAME> can be any string, but it’s recommended to use a name that describes the functionality of the plugin.

    2. -

  2. the top module of the package must have a dictionary named patches.

    3. -
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  1. The dictionary must be keyed with each class that you want to monkeypatch. The value of the key must be an iterable of functions that will be monkeypatched to the class.

    2. -

  2. The function must be a callable, and it must take the class instance as the first argument, so that when monkeypatched to a class, it can be called as a method of the class instance.

    3. -
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-

Here’s a minimal example code snippet of a mmif-utils- plugin.

-
import cv2
-from mmif.serialize import Mmif
-from mmif.vocabulary import AnnotationTypes, DocumentTypes
-
-
-def get_framerate(mmif: Mmif, video_doc_id: str):  # first argument must be the class instance
-    video_doc = mmif.get_document_by_id(video_doc_id)
-    if video_doc is None or video_doc.at_type != DocumentTypes.VideoDocument:
-        raise ValueError(f'Video document with id "{video_doc_id}" does not exist.')
-    for v in mmif.get_views_for_document(video_doc_id):
-        for a in v.get_annotations(AnnotationTypes.Annotation):
-            framerate_keys = ('fps', 'framerate')
-            for k, v in a.properties.items():
-                if k.lower() in framerate_keys:
-                    return v
-    cap = cv2.VideoCapture(video_doc.location_path())
-    return cap.get(cv2.CAP_PROP_FPS)
-
-patches = {Mmif: [get_framerate]}  # all callables in the list must have `Mmif` instance as the first argument
-
-
-

Then when this code is loaded as a mmif-utils- plugin, the get_framerate function will be monkeypatched to the mmif.serialize.mmif.Mmif class, and it can be called as a method of the class instance. -NOTE that a monkeypatch will “overwrite” the original method of the class, so it’s important to make sure that the monkeypatched method has the same signature as the original method. -Also if there’s no original method, the method from a plugin will be simply added to the class, not altering any existing code.

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null]], "mmif package": [[5, null]], "mmif.serialize module": [[0, null]], "mmif.serialize.annotation module": [[0, "module-mmif.serialize.annotation"]], "mmif.serialize.mmif module": [[0, "module-mmif.serialize.mmif"]], "mmif.serialize.model module": [[0, "module-mmif.serialize.model"]], "mmif.serialize.view module": [[0, "module-mmif.serialize.view"]], "mmif.vocabulary module": [[1, null]], "mmif.vocabulary.annotation_types module": [[1, "module-mmif.vocabulary.annotation_types"]], "mmif.vocabulary.document_types module": [[1, "module-mmif.vocabulary.document_types"]]}, "docnames": ["autodoc/mmif.serialize", "autodoc/mmif.vocabulary", "consumer-tutorial", "index", "introduction", "modules", "plugins", "target-versions"], "envversion": {"sphinx": 64, "sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, 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documentation!", "Getting Started", "mmif package", "Developing plugins for MMIF Python SDK", "Target MMIF Versions"], "titleterms": {"": 3, "annot": 0, "annotation_typ": 1, "api": 3, "consum": 2, "content": 3, "develop": 6, "document": [3, 6], "document_typ": 1, "format": 3, "get": 4, "indic": 3, "instal": 4, "interchang": 3, "locat": 6, "mmif": [0, 1, 2, 3, 4, 5, 6, 7], "model": 0, "modul": [0, 1], "multimedia": 3, "overview": [4, 6], "packag": 5, "plugin": 6, "prerequisit": 4, "python": [3, 6], "scheme": 6, "sdk": 6, "serial": [0, 4], "specif": 7, "start": 4, "tabl": 3, "target": 7, "util": 6, "version": 7, "view": 0, "vocabulari": 1, "welcom": 3}}) \ No newline at end of file diff --git a/docs/1.0.2/target-versions.html b/docs/1.0.2/target-versions.html deleted file mode 100644 index a84add18..00000000 --- a/docs/1.0.2/target-versions.html +++ /dev/null @@ -1,248 +0,0 @@ - - - - - - - - - Target MMIF Versions — mmif-python documentation - - - - - - - - - - - - - - - - - -
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Target MMIF Versions

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This article provides targeting MMIF specification versions of different versions of mmif-python SDK.

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Target Specification Versions

mmif-python version

Target MMIF Specification

1.0.2

1.1.0

1.0.1

1.0.0

1.0.0

0.5.0

0.5.2

0.5.0

0.5.1

0.5.0

0.5.0

0.5.0

0.4.8

0.4.2

0.4.7

0.4.1

0.4.6

0.4.0

0.4.5

0.4.0

0.4.4

0.4.0

0.4.3

0.4.0

0.4.2

0.4.0

0.4.1

0.4.0

0.4.0

0.4.0

0.3.5

0.3.1

0.3.4

0.3.1

0.3.3

0.3.1

0.3.2

0.3.1

0.3.1

0.3.0

0.3.0

0.3.0

0.2.2

0.2.1

0.2.1

0.2.1

0.2.0

0.2.1

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0.3.4
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0.3.5
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0.4.0
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0.4.1
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0.4.2
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0.4.3
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0.4.4
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0.4.5
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0.4.6
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0.4.7
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0.4.8
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0.5.0
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0.5.1
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0.5.2
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1.0.0
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1.0.1
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1.0.10
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1.0.11
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1.0.12
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1.0.13
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1.0.14
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1.0.15
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1.0.16
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1.0.17
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1.0.18
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1.0.19
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1.0.2
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1.0.3
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1.0.4
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1.0.5
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1.0.6
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1.0.7
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1.0.8
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1.0.9
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The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the `appliance documentation `_ to learn more about the appliance. - -MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance. - -#. The code must be hosted on a public git repository (e.g. Github, Gitlab, ...) -#. Must listen to ``5000`` port. -#. Must expose ``/display`` route . -#. ``/display`` router should response to ``GET`` requests. -#. In the ``GET`` request, a public URL of the input MMIF file is passed via ``file`` URL parameter. -#. On the codebase root, there must be a ``Dockerfile`` that can build a `docker `_ image that runs the web app. - -We provide an example consumer at https://github.com/clamsproject/mmif-visualizer. diff --git a/docs/1.0.3/_sources/index.rst.txt b/docs/1.0.3/_sources/index.rst.txt deleted file mode 100644 index beb56aae..00000000 --- a/docs/1.0.3/_sources/index.rst.txt +++ /dev/null @@ -1,26 +0,0 @@ -Welcome to mmif-python's documentation! -======================================= - -.. mdinclude:: ../README.md - -.. toctree:: - :maxdepth: 2 - :caption: Contents - - introduction - plugins - target-versions - -.. toctree:: - :maxdepth: 2 - :caption: API documentation: - - modules - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/docs/1.0.3/_sources/introduction.rst.txt b/docs/1.0.3/_sources/introduction.rst.txt deleted file mode 100644 index cfd9eaf7..00000000 --- a/docs/1.0.3/_sources/introduction.rst.txt +++ /dev/null @@ -1,89 +0,0 @@ -.. _introduction: - -Getting Started -=============== - - -Overview ---------- - -MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for reproducibility, transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF website `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects. - -Prerequisites -------------- - -* `Python `_: the latest ``mmif-python`` requires Python 3.8 or newer. We have no plan to support `Python 2.7 `_. - -Installation ---------------- - -Package ``mmif-python`` is distributed via the official PyPI. Users are supposed to pip-install to get latest release. - -.. code-block:: bash - - pip install mmif-python - -This will install a package `mmif` to local python. - -The MMIF format and specification is evolving over time, and ``mmif-python`` package will be updated along with the changes in MMIF format. - -.. note:: MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and ``mmif-python`` versions, please take time to read our decision on the subject `here `_. If you need to know which python SDK supports which specification version, see :ref:`target-versions` page. - -MMIF Serialization ---------------------------- - -:class:`mmif.serialize.mmif.Mmif` represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of :class:`mmif.serialize.model.MmifObject`, including the :class:`mmif.serialize.mmif.Mmif`. To start with an existing MMIF :class:`str`, simple initiate a new ``Mmif`` object with the file. - -.. code-block:: python - - import mmif - from mmif import Mmif - - mmif_str = """{ - "metadata": { - "mmif": "http://mmif.clams.ai/1.0.0" - }, - "documents": [ - { - "@type": "http://mmif.clams.ai/vocabulary/VideoDocument/v1", - "properties": { - "id": "m1", - "mime": "video/mp4", - "location": "file:///var/archive/video-0012.mp4" - } - }, - { - "@type": "http://mmif.clams.ai/vocabulary/TextDocument/v1", - "properties": { - "id": "m2", - "mime": "text/plain", - "location": "file:///var/archive/video-0012-transcript.txt" - } - } - ], - "views": []}""" - mmif_obj = Mmif(mmif_str) - - -Few notes; - -#. MMIF does not carry the primary source files in it. -#. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version ``mmif-python`` implementation of the MMIF might not be able to load an unsupported version of MMIF string. - -When serializing back to :class:`str`, call :meth:`mmif.serialize.model.MmifObject.serialize` on the object. - -To get subcomponents, you can use various getters implemented in subclasses. For example; - -.. code-block:: python - - from mmif.vocabulary.document_types import DocumentTypes - - for video in mmif_obj.Mmif.get_documents_by_type(DocumentTypes.VideoDocument): - with open(video.location_path(), 'b') as in_video: - # do something with the video file - - -For a full list of available helper methods, please refer to :ref:`the API documentation `. - diff --git a/docs/1.0.3/_sources/modules.rst.txt b/docs/1.0.3/_sources/modules.rst.txt deleted file mode 100644 index e4269c6d..00000000 --- a/docs/1.0.3/_sources/modules.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _apidoc: - -mmif package -============ - -.. toctree:: - :maxdepth: 4 - - autodoc/mmif.serialize - autodoc/mmif.vocabulary diff --git a/docs/1.0.3/_sources/plugins.rst.txt b/docs/1.0.3/_sources/plugins.rst.txt deleted file mode 100644 index 9e1505e9..00000000 --- a/docs/1.0.3/_sources/plugins.rst.txt +++ /dev/null @@ -1,75 +0,0 @@ -.. _plugins: - -Developing plugins for MMIF Python SDK -====================================== - - -Overview --------- - -As MMIF JSON files can carry information about media document files without actually carrying file contents, file accessing modules in ``mmif`` Python package (distributed as ``mmif-python`` on PyPI) are designed to be lightweight and flexible so that it can work with additional "plugin" Python packages that can handle concrete file access. - - -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF website `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects. - -Developer can write simple plugins that can provide additional functionalities to ``mmif-python``. For example, ``mmif-python`` does not provide any file access functionality beyond a local file system (with ``file`` scheme), but it can be extended with a plugin that can handle file access over different protocols (e.g. ``http``, ``s3``, ``ftp``, etc). - -This document contains information about how to write plugins for ``mmif-python``. - -Document Location Scheme Plugins -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -:class:`mmif.serialize.annotation.Document` class has various methods to access parts of ``location`` property of the document. The location is in `URI/IRI format `_ (``SCHEME://HOSTNAME/PATH``, in a nutshell) and it has to be resolved to a local file for CLAMS Apps to process the local file to analyze and extract information about the media and its contents. The core ``mmif-python`` distribution only provides a default implementation that can handle ``file`` scheme URIs. - -To add a document location handler plugin, you need to implement a Python `"package" `_ (do not confuse with PYPI distribution), that meets these requirements; - -#. the package must be named ``mmif_docloc_``. For example, to implement a handler for ``s3`` scheme, the package name must be ``mmif_docloc_s3``. The prefix is important as it's used in the plugin discovery process from the core ``mmif-python`` modules. -#. the top module of the package must have a function named ``resolve``. The function must take a single argument, which is a :class:`str` of the document location URI. The function must return a :class:`str` of the local file path. For example, if the document location is ``s3://mybucket/myfile.mp4``, a Python user should be able to to something like this; - -.. code-block:: python - - import mmif_docloc_s3 - resolved = mmif_docloc_s3.resolve('s3://mybucket/myfile.mp4') - # then resolved must be a local file path that can be used to open the file - - -Here's a minimal example codebase that you refer to when you develop a ``docloc`` plugin. - -(However, before you start writing your own plugin for a specific URI scheme, checking `if there's already a PyPI distribution `_ for the scheme might be a good idea.) - -.. code-block:: sh - - $ tree . - . - ├── mmif_docloc_dummy - │ └── __init__.py - ├── pyproject.toml - └── setup.cfg - - $ cat pyproject.toml - [build-system] - requires = ["setuptools"] - build-backend = "setuptools.build_meta" - - $ cat setup.cfg - [metadata] - name = mmif_docloc_dummy # this name is IMPORTANT - version = 0.0.1 - description = a plugin to mmif-pyhon to handle `dummy` location scheme - - -And the plugin code. - -.. code-block:: python - - # mmif_docloc_dummy/__init__.py - doc_types = {'video': 'mp4'} - - def resolve(docloc): - scheme = 'dummy' - if docloc.startswith(f'{scheme}://'): - doc_id, doc_type = docloc.split('.') - return f'/path/to/{doc_id}.{doc_types[doc_type]}' - else: - raise ValueError(f'cannot handle document location scheme: {docloc}') diff --git a/docs/1.0.3/_sources/target-versions.rst.txt b/docs/1.0.3/_sources/target-versions.rst.txt deleted file mode 100644 index 34216d3e..00000000 --- a/docs/1.0.3/_sources/target-versions.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _target-versions: - -Target MMIF Versions -==================== - -This article provides targeting MMIF specification versions of different versions of ``mmif-python`` SDK. - -.. csv-table:: Target Specification Versions - :file: target-versions.csv - :header-rows: 1 diff --git a/docs/1.0.3/_static/_sphinx_javascript_frameworks_compat.js b/docs/1.0.3/_static/_sphinx_javascript_frameworks_compat.js deleted file mode 100644 index 81415803..00000000 --- a/docs/1.0.3/_static/_sphinx_javascript_frameworks_compat.js +++ /dev/null @@ -1,123 +0,0 @@ -/* Compatability shim for jQuery and underscores.js. - * - * Copyright Sphinx contributors - * Released under the two clause BSD licence - */ - -/** - * small helper function to urldecode strings - * - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL - */ -jQuery.urldecode = function(x) { - if (!x) { - return x - } - return decodeURIComponent(x.replace(/\+/g, ' ')); -}; - -/** - * small helper function to urlencode strings - */ -jQuery.urlencode = encodeURIComponent; - -/** - * This function returns the parsed url parameters of the - * current request. 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- -/** - * Simple result scoring code. - */ -if (typeof Scorer === "undefined") { - var Scorer = { - // Implement the following function to further tweak the score for each result - // The function takes a result array [docname, title, anchor, descr, score, filename] - // and returns the new score. - /* - score: result => { - const [docname, title, anchor, descr, score, filename, kind] = result - return score - }, - */ - - // query matches the full name of an object - objNameMatch: 11, - // or matches in the last dotted part of the object name - objPartialMatch: 6, - // Additive scores depending on the priority of the object - objPrio: { - 0: 15, // used to be importantResults - 1: 5, // used to be objectResults - 2: -5, // used to be unimportantResults - }, - // Used when the priority is not in the mapping. - objPrioDefault: 0, - - // query found in title - title: 15, - partialTitle: 7, - // query found in terms - term: 5, - partialTerm: 2, - }; -} - -// Global search result kind enum, used by themes to style search results. -class SearchResultKind { - static get index() { return "index"; } - static get object() { return "object"; } - static get text() { return "text"; } - static get title() { return "title"; } -} - -const _removeChildren = (element) => { - while (element && element.lastChild) element.removeChild(element.lastChild); -}; - -/** - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping - */ -const _escapeRegExp = (string) => - string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string - -const _displayItem = (item, searchTerms, highlightTerms) => { - const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; - const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; - const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; - const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; - const contentRoot = document.documentElement.dataset.content_root; - - const [docName, title, anchor, descr, score, _filename, kind] = item; - - let listItem = document.createElement("li"); - // Add a class representing the item's type: - // can be used by a theme's CSS selector for styling - // See SearchResultKind for the class names. - listItem.classList.add(`kind-${kind}`); - let requestUrl; - let linkUrl; - if (docBuilder === "dirhtml") { - // dirhtml builder - let dirname = docName + "/"; - if (dirname.match(/\/index\/$/)) - dirname = dirname.substring(0, dirname.length - 6); - else if (dirname === "index/") dirname = ""; - requestUrl = contentRoot + dirname; - linkUrl = requestUrl; - } else { - // normal html builders - requestUrl = contentRoot + docName + docFileSuffix; - linkUrl = docName + docLinkSuffix; - } - let linkEl = listItem.appendChild(document.createElement("a")); - linkEl.href = linkUrl + anchor; - linkEl.dataset.score = score; - linkEl.innerHTML = title; - if (descr) { - listItem.appendChild(document.createElement("span")).innerHTML = - " (" + descr + ")"; - // highlight search terms in the description - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - } - else if (showSearchSummary) - fetch(requestUrl) - .then((responseData) => responseData.text()) - .then((data) => { - if (data) - listItem.appendChild( - Search.makeSearchSummary(data, searchTerms, anchor) - ); - // highlight search terms in the summary - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - }); - Search.output.appendChild(listItem); -}; -const _finishSearch = (resultCount) => { - Search.stopPulse(); - Search.title.innerText = _("Search Results"); - if (!resultCount) - Search.status.innerText = Documentation.gettext( - "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." - ); - else - Search.status.innerText = Documentation.ngettext( - "Search finished, found one page matching the search query.", - "Search finished, found ${resultCount} pages matching the search query.", - resultCount, - ).replace('${resultCount}', resultCount); -}; -const _displayNextItem = ( - results, - resultCount, - searchTerms, - highlightTerms, -) => { - // results left, load the summary and display it - // this is intended to be dynamic (don't sub resultsCount) - if (results.length) { - _displayItem(results.pop(), searchTerms, highlightTerms); - setTimeout( - () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), - 5 - ); - } - // search finished, update title and status message - else _finishSearch(resultCount); -}; -// Helper function used by query() to order search results. -// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. -// Order the results by score (in opposite order of appearance, since the -// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. -const _orderResultsByScoreThenName = (a, b) => { - const leftScore = a[4]; - const rightScore = b[4]; - if (leftScore === rightScore) { - // same score: sort alphabetically - const leftTitle = a[1].toLowerCase(); - const rightTitle = b[1].toLowerCase(); - if (leftTitle === rightTitle) return 0; - return leftTitle > rightTitle ? -1 : 1; // inverted is intentional - } - return leftScore > rightScore ? 1 : -1; -}; - -/** - * Default splitQuery function. Can be overridden in ``sphinx.search`` with a - * custom function per language. - * - * The regular expression works by splitting the string on consecutive characters - * that are not Unicode letters, numbers, underscores, or emoji characters. - * This is the same as ``\W+`` in Python, preserving the surrogate pair area. - */ -if (typeof splitQuery === "undefined") { - var splitQuery = (query) => query - .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) - .filter(term => term) // remove remaining empty strings -} - -/** - * Search Module - */ -const Search = { - _index: null, - _queued_query: null, - _pulse_status: -1, - - htmlToText: (htmlString, anchor) => { - const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - for (const removalQuery of [".headerlink", "script", "style"]) { - htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); - } - if (anchor) { - const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); - if (anchorContent) return anchorContent.textContent; - - console.warn( - `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` - ); - } - - // if anchor not specified or not found, fall back to main content - const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent) return docContent.textContent; - - console.warn( - "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." - ); - return ""; - }, - - init: () => { - const query = new URLSearchParams(window.location.search).get("q"); - document - .querySelectorAll('input[name="q"]') - .forEach((el) => (el.value = query)); - if (query) Search.performSearch(query); - }, - - loadIndex: (url) => - (document.body.appendChild(document.createElement("script")).src = url), - - setIndex: (index) => { - Search._index = index; - if (Search._queued_query !== null) { - const query = Search._queued_query; - Search._queued_query = null; - Search.query(query); - } - }, - - hasIndex: () => Search._index !== null, - - deferQuery: (query) => (Search._queued_query = query), - - stopPulse: () => (Search._pulse_status = -1), - - startPulse: () => { - if (Search._pulse_status >= 0) return; - - const pulse = () => { - Search._pulse_status = (Search._pulse_status + 1) % 4; - Search.dots.innerText = ".".repeat(Search._pulse_status); - if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); - }; - pulse(); - }, - - /** - * perform a search for something (or wait until index is loaded) - */ - performSearch: (query) => { - // create the required interface elements - const searchText = document.createElement("h2"); - searchText.textContent = _("Searching"); - const searchSummary = document.createElement("p"); - searchSummary.classList.add("search-summary"); - searchSummary.innerText = ""; - const searchList = document.createElement("ul"); - searchList.setAttribute("role", "list"); - searchList.classList.add("search"); - - const out = document.getElementById("search-results"); - Search.title = out.appendChild(searchText); - Search.dots = Search.title.appendChild(document.createElement("span")); - Search.status = out.appendChild(searchSummary); - Search.output = out.appendChild(searchList); - - const searchProgress = document.getElementById("search-progress"); - // Some themes don't use the search progress node - if (searchProgress) { - searchProgress.innerText = _("Preparing search..."); - } - Search.startPulse(); - - // index already loaded, the browser was quick! - if (Search.hasIndex()) Search.query(query); - else Search.deferQuery(query); - }, - - _parseQuery: (query) => { - // stem the search terms and add them to the correct list - const stemmer = new Stemmer(); - const searchTerms = new Set(); - const excludedTerms = new Set(); - const highlightTerms = new Set(); - const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); - splitQuery(query.trim()).forEach((queryTerm) => { - const queryTermLower = queryTerm.toLowerCase(); - - // maybe skip this "word" - // stopwords array is from language_data.js - if ( - stopwords.indexOf(queryTermLower) !== -1 || - queryTerm.match(/^\d+$/) - ) - return; - - // stem the word - let word = stemmer.stemWord(queryTermLower); - // select the correct list - if (word[0] === "-") excludedTerms.add(word.substr(1)); - else { - searchTerms.add(word); - highlightTerms.add(queryTermLower); - } - }); - - if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js - localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) - } - - // console.debug("SEARCH: searching for:"); - // console.info("required: ", [...searchTerms]); - // console.info("excluded: ", [...excludedTerms]); - - return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; - }, - - /** - * execute search (requires search index to be loaded) - */ - _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - - // Collect multiple result groups to be sorted separately and then ordered. - // Each is an array of [docname, title, anchor, descr, score, filename, kind]. - const normalResults = []; - const nonMainIndexResults = []; - - _removeChildren(document.getElementById("search-progress")); - - const queryLower = query.toLowerCase().trim(); - for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { - for (const [file, id] of foundTitles) { - const score = Math.round(Scorer.title * queryLower.length / title.length); - const boost = titles[file] === title ? 1 : 0; // add a boost for document titles - normalResults.push([ - docNames[file], - titles[file] !== title ? `${titles[file]} > ${title}` : title, - id !== null ? "#" + id : "", - null, - score + boost, - filenames[file], - SearchResultKind.title, - ]); - } - } - } - - // search for explicit entries in index directives - for (const [entry, foundEntries] of Object.entries(indexEntries)) { - if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id, isMain] of foundEntries) { - const score = Math.round(100 * queryLower.length / entry.length); - const result = [ - docNames[file], - titles[file], - id ? "#" + id : "", - null, - score, - filenames[file], - SearchResultKind.index, - ]; - if (isMain) { - normalResults.push(result); - } else { - nonMainIndexResults.push(result); - } - } - } - } - - // lookup as object - objectTerms.forEach((term) => - normalResults.push(...Search.performObjectSearch(term, objectTerms)) - ); - - // lookup as search terms in fulltext - normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); - - // let the scorer override scores with a custom scoring function - if (Scorer.score) { - normalResults.forEach((item) => (item[4] = Scorer.score(item))); - nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); - } - - // Sort each group of results by score and then alphabetically by name. - normalResults.sort(_orderResultsByScoreThenName); - nonMainIndexResults.sort(_orderResultsByScoreThenName); - - // Combine the result groups in (reverse) order. - // Non-main index entries are typically arbitrary cross-references, - // so display them after other results. - let results = [...nonMainIndexResults, ...normalResults]; - - // remove duplicate search results - // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept - let seen = new Set(); - results = results.reverse().reduce((acc, result) => { - let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); - if (!seen.has(resultStr)) { - acc.push(result); - seen.add(resultStr); - } - return acc; - }, []); - - return results.reverse(); - }, - - query: (query) => { - const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); - const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); - - // for debugging - //Search.lastresults = results.slice(); // a copy - // console.info("search results:", Search.lastresults); - - // print the results - _displayNextItem(results, results.length, searchTerms, highlightTerms); - }, - - /** - * search for object names - */ - performObjectSearch: (object, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const objects = Search._index.objects; - const objNames = Search._index.objnames; - const titles = Search._index.titles; - - const results = []; - - const objectSearchCallback = (prefix, match) => { - const name = match[4] - const fullname = (prefix ? prefix + "." : "") + name; - const fullnameLower = fullname.toLowerCase(); - if (fullnameLower.indexOf(object) < 0) return; - - let score = 0; - const parts = fullnameLower.split("."); - - // check for different match types: exact matches of full name or - // "last name" (i.e. last dotted part) - if (fullnameLower === object || parts.slice(-1)[0] === object) - score += Scorer.objNameMatch; - else if (parts.slice(-1)[0].indexOf(object) > -1) - score += Scorer.objPartialMatch; // matches in last name - - const objName = objNames[match[1]][2]; - const title = titles[match[0]]; - - // If more than one term searched for, we require other words to be - // found in the name/title/description - const otherTerms = new Set(objectTerms); - otherTerms.delete(object); - if (otherTerms.size > 0) { - const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); - if ( - [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) - ) - return; - } - - let anchor = match[3]; - if (anchor === "") anchor = fullname; - else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; - - const descr = objName + _(", in ") + title; - - // add custom score for some objects according to scorer - if (Scorer.objPrio.hasOwnProperty(match[2])) - score += Scorer.objPrio[match[2]]; - else score += Scorer.objPrioDefault; - - results.push([ - docNames[match[0]], - fullname, - "#" + anchor, - descr, - score, - filenames[match[0]], - SearchResultKind.object, - ]); - }; - Object.keys(objects).forEach((prefix) => - objects[prefix].forEach((array) => - objectSearchCallback(prefix, array) - ) - ); - return results; - }, - - /** - * search for full-text terms in the index - */ - performTermsSearch: (searchTerms, excludedTerms) => { - // prepare search - const terms = Search._index.terms; - const titleTerms = Search._index.titleterms; - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - - const scoreMap = new Map(); - const fileMap = new Map(); - - // perform the search on the required terms - searchTerms.forEach((word) => { - const files = []; - const arr = [ - { files: terms[word], score: Scorer.term }, - { files: titleTerms[word], score: Scorer.title }, - ]; - // add support for partial matches - if (word.length > 2) { - const escapedWord = _escapeRegExp(word); - if (!terms.hasOwnProperty(word)) { - Object.keys(terms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: terms[term], score: Scorer.partialTerm }); - }); - } - if (!titleTerms.hasOwnProperty(word)) { - Object.keys(titleTerms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); - }); - } - } - - // no match but word was a required one - if (arr.every((record) => record.files === undefined)) return; - - // found search word in contents - arr.forEach((record) => { - if (record.files === undefined) return; - - let recordFiles = record.files; - if (recordFiles.length === undefined) recordFiles = [recordFiles]; - files.push(...recordFiles); - - // set score for the word in each file - recordFiles.forEach((file) => { - if (!scoreMap.has(file)) scoreMap.set(file, {}); - scoreMap.get(file)[word] = record.score; - }); - }); - - // create the mapping - files.forEach((file) => { - if (!fileMap.has(file)) fileMap.set(file, [word]); - else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); - }); - }); - - // now check if the files don't contain excluded terms - const results = []; - for (const [file, wordList] of fileMap) { - // check if all requirements are matched - - // as search terms with length < 3 are discarded - const filteredTermCount = [...searchTerms].filter( - (term) => term.length > 2 - ).length; - if ( - wordList.length !== searchTerms.size && - wordList.length !== filteredTermCount - ) - continue; - - // ensure that none of the excluded terms is in the search result - if ( - [...excludedTerms].some( - (term) => - terms[term] === file || - titleTerms[term] === file || - (terms[term] || []).includes(file) || - (titleTerms[term] || []).includes(file) - ) - ) - break; - - // select one (max) score for the file. - const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); - // add result to the result list - results.push([ - docNames[file], - titles[file], - "", - null, - score, - filenames[file], - SearchResultKind.text, - ]); - } - return results; - }, - - /** - * helper function to return a node containing the - * search summary for a given text. keywords is a list - * of stemmed words. - */ - makeSearchSummary: (htmlText, keywords, anchor) => { - const text = Search.htmlToText(htmlText, anchor); - if (text === "") return null; - - const textLower = text.toLowerCase(); - const actualStartPosition = [...keywords] - .map((k) => textLower.indexOf(k.toLowerCase())) - .filter((i) => i > -1) - .slice(-1)[0]; - const startWithContext = Math.max(actualStartPosition - 120, 0); - - const top = startWithContext === 0 ? "" : "..."; - const tail = startWithContext + 240 < text.length ? "..." : ""; - - let summary = document.createElement("p"); - summary.classList.add("context"); - summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; - - return summary; - }, -}; - -_ready(Search.init); diff --git a/docs/1.0.3/_static/sphinx_highlight.js b/docs/1.0.3/_static/sphinx_highlight.js deleted file mode 100644 index 8a96c69a..00000000 --- a/docs/1.0.3/_static/sphinx_highlight.js +++ /dev/null @@ -1,154 +0,0 @@ -/* Highlighting utilities for Sphinx HTML documentation. */ -"use strict"; - -const SPHINX_HIGHLIGHT_ENABLED = true - -/** - * highlight a given string on a node by wrapping it in - * span elements with the given class name. - */ -const _highlight = (node, addItems, text, className) => { - if (node.nodeType === Node.TEXT_NODE) { - const val = node.nodeValue; - const parent = node.parentNode; - const pos = val.toLowerCase().indexOf(text); - if ( - pos >= 0 && - !parent.classList.contains(className) && - !parent.classList.contains("nohighlight") - ) { - let span; - - const closestNode = parent.closest("body, svg, foreignObject"); - const isInSVG = closestNode && closestNode.matches("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.classList.add(className); - } - - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - const rest = document.createTextNode(val.substr(pos + text.length)); - parent.insertBefore( - span, - parent.insertBefore( - rest, - node.nextSibling - ) - ); - node.nodeValue = val.substr(0, pos); - /* There may be more occurrences of search term in this node. So call this - * function recursively on the remaining fragment. - */ - _highlight(rest, addItems, text, className); - - if (isInSVG) { - const rect = document.createElementNS( - "http://www.w3.org/2000/svg", - "rect" - ); - const bbox = parent.getBBox(); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute("class", className); - addItems.push({ parent: parent, target: rect }); - } - } - } else if (node.matches && !node.matches("button, select, textarea")) { - node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); - } -}; -const _highlightText = (thisNode, text, className) => { - let addItems = []; - _highlight(thisNode, addItems, text, className); - addItems.forEach((obj) => - obj.parent.insertAdjacentElement("beforebegin", obj.target) - ); -}; - -/** - * Small JavaScript module for the documentation. - */ -const SphinxHighlight = { - - /** - * highlight the search words provided in localstorage in the text - */ - highlightSearchWords: () => { - if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight - - // get and clear terms from localstorage - const url = new URL(window.location); - const highlight = - localStorage.getItem("sphinx_highlight_terms") - || url.searchParams.get("highlight") - || ""; - localStorage.removeItem("sphinx_highlight_terms") - url.searchParams.delete("highlight"); - window.history.replaceState({}, "", url); - - // get individual terms from highlight string - const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); - if (terms.length === 0) return; // nothing to do - - // There should never be more than one element matching "div.body" - const divBody = document.querySelectorAll("div.body"); - const body = divBody.length ? divBody[0] : document.querySelector("body"); - window.setTimeout(() => { - terms.forEach((term) => _highlightText(body, term, "highlighted")); - }, 10); - - const searchBox = document.getElementById("searchbox"); - if (searchBox === null) return; - searchBox.appendChild( - document - .createRange() - .createContextualFragment( - '

' + - '' + - _("Hide Search Matches") + - "

" - ) - ); - }, - - /** - * helper function to hide the search marks again - */ - hideSearchWords: () => { - document - .querySelectorAll("#searchbox .highlight-link") - .forEach((el) => el.remove()); - document - .querySelectorAll("span.highlighted") - .forEach((el) => el.classList.remove("highlighted")); - localStorage.removeItem("sphinx_highlight_terms") - }, - - initEscapeListener: () => { - // only install a listener if it is really needed - if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; - - document.addEventListener("keydown", (event) => { - // bail for input elements - if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; - // bail with special keys - if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; - if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { - SphinxHighlight.hideSearchWords(); - event.preventDefault(); - } - }); - }, -}; - -_ready(() => { - /* Do not call highlightSearchWords() when we are on the search page. - * It will highlight words from the *previous* search query. - */ - if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); - SphinxHighlight.initEscapeListener(); -}); diff --git a/docs/1.0.3/autodoc/mmif.serialize.html b/docs/1.0.3/autodoc/mmif.serialize.html deleted file mode 100644 index ebe20af5..00000000 --- a/docs/1.0.3/autodoc/mmif.serialize.html +++ /dev/null @@ -1,1271 +0,0 @@ - - - - - - - - - mmif.serialize module — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
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mmif.serialize module

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mmif.serialize.model module

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The model module contains the classes used to represent an -abstract MMIF object as a live Python object.

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The MmifObject class or one of its derivatives is subclassed by -all other classes defined in this SDK, except for MmifObjectEncoder.

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These objects are generally instantiated from JSON, either as a string -or as an already-loaded Python dictionary. This base class provides the -core functionality for deserializing MMIF JSON data into live objects -and serializing live objects into MMIF JSON data. Specialized behavior -for the different components of MMIF is added in the subclasses.

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-class mmif.serialize.model.DataDict(mmif_obj: bytes | str | dict | None = None)[source]
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Bases: MmifObject, Generic[T, S]

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-empty()[source]
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-get(key: T, default=None) → S | None[source]
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-items()[source]
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-keys()[source]
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-update(other, overwrite)[source]
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-values()[source]
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-class mmif.serialize.model.DataList(mmif_obj: bytes | str | list | None = None)[source]
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Bases: MmifObject, Generic[T]

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The DataList class is an abstraction that represents the -various lists found in a MMIF file, such as documents, subdocuments, -views, and annotations.

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Parameters:
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mmif_obj (Union[str, list]) – the data that the list contains

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-append(value, overwrite)[source]
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-deserialize(mmif_json: str | list) → None[source]
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Passes the input data into the internal deserializer.

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-empty()[source]
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-get(key: str) → T | None[source]
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Standard dictionary-style get() method, albeit with no default -parameter. Relies on the implementation of __getitem__.

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Will return None if the key is not found.

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Parameters:
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key – the key to search for

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Returns:
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the value matching that key

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-class mmif.serialize.model.MmifObject(mmif_obj: bytes | str | dict | None = None)[source]
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Bases: object

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Abstract superclass for MMIF related key-value pair objects.

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Any MMIF object can be initialized as an empty placeholder or -an actual representation with a JSON formatted string or equivalent -dict object argument.

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This superclass has four specially designed instance variables, and these -variable names cannot be used as attribute names for MMIF objects.

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  1. _unnamed_attributes: -Only can be either None or an empty dictionary. If it’s set to None, -it means the class won’t take any Additional Attributes in the JSON -schema sense. If it’s a dict, users can throw any k-v pairs to the -class, EXCEPT for the reserved two key names.

    2. -

  2. _attribute_classes: -This is a dict from a key name to a specific python class to use for -deserialize the value. Note that a key name in this dict does NOT -have to be a named attribute, but is recommended to be one.

    3. -

  3. _required_attributes: -This is a simple list of names of attributes that are required in the object. -When serialize, an object will skip its empty (e.g. zero-length, or None) -attributes unless they are in this list. Otherwise, the serialized JSON -string would have empty representations (e.g. "", []).

    4. -

  4. _exclude_from_diff: -This is a simple list of names of attributes that should be excluded from -the diff calculation in __eq__.

    5. -
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# TODO (krim @ 8/17/20): this dict is however, a duplicate with the type hints in the class definition. -Maybe there is a better way to utilize type hints (e.g. getting them as a programmatically), but for now -developers should be careful to add types to hints as well as to this dict.

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Also note that those special attributes MUST be set in the __init__() -before calling super method, otherwise deserialization will not work.

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And also, a subclass that has one or more named attributes, it must -set those attributes in the __init__() before calling super method. When -serializing a MmifObject, all empty attributes will be ignored, so for -optional named attributes, you must leave the values empty (len == 0), but -NOT None. Any None-valued named attributes will cause issues with current -implementation.

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Parameters:
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mmif_obj – JSON string or dict to initialize an object. -If not given, an empty object will be initialized, sometimes with -an ID value automatically generated, based on its parent object.

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-deserialize(mmif_json: str | dict) → None[source]
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Takes a JSON-formatted string or a simple dict that’s json-loaded from -such a string as an input and populates object’s fields with the values -specified in the input.

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Parameters:
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mmif_json – JSON-formatted string or dict from such a string -that represents a MMIF object

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-disallow_additional_properties() → None[source]
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Call this method in __init__() to prevent the insertion -of unnamed attributes after initialization.

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-static is_empty(obj) → bool[source]
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return True if the obj is None or “emtpy”. The emptiness first defined as -having zero length. But for objects that lack __len__ method, we need -additional check.

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-reserved_names: Set[str] = {'_attribute_classes', '_exclude_from_diff', '_required_attributes', '_unnamed_attributes', 'reserved_names'}[source]
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-serialize(pretty: bool = False) → str[source]
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Generates JSON representation of an object.

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Parameters:
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pretty – If True, returns string representation with indentation.

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Returns:
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JSON string of the object.

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-set_additional_property(key: str, value: Any) → None[source]
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Method to set values in _unnamed_attributes.

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Parameters:
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  • key – the attribute name

    • -

  • value – the desired value

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Returns:
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None

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Raise:
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AttributeError if additional properties are disallowed by disallow_additional_properties()

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-class mmif.serialize.model.MmifObjectEncoder(*, skipkeys=False, ensure_ascii=True, check_circular=True, allow_nan=True, sort_keys=False, indent=None, separators=None, default=None)[source]
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Bases: JSONEncoder

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Encoder class to define behaviors of de-/serialization

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-default(obj: MmifObject)[source]
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Overrides default encoding behavior to prioritize MmifObject.serialize().

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mmif.serialize.mmif module

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The mmif module contains the classes used to represent a full MMIF -file as a live Python object.

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See the specification docs and the JSON Schema file for more information.

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-class mmif.serialize.mmif.Mmif(mmif_obj: bytes | str | dict | None = None, *, validate: bool = True)[source]
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Bases: MmifObject

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MmifObject that represents a full MMIF file.

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Parameters:
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  • mmif_obj – the JSON data

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  • validate – whether to validate the data against the MMIF JSON schema.

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-add_document(document: Document, overwrite=False) → None[source]
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Appends a Document object to the documents list.

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Fails if there is already a document with the same ID in the MMIF object.

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Parameters:
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  • document – the Document object to add

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  • overwrite – if set to True, will overwrite -an existing view with the same ID

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Returns:
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None

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-add_view(view: View, overwrite=False) → None[source]
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Appends a View object to the views list.

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Fails if there is already a view with the same ID in the MMIF object.

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Parameters:
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  • view – the Document object to add

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  • overwrite – if set to True, will overwrite -an existing view with the same ID

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Returns:
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None

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-generate_capital_annotations()[source]
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Automatically convert any “pending” temporary properties from -Document objects to Annotation objects . The generated Annotation -objects are then added to the last View in the views lists.

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See https://github.com/clamsproject/mmif-python/issues/226 for rationale -behind this behavior and discussion.

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-get_alignments(at_type1: str | TypesBase, at_type2: str | TypesBase) → Dict[str, List[Annotation]][source]
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Finds views where alignments between two given annotation types occurred.

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Returns:
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a dict that keyed by view IDs (str) and has lists of alignment Annotation objects as values.

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-get_all_views_contain(at_types: TypesBase | str | List[str | TypesBase]) → List[View][source]
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Returns the list of all views in the MMIF if given types -are present in that view’s ‘contains’ metadata.

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Parameters:
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at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

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Returns:
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the list of views that contain the type

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-get_document_by_id(doc_id: str) → Document[source]
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Finds a Document object with the given ID.

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Parameters:
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doc_id – the ID to search for

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Returns:
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a reference to the corresponding document, if it exists

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Raises:
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KeyError – if there is no corresponding document

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-get_document_location(m_type: DocumentTypes | str, path_only=False) → str | None[source]
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Method to get the location of first document of given type.

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Parameters:
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m_type – the type to search for

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Returns:
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the value of the location field in the corresponding document

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-get_documents_by_app(app_id: str) → List[Document][source]
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Method to get all documents object queries by its originated app name.

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Parameters:
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app_id – the app name to search for

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Returns:
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a list of documents matching the requested app name, or an empty list if the app not found

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-get_documents_by_property(prop_key: str, prop_value: str) → List[Document][source]
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Method to retrieve documents by an arbitrary key-value pair in the document properties objects.

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Parameters:
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  • prop_key – the metadata key to search for

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  • prop_value – the metadata value to match

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Returns:
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a list of documents matching the requested metadata key-value pair

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-get_documents_by_type(doc_type: str | DocumentTypes) → List[Document][source]
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Method to get all documents where the type matches a particular document type, which should be one of the CLAMS document types.

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Parameters:
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doc_type – the type of documents to search for, must be one of Document type defined in the CLAMS vocabulary.

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Returns:
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a list of documents matching the requested type, or an empty list if none found.

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-get_documents_in_view(vid: str | None = None) → List[Document][source]
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Method to get all documents object queries by a view id.

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Parameters:
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vid – the source view ID to search for

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Returns:
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a list of documents matching the requested source view ID, or an empty list if the view not found

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-get_documents_locations(m_type: DocumentTypes | str, path_only=False) → List[str | None][source]
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This method returns the file paths of documents of given type. -Only top-level documents have locations, so we only check them.

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Parameters:
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m_type – the type to search for

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Returns:
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a list of the values of the location fields in the corresponding documents

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-get_view_by_id(req_view_id: str) → View[source]
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Finds a View object with the given ID.

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Parameters:
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req_view_id – the ID to search for

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Returns:
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a reference to the corresponding view, if it exists

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Raises:
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Exception – if there is no corresponding view

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-get_view_contains(at_types: TypesBase | str | List[str | TypesBase]) → View | None[source]
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Returns the last view appended that contains the given -types in its ‘contains’ metadata.

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Parameters:
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at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

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Returns:
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the view, or None if the type is not found

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-get_views_contain(at_types: TypesBase | str | List[str | TypesBase]) → List[View][source]
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An alias to get_all_views_contain method.

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-get_views_for_document(doc_id: str) → List[View][source]
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Returns the list of all views that have annotations anchored on a particular document. -Note that when the document is inside a view (generated during the pipeline’s running), -doc_id must be prefixed with the view_id.

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-id_delimiter: ClassVar[str] = ':'[source]
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-new_view() → View[source]
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Creates an empty view with a new ID and appends it to the views list.

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Returns:
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a reference to the new View object

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-new_view_id() → str[source]
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Fetches an ID for a new view.

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Returns:
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the ID

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-sanitize()[source]
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Sanitizes a Mmif object by running some safeguards. -Concretely, it performs the following before returning the JSON string.

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  1. validating output using built-in MMIF jsonschema

    2. -

  2. remove non-existing annotation types from contains metadata

    3. -
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-serialize(pretty: bool = False, sanitize: bool = False, autogenerate_capital_annotations=True) → str[source]
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Serializes the MMIF object to a JSON string.

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Parameters:
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  • sanitize – If True, performs some sanitization of before returning -the JSON string. See sanitize() for details.

    • -

  • autogenerate_capital_annotations – If True, automatically convert -any “pending” temporary properties from Document objects to -Annotation objects. See generate_capital_annotations() for -details.

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  • pretty – If True, returns string representation with indentation.

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Returns:
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JSON string of the MMIF object.

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-static validate(json_str: bytes | str | dict) → None[source]
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Validates a MMIF JSON object against the MMIF Schema. -Note that this method operates before processing by MmifObject._load_str, -so it expects @ and not _ for the JSON-LD @-keys.

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Raises:
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jsonschema.exceptions.ValidationError – if the input fails validation

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Parameters:
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json_str – a MMIF JSON dict or string

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Returns:
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None

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-view_prefix: ClassVar[str] = 'v_'[source]
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mmif.serialize.view module

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The view module contains the classes used to represent a MMIF view -as a live Python object.

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In MMIF, views are created by apps in a pipeline that are annotating -data that was previously present in the MMIF file.

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-class mmif.serialize.view.Contain(mmif_obj: bytes | str | dict | None = None)[source]
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Bases: DataDict[str, str]

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Contain object that represents the metadata of a single -annotation type in the contains metadata of a MMIF view.

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-class mmif.serialize.view.View(view_obj: bytes | str | dict | None = None)[source]
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Bases: MmifObject

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View object that represents a single view in a MMIF file.

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A view is identified by an ID, and contains certain metadata, -a list of annotations, and potentially a JSON-LD @context -IRI.

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If view_obj is not provided, an empty View will be generated.

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Parameters:
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view_obj – the JSON data that defines the view

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-add_annotation(annotation: Annotation, overwrite=False) → Annotation[source]
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Adds an annotation to the current view.

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Fails if there is already an annotation with the same ID -in the view, unless overwrite is set to True.

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Parameters:
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Raises:
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KeyError – if overwrite is set to False and -an annotation with the same ID exists -in the view

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Returns:
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the same Annotation object passed in as annotation

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-add_document(document: Document, overwrite=False) → Annotation[source]
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Appends a Document object to the annotations list.

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Fails if there is already a document with the same ID in the annotations list.

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Parameters:
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  • document – the Document object to add

    • -

  • overwrite – if set to True, will overwrite -an existing view with the same ID

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Returns:
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None

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-get_annotation_by_id(ann_id)[source]
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-get_annotations(at_type: str | TypesBase | None = None, **properties) → Generator[Annotation, None, None][source]
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Look for certain annotations in this view, specified by parameters

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Parameters:
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  • at_type – @type of the annotations to look for. When this is None, any @type will match.

    • -

  • properties – properties of the annotations to look for. When given more than one property, all properties must match. Note that annotation type metadata are specified in the contains view metadata, not in individual annotation objects.

    • -
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-get_document_by_id(doc_id) → Document[source]
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-get_documents() → List[Document][source]
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-new_annotation(at_type: str | TypesBase, aid: str | None = None, overwrite=False, **properties) → Annotation[source]
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Generates a new mmif.serialize.annotation.Annotation -object and adds it to the current view.

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Fails if there is already an annotation with the same ID -in the view, unless overwrite is set to True.

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Parameters:
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  • at_type – the desired @type of the annotation.

    • -

  • aid – the desired ID of the annotation, when not given, -the mmif SDK tries to automatically generate an ID based on -Annotation type and existing annotations in the view.

    • -

  • overwrite – if set to True, will overwrite an -existing annotation with the same ID.

    • -
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Raises:
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KeyError – if overwrite is set to False and -an annotation with the same ID exists -in the view.

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Returns:
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the generated mmif.serialize.annotation.Annotation

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-new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
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Adds a new element to the contains metadata.

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Parameters:
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  • at_type – the @type of the annotation type being added

    • -

  • contains_metadata – any metadata associated with the annotation type

    • -
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Returns:
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the generated Contain object

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-new_textdocument(text: str, lang: str = 'en', did: str | None = None, overwrite=False, **properties) → Document[source]
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Generates a new mmif.serialize.annotation.Document -object, particularly typed as TextDocument and adds it to the current view.

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Fails if there is already a text document with the same ID -in the view, unless overwrite is set to True.

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Parameters:
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  • text – text content of the new document

    • -

  • lang – ISO 639-1 code of the language used in the new document

    • -

  • did – the desired ID of the document, when not given, -the mmif SDK tries to automatically generate an ID based on -Annotation type and existing documents in the view.

    • -

  • overwrite – if set to True, will overwrite an -existing document with the same ID

    • -
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Raises:
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KeyError – if overwrite is set to False and -an document with the same ID exists -in the view

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Returns:
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the generated mmif.serialize.annotation.Document

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-set_error(err_message: str, err_trace: str) → None[source]
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-class mmif.serialize.view.ViewMetadata(viewmetadata_obj: bytes | str | dict | None = None)[source]
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Bases: MmifObject

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ViewMetadata object that represents the metadata object within a MMIF view.

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Parameters:
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viewmetadata_obj – the JSON data that defines the metadata

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-add_contain(contain: Contain, at_type: str | TypesBase)[source]
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-add_parameter(param_key, param_value)[source]
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-add_parameters(**runtime_params)[source]
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-add_warnings(*warnings: Warning)[source]
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-emtpy_warnings()[source]
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-get_parameter(param_key)[source]
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-new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
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Adds a new element to the contains dictionary.

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Parameters:
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    -

  • at_type – the @type of the annotation type being added

    • -

  • contains_metadata – any metadata associated with the annotation type

    • -
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Returns:
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the generated Contain object

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-set_error(message: str, stack_trace: str)[source]
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mmif.serialize.annotation module

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The annotation module contains the classes used to represent a -MMIF annotation as a live Python object.

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In MMIF, annotations are created by apps in a pipeline as a part -of a view. For documentation on how views are represented, see -mmif.serialize.view.

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-class mmif.serialize.annotation.Annotation(anno_obj: bytes | str | dict | None = None)[source]
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Bases: MmifObject

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MmifObject that represents an annotation in a MMIF view.

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-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]]) → None[source]
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Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

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- -
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-property at_type: TypesBase[source]
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- -
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-static check_prop_value_is_simple_enough(value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]])[source]
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- -
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-get(prop_name: str) → AnnotationProperties | str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]][source]
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A special getter for Annotation properties. This is to allow for -directly accessing properties without having to go through the -properties object.

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- -
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-get_property(prop_name: str) → AnnotationProperties | str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]][source]
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A special getter for Annotation properties. This is to allow for -directly accessing properties without having to go through the -properties object.

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- -
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-property id: str[source]
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- -
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-is_document()[source]
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- -
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-is_type(at_type: str | TypesBase) → bool[source]
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Check if the @type of this object matches.

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- -
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-property parent: str[source]
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- -
- -
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-class mmif.serialize.annotation.AnnotationProperties(mmif_obj: bytes | str | dict | None = None)[source]
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Bases: MmifObject, MutableMapping[str, T]

-

AnnotationProperties object that represents the -properties object within a MMIF annotation.

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Parameters:
-

mmif_obj – the JSON data that defines the properties

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- -
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-class mmif.serialize.annotation.Document(doc_obj: bytes | str | dict | None = None)[source]
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Bases: Annotation

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Document object that represents a single document in a MMIF file.

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A document is identified by an ID, and contains certain attributes -and potentially contains the contents of the document itself, -metadata about how the document was created, and/or a list of -subdocuments grouped together logically.

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If document_obj is not provided, an empty Document will be generated.

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Parameters:
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document_obj – the JSON data that defines the document

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-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None]) → None[source]
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Adds a property to the document’s properties.

-

Unlike the parent Annotation class, added properties of a -Document object can be lost during serialization unless it belongs -to somewhere in a Mmif object. This is because we want to keep -Document object as “read-only” as possible. Thus, if you want to add -a property to a Document object,

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    -

  • add the document to a Mmif object (either in the documents list or -in a view from the views list), or

    • -

  • directly write to Document.properties instead of using this method -(which is not recommended).

    • -
-

With the former method, the SDK will record the added property as a -Annotation annotation object, separate from the original Document -object. See Mmif.generate_capital_annotations() for more.

-

A few notes to keep in mind:

-
    -

  1. You can’t overwrite an existing property of a Document object.

    2. -

  2. A MMIF can have multiple Annotation objects with the same -property name but different values. When this happens, the SDK will -only keep the latest value (in order of appearances in views list) of -the property, effectively overwriting the previous values.

    3. -
-
- -
-
-get(prop_name)[source]
-

A special getter for Document properties. This is to allow for reading -the three properties in a specific order so that the latest value is -returned, in case there are multiple values for the same key.

-
- -
-
-get_property(prop_name)[source]
-

A special getter for Document properties. This is to allow for reading -the three properties in a specific order so that the latest value is -returned, in case there are multiple values for the same key.

-
- -
-
-property location: str | None[source]
-

location property must be a legitimate URI. That is, should the document be a local file -then the file:// scheme must be used. -Returns None when no location is set.

-
- -
-
-location_address() → str | None[source]
-

Retrieves the full address from the document location URI. -Returns None when no location is set.

-
- -
-
-location_path() → str | None[source]
-

Retrieves a path that’s resolved to a pathname in the local file system. -To obtain the original value of the “path” part in the location string -(before resolving), use properties.location_path_literal method. -Returns None when no location is set.

-
- -
-
-location_scheme() → str | None[source]
-

Retrieves URI scheme of the document location. -Returns None when no location is set.

-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.DocumentProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: AnnotationProperties

-

DocumentProperties object that represents the -properties object within a MMIF document.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
-
-property location: str | None[source]
-

location property must be a legitimate URI. That is, should the document be a local file -then the file:// scheme must be used. -Returns None when no location is set.

-
- -
-
-location_address() → str | None[source]
-

Retrieves the full address from the document location URI. -Returns None when no location is set.

-
- -
-
-location_path() → str | None[source]
-
- -
-
-location_path_literal() → str | None[source]
-

Retrieves only path name of the document location (hostname is ignored). -Returns None when no location is set.

-
- -
-
-location_path_resolved(nonexist_ok=True) → str | None[source]
-

Retrieves only path name of the document location (hostname is ignored), -and then try to resolve the path name in the local file system. -This method should be used when the document scheme is file or empty. -For other schemes, users should install mmif-locdoc-<scheme> plugin.

-

Returns None when no location is set. -Raise ValueError when no code found to resolve the given location scheme.

-
- -
-
-location_scheme() → str | None[source]
-

Retrieves URI scheme of the document location. -Returns None when no location is set.

-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.Text(text_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-
-
-property lang: str[source]
-
- -
-
-property value: str[source]
-
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- - - \ No newline at end of file diff --git a/docs/1.0.3/autodoc/mmif.vocabulary.html b/docs/1.0.3/autodoc/mmif.vocabulary.html deleted file mode 100644 index 503f25c1..00000000 --- a/docs/1.0.3/autodoc/mmif.vocabulary.html +++ /dev/null @@ -1,325 +0,0 @@ - - - - - - - - - mmif.vocabulary module — mmif-python documentation - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.vocabulary module

-
-

mmif.vocabulary.annotation_types module

-
-
-class mmif.vocabulary.annotation_types.AnnotationTypes(type_uri, fuzzymode=True)[source]
-

Bases: AnnotationTypesBase

-

This class contains the CLAMS annotation types -defined in the spec version 1.1.0 as class variables.

-
-
-Alignment = http://mmif.clams.ai/vocabulary/Alignment/v1[source]
-
- -
-
-Annotation = http://mmif.clams.ai/vocabulary/Annotation/v6[source]
-
- -
-
-BoundingBox = http://mmif.clams.ai/vocabulary/BoundingBox/v5[source]
-
- -
-
-Chapter = http://mmif.clams.ai/vocabulary/Chapter/v6[source]
-
- -
-
-Interval = http://mmif.clams.ai/vocabulary/Interval/v5[source]
-
- -
-
-NamedEntity = http://mmif.clams.ai/vocabulary/NamedEntity/v1[source]
-
- -
-
-NounChunk = http://mmif.clams.ai/vocabulary/NounChunk/v1[source]
-
- -
-
-Paragraph = http://mmif.clams.ai/vocabulary/Paragraph/v1[source]
-
- -
-
-Polygon = http://mmif.clams.ai/vocabulary/Polygon/v5[source]
-
- -
-
-Region = http://mmif.clams.ai/vocabulary/Region/v5[source]
-
- -
-
-Relation = http://mmif.clams.ai/vocabulary/Relation/v5[source]
-
- -
-
-Sentence = http://mmif.clams.ai/vocabulary/Sentence/v1[source]
-
- -
-
-Span = http://mmif.clams.ai/vocabulary/Span/v5[source]
-
- -
-
-TimeFrame = http://mmif.clams.ai/vocabulary/TimeFrame/v6[source]
-
- -
-
-TimePoint = http://mmif.clams.ai/vocabulary/TimePoint/v5[source]
-
- -
-
-Token = http://mmif.clams.ai/vocabulary/Token/v1[source]
-
- -
-
-VerbChunk = http://mmif.clams.ai/vocabulary/VerbChunk/v1[source]
-
- -
-
-VideoObject = http://mmif.clams.ai/vocabulary/VideoObject/v5[source]
-
- -
-
-typevers = {'Alignment': 'v1', 'Annotation': 'v6', 'BoundingBox': 'v5', 'Chapter': 'v6', 'Interval': 'v5', 'NamedEntity': 'v1', 'NounChunk': 'v1', 'Paragraph': 'v1', 'Polygon': 'v5', 'Region': 'v5', 'Relation': 'v5', 'Sentence': 'v1', 'Span': 'v5', 'TimeFrame': 'v6', 'TimePoint': 'v5', 'Token': 'v1', 'VerbChunk': 'v1', 'VideoObject': 'v5'}[source]
-
- -
- -
-
-

mmif.vocabulary.document_types module

-
-
-class mmif.vocabulary.document_types.DocumentTypes(type_uri, fuzzymode=True)[source]
-

Bases: DocumentTypesBase

-

This class contains the CLAMS document types -defined in the spec version 1.1.0 as class variables.

-
-
-AudioDocument = http://mmif.clams.ai/vocabulary/AudioDocument/v1[source]
-
- -
-
-Document = http://mmif.clams.ai/vocabulary/Document/v1[source]
-
- -
-
-ImageDocument = http://mmif.clams.ai/vocabulary/ImageDocument/v1[source]
-
- -
-
-TextDocument = http://mmif.clams.ai/vocabulary/TextDocument/v1[source]
-
- -
-
-VideoDocument = http://mmif.clams.ai/vocabulary/VideoDocument/v1[source]
-
- -
-
-typevers = {'AudioDocument': 'v1', 'Document': 'v1', 'ImageDocument': 'v1', 'TextDocument': 'v1', 'VideoDocument': 'v1'}[source]
-
- -
- -
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 1.0.3 - - -
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0.3.3
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- - - \ No newline at end of file diff --git a/docs/1.0.3/consumer-tutorial.html b/docs/1.0.3/consumer-tutorial.html deleted file mode 100644 index 95d0e9c3..00000000 --- a/docs/1.0.3/consumer-tutorial.html +++ /dev/null @@ -1,171 +0,0 @@ - - - - - - - - - MMIF consumer — mmif-python documentation - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • MMIF consumer
    • -
  • -
    • -
-
-
-
-
- -
-

MMIF consumer

-

A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the appliance documentation to learn more about the appliance.

-

MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance.

-
    -

  1. The code must be hosted on a public git repository (e.g. Github, Gitlab, …)

    2. -

  2. Must listen to 5000 port.

    3. -

  3. Must expose /display route .

    4. -

  4. /display router should response to GET requests.

    5. -

  5. In the GET request, a public URL of the input MMIF file is passed via file URL parameter.

    6. -

  6. On the codebase root, there must be a Dockerfile that can build a docker image that runs the web app.

    7. -
-

We provide an example consumer at https://github.com/clamsproject/mmif-visualizer.

-
- - -
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- -
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-
-
- -
- - Other Versions - v: 1.0.3 - - -
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- - -
- -
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    -
    • -
  • Index
    • -
  • -
    • -
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Index

- -
- A - | B - | C - | D - | E - | G - | I - | K - | L - | M - | N - | P - | R - | S - | T - | U - | V - -
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A

- - - -
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B

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- - -
- -
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  • Welcome to mmif-python’s documentation!
    • -
  • -
    • -
-
-
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- -
-

Welcome to mmif-python’s documentation!

-
-

MultiMedia Interchange Format

-

MMIF is a JSON(-LD)-based data format designed for transferring annotation data between computational analysis applications in CLAMS project.

-
-

Contents

- -
-
-

API documentation:

- -
-
-
-
-

Indices and tables

- -
- - -
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- - -
- -
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  • Getting Started
    • -
  • -
    • -
-
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-
- -
-

Getting Started

-
-

Overview

-

MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for reproducibility, transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF website. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects.

-
-
-

Prerequisites

-
    -

  • Python: the latest mmif-python requires Python 3.8 or newer. We have no plan to support Python 2.7.

    • -
-
-
-

Installation

-

Package mmif-python is distributed via the official PyPI. Users are supposed to pip-install to get latest release.

-
pip install mmif-python
-
-
-

This will install a package mmif to local python.

-

The MMIF format and specification is evolving over time, and mmif-python package will be updated along with the changes in MMIF format.

-
-

Note

-

MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and mmif-python versions, please take time to read our decision on the subject here. If you need to know which python SDK supports which specification version, see Target MMIF Versions page.

-
-
-
-

MMIF Serialization

-

mmif.serialize.mmif.Mmif represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of mmif.serialize.model.MmifObject, including the mmif.serialize.mmif.Mmif. To start with an existing MMIF str, simple initiate a new Mmif object with the file.

-
import mmif
-from mmif import Mmif
-
-mmif_str = """{
-"metadata": {
-  "mmif": "http://mmif.clams.ai/1.0.0"
-},
-"documents": [
-  {
-    "@type": "http://mmif.clams.ai/vocabulary/VideoDocument/v1",
-    "properties": {
-      "id": "m1",
-      "mime": "video/mp4",
-      "location": "file:///var/archive/video-0012.mp4"
-    }
-  },
-  {
-    "@type": "http://mmif.clams.ai/vocabulary/TextDocument/v1",
-    "properties": {
-      "id": "m2",
-      "mime": "text/plain",
-      "location": "file:///var/archive/video-0012-transcript.txt"
-    }
-  }
-],
-"views": []}"""
-mmif_obj = Mmif(mmif_str)
-
-
-

Few notes;

-
    -

  1. MMIF does not carry the primary source files in it.

    2. -

  2. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version mmif-python implementation of the MMIF might not be able to load an unsupported version of MMIF string.

    3. -
-

When serializing back to str, call mmif.serialize.model.MmifObject.serialize() on the object.

-

To get subcomponents, you can use various getters implemented in subclasses. For example;

-
from mmif.vocabulary.document_types import DocumentTypes
-
-for video in mmif_obj.Mmif.get_documents_by_type(DocumentTypes.VideoDocument):
-  with open(video.location_path(), 'b') as in_video:
-    # do something with the video file
-
-
-

For a full list of available helper methods, please refer to the API documentation.

-
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- -
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- - Other Versions - v: 1.0.3 - - -
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- - - \ No newline at end of file diff --git a/docs/1.0.3/modules.html b/docs/1.0.3/modules.html deleted file mode 100644 index 5023494f..00000000 --- a/docs/1.0.3/modules.html +++ /dev/null @@ -1,349 +0,0 @@ - - - - - - - - - mmif package — mmif-python documentation - - - - - - - - - - - - - - - - - -
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  • mmif package
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  • -
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mmif package

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- - - \ No newline at end of file diff --git a/docs/1.0.3/objects.inv b/docs/1.0.3/objects.inv deleted file mode 100644 index 0b570e52..00000000 Binary files a/docs/1.0.3/objects.inv and /dev/null differ diff --git a/docs/1.0.3/plugins.html b/docs/1.0.3/plugins.html deleted file mode 100644 index 7156f9ea..00000000 --- a/docs/1.0.3/plugins.html +++ /dev/null @@ -1,227 +0,0 @@ - - - - - - - - - Developing plugins for MMIF Python SDK — mmif-python documentation - - - - - - - - - - - - - - - - - -
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  • Developing plugins for MMIF Python SDK
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Developing plugins for MMIF Python SDK

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Overview

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As MMIF JSON files can carry information about media document files without actually carrying file contents, file accessing modules in mmif Python package (distributed as mmif-python on PyPI) are designed to be lightweight and flexible so that it can work with additional “plugin” Python packages that can handle concrete file access.

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This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF website. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects.

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Developer can write simple plugins that can provide additional functionalities to mmif-python. For example, mmif-python does not provide any file access functionality beyond a local file system (with file scheme), but it can be extended with a plugin that can handle file access over different protocols (e.g. http, s3, ftp, etc).

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This document contains information about how to write plugins for mmif-python.

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Document Location Scheme Plugins

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mmif.serialize.annotation.Document class has various methods to access parts of location property of the document. The location is in URI/IRI format (SCHEME://HOSTNAME/PATH, in a nutshell) and it has to be resolved to a local file for CLAMS Apps to process the local file to analyze and extract information about the media and its contents. The core mmif-python distribution only provides a default implementation that can handle file scheme URIs.

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To add a document location handler plugin, you need to implement a Python “package” (do not confuse with PYPI distribution), that meets these requirements;

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  1. the package must be named mmif_docloc_<SCHEME>. For example, to implement a handler for s3 scheme, the package name must be mmif_docloc_s3. The prefix is important as it’s used in the plugin discovery process from the core mmif-python modules.

    2. -

  2. the top module of the package must have a function named resolve. The function must take a single argument, which is a str of the document location URI. The function must return a str of the local file path. For example, if the document location is s3://mybucket/myfile.mp4, a Python user should be able to to something like this;

    3. -
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import mmif_docloc_s3
-resolved = mmif_docloc_s3.resolve('s3://mybucket/myfile.mp4')
-# then resolved must be a local file path that can be used to open the file
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Here’s a minimal example codebase that you refer to when you develop a docloc plugin.

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(However, before you start writing your own plugin for a specific URI scheme, checking if there’s already a PyPI distribution for the scheme might be a good idea.)

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$ tree .
-.
-├── mmif_docloc_dummy
-│   └── __init__.py
-├── pyproject.toml
-└── setup.cfg
-
- $ cat pyproject.toml
-[build-system]
-requires = ["setuptools"]
-build-backend = "setuptools.build_meta"
-
-$ cat setup.cfg
-[metadata]
-name = mmif_docloc_dummy  # this name is IMPORTANT
-version = 0.0.1
-description = a plugin to mmif-pyhon to handle `dummy` location scheme
-
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And the plugin code.

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# mmif_docloc_dummy/__init__.py
-doc_types = {'video': 'mp4'}
-
-def resolve(docloc):
-    scheme = 'dummy'
-    if docloc.startswith(f'{scheme}://'):
-        doc_id, doc_type = docloc.split('.')
-        return f'/path/to/{doc_id}.{doc_types[doc_type]}'
-    else:
-        raise ValueError(f'cannot handle document location scheme: {docloc}')
-
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Python Module Index

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- - - - - - - - \ No newline at end of file diff --git a/docs/1.0.3/searchindex.js b/docs/1.0.3/searchindex.js deleted file mode 100644 index 028638e0..00000000 --- a/docs/1.0.3/searchindex.js +++ /dev/null @@ -1 +0,0 @@ -Search.setIndex({"alltitles": {"API documentation:": [[3, null]], "Contents": [[3, null]], "Developing plugins for MMIF Python SDK": [[6, null]], "Document Location Scheme Plugins": [[6, "document-location-scheme-plugins"]], "Getting Started": [[4, null]], "Indices and tables": [[3, "indices-and-tables"]], "Installation": [[4, "installation"]], "MMIF Serialization": [[4, "mmif-serialization"]], "MMIF consumer": [[2, null]], "MultiMedia Interchange Format": [[3, "multimedia-interchange-format"]], "Overview": [[4, "overview"], [6, "overview"]], "Prerequisites": [[4, "prerequisites"]], "Target MMIF Versions": [[7, null]], "Target Specification Versions": [[7, "id1"]], "Welcome to mmif-python\u2019s documentation!": [[3, null]], "mmif package": [[5, null]], 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[0, 4, 6], "when": [0, 4, 6], "where": 0, "whether": 0, "which": [0, 4, 6], "within": 0, "without": [0, 6], "won": 0, "work": [0, 6], "workflow": 4, "would": 0, "write": [0, 6], "you": [0, 4, 6], "your": 6, "zero": 0}, "titles": ["mmif.serialize module", "mmif.vocabulary module", "MMIF consumer", "Welcome to mmif-python\u2019s documentation!", "Getting Started", "mmif package", "Developing plugins for MMIF Python SDK", "Target MMIF Versions"], "titleterms": {"": 3, "annot": 0, "annotation_typ": 1, "api": 3, "consum": 2, "content": 3, "develop": 6, "document": [3, 6], "document_typ": 1, "format": 3, "get": 4, "indic": 3, "instal": 4, "interchang": 3, "locat": 6, "mmif": [0, 1, 2, 3, 4, 5, 6, 7], "model": 0, "modul": [0, 1], "multimedia": 3, "overview": [4, 6], "packag": 5, "plugin": 6, "prerequisit": 4, "python": [3, 6], "scheme": 6, "sdk": 6, "serial": [0, 4], "specif": 7, "start": 4, "tabl": 3, "target": 7, "version": 7, "view": 0, "vocabulari": 1, "welcom": 3}}) \ No newline at end of file diff --git a/docs/1.0.3/target-versions.html b/docs/1.0.3/target-versions.html deleted file mode 100644 index 80e354d5..00000000 --- a/docs/1.0.3/target-versions.html +++ /dev/null @@ -1,251 +0,0 @@ - - - - - - - - - Target MMIF Versions — mmif-python documentation - - - - - - - - - - - - - - - - - -
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This article provides targeting MMIF specification versions of different versions of mmif-python SDK.

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Target Specification Versions

mmif-python version

Target MMIF Specification

1.0.3

1.1.0

1.0.2

1.0.0

1.0.1

1.0.0

1.0.0

0.5.0

0.5.2

0.5.0

0.5.1

0.5.0

0.5.0

0.5.0

0.4.8

0.4.2

0.4.7

0.4.1

0.4.6

0.4.0

0.4.5

0.4.0

0.4.4

0.4.0

0.4.3

0.4.0

0.4.2

0.4.0

0.4.1

0.4.0

0.4.0

0.4.0

0.3.5

0.3.1

0.3.4

0.3.1

0.3.3

0.3.1

0.3.2

0.3.1

0.3.1

0.3.0

0.3.0

0.3.0

0.2.2

0.2.1

0.2.1

0.2.1

0.2.0

0.2.1

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0.4.0
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0.4.1
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0.4.2
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0.4.3
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0.4.4
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0.4.5
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0.4.6
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0.4.7
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0.4.8
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0.5.0
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0.5.1
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0.5.2
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1.0.0
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1.0.1
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1.0.10
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1.0.11
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1.0.12
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1.0.13
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1.0.14
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1.0.15
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1.0.16
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1.0.17
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1.0.18
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1.0.19
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1.0.2
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1.0.3
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1.0.4
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1.0.5
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1.0.6
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The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the `appliance documentation `_ to learn more about the appliance. - -MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance. - -#. The code must be hosted on a public git repository (e.g. Github, Gitlab, ...) -#. Must listen to ``5000`` port. -#. Must expose ``/display`` route . -#. ``/display`` router should response to ``GET`` requests. -#. In the ``GET`` request, a public URL of the input MMIF file is passed via ``file`` URL parameter. -#. On the codebase root, there must be a ``Dockerfile`` that can build a `docker `_ image that runs the web app. - -We provide an example consumer at https://github.com/clamsproject/mmif-visualizer. diff --git a/docs/1.0.4/_sources/index.rst.txt b/docs/1.0.4/_sources/index.rst.txt deleted file mode 100644 index beb56aae..00000000 --- a/docs/1.0.4/_sources/index.rst.txt +++ /dev/null @@ -1,26 +0,0 @@ -Welcome to mmif-python's documentation! -======================================= - -.. mdinclude:: ../README.md - -.. toctree:: - :maxdepth: 2 - :caption: Contents - - introduction - plugins - target-versions - -.. toctree:: - :maxdepth: 2 - :caption: API documentation: - - modules - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/docs/1.0.4/_sources/introduction.rst.txt b/docs/1.0.4/_sources/introduction.rst.txt deleted file mode 100644 index cfd9eaf7..00000000 --- a/docs/1.0.4/_sources/introduction.rst.txt +++ /dev/null @@ -1,89 +0,0 @@ -.. _introduction: - -Getting Started -=============== - - -Overview ---------- - -MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for reproducibility, transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF website `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects. - -Prerequisites -------------- - -* `Python `_: the latest ``mmif-python`` requires Python 3.8 or newer. We have no plan to support `Python 2.7 `_. - -Installation ---------------- - -Package ``mmif-python`` is distributed via the official PyPI. Users are supposed to pip-install to get latest release. - -.. code-block:: bash - - pip install mmif-python - -This will install a package `mmif` to local python. - -The MMIF format and specification is evolving over time, and ``mmif-python`` package will be updated along with the changes in MMIF format. - -.. note:: MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and ``mmif-python`` versions, please take time to read our decision on the subject `here `_. If you need to know which python SDK supports which specification version, see :ref:`target-versions` page. - -MMIF Serialization ---------------------------- - -:class:`mmif.serialize.mmif.Mmif` represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of :class:`mmif.serialize.model.MmifObject`, including the :class:`mmif.serialize.mmif.Mmif`. To start with an existing MMIF :class:`str`, simple initiate a new ``Mmif`` object with the file. - -.. code-block:: python - - import mmif - from mmif import Mmif - - mmif_str = """{ - "metadata": { - "mmif": "http://mmif.clams.ai/1.0.0" - }, - "documents": [ - { - "@type": "http://mmif.clams.ai/vocabulary/VideoDocument/v1", - "properties": { - "id": "m1", - "mime": "video/mp4", - "location": "file:///var/archive/video-0012.mp4" - } - }, - { - "@type": "http://mmif.clams.ai/vocabulary/TextDocument/v1", - "properties": { - "id": "m2", - "mime": "text/plain", - "location": "file:///var/archive/video-0012-transcript.txt" - } - } - ], - "views": []}""" - mmif_obj = Mmif(mmif_str) - - -Few notes; - -#. MMIF does not carry the primary source files in it. -#. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version ``mmif-python`` implementation of the MMIF might not be able to load an unsupported version of MMIF string. - -When serializing back to :class:`str`, call :meth:`mmif.serialize.model.MmifObject.serialize` on the object. - -To get subcomponents, you can use various getters implemented in subclasses. For example; - -.. code-block:: python - - from mmif.vocabulary.document_types import DocumentTypes - - for video in mmif_obj.Mmif.get_documents_by_type(DocumentTypes.VideoDocument): - with open(video.location_path(), 'b') as in_video: - # do something with the video file - - -For a full list of available helper methods, please refer to :ref:`the API documentation `. - diff --git a/docs/1.0.4/_sources/modules.rst.txt b/docs/1.0.4/_sources/modules.rst.txt deleted file mode 100644 index e4269c6d..00000000 --- a/docs/1.0.4/_sources/modules.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _apidoc: - -mmif package -============ - -.. toctree:: - :maxdepth: 4 - - autodoc/mmif.serialize - autodoc/mmif.vocabulary diff --git a/docs/1.0.4/_sources/plugins.rst.txt b/docs/1.0.4/_sources/plugins.rst.txt deleted file mode 100644 index 9e1505e9..00000000 --- a/docs/1.0.4/_sources/plugins.rst.txt +++ /dev/null @@ -1,75 +0,0 @@ -.. _plugins: - -Developing plugins for MMIF Python SDK -====================================== - - -Overview --------- - -As MMIF JSON files can carry information about media document files without actually carrying file contents, file accessing modules in ``mmif`` Python package (distributed as ``mmif-python`` on PyPI) are designed to be lightweight and flexible so that it can work with additional "plugin" Python packages that can handle concrete file access. - - -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF website `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects. - -Developer can write simple plugins that can provide additional functionalities to ``mmif-python``. For example, ``mmif-python`` does not provide any file access functionality beyond a local file system (with ``file`` scheme), but it can be extended with a plugin that can handle file access over different protocols (e.g. ``http``, ``s3``, ``ftp``, etc). - -This document contains information about how to write plugins for ``mmif-python``. - -Document Location Scheme Plugins -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -:class:`mmif.serialize.annotation.Document` class has various methods to access parts of ``location`` property of the document. The location is in `URI/IRI format `_ (``SCHEME://HOSTNAME/PATH``, in a nutshell) and it has to be resolved to a local file for CLAMS Apps to process the local file to analyze and extract information about the media and its contents. The core ``mmif-python`` distribution only provides a default implementation that can handle ``file`` scheme URIs. - -To add a document location handler plugin, you need to implement a Python `"package" `_ (do not confuse with PYPI distribution), that meets these requirements; - -#. the package must be named ``mmif_docloc_``. For example, to implement a handler for ``s3`` scheme, the package name must be ``mmif_docloc_s3``. The prefix is important as it's used in the plugin discovery process from the core ``mmif-python`` modules. -#. the top module of the package must have a function named ``resolve``. The function must take a single argument, which is a :class:`str` of the document location URI. The function must return a :class:`str` of the local file path. For example, if the document location is ``s3://mybucket/myfile.mp4``, a Python user should be able to to something like this; - -.. code-block:: python - - import mmif_docloc_s3 - resolved = mmif_docloc_s3.resolve('s3://mybucket/myfile.mp4') - # then resolved must be a local file path that can be used to open the file - - -Here's a minimal example codebase that you refer to when you develop a ``docloc`` plugin. - -(However, before you start writing your own plugin for a specific URI scheme, checking `if there's already a PyPI distribution `_ for the scheme might be a good idea.) - -.. code-block:: sh - - $ tree . - . - ├── mmif_docloc_dummy - │ └── __init__.py - ├── pyproject.toml - └── setup.cfg - - $ cat pyproject.toml - [build-system] - requires = ["setuptools"] - build-backend = "setuptools.build_meta" - - $ cat setup.cfg - [metadata] - name = mmif_docloc_dummy # this name is IMPORTANT - version = 0.0.1 - description = a plugin to mmif-pyhon to handle `dummy` location scheme - - -And the plugin code. - -.. code-block:: python - - # mmif_docloc_dummy/__init__.py - doc_types = {'video': 'mp4'} - - def resolve(docloc): - scheme = 'dummy' - if docloc.startswith(f'{scheme}://'): - doc_id, doc_type = docloc.split('.') - return f'/path/to/{doc_id}.{doc_types[doc_type]}' - else: - raise ValueError(f'cannot handle document location scheme: {docloc}') diff --git a/docs/1.0.4/_sources/target-versions.rst.txt b/docs/1.0.4/_sources/target-versions.rst.txt deleted file mode 100644 index 34216d3e..00000000 --- a/docs/1.0.4/_sources/target-versions.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _target-versions: - -Target MMIF Versions -==================== - -This article provides targeting MMIF specification versions of different versions of ``mmif-python`` SDK. - -.. csv-table:: Target Specification Versions - :file: target-versions.csv - :header-rows: 1 diff --git a/docs/1.0.4/_static/_sphinx_javascript_frameworks_compat.js b/docs/1.0.4/_static/_sphinx_javascript_frameworks_compat.js deleted file mode 100644 index 81415803..00000000 --- a/docs/1.0.4/_static/_sphinx_javascript_frameworks_compat.js +++ /dev/null @@ -1,123 +0,0 @@ -/* Compatability shim for jQuery and underscores.js. - * - * Copyright Sphinx contributors - * Released under the two clause BSD licence - */ - -/** - * small helper function to urldecode strings - * - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL - */ -jQuery.urldecode = function(x) { - if (!x) { - return x - } - return decodeURIComponent(x.replace(/\+/g, ' ')); -}; - -/** - * small helper function to urlencode strings - */ -jQuery.urlencode = encodeURIComponent; - -/** - * This function returns the parsed url parameters of the - * current request. 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span; - var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.className = className; - } - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - node.parentNode.insertBefore(span, node.parentNode.insertBefore( - document.createTextNode(val.substr(pos + text.length)), - node.nextSibling)); - node.nodeValue = val.substr(0, pos); - if (isInSVG) { - var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect"); - var bbox = node.parentElement.getBBox(); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute('class', className); - addItems.push({ - "parent": node.parentNode, - "target": rect}); - } - } - } - else if (!jQuery(node).is("button, select, textarea")) { - jQuery.each(node.childNodes, function() { - highlight(this, addItems); - }); - } - } - var addItems = []; - var result = this.each(function() { - highlight(this, addItems); - }); - for (var i = 0; i < addItems.length; ++i) { - jQuery(addItems[i].parent).before(addItems[i].target); - } - return result; -}; - -/* - * backward compatibility for jQuery.browser - * This will be supported until firefox bug is fixed. - */ -if (!jQuery.browser) { - jQuery.uaMatch = function(ua) { - ua = ua.toLowerCase(); - - var match = /(chrome)[ \/]([\w.]+)/.exec(ua) || - /(webkit)[ \/]([\w.]+)/.exec(ua) || - /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) || - /(msie) ([\w.]+)/.exec(ua) || - ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) || - []; - - return { - browser: match[ 1 ] || "", - version: match[ 2 ] || "0" - }; - }; - jQuery.browser = {}; - jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true; -} diff --git a/docs/1.0.4/_static/basic.css 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- -/** - * Simple result scoring code. - */ -if (typeof Scorer === "undefined") { - var Scorer = { - // Implement the following function to further tweak the score for each result - // The function takes a result array [docname, title, anchor, descr, score, filename] - // and returns the new score. - /* - score: result => { - const [docname, title, anchor, descr, score, filename, kind] = result - return score - }, - */ - - // query matches the full name of an object - objNameMatch: 11, - // or matches in the last dotted part of the object name - objPartialMatch: 6, - // Additive scores depending on the priority of the object - objPrio: { - 0: 15, // used to be importantResults - 1: 5, // used to be objectResults - 2: -5, // used to be unimportantResults - }, - // Used when the priority is not in the mapping. - objPrioDefault: 0, - - // query found in title - title: 15, - partialTitle: 7, - // query found in terms - term: 5, - partialTerm: 2, - }; -} - -// Global search result kind enum, used by themes to style search results. -class SearchResultKind { - static get index() { return "index"; } - static get object() { return "object"; } - static get text() { return "text"; } - static get title() { return "title"; } -} - -const _removeChildren = (element) => { - while (element && element.lastChild) element.removeChild(element.lastChild); -}; - -/** - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping - */ -const _escapeRegExp = (string) => - string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string - -const _displayItem = (item, searchTerms, highlightTerms) => { - const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; - const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; - const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; - const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; - const contentRoot = document.documentElement.dataset.content_root; - - const [docName, title, anchor, descr, score, _filename, kind] = item; - - let listItem = document.createElement("li"); - // Add a class representing the item's type: - // can be used by a theme's CSS selector for styling - // See SearchResultKind for the class names. - listItem.classList.add(`kind-${kind}`); - let requestUrl; - let linkUrl; - if (docBuilder === "dirhtml") { - // dirhtml builder - let dirname = docName + "/"; - if (dirname.match(/\/index\/$/)) - dirname = dirname.substring(0, dirname.length - 6); - else if (dirname === "index/") dirname = ""; - requestUrl = contentRoot + dirname; - linkUrl = requestUrl; - } else { - // normal html builders - requestUrl = contentRoot + docName + docFileSuffix; - linkUrl = docName + docLinkSuffix; - } - let linkEl = listItem.appendChild(document.createElement("a")); - linkEl.href = linkUrl + anchor; - linkEl.dataset.score = score; - linkEl.innerHTML = title; - if (descr) { - listItem.appendChild(document.createElement("span")).innerHTML = - " (" + descr + ")"; - // highlight search terms in the description - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - } - else if (showSearchSummary) - fetch(requestUrl) - .then((responseData) => responseData.text()) - .then((data) => { - if (data) - listItem.appendChild( - Search.makeSearchSummary(data, searchTerms, anchor) - ); - // highlight search terms in the summary - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - }); - Search.output.appendChild(listItem); -}; -const _finishSearch = (resultCount) => { - Search.stopPulse(); - Search.title.innerText = _("Search Results"); - if (!resultCount) - Search.status.innerText = Documentation.gettext( - "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." - ); - else - Search.status.innerText = Documentation.ngettext( - "Search finished, found one page matching the search query.", - "Search finished, found ${resultCount} pages matching the search query.", - resultCount, - ).replace('${resultCount}', resultCount); -}; -const _displayNextItem = ( - results, - resultCount, - searchTerms, - highlightTerms, -) => { - // results left, load the summary and display it - // this is intended to be dynamic (don't sub resultsCount) - if (results.length) { - _displayItem(results.pop(), searchTerms, highlightTerms); - setTimeout( - () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), - 5 - ); - } - // search finished, update title and status message - else _finishSearch(resultCount); -}; -// Helper function used by query() to order search results. -// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. -// Order the results by score (in opposite order of appearance, since the -// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. -const _orderResultsByScoreThenName = (a, b) => { - const leftScore = a[4]; - const rightScore = b[4]; - if (leftScore === rightScore) { - // same score: sort alphabetically - const leftTitle = a[1].toLowerCase(); - const rightTitle = b[1].toLowerCase(); - if (leftTitle === rightTitle) return 0; - return leftTitle > rightTitle ? -1 : 1; // inverted is intentional - } - return leftScore > rightScore ? 1 : -1; -}; - -/** - * Default splitQuery function. Can be overridden in ``sphinx.search`` with a - * custom function per language. - * - * The regular expression works by splitting the string on consecutive characters - * that are not Unicode letters, numbers, underscores, or emoji characters. - * This is the same as ``\W+`` in Python, preserving the surrogate pair area. - */ -if (typeof splitQuery === "undefined") { - var splitQuery = (query) => query - .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) - .filter(term => term) // remove remaining empty strings -} - -/** - * Search Module - */ -const Search = { - _index: null, - _queued_query: null, - _pulse_status: -1, - - htmlToText: (htmlString, anchor) => { - const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - for (const removalQuery of [".headerlink", "script", "style"]) { - htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); - } - if (anchor) { - const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); - if (anchorContent) return anchorContent.textContent; - - console.warn( - `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` - ); - } - - // if anchor not specified or not found, fall back to main content - const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent) return docContent.textContent; - - console.warn( - "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." - ); - return ""; - }, - - init: () => { - const query = new URLSearchParams(window.location.search).get("q"); - document - .querySelectorAll('input[name="q"]') - .forEach((el) => (el.value = query)); - if (query) Search.performSearch(query); - }, - - loadIndex: (url) => - (document.body.appendChild(document.createElement("script")).src = url), - - setIndex: (index) => { - Search._index = index; - if (Search._queued_query !== null) { - const query = Search._queued_query; - Search._queued_query = null; - Search.query(query); - } - }, - - hasIndex: () => Search._index !== null, - - deferQuery: (query) => (Search._queued_query = query), - - stopPulse: () => (Search._pulse_status = -1), - - startPulse: () => { - if (Search._pulse_status >= 0) return; - - const pulse = () => { - Search._pulse_status = (Search._pulse_status + 1) % 4; - Search.dots.innerText = ".".repeat(Search._pulse_status); - if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); - }; - pulse(); - }, - - /** - * perform a search for something (or wait until index is loaded) - */ - performSearch: (query) => { - // create the required interface elements - const searchText = document.createElement("h2"); - searchText.textContent = _("Searching"); - const searchSummary = document.createElement("p"); - searchSummary.classList.add("search-summary"); - searchSummary.innerText = ""; - const searchList = document.createElement("ul"); - searchList.setAttribute("role", "list"); - searchList.classList.add("search"); - - const out = document.getElementById("search-results"); - Search.title = out.appendChild(searchText); - Search.dots = Search.title.appendChild(document.createElement("span")); - Search.status = out.appendChild(searchSummary); - Search.output = out.appendChild(searchList); - - const searchProgress = document.getElementById("search-progress"); - // Some themes don't use the search progress node - if (searchProgress) { - searchProgress.innerText = _("Preparing search..."); - } - Search.startPulse(); - - // index already loaded, the browser was quick! - if (Search.hasIndex()) Search.query(query); - else Search.deferQuery(query); - }, - - _parseQuery: (query) => { - // stem the search terms and add them to the correct list - const stemmer = new Stemmer(); - const searchTerms = new Set(); - const excludedTerms = new Set(); - const highlightTerms = new Set(); - const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); - splitQuery(query.trim()).forEach((queryTerm) => { - const queryTermLower = queryTerm.toLowerCase(); - - // maybe skip this "word" - // stopwords array is from language_data.js - if ( - stopwords.indexOf(queryTermLower) !== -1 || - queryTerm.match(/^\d+$/) - ) - return; - - // stem the word - let word = stemmer.stemWord(queryTermLower); - // select the correct list - if (word[0] === "-") excludedTerms.add(word.substr(1)); - else { - searchTerms.add(word); - highlightTerms.add(queryTermLower); - } - }); - - if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js - localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) - } - - // console.debug("SEARCH: searching for:"); - // console.info("required: ", [...searchTerms]); - // console.info("excluded: ", [...excludedTerms]); - - return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; - }, - - /** - * execute search (requires search index to be loaded) - */ - _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - - // Collect multiple result groups to be sorted separately and then ordered. - // Each is an array of [docname, title, anchor, descr, score, filename, kind]. - const normalResults = []; - const nonMainIndexResults = []; - - _removeChildren(document.getElementById("search-progress")); - - const queryLower = query.toLowerCase().trim(); - for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { - for (const [file, id] of foundTitles) { - const score = Math.round(Scorer.title * queryLower.length / title.length); - const boost = titles[file] === title ? 1 : 0; // add a boost for document titles - normalResults.push([ - docNames[file], - titles[file] !== title ? `${titles[file]} > ${title}` : title, - id !== null ? "#" + id : "", - null, - score + boost, - filenames[file], - SearchResultKind.title, - ]); - } - } - } - - // search for explicit entries in index directives - for (const [entry, foundEntries] of Object.entries(indexEntries)) { - if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id, isMain] of foundEntries) { - const score = Math.round(100 * queryLower.length / entry.length); - const result = [ - docNames[file], - titles[file], - id ? "#" + id : "", - null, - score, - filenames[file], - SearchResultKind.index, - ]; - if (isMain) { - normalResults.push(result); - } else { - nonMainIndexResults.push(result); - } - } - } - } - - // lookup as object - objectTerms.forEach((term) => - normalResults.push(...Search.performObjectSearch(term, objectTerms)) - ); - - // lookup as search terms in fulltext - normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); - - // let the scorer override scores with a custom scoring function - if (Scorer.score) { - normalResults.forEach((item) => (item[4] = Scorer.score(item))); - nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); - } - - // Sort each group of results by score and then alphabetically by name. - normalResults.sort(_orderResultsByScoreThenName); - nonMainIndexResults.sort(_orderResultsByScoreThenName); - - // Combine the result groups in (reverse) order. - // Non-main index entries are typically arbitrary cross-references, - // so display them after other results. - let results = [...nonMainIndexResults, ...normalResults]; - - // remove duplicate search results - // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept - let seen = new Set(); - results = results.reverse().reduce((acc, result) => { - let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); - if (!seen.has(resultStr)) { - acc.push(result); - seen.add(resultStr); - } - return acc; - }, []); - - return results.reverse(); - }, - - query: (query) => { - const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); - const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); - - // for debugging - //Search.lastresults = results.slice(); // a copy - // console.info("search results:", Search.lastresults); - - // print the results - _displayNextItem(results, results.length, searchTerms, highlightTerms); - }, - - /** - * search for object names - */ - performObjectSearch: (object, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const objects = Search._index.objects; - const objNames = Search._index.objnames; - const titles = Search._index.titles; - - const results = []; - - const objectSearchCallback = (prefix, match) => { - const name = match[4] - const fullname = (prefix ? prefix + "." : "") + name; - const fullnameLower = fullname.toLowerCase(); - if (fullnameLower.indexOf(object) < 0) return; - - let score = 0; - const parts = fullnameLower.split("."); - - // check for different match types: exact matches of full name or - // "last name" (i.e. last dotted part) - if (fullnameLower === object || parts.slice(-1)[0] === object) - score += Scorer.objNameMatch; - else if (parts.slice(-1)[0].indexOf(object) > -1) - score += Scorer.objPartialMatch; // matches in last name - - const objName = objNames[match[1]][2]; - const title = titles[match[0]]; - - // If more than one term searched for, we require other words to be - // found in the name/title/description - const otherTerms = new Set(objectTerms); - otherTerms.delete(object); - if (otherTerms.size > 0) { - const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); - if ( - [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) - ) - return; - } - - let anchor = match[3]; - if (anchor === "") anchor = fullname; - else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; - - const descr = objName + _(", in ") + title; - - // add custom score for some objects according to scorer - if (Scorer.objPrio.hasOwnProperty(match[2])) - score += Scorer.objPrio[match[2]]; - else score += Scorer.objPrioDefault; - - results.push([ - docNames[match[0]], - fullname, - "#" + anchor, - descr, - score, - filenames[match[0]], - SearchResultKind.object, - ]); - }; - Object.keys(objects).forEach((prefix) => - objects[prefix].forEach((array) => - objectSearchCallback(prefix, array) - ) - ); - return results; - }, - - /** - * search for full-text terms in the index - */ - performTermsSearch: (searchTerms, excludedTerms) => { - // prepare search - const terms = Search._index.terms; - const titleTerms = Search._index.titleterms; - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - - const scoreMap = new Map(); - const fileMap = new Map(); - - // perform the search on the required terms - searchTerms.forEach((word) => { - const files = []; - const arr = [ - { files: terms[word], score: Scorer.term }, - { files: titleTerms[word], score: Scorer.title }, - ]; - // add support for partial matches - if (word.length > 2) { - const escapedWord = _escapeRegExp(word); - if (!terms.hasOwnProperty(word)) { - Object.keys(terms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: terms[term], score: Scorer.partialTerm }); - }); - } - if (!titleTerms.hasOwnProperty(word)) { - Object.keys(titleTerms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); - }); - } - } - - // no match but word was a required one - if (arr.every((record) => record.files === undefined)) return; - - // found search word in contents - arr.forEach((record) => { - if (record.files === undefined) return; - - let recordFiles = record.files; - if (recordFiles.length === undefined) recordFiles = [recordFiles]; - files.push(...recordFiles); - - // set score for the word in each file - recordFiles.forEach((file) => { - if (!scoreMap.has(file)) scoreMap.set(file, {}); - scoreMap.get(file)[word] = record.score; - }); - }); - - // create the mapping - files.forEach((file) => { - if (!fileMap.has(file)) fileMap.set(file, [word]); - else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); - }); - }); - - // now check if the files don't contain excluded terms - const results = []; - for (const [file, wordList] of fileMap) { - // check if all requirements are matched - - // as search terms with length < 3 are discarded - const filteredTermCount = [...searchTerms].filter( - (term) => term.length > 2 - ).length; - if ( - wordList.length !== searchTerms.size && - wordList.length !== filteredTermCount - ) - continue; - - // ensure that none of the excluded terms is in the search result - if ( - [...excludedTerms].some( - (term) => - terms[term] === file || - titleTerms[term] === file || - (terms[term] || []).includes(file) || - (titleTerms[term] || []).includes(file) - ) - ) - break; - - // select one (max) score for the file. - const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); - // add result to the result list - results.push([ - docNames[file], - titles[file], - "", - null, - score, - filenames[file], - SearchResultKind.text, - ]); - } - return results; - }, - - /** - * helper function to return a node containing the - * search summary for a given text. keywords is a list - * of stemmed words. - */ - makeSearchSummary: (htmlText, keywords, anchor) => { - const text = Search.htmlToText(htmlText, anchor); - if (text === "") return null; - - const textLower = text.toLowerCase(); - const actualStartPosition = [...keywords] - .map((k) => textLower.indexOf(k.toLowerCase())) - .filter((i) => i > -1) - .slice(-1)[0]; - const startWithContext = Math.max(actualStartPosition - 120, 0); - - const top = startWithContext === 0 ? "" : "..."; - const tail = startWithContext + 240 < text.length ? "..." : ""; - - let summary = document.createElement("p"); - summary.classList.add("context"); - summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; - - return summary; - }, -}; - -_ready(Search.init); diff --git a/docs/1.0.4/_static/sphinx_highlight.js b/docs/1.0.4/_static/sphinx_highlight.js deleted file mode 100644 index 8a96c69a..00000000 --- a/docs/1.0.4/_static/sphinx_highlight.js +++ /dev/null @@ -1,154 +0,0 @@ -/* Highlighting utilities for Sphinx HTML documentation. */ -"use strict"; - -const SPHINX_HIGHLIGHT_ENABLED = true - -/** - * highlight a given string on a node by wrapping it in - * span elements with the given class name. - */ -const _highlight = (node, addItems, text, className) => { - if (node.nodeType === Node.TEXT_NODE) { - const val = node.nodeValue; - const parent = node.parentNode; - const pos = val.toLowerCase().indexOf(text); - if ( - pos >= 0 && - !parent.classList.contains(className) && - !parent.classList.contains("nohighlight") - ) { - let span; - - const closestNode = parent.closest("body, svg, foreignObject"); - const isInSVG = closestNode && closestNode.matches("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.classList.add(className); - } - - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - const rest = document.createTextNode(val.substr(pos + text.length)); - parent.insertBefore( - span, - parent.insertBefore( - rest, - node.nextSibling - ) - ); - node.nodeValue = val.substr(0, pos); - /* There may be more occurrences of search term in this node. So call this - * function recursively on the remaining fragment. - */ - _highlight(rest, addItems, text, className); - - if (isInSVG) { - const rect = document.createElementNS( - "http://www.w3.org/2000/svg", - "rect" - ); - const bbox = parent.getBBox(); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute("class", className); - addItems.push({ parent: parent, target: rect }); - } - } - } else if (node.matches && !node.matches("button, select, textarea")) { - node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); - } -}; -const _highlightText = (thisNode, text, className) => { - let addItems = []; - _highlight(thisNode, addItems, text, className); - addItems.forEach((obj) => - obj.parent.insertAdjacentElement("beforebegin", obj.target) - ); -}; - -/** - * Small JavaScript module for the documentation. - */ -const SphinxHighlight = { - - /** - * highlight the search words provided in localstorage in the text - */ - highlightSearchWords: () => { - if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight - - // get and clear terms from localstorage - const url = new URL(window.location); - const highlight = - localStorage.getItem("sphinx_highlight_terms") - || url.searchParams.get("highlight") - || ""; - localStorage.removeItem("sphinx_highlight_terms") - url.searchParams.delete("highlight"); - window.history.replaceState({}, "", url); - - // get individual terms from highlight string - const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); - if (terms.length === 0) return; // nothing to do - - // There should never be more than one element matching "div.body" - const divBody = document.querySelectorAll("div.body"); - const body = divBody.length ? divBody[0] : document.querySelector("body"); - window.setTimeout(() => { - terms.forEach((term) => _highlightText(body, term, "highlighted")); - }, 10); - - const searchBox = document.getElementById("searchbox"); - if (searchBox === null) return; - searchBox.appendChild( - document - .createRange() - .createContextualFragment( - '

' + - '' + - _("Hide Search Matches") + - "

" - ) - ); - }, - - /** - * helper function to hide the search marks again - */ - hideSearchWords: () => { - document - .querySelectorAll("#searchbox .highlight-link") - .forEach((el) => el.remove()); - document - .querySelectorAll("span.highlighted") - .forEach((el) => el.classList.remove("highlighted")); - localStorage.removeItem("sphinx_highlight_terms") - }, - - initEscapeListener: () => { - // only install a listener if it is really needed - if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; - - document.addEventListener("keydown", (event) => { - // bail for input elements - if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; - // bail with special keys - if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; - if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { - SphinxHighlight.hideSearchWords(); - event.preventDefault(); - } - }); - }, -}; - -_ready(() => { - /* Do not call highlightSearchWords() when we are on the search page. - * It will highlight words from the *previous* search query. - */ - if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); - SphinxHighlight.initEscapeListener(); -}); diff --git a/docs/1.0.4/autodoc/mmif.serialize.html b/docs/1.0.4/autodoc/mmif.serialize.html deleted file mode 100644 index fca9e767..00000000 --- a/docs/1.0.4/autodoc/mmif.serialize.html +++ /dev/null @@ -1,1271 +0,0 @@ - - - - - - - - - mmif.serialize module — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
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mmif.serialize module

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mmif.serialize.model module

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The model module contains the classes used to represent an -abstract MMIF object as a live Python object.

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The MmifObject class or one of its derivatives is subclassed by -all other classes defined in this SDK, except for MmifObjectEncoder.

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These objects are generally instantiated from JSON, either as a string -or as an already-loaded Python dictionary. This base class provides the -core functionality for deserializing MMIF JSON data into live objects -and serializing live objects into MMIF JSON data. Specialized behavior -for the different components of MMIF is added in the subclasses.

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-class mmif.serialize.model.DataDict(mmif_obj: bytes | str | dict | None = None)[source]
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Bases: MmifObject, Generic[T, S]

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-empty()[source]
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-get(key: T, default=None) → S | None[source]
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-items()[source]
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-keys()[source]
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-update(other, overwrite)[source]
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-values()[source]
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-class mmif.serialize.model.DataList(mmif_obj: bytes | str | list | None = None)[source]
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Bases: MmifObject, Generic[T]

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The DataList class is an abstraction that represents the -various lists found in a MMIF file, such as documents, subdocuments, -views, and annotations.

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Parameters:
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mmif_obj (Union[str, list]) – the data that the list contains

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-append(value, overwrite)[source]
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-deserialize(mmif_json: str | list) → None[source]
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Passes the input data into the internal deserializer.

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-empty()[source]
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-get(key: str) → T | None[source]
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Standard dictionary-style get() method, albeit with no default -parameter. Relies on the implementation of __getitem__.

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Will return None if the key is not found.

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Parameters:
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key – the key to search for

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Returns:
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the value matching that key

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-class mmif.serialize.model.MmifObject(mmif_obj: bytes | str | dict | None = None)[source]
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Bases: object

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Abstract superclass for MMIF related key-value pair objects.

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Any MMIF object can be initialized as an empty placeholder or -an actual representation with a JSON formatted string or equivalent -dict object argument.

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This superclass has four specially designed instance variables, and these -variable names cannot be used as attribute names for MMIF objects.

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  1. _unnamed_attributes: -Only can be either None or an empty dictionary. If it’s set to None, -it means the class won’t take any Additional Attributes in the JSON -schema sense. If it’s a dict, users can throw any k-v pairs to the -class, EXCEPT for the reserved two key names.

    2. -

  2. _attribute_classes: -This is a dict from a key name to a specific python class to use for -deserialize the value. Note that a key name in this dict does NOT -have to be a named attribute, but is recommended to be one.

    3. -

  3. _required_attributes: -This is a simple list of names of attributes that are required in the object. -When serialize, an object will skip its empty (e.g. zero-length, or None) -attributes unless they are in this list. Otherwise, the serialized JSON -string would have empty representations (e.g. "", []).

    4. -

  4. _exclude_from_diff: -This is a simple list of names of attributes that should be excluded from -the diff calculation in __eq__.

    5. -
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# TODO (krim @ 8/17/20): this dict is however, a duplicate with the type hints in the class definition. -Maybe there is a better way to utilize type hints (e.g. getting them as a programmatically), but for now -developers should be careful to add types to hints as well as to this dict.

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Also note that those special attributes MUST be set in the __init__() -before calling super method, otherwise deserialization will not work.

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And also, a subclass that has one or more named attributes, it must -set those attributes in the __init__() before calling super method. When -serializing a MmifObject, all empty attributes will be ignored, so for -optional named attributes, you must leave the values empty (len == 0), but -NOT None. Any None-valued named attributes will cause issues with current -implementation.

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Parameters:
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mmif_obj – JSON string or dict to initialize an object. -If not given, an empty object will be initialized, sometimes with -an ID value automatically generated, based on its parent object.

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-deserialize(mmif_json: str | dict) → None[source]
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Takes a JSON-formatted string or a simple dict that’s json-loaded from -such a string as an input and populates object’s fields with the values -specified in the input.

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Parameters:
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mmif_json – JSON-formatted string or dict from such a string -that represents a MMIF object

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-disallow_additional_properties() → None[source]
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Call this method in __init__() to prevent the insertion -of unnamed attributes after initialization.

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-static is_empty(obj) → bool[source]
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return True if the obj is None or “emtpy”. The emptiness first defined as -having zero length. But for objects that lack __len__ method, we need -additional check.

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-reserved_names: Set[str] = {'_attribute_classes', '_exclude_from_diff', '_required_attributes', '_unnamed_attributes', 'reserved_names'}[source]
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-serialize(pretty: bool = False) → str[source]
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Generates JSON representation of an object.

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Parameters:
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pretty – If True, returns string representation with indentation.

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Returns:
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JSON string of the object.

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-set_additional_property(key: str, value: Any) → None[source]
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Method to set values in _unnamed_attributes.

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Parameters:
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  • key – the attribute name

    • -

  • value – the desired value

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Returns:
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None

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Raise:
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AttributeError if additional properties are disallowed by disallow_additional_properties()

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-class mmif.serialize.model.MmifObjectEncoder(*, skipkeys=False, ensure_ascii=True, check_circular=True, allow_nan=True, sort_keys=False, indent=None, separators=None, default=None)[source]
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Bases: JSONEncoder

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Encoder class to define behaviors of de-/serialization

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-default(obj: MmifObject)[source]
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Overrides default encoding behavior to prioritize MmifObject.serialize().

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mmif.serialize.mmif module

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The mmif module contains the classes used to represent a full MMIF -file as a live Python object.

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See the specification docs and the JSON Schema file for more information.

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-class mmif.serialize.mmif.Mmif(mmif_obj: bytes | str | dict | None = None, *, validate: bool = True)[source]
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Bases: MmifObject

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MmifObject that represents a full MMIF file.

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Parameters:
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  • mmif_obj – the JSON data

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  • validate – whether to validate the data against the MMIF JSON schema.

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-add_document(document: Document, overwrite=False) → None[source]
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Appends a Document object to the documents list.

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Fails if there is already a document with the same ID in the MMIF object.

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Parameters:
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  • document – the Document object to add

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  • overwrite – if set to True, will overwrite -an existing view with the same ID

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Returns:
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None

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-add_view(view: View, overwrite=False) → None[source]
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Appends a View object to the views list.

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Fails if there is already a view with the same ID in the MMIF object.

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Parameters:
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  • view – the Document object to add

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  • overwrite – if set to True, will overwrite -an existing view with the same ID

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Returns:
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None

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-generate_capital_annotations()[source]
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Automatically convert any “pending” temporary properties from -Document objects to Annotation objects . The generated Annotation -objects are then added to the last View in the views lists.

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See https://github.com/clamsproject/mmif-python/issues/226 for rationale -behind this behavior and discussion.

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-get_alignments(at_type1: str | TypesBase, at_type2: str | TypesBase) → Dict[str, List[Annotation]][source]
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Finds views where alignments between two given annotation types occurred.

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Returns:
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a dict that keyed by view IDs (str) and has lists of alignment Annotation objects as values.

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-get_all_views_contain(at_types: TypesBase | str | List[str | TypesBase]) → List[View][source]
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Returns the list of all views in the MMIF if given types -are present in that view’s ‘contains’ metadata.

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Parameters:
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at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

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Returns:
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the list of views that contain the type

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-get_document_by_id(doc_id: str) → Document[source]
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Finds a Document object with the given ID.

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Parameters:
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doc_id – the ID to search for

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Returns:
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a reference to the corresponding document, if it exists

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Raises:
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KeyError – if there is no corresponding document

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-get_document_location(m_type: DocumentTypes | str, path_only=False) → str | None[source]
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Method to get the location of first document of given type.

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Parameters:
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m_type – the type to search for

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Returns:
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the value of the location field in the corresponding document

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-get_documents_by_app(app_id: str) → List[Document][source]
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Method to get all documents object queries by its originated app name.

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Parameters:
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app_id – the app name to search for

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Returns:
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a list of documents matching the requested app name, or an empty list if the app not found

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-get_documents_by_property(prop_key: str, prop_value: str) → List[Document][source]
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Method to retrieve documents by an arbitrary key-value pair in the document properties objects.

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Parameters:
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  • prop_key – the metadata key to search for

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  • prop_value – the metadata value to match

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Returns:
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a list of documents matching the requested metadata key-value pair

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-get_documents_by_type(doc_type: str | DocumentTypes) → List[Document][source]
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Method to get all documents where the type matches a particular document type, which should be one of the CLAMS document types.

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Parameters:
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doc_type – the type of documents to search for, must be one of Document type defined in the CLAMS vocabulary.

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Returns:
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a list of documents matching the requested type, or an empty list if none found.

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-get_documents_in_view(vid: str | None = None) → List[Document][source]
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Method to get all documents object queries by a view id.

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Parameters:
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vid – the source view ID to search for

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Returns:
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a list of documents matching the requested source view ID, or an empty list if the view not found

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-get_documents_locations(m_type: DocumentTypes | str, path_only=False) → List[str | None][source]
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This method returns the file paths of documents of given type. -Only top-level documents have locations, so we only check them.

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Parameters:
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m_type – the type to search for

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Returns:
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a list of the values of the location fields in the corresponding documents

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-get_view_by_id(req_view_id: str) → View[source]
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Finds a View object with the given ID.

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Parameters:
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req_view_id – the ID to search for

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Returns:
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a reference to the corresponding view, if it exists

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Raises:
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Exception – if there is no corresponding view

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-get_view_contains(at_types: TypesBase | str | List[str | TypesBase]) → View | None[source]
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Returns the last view appended that contains the given -types in its ‘contains’ metadata.

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Parameters:
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at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

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Returns:
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the view, or None if the type is not found

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-get_views_contain(at_types: TypesBase | str | List[str | TypesBase]) → List[View][source]
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An alias to get_all_views_contain method.

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-get_views_for_document(doc_id: str) → List[View][source]
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Returns the list of all views that have annotations anchored on a particular document. -Note that when the document is inside a view (generated during the pipeline’s running), -doc_id must be prefixed with the view_id.

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-id_delimiter: ClassVar[str] = ':'[source]
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-new_view() → View[source]
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Creates an empty view with a new ID and appends it to the views list.

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Returns:
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a reference to the new View object

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-new_view_id() → str[source]
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Fetches an ID for a new view.

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Returns:
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the ID

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-sanitize()[source]
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Sanitizes a Mmif object by running some safeguards. -Concretely, it performs the following before returning the JSON string.

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  1. validating output using built-in MMIF jsonschema

    2. -

  2. remove non-existing annotation types from contains metadata

    3. -
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-serialize(pretty: bool = False, sanitize: bool = False, autogenerate_capital_annotations=True) → str[source]
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Serializes the MMIF object to a JSON string.

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Parameters:
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  • sanitize – If True, performs some sanitization of before returning -the JSON string. See sanitize() for details.

    • -

  • autogenerate_capital_annotations – If True, automatically convert -any “pending” temporary properties from Document objects to -Annotation objects. See generate_capital_annotations() for -details.

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  • pretty – If True, returns string representation with indentation.

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Returns:
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JSON string of the MMIF object.

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-static validate(json_str: bytes | str | dict) → None[source]
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Validates a MMIF JSON object against the MMIF Schema. -Note that this method operates before processing by MmifObject._load_str, -so it expects @ and not _ for the JSON-LD @-keys.

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Raises:
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jsonschema.exceptions.ValidationError – if the input fails validation

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Parameters:
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json_str – a MMIF JSON dict or string

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Returns:
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None

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-view_prefix: ClassVar[str] = 'v_'[source]
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mmif.serialize.view module

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The view module contains the classes used to represent a MMIF view -as a live Python object.

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In MMIF, views are created by apps in a pipeline that are annotating -data that was previously present in the MMIF file.

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-class mmif.serialize.view.Contain(mmif_obj: bytes | str | dict | None = None)[source]
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Bases: DataDict[str, str]

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Contain object that represents the metadata of a single -annotation type in the contains metadata of a MMIF view.

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-class mmif.serialize.view.View(view_obj: bytes | str | dict | None = None)[source]
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Bases: MmifObject

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View object that represents a single view in a MMIF file.

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A view is identified by an ID, and contains certain metadata, -a list of annotations, and potentially a JSON-LD @context -IRI.

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If view_obj is not provided, an empty View will be generated.

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Parameters:
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view_obj – the JSON data that defines the view

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-add_annotation(annotation: Annotation, overwrite=False) → Annotation[source]
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Adds an annotation to the current view.

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Fails if there is already an annotation with the same ID -in the view, unless overwrite is set to True.

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Parameters:
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Raises:
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KeyError – if overwrite is set to False and -an annotation with the same ID exists -in the view

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Returns:
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the same Annotation object passed in as annotation

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-add_document(document: Document, overwrite=False) → Annotation[source]
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Appends a Document object to the annotations list.

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Fails if there is already a document with the same ID in the annotations list.

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Parameters:
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  • document – the Document object to add

    • -

  • overwrite – if set to True, will overwrite -an existing view with the same ID

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Returns:
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None

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-get_annotation_by_id(ann_id)[source]
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-get_annotations(at_type: str | TypesBase | None = None, **properties) → Generator[Annotation, None, None][source]
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Look for certain annotations in this view, specified by parameters

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Parameters:
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  • at_type – @type of the annotations to look for. When this is None, any @type will match.

    • -

  • properties – properties of the annotations to look for. When given more than one property, all properties must match. Note that annotation type metadata are specified in the contains view metadata, not in individual annotation objects.

    • -
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-get_document_by_id(doc_id) → Document[source]
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-get_documents() → List[Document][source]
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-new_annotation(at_type: str | TypesBase, aid: str | None = None, overwrite=False, **properties) → Annotation[source]
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Generates a new mmif.serialize.annotation.Annotation -object and adds it to the current view.

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Fails if there is already an annotation with the same ID -in the view, unless overwrite is set to True.

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Parameters:
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  • at_type – the desired @type of the annotation.

    • -

  • aid – the desired ID of the annotation, when not given, -the mmif SDK tries to automatically generate an ID based on -Annotation type and existing annotations in the view.

    • -

  • overwrite – if set to True, will overwrite an -existing annotation with the same ID.

    • -
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Raises:
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KeyError – if overwrite is set to False and -an annotation with the same ID exists -in the view.

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Returns:
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the generated mmif.serialize.annotation.Annotation

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-new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
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Adds a new element to the contains metadata.

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Parameters:
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  • at_type – the @type of the annotation type being added

    • -

  • contains_metadata – any metadata associated with the annotation type

    • -
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Returns:
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the generated Contain object

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-new_textdocument(text: str, lang: str = 'en', did: str | None = None, overwrite=False, **properties) → Document[source]
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Generates a new mmif.serialize.annotation.Document -object, particularly typed as TextDocument and adds it to the current view.

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Fails if there is already a text document with the same ID -in the view, unless overwrite is set to True.

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Parameters:
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  • text – text content of the new document

    • -

  • lang – ISO 639-1 code of the language used in the new document

    • -

  • did – the desired ID of the document, when not given, -the mmif SDK tries to automatically generate an ID based on -Annotation type and existing documents in the view.

    • -

  • overwrite – if set to True, will overwrite an -existing document with the same ID

    • -
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Raises:
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KeyError – if overwrite is set to False and -an document with the same ID exists -in the view

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Returns:
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the generated mmif.serialize.annotation.Document

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-set_error(err_message: str, err_trace: str) → None[source]
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-class mmif.serialize.view.ViewMetadata(viewmetadata_obj: bytes | str | dict | None = None)[source]
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Bases: MmifObject

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ViewMetadata object that represents the metadata object within a MMIF view.

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Parameters:
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viewmetadata_obj – the JSON data that defines the metadata

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-add_contain(contain: Contain, at_type: str | TypesBase)[source]
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-add_parameter(param_key, param_value)[source]
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-add_parameters(**runtime_params)[source]
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-add_warnings(*warnings: Warning)[source]
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-emtpy_warnings()[source]
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-get_parameter(param_key)[source]
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-new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
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Adds a new element to the contains dictionary.

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Parameters:
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    -

  • at_type – the @type of the annotation type being added

    • -

  • contains_metadata – any metadata associated with the annotation type

    • -
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Returns:
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the generated Contain object

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-set_error(message: str, stack_trace: str)[source]
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mmif.serialize.annotation module

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The annotation module contains the classes used to represent a -MMIF annotation as a live Python object.

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In MMIF, annotations are created by apps in a pipeline as a part -of a view. For documentation on how views are represented, see -mmif.serialize.view.

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-class mmif.serialize.annotation.Annotation(anno_obj: bytes | str | dict | None = None)[source]
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Bases: MmifObject

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MmifObject that represents an annotation in a MMIF view.

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-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]]) → None[source]
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Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

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- -
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-property at_type: TypesBase[source]
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- -
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-static check_prop_value_is_simple_enough(value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]])[source]
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- -
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-get(prop_name: str) → AnnotationProperties | str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]][source]
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A special getter for Annotation properties. This is to allow for -directly accessing properties without having to go through the -properties object.

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- -
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-get_property(prop_name: str) → AnnotationProperties | str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]][source]
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A special getter for Annotation properties. This is to allow for -directly accessing properties without having to go through the -properties object.

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- -
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-property id: str[source]
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- -
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-is_document()[source]
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- -
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-is_type(at_type: str | TypesBase) → bool[source]
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Check if the @type of this object matches.

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- -
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-property parent: str[source]
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- -
- -
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-class mmif.serialize.annotation.AnnotationProperties(mmif_obj: bytes | str | dict | None = None)[source]
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Bases: MmifObject, MutableMapping[str, T]

-

AnnotationProperties object that represents the -properties object within a MMIF annotation.

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Parameters:
-

mmif_obj – the JSON data that defines the properties

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- -
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-class mmif.serialize.annotation.Document(doc_obj: bytes | str | dict | None = None)[source]
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Bases: Annotation

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Document object that represents a single document in a MMIF file.

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A document is identified by an ID, and contains certain attributes -and potentially contains the contents of the document itself, -metadata about how the document was created, and/or a list of -subdocuments grouped together logically.

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If document_obj is not provided, an empty Document will be generated.

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Parameters:
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document_obj – the JSON data that defines the document

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-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None]) → None[source]
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Adds a property to the document’s properties.

-

Unlike the parent Annotation class, added properties of a -Document object can be lost during serialization unless it belongs -to somewhere in a Mmif object. This is because we want to keep -Document object as “read-only” as possible. Thus, if you want to add -a property to a Document object,

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    -

  • add the document to a Mmif object (either in the documents list or -in a view from the views list), or

    • -

  • directly write to Document.properties instead of using this method -(which is not recommended).

    • -
-

With the former method, the SDK will record the added property as a -Annotation annotation object, separate from the original Document -object. See Mmif.generate_capital_annotations() for more.

-

A few notes to keep in mind:

-
    -

  1. You can’t overwrite an existing property of a Document object.

    2. -

  2. A MMIF can have multiple Annotation objects with the same -property name but different values. When this happens, the SDK will -only keep the latest value (in order of appearances in views list) of -the property, effectively overwriting the previous values.

    3. -
-
- -
-
-get(prop_name)[source]
-

A special getter for Document properties. This is to allow for reading -the three properties in a specific order so that the latest value is -returned, in case there are multiple values for the same key.

-
- -
-
-get_property(prop_name)[source]
-

A special getter for Document properties. This is to allow for reading -the three properties in a specific order so that the latest value is -returned, in case there are multiple values for the same key.

-
- -
-
-property location: str | None[source]
-

location property must be a legitimate URI. That is, should the document be a local file -then the file:// scheme must be used. -Returns None when no location is set.

-
- -
-
-location_address() → str | None[source]
-

Retrieves the full address from the document location URI. -Returns None when no location is set.

-
- -
-
-location_path() → str | None[source]
-

Retrieves a path that’s resolved to a pathname in the local file system. -To obtain the original value of the “path” part in the location string -(before resolving), use properties.location_path_literal method. -Returns None when no location is set.

-
- -
-
-location_scheme() → str | None[source]
-

Retrieves URI scheme of the document location. -Returns None when no location is set.

-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.DocumentProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: AnnotationProperties

-

DocumentProperties object that represents the -properties object within a MMIF document.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
-
-property location: str | None[source]
-

location property must be a legitimate URI. That is, should the document be a local file -then the file:// scheme must be used. -Returns None when no location is set.

-
- -
-
-location_address() → str | None[source]
-

Retrieves the full address from the document location URI. -Returns None when no location is set.

-
- -
-
-location_path() → str | None[source]
-
- -
-
-location_path_literal() → str | None[source]
-

Retrieves only path name of the document location (hostname is ignored). -Returns None when no location is set.

-
- -
-
-location_path_resolved(nonexist_ok=True) → str | None[source]
-

Retrieves only path name of the document location (hostname is ignored), -and then try to resolve the path name in the local file system. -This method should be used when the document scheme is file or empty. -For other schemes, users should install mmif-locdoc-<scheme> plugin.

-

Returns None when no location is set. -Raise ValueError when no code found to resolve the given location scheme.

-
- -
-
-location_scheme() → str | None[source]
-

Retrieves URI scheme of the document location. -Returns None when no location is set.

-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.Text(text_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-
-
-property lang: str[source]
-
- -
-
-property value: str[source]
-
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- - - \ No newline at end of file diff --git a/docs/1.0.4/autodoc/mmif.vocabulary.html b/docs/1.0.4/autodoc/mmif.vocabulary.html deleted file mode 100644 index bae5e232..00000000 --- a/docs/1.0.4/autodoc/mmif.vocabulary.html +++ /dev/null @@ -1,325 +0,0 @@ - - - - - - - - - mmif.vocabulary module — mmif-python documentation - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.vocabulary module

-
-

mmif.vocabulary.annotation_types module

-
-
-class mmif.vocabulary.annotation_types.AnnotationTypes(type_uri, fuzzymode=True)[source]
-

Bases: AnnotationTypesBase

-

This class contains the CLAMS annotation types -defined in the spec version 1.1.0 as class variables.

-
-
-Alignment = http://mmif.clams.ai/vocabulary/Alignment/v1[source]
-
- -
-
-Annotation = http://mmif.clams.ai/vocabulary/Annotation/v6[source]
-
- -
-
-BoundingBox = http://mmif.clams.ai/vocabulary/BoundingBox/v5[source]
-
- -
-
-Chapter = http://mmif.clams.ai/vocabulary/Chapter/v6[source]
-
- -
-
-Interval = http://mmif.clams.ai/vocabulary/Interval/v5[source]
-
- -
-
-NamedEntity = http://mmif.clams.ai/vocabulary/NamedEntity/v1[source]
-
- -
-
-NounChunk = http://mmif.clams.ai/vocabulary/NounChunk/v1[source]
-
- -
-
-Paragraph = http://mmif.clams.ai/vocabulary/Paragraph/v1[source]
-
- -
-
-Polygon = http://mmif.clams.ai/vocabulary/Polygon/v5[source]
-
- -
-
-Region = http://mmif.clams.ai/vocabulary/Region/v5[source]
-
- -
-
-Relation = http://mmif.clams.ai/vocabulary/Relation/v5[source]
-
- -
-
-Sentence = http://mmif.clams.ai/vocabulary/Sentence/v1[source]
-
- -
-
-Span = http://mmif.clams.ai/vocabulary/Span/v5[source]
-
- -
-
-TimeFrame = http://mmif.clams.ai/vocabulary/TimeFrame/v6[source]
-
- -
-
-TimePoint = http://mmif.clams.ai/vocabulary/TimePoint/v5[source]
-
- -
-
-Token = http://mmif.clams.ai/vocabulary/Token/v1[source]
-
- -
-
-VerbChunk = http://mmif.clams.ai/vocabulary/VerbChunk/v1[source]
-
- -
-
-VideoObject = http://mmif.clams.ai/vocabulary/VideoObject/v5[source]
-
- -
-
-typevers = {'Alignment': 'v1', 'Annotation': 'v6', 'BoundingBox': 'v5', 'Chapter': 'v6', 'Interval': 'v5', 'NamedEntity': 'v1', 'NounChunk': 'v1', 'Paragraph': 'v1', 'Polygon': 'v5', 'Region': 'v5', 'Relation': 'v5', 'Sentence': 'v1', 'Span': 'v5', 'TimeFrame': 'v6', 'TimePoint': 'v5', 'Token': 'v1', 'VerbChunk': 'v1', 'VideoObject': 'v5'}[source]
-
- -
- -
-
-

mmif.vocabulary.document_types module

-
-
-class mmif.vocabulary.document_types.DocumentTypes(type_uri, fuzzymode=True)[source]
-

Bases: DocumentTypesBase

-

This class contains the CLAMS document types -defined in the spec version 1.1.0 as class variables.

-
-
-AudioDocument = http://mmif.clams.ai/vocabulary/AudioDocument/v1[source]
-
- -
-
-Document = http://mmif.clams.ai/vocabulary/Document/v1[source]
-
- -
-
-ImageDocument = http://mmif.clams.ai/vocabulary/ImageDocument/v1[source]
-
- -
-
-TextDocument = http://mmif.clams.ai/vocabulary/TextDocument/v1[source]
-
- -
-
-VideoDocument = http://mmif.clams.ai/vocabulary/VideoDocument/v1[source]
-
- -
-
-typevers = {'AudioDocument': 'v1', 'Document': 'v1', 'ImageDocument': 'v1', 'TextDocument': 'v1', 'VideoDocument': 'v1'}[source]
-
- -
- -
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 1.0.4 - - -
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- - - \ No newline at end of file diff --git a/docs/1.0.4/consumer-tutorial.html b/docs/1.0.4/consumer-tutorial.html deleted file mode 100644 index 610967de..00000000 --- a/docs/1.0.4/consumer-tutorial.html +++ /dev/null @@ -1,171 +0,0 @@ - - - - - - - - - MMIF consumer — mmif-python documentation - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • MMIF consumer
    • -
  • -
    • -
-
-
-
-
- -
-

MMIF consumer

-

A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the appliance documentation to learn more about the appliance.

-

MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance.

-
    -

  1. The code must be hosted on a public git repository (e.g. Github, Gitlab, …)

    2. -

  2. Must listen to 5000 port.

    3. -

  3. Must expose /display route .

    4. -

  4. /display router should response to GET requests.

    5. -

  5. In the GET request, a public URL of the input MMIF file is passed via file URL parameter.

    6. -

  6. On the codebase root, there must be a Dockerfile that can build a docker image that runs the web app.

    7. -
-

We provide an example consumer at https://github.com/clamsproject/mmif-visualizer.

-
- - -
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- -
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- -
- - Other Versions - v: 1.0.4 - - -
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- - -
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    • -
  • Index
    • -
  • -
    • -
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Index

- -
- A - | B - | C - | D - | E - | G - | I - | K - | L - | M - | N - | P - | R - | S - | T - | U - | V - -
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A

- - - -
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- - -
- -
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  • Welcome to mmif-python’s documentation!
    • -
  • -
    • -
-
-
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- -
-

Welcome to mmif-python’s documentation!

-
-

MultiMedia Interchange Format

-

MMIF is a JSON(-LD)-based data format designed for transferring annotation data between computational analysis applications in CLAMS project.

-
-

Contents

- -
-
-

API documentation:

- -
-
-
-
-

Indices and tables

- -
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- - -
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  • Getting Started
    • -
  • -
    • -
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- -
-

Getting Started

-
-

Overview

-

MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for reproducibility, transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF website. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects.

-
-
-

Prerequisites

-
    -

  • Python: the latest mmif-python requires Python 3.8 or newer. We have no plan to support Python 2.7.

    • -
-
-
-

Installation

-

Package mmif-python is distributed via the official PyPI. Users are supposed to pip-install to get latest release.

-
pip install mmif-python
-
-
-

This will install a package mmif to local python.

-

The MMIF format and specification is evolving over time, and mmif-python package will be updated along with the changes in MMIF format.

-
-

Note

-

MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and mmif-python versions, please take time to read our decision on the subject here. If you need to know which python SDK supports which specification version, see Target MMIF Versions page.

-
-
-
-

MMIF Serialization

-

mmif.serialize.mmif.Mmif represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of mmif.serialize.model.MmifObject, including the mmif.serialize.mmif.Mmif. To start with an existing MMIF str, simple initiate a new Mmif object with the file.

-
import mmif
-from mmif import Mmif
-
-mmif_str = """{
-"metadata": {
-  "mmif": "http://mmif.clams.ai/1.0.0"
-},
-"documents": [
-  {
-    "@type": "http://mmif.clams.ai/vocabulary/VideoDocument/v1",
-    "properties": {
-      "id": "m1",
-      "mime": "video/mp4",
-      "location": "file:///var/archive/video-0012.mp4"
-    }
-  },
-  {
-    "@type": "http://mmif.clams.ai/vocabulary/TextDocument/v1",
-    "properties": {
-      "id": "m2",
-      "mime": "text/plain",
-      "location": "file:///var/archive/video-0012-transcript.txt"
-    }
-  }
-],
-"views": []}"""
-mmif_obj = Mmif(mmif_str)
-
-
-

Few notes;

-
    -

  1. MMIF does not carry the primary source files in it.

    2. -

  2. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version mmif-python implementation of the MMIF might not be able to load an unsupported version of MMIF string.

    3. -
-

When serializing back to str, call mmif.serialize.model.MmifObject.serialize() on the object.

-

To get subcomponents, you can use various getters implemented in subclasses. For example;

-
from mmif.vocabulary.document_types import DocumentTypes
-
-for video in mmif_obj.Mmif.get_documents_by_type(DocumentTypes.VideoDocument):
-  with open(video.location_path(), 'b') as in_video:
-    # do something with the video file
-
-
-

For a full list of available helper methods, please refer to the API documentation.

-
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- -
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- - Other Versions - v: 1.0.4 - - -
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  • mmif package
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mmif package

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- - - \ No newline at end of file diff --git a/docs/1.0.4/objects.inv b/docs/1.0.4/objects.inv deleted file mode 100644 index 360bdc60..00000000 Binary files a/docs/1.0.4/objects.inv and /dev/null differ diff --git a/docs/1.0.4/plugins.html b/docs/1.0.4/plugins.html deleted file mode 100644 index d6a9a770..00000000 --- a/docs/1.0.4/plugins.html +++ /dev/null @@ -1,227 +0,0 @@ - - - - - - - - - Developing plugins for MMIF Python SDK — mmif-python documentation - - - - - - - - - - - - - - - - - -
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  • Developing plugins for MMIF Python SDK
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Developing plugins for MMIF Python SDK

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Overview

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As MMIF JSON files can carry information about media document files without actually carrying file contents, file accessing modules in mmif Python package (distributed as mmif-python on PyPI) are designed to be lightweight and flexible so that it can work with additional “plugin” Python packages that can handle concrete file access.

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This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF website. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects.

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Developer can write simple plugins that can provide additional functionalities to mmif-python. For example, mmif-python does not provide any file access functionality beyond a local file system (with file scheme), but it can be extended with a plugin that can handle file access over different protocols (e.g. http, s3, ftp, etc).

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This document contains information about how to write plugins for mmif-python.

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Document Location Scheme Plugins

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mmif.serialize.annotation.Document class has various methods to access parts of location property of the document. The location is in URI/IRI format (SCHEME://HOSTNAME/PATH, in a nutshell) and it has to be resolved to a local file for CLAMS Apps to process the local file to analyze and extract information about the media and its contents. The core mmif-python distribution only provides a default implementation that can handle file scheme URIs.

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To add a document location handler plugin, you need to implement a Python “package” (do not confuse with PYPI distribution), that meets these requirements;

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  1. the package must be named mmif_docloc_<SCHEME>. For example, to implement a handler for s3 scheme, the package name must be mmif_docloc_s3. The prefix is important as it’s used in the plugin discovery process from the core mmif-python modules.

    2. -

  2. the top module of the package must have a function named resolve. The function must take a single argument, which is a str of the document location URI. The function must return a str of the local file path. For example, if the document location is s3://mybucket/myfile.mp4, a Python user should be able to to something like this;

    3. -
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import mmif_docloc_s3
-resolved = mmif_docloc_s3.resolve('s3://mybucket/myfile.mp4')
-# then resolved must be a local file path that can be used to open the file
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Here’s a minimal example codebase that you refer to when you develop a docloc plugin.

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(However, before you start writing your own plugin for a specific URI scheme, checking if there’s already a PyPI distribution for the scheme might be a good idea.)

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$ tree .
-.
-├── mmif_docloc_dummy
-│   └── __init__.py
-├── pyproject.toml
-└── setup.cfg
-
- $ cat pyproject.toml
-[build-system]
-requires = ["setuptools"]
-build-backend = "setuptools.build_meta"
-
-$ cat setup.cfg
-[metadata]
-name = mmif_docloc_dummy  # this name is IMPORTANT
-version = 0.0.1
-description = a plugin to mmif-pyhon to handle `dummy` location scheme
-
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And the plugin code.

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# mmif_docloc_dummy/__init__.py
-doc_types = {'video': 'mp4'}
-
-def resolve(docloc):
-    scheme = 'dummy'
-    if docloc.startswith(f'{scheme}://'):
-        doc_id, doc_type = docloc.split('.')
-        return f'/path/to/{doc_id}.{doc_types[doc_type]}'
-    else:
-        raise ValueError(f'cannot handle document location scheme: {docloc}')
-
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Python Module Index

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- - - - - - - - \ No newline at end of file diff --git a/docs/1.0.4/searchindex.js b/docs/1.0.4/searchindex.js deleted file mode 100644 index 028638e0..00000000 --- a/docs/1.0.4/searchindex.js +++ /dev/null @@ -1 +0,0 @@ -Search.setIndex({"alltitles": {"API documentation:": [[3, null]], "Contents": [[3, null]], "Developing plugins for MMIF Python SDK": [[6, null]], "Document Location Scheme Plugins": [[6, "document-location-scheme-plugins"]], "Getting Started": [[4, null]], "Indices and tables": [[3, "indices-and-tables"]], "Installation": [[4, "installation"]], "MMIF Serialization": [[4, "mmif-serialization"]], "MMIF consumer": [[2, null]], "MultiMedia Interchange Format": [[3, "multimedia-interchange-format"]], "Overview": [[4, "overview"], [6, "overview"]], "Prerequisites": [[4, "prerequisites"]], "Target MMIF Versions": [[7, null]], "Target Specification Versions": [[7, "id1"]], "Welcome to mmif-python\u2019s documentation!": [[3, null]], "mmif package": [[5, null]], 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[0, 4, 6], "when": [0, 4, 6], "where": 0, "whether": 0, "which": [0, 4, 6], "within": 0, "without": [0, 6], "won": 0, "work": [0, 6], "workflow": 4, "would": 0, "write": [0, 6], "you": [0, 4, 6], "your": 6, "zero": 0}, "titles": ["mmif.serialize module", "mmif.vocabulary module", "MMIF consumer", "Welcome to mmif-python\u2019s documentation!", "Getting Started", "mmif package", "Developing plugins for MMIF Python SDK", "Target MMIF Versions"], "titleterms": {"": 3, "annot": 0, "annotation_typ": 1, "api": 3, "consum": 2, "content": 3, "develop": 6, "document": [3, 6], "document_typ": 1, "format": 3, "get": 4, "indic": 3, "instal": 4, "interchang": 3, "locat": 6, "mmif": [0, 1, 2, 3, 4, 5, 6, 7], "model": 0, "modul": [0, 1], "multimedia": 3, "overview": [4, 6], "packag": 5, "plugin": 6, "prerequisit": 4, "python": [3, 6], "scheme": 6, "sdk": 6, "serial": [0, 4], "specif": 7, "start": 4, "tabl": 3, "target": 7, "version": 7, "view": 0, "vocabulari": 1, "welcom": 3}}) \ No newline at end of file diff --git a/docs/1.0.4/target-versions.html b/docs/1.0.4/target-versions.html deleted file mode 100644 index de1f6861..00000000 --- a/docs/1.0.4/target-versions.html +++ /dev/null @@ -1,254 +0,0 @@ - - - - - - - - - Target MMIF Versions — mmif-python documentation - - - - - - - - - - - - - - - - - -
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Target MMIF Versions

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This article provides targeting MMIF specification versions of different versions of mmif-python SDK.

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Target Specification Versions

mmif-python version

Target MMIF Specification

1.0.4

1.1.0

1.0.3

1.0.0

1.0.2

1.0.0

1.0.1

1.0.0

1.0.0

0.5.0

0.5.2

0.5.0

0.5.1

0.5.0

0.5.0

0.5.0

0.4.8

0.4.2

0.4.7

0.4.1

0.4.6

0.4.0

0.4.5

0.4.0

0.4.4

0.4.0

0.4.3

0.4.0

0.4.2

0.4.0

0.4.1

0.4.0

0.4.0

0.4.0

0.3.5

0.3.1

0.3.4

0.3.1

0.3.3

0.3.1

0.3.2

0.3.1

0.3.1

0.3.0

0.3.0

0.3.0

0.2.2

0.2.1

0.2.1

0.2.1

0.2.0

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0.3.3
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0.3.4
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0.3.5
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0.4.0
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0.4.1
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0.4.2
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0.4.3
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0.4.4
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0.4.5
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0.4.6
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0.4.7
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0.4.8
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0.5.0
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0.5.1
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0.5.2
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1.0.0
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1.0.1
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1.0.10
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1.0.11
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1.0.12
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1.0.13
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1.0.14
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1.0.15
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1.0.16
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1.0.17
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1.0.18
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1.0.19
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1.0.2
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1.0.3
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1.0.4
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1.0.5
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1.0.6
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1.0.7
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The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the `appliance documentation `_ to learn more about the appliance. - -MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance. - -#. The code must be hosted on a public git repository (e.g. Github, Gitlab, ...) -#. Must listen to ``5000`` port. -#. Must expose ``/display`` route . -#. ``/display`` router should response to ``GET`` requests. -#. In the ``GET`` request, a public URL of the input MMIF file is passed via ``file`` URL parameter. -#. On the codebase root, there must be a ``Dockerfile`` that can build a `docker `_ image that runs the web app. - -We provide an example consumer at https://github.com/clamsproject/mmif-visualizer. diff --git a/docs/1.0.5/_sources/index.rst.txt b/docs/1.0.5/_sources/index.rst.txt deleted file mode 100644 index beb56aae..00000000 --- a/docs/1.0.5/_sources/index.rst.txt +++ /dev/null @@ -1,26 +0,0 @@ -Welcome to mmif-python's documentation! -======================================= - -.. mdinclude:: ../README.md - -.. toctree:: - :maxdepth: 2 - :caption: Contents - - introduction - plugins - target-versions - -.. toctree:: - :maxdepth: 2 - :caption: API documentation: - - modules - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/docs/1.0.5/_sources/introduction.rst.txt b/docs/1.0.5/_sources/introduction.rst.txt deleted file mode 100644 index cfd9eaf7..00000000 --- a/docs/1.0.5/_sources/introduction.rst.txt +++ /dev/null @@ -1,89 +0,0 @@ -.. _introduction: - -Getting Started -=============== - - -Overview ---------- - -MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for reproducibility, transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF website `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects. - -Prerequisites -------------- - -* `Python `_: the latest ``mmif-python`` requires Python 3.8 or newer. We have no plan to support `Python 2.7 `_. - -Installation ---------------- - -Package ``mmif-python`` is distributed via the official PyPI. Users are supposed to pip-install to get latest release. - -.. code-block:: bash - - pip install mmif-python - -This will install a package `mmif` to local python. - -The MMIF format and specification is evolving over time, and ``mmif-python`` package will be updated along with the changes in MMIF format. - -.. note:: MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and ``mmif-python`` versions, please take time to read our decision on the subject `here `_. If you need to know which python SDK supports which specification version, see :ref:`target-versions` page. - -MMIF Serialization ---------------------------- - -:class:`mmif.serialize.mmif.Mmif` represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of :class:`mmif.serialize.model.MmifObject`, including the :class:`mmif.serialize.mmif.Mmif`. To start with an existing MMIF :class:`str`, simple initiate a new ``Mmif`` object with the file. - -.. code-block:: python - - import mmif - from mmif import Mmif - - mmif_str = """{ - "metadata": { - "mmif": "http://mmif.clams.ai/1.0.0" - }, - "documents": [ - { - "@type": "http://mmif.clams.ai/vocabulary/VideoDocument/v1", - "properties": { - "id": "m1", - "mime": "video/mp4", - "location": "file:///var/archive/video-0012.mp4" - } - }, - { - "@type": "http://mmif.clams.ai/vocabulary/TextDocument/v1", - "properties": { - "id": "m2", - "mime": "text/plain", - "location": "file:///var/archive/video-0012-transcript.txt" - } - } - ], - "views": []}""" - mmif_obj = Mmif(mmif_str) - - -Few notes; - -#. MMIF does not carry the primary source files in it. -#. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version ``mmif-python`` implementation of the MMIF might not be able to load an unsupported version of MMIF string. - -When serializing back to :class:`str`, call :meth:`mmif.serialize.model.MmifObject.serialize` on the object. - -To get subcomponents, you can use various getters implemented in subclasses. For example; - -.. code-block:: python - - from mmif.vocabulary.document_types import DocumentTypes - - for video in mmif_obj.Mmif.get_documents_by_type(DocumentTypes.VideoDocument): - with open(video.location_path(), 'b') as in_video: - # do something with the video file - - -For a full list of available helper methods, please refer to :ref:`the API documentation `. - diff --git a/docs/1.0.5/_sources/modules.rst.txt b/docs/1.0.5/_sources/modules.rst.txt deleted file mode 100644 index e4269c6d..00000000 --- a/docs/1.0.5/_sources/modules.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _apidoc: - -mmif package -============ - -.. toctree:: - :maxdepth: 4 - - autodoc/mmif.serialize - autodoc/mmif.vocabulary diff --git a/docs/1.0.5/_sources/plugins.rst.txt b/docs/1.0.5/_sources/plugins.rst.txt deleted file mode 100644 index 9e1505e9..00000000 --- a/docs/1.0.5/_sources/plugins.rst.txt +++ /dev/null @@ -1,75 +0,0 @@ -.. _plugins: - -Developing plugins for MMIF Python SDK -====================================== - - -Overview --------- - -As MMIF JSON files can carry information about media document files without actually carrying file contents, file accessing modules in ``mmif`` Python package (distributed as ``mmif-python`` on PyPI) are designed to be lightweight and flexible so that it can work with additional "plugin" Python packages that can handle concrete file access. - - -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF website `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects. - -Developer can write simple plugins that can provide additional functionalities to ``mmif-python``. For example, ``mmif-python`` does not provide any file access functionality beyond a local file system (with ``file`` scheme), but it can be extended with a plugin that can handle file access over different protocols (e.g. ``http``, ``s3``, ``ftp``, etc). - -This document contains information about how to write plugins for ``mmif-python``. - -Document Location Scheme Plugins -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -:class:`mmif.serialize.annotation.Document` class has various methods to access parts of ``location`` property of the document. The location is in `URI/IRI format `_ (``SCHEME://HOSTNAME/PATH``, in a nutshell) and it has to be resolved to a local file for CLAMS Apps to process the local file to analyze and extract information about the media and its contents. The core ``mmif-python`` distribution only provides a default implementation that can handle ``file`` scheme URIs. - -To add a document location handler plugin, you need to implement a Python `"package" `_ (do not confuse with PYPI distribution), that meets these requirements; - -#. the package must be named ``mmif_docloc_``. For example, to implement a handler for ``s3`` scheme, the package name must be ``mmif_docloc_s3``. The prefix is important as it's used in the plugin discovery process from the core ``mmif-python`` modules. -#. the top module of the package must have a function named ``resolve``. The function must take a single argument, which is a :class:`str` of the document location URI. The function must return a :class:`str` of the local file path. For example, if the document location is ``s3://mybucket/myfile.mp4``, a Python user should be able to to something like this; - -.. code-block:: python - - import mmif_docloc_s3 - resolved = mmif_docloc_s3.resolve('s3://mybucket/myfile.mp4') - # then resolved must be a local file path that can be used to open the file - - -Here's a minimal example codebase that you refer to when you develop a ``docloc`` plugin. - -(However, before you start writing your own plugin for a specific URI scheme, checking `if there's already a PyPI distribution `_ for the scheme might be a good idea.) - -.. code-block:: sh - - $ tree . - . - ├── mmif_docloc_dummy - │ └── __init__.py - ├── pyproject.toml - └── setup.cfg - - $ cat pyproject.toml - [build-system] - requires = ["setuptools"] - build-backend = "setuptools.build_meta" - - $ cat setup.cfg - [metadata] - name = mmif_docloc_dummy # this name is IMPORTANT - version = 0.0.1 - description = a plugin to mmif-pyhon to handle `dummy` location scheme - - -And the plugin code. - -.. code-block:: python - - # mmif_docloc_dummy/__init__.py - doc_types = {'video': 'mp4'} - - def resolve(docloc): - scheme = 'dummy' - if docloc.startswith(f'{scheme}://'): - doc_id, doc_type = docloc.split('.') - return f'/path/to/{doc_id}.{doc_types[doc_type]}' - else: - raise ValueError(f'cannot handle document location scheme: {docloc}') diff --git a/docs/1.0.5/_sources/target-versions.rst.txt b/docs/1.0.5/_sources/target-versions.rst.txt deleted file mode 100644 index 34216d3e..00000000 --- a/docs/1.0.5/_sources/target-versions.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _target-versions: - -Target MMIF Versions -==================== - -This article provides targeting MMIF specification versions of different versions of ``mmif-python`` SDK. - -.. csv-table:: Target Specification Versions - :file: target-versions.csv - :header-rows: 1 diff --git a/docs/1.0.5/_static/_sphinx_javascript_frameworks_compat.js b/docs/1.0.5/_static/_sphinx_javascript_frameworks_compat.js deleted file mode 100644 index 81415803..00000000 --- a/docs/1.0.5/_static/_sphinx_javascript_frameworks_compat.js +++ /dev/null @@ -1,123 +0,0 @@ -/* Compatability shim for jQuery and underscores.js. - * - * Copyright Sphinx contributors - * Released under the two clause BSD licence - */ - -/** - * small helper function to urldecode strings - * - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL - */ -jQuery.urldecode = function(x) { - if (!x) { - return x - } - return decodeURIComponent(x.replace(/\+/g, ' ')); -}; - -/** - * small helper function to urlencode strings - */ -jQuery.urlencode = encodeURIComponent; - -/** - * This function returns the parsed url parameters of the - * current request. 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span; - var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.className = className; - } - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - node.parentNode.insertBefore(span, node.parentNode.insertBefore( - document.createTextNode(val.substr(pos + text.length)), - node.nextSibling)); - node.nodeValue = val.substr(0, pos); - if (isInSVG) { - var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect"); - var bbox = node.parentElement.getBBox(); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute('class', className); - addItems.push({ - "parent": node.parentNode, - "target": rect}); - } - } - } - else if (!jQuery(node).is("button, select, textarea")) { - jQuery.each(node.childNodes, function() { - highlight(this, addItems); - }); - } - } - var addItems = []; - var result = this.each(function() { - highlight(this, addItems); - }); - for (var i = 0; i < addItems.length; ++i) { - jQuery(addItems[i].parent).before(addItems[i].target); - } - return result; -}; - -/* - * backward compatibility for jQuery.browser - * This will be supported until firefox bug is fixed. - */ -if (!jQuery.browser) { - jQuery.uaMatch = function(ua) { - ua = ua.toLowerCase(); - - var match = /(chrome)[ \/]([\w.]+)/.exec(ua) || - /(webkit)[ \/]([\w.]+)/.exec(ua) || - /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) || - /(msie) ([\w.]+)/.exec(ua) || - ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) || - []; - - return { - browser: match[ 1 ] || "", - version: match[ 2 ] || "0" - }; - }; - jQuery.browser = {}; - jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true; -} diff --git a/docs/1.0.5/_static/basic.css 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- -/** - * Simple result scoring code. - */ -if (typeof Scorer === "undefined") { - var Scorer = { - // Implement the following function to further tweak the score for each result - // The function takes a result array [docname, title, anchor, descr, score, filename] - // and returns the new score. - /* - score: result => { - const [docname, title, anchor, descr, score, filename, kind] = result - return score - }, - */ - - // query matches the full name of an object - objNameMatch: 11, - // or matches in the last dotted part of the object name - objPartialMatch: 6, - // Additive scores depending on the priority of the object - objPrio: { - 0: 15, // used to be importantResults - 1: 5, // used to be objectResults - 2: -5, // used to be unimportantResults - }, - // Used when the priority is not in the mapping. - objPrioDefault: 0, - - // query found in title - title: 15, - partialTitle: 7, - // query found in terms - term: 5, - partialTerm: 2, - }; -} - -// Global search result kind enum, used by themes to style search results. -class SearchResultKind { - static get index() { return "index"; } - static get object() { return "object"; } - static get text() { return "text"; } - static get title() { return "title"; } -} - -const _removeChildren = (element) => { - while (element && element.lastChild) element.removeChild(element.lastChild); -}; - -/** - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping - */ -const _escapeRegExp = (string) => - string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string - -const _displayItem = (item, searchTerms, highlightTerms) => { - const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; - const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; - const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; - const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; - const contentRoot = document.documentElement.dataset.content_root; - - const [docName, title, anchor, descr, score, _filename, kind] = item; - - let listItem = document.createElement("li"); - // Add a class representing the item's type: - // can be used by a theme's CSS selector for styling - // See SearchResultKind for the class names. - listItem.classList.add(`kind-${kind}`); - let requestUrl; - let linkUrl; - if (docBuilder === "dirhtml") { - // dirhtml builder - let dirname = docName + "/"; - if (dirname.match(/\/index\/$/)) - dirname = dirname.substring(0, dirname.length - 6); - else if (dirname === "index/") dirname = ""; - requestUrl = contentRoot + dirname; - linkUrl = requestUrl; - } else { - // normal html builders - requestUrl = contentRoot + docName + docFileSuffix; - linkUrl = docName + docLinkSuffix; - } - let linkEl = listItem.appendChild(document.createElement("a")); - linkEl.href = linkUrl + anchor; - linkEl.dataset.score = score; - linkEl.innerHTML = title; - if (descr) { - listItem.appendChild(document.createElement("span")).innerHTML = - " (" + descr + ")"; - // highlight search terms in the description - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - } - else if (showSearchSummary) - fetch(requestUrl) - .then((responseData) => responseData.text()) - .then((data) => { - if (data) - listItem.appendChild( - Search.makeSearchSummary(data, searchTerms, anchor) - ); - // highlight search terms in the summary - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - }); - Search.output.appendChild(listItem); -}; -const _finishSearch = (resultCount) => { - Search.stopPulse(); - Search.title.innerText = _("Search Results"); - if (!resultCount) - Search.status.innerText = Documentation.gettext( - "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." - ); - else - Search.status.innerText = Documentation.ngettext( - "Search finished, found one page matching the search query.", - "Search finished, found ${resultCount} pages matching the search query.", - resultCount, - ).replace('${resultCount}', resultCount); -}; -const _displayNextItem = ( - results, - resultCount, - searchTerms, - highlightTerms, -) => { - // results left, load the summary and display it - // this is intended to be dynamic (don't sub resultsCount) - if (results.length) { - _displayItem(results.pop(), searchTerms, highlightTerms); - setTimeout( - () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), - 5 - ); - } - // search finished, update title and status message - else _finishSearch(resultCount); -}; -// Helper function used by query() to order search results. -// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. -// Order the results by score (in opposite order of appearance, since the -// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. -const _orderResultsByScoreThenName = (a, b) => { - const leftScore = a[4]; - const rightScore = b[4]; - if (leftScore === rightScore) { - // same score: sort alphabetically - const leftTitle = a[1].toLowerCase(); - const rightTitle = b[1].toLowerCase(); - if (leftTitle === rightTitle) return 0; - return leftTitle > rightTitle ? -1 : 1; // inverted is intentional - } - return leftScore > rightScore ? 1 : -1; -}; - -/** - * Default splitQuery function. Can be overridden in ``sphinx.search`` with a - * custom function per language. - * - * The regular expression works by splitting the string on consecutive characters - * that are not Unicode letters, numbers, underscores, or emoji characters. - * This is the same as ``\W+`` in Python, preserving the surrogate pair area. - */ -if (typeof splitQuery === "undefined") { - var splitQuery = (query) => query - .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) - .filter(term => term) // remove remaining empty strings -} - -/** - * Search Module - */ -const Search = { - _index: null, - _queued_query: null, - _pulse_status: -1, - - htmlToText: (htmlString, anchor) => { - const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - for (const removalQuery of [".headerlink", "script", "style"]) { - htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); - } - if (anchor) { - const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); - if (anchorContent) return anchorContent.textContent; - - console.warn( - `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` - ); - } - - // if anchor not specified or not found, fall back to main content - const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent) return docContent.textContent; - - console.warn( - "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." - ); - return ""; - }, - - init: () => { - const query = new URLSearchParams(window.location.search).get("q"); - document - .querySelectorAll('input[name="q"]') - .forEach((el) => (el.value = query)); - if (query) Search.performSearch(query); - }, - - loadIndex: (url) => - (document.body.appendChild(document.createElement("script")).src = url), - - setIndex: (index) => { - Search._index = index; - if (Search._queued_query !== null) { - const query = Search._queued_query; - Search._queued_query = null; - Search.query(query); - } - }, - - hasIndex: () => Search._index !== null, - - deferQuery: (query) => (Search._queued_query = query), - - stopPulse: () => (Search._pulse_status = -1), - - startPulse: () => { - if (Search._pulse_status >= 0) return; - - const pulse = () => { - Search._pulse_status = (Search._pulse_status + 1) % 4; - Search.dots.innerText = ".".repeat(Search._pulse_status); - if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); - }; - pulse(); - }, - - /** - * perform a search for something (or wait until index is loaded) - */ - performSearch: (query) => { - // create the required interface elements - const searchText = document.createElement("h2"); - searchText.textContent = _("Searching"); - const searchSummary = document.createElement("p"); - searchSummary.classList.add("search-summary"); - searchSummary.innerText = ""; - const searchList = document.createElement("ul"); - searchList.setAttribute("role", "list"); - searchList.classList.add("search"); - - const out = document.getElementById("search-results"); - Search.title = out.appendChild(searchText); - Search.dots = Search.title.appendChild(document.createElement("span")); - Search.status = out.appendChild(searchSummary); - Search.output = out.appendChild(searchList); - - const searchProgress = document.getElementById("search-progress"); - // Some themes don't use the search progress node - if (searchProgress) { - searchProgress.innerText = _("Preparing search..."); - } - Search.startPulse(); - - // index already loaded, the browser was quick! - if (Search.hasIndex()) Search.query(query); - else Search.deferQuery(query); - }, - - _parseQuery: (query) => { - // stem the search terms and add them to the correct list - const stemmer = new Stemmer(); - const searchTerms = new Set(); - const excludedTerms = new Set(); - const highlightTerms = new Set(); - const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); - splitQuery(query.trim()).forEach((queryTerm) => { - const queryTermLower = queryTerm.toLowerCase(); - - // maybe skip this "word" - // stopwords array is from language_data.js - if ( - stopwords.indexOf(queryTermLower) !== -1 || - queryTerm.match(/^\d+$/) - ) - return; - - // stem the word - let word = stemmer.stemWord(queryTermLower); - // select the correct list - if (word[0] === "-") excludedTerms.add(word.substr(1)); - else { - searchTerms.add(word); - highlightTerms.add(queryTermLower); - } - }); - - if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js - localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) - } - - // console.debug("SEARCH: searching for:"); - // console.info("required: ", [...searchTerms]); - // console.info("excluded: ", [...excludedTerms]); - - return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; - }, - - /** - * execute search (requires search index to be loaded) - */ - _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - - // Collect multiple result groups to be sorted separately and then ordered. - // Each is an array of [docname, title, anchor, descr, score, filename, kind]. - const normalResults = []; - const nonMainIndexResults = []; - - _removeChildren(document.getElementById("search-progress")); - - const queryLower = query.toLowerCase().trim(); - for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { - for (const [file, id] of foundTitles) { - const score = Math.round(Scorer.title * queryLower.length / title.length); - const boost = titles[file] === title ? 1 : 0; // add a boost for document titles - normalResults.push([ - docNames[file], - titles[file] !== title ? `${titles[file]} > ${title}` : title, - id !== null ? "#" + id : "", - null, - score + boost, - filenames[file], - SearchResultKind.title, - ]); - } - } - } - - // search for explicit entries in index directives - for (const [entry, foundEntries] of Object.entries(indexEntries)) { - if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id, isMain] of foundEntries) { - const score = Math.round(100 * queryLower.length / entry.length); - const result = [ - docNames[file], - titles[file], - id ? "#" + id : "", - null, - score, - filenames[file], - SearchResultKind.index, - ]; - if (isMain) { - normalResults.push(result); - } else { - nonMainIndexResults.push(result); - } - } - } - } - - // lookup as object - objectTerms.forEach((term) => - normalResults.push(...Search.performObjectSearch(term, objectTerms)) - ); - - // lookup as search terms in fulltext - normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); - - // let the scorer override scores with a custom scoring function - if (Scorer.score) { - normalResults.forEach((item) => (item[4] = Scorer.score(item))); - nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); - } - - // Sort each group of results by score and then alphabetically by name. - normalResults.sort(_orderResultsByScoreThenName); - nonMainIndexResults.sort(_orderResultsByScoreThenName); - - // Combine the result groups in (reverse) order. - // Non-main index entries are typically arbitrary cross-references, - // so display them after other results. - let results = [...nonMainIndexResults, ...normalResults]; - - // remove duplicate search results - // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept - let seen = new Set(); - results = results.reverse().reduce((acc, result) => { - let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); - if (!seen.has(resultStr)) { - acc.push(result); - seen.add(resultStr); - } - return acc; - }, []); - - return results.reverse(); - }, - - query: (query) => { - const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); - const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); - - // for debugging - //Search.lastresults = results.slice(); // a copy - // console.info("search results:", Search.lastresults); - - // print the results - _displayNextItem(results, results.length, searchTerms, highlightTerms); - }, - - /** - * search for object names - */ - performObjectSearch: (object, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const objects = Search._index.objects; - const objNames = Search._index.objnames; - const titles = Search._index.titles; - - const results = []; - - const objectSearchCallback = (prefix, match) => { - const name = match[4] - const fullname = (prefix ? prefix + "." : "") + name; - const fullnameLower = fullname.toLowerCase(); - if (fullnameLower.indexOf(object) < 0) return; - - let score = 0; - const parts = fullnameLower.split("."); - - // check for different match types: exact matches of full name or - // "last name" (i.e. last dotted part) - if (fullnameLower === object || parts.slice(-1)[0] === object) - score += Scorer.objNameMatch; - else if (parts.slice(-1)[0].indexOf(object) > -1) - score += Scorer.objPartialMatch; // matches in last name - - const objName = objNames[match[1]][2]; - const title = titles[match[0]]; - - // If more than one term searched for, we require other words to be - // found in the name/title/description - const otherTerms = new Set(objectTerms); - otherTerms.delete(object); - if (otherTerms.size > 0) { - const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); - if ( - [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) - ) - return; - } - - let anchor = match[3]; - if (anchor === "") anchor = fullname; - else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; - - const descr = objName + _(", in ") + title; - - // add custom score for some objects according to scorer - if (Scorer.objPrio.hasOwnProperty(match[2])) - score += Scorer.objPrio[match[2]]; - else score += Scorer.objPrioDefault; - - results.push([ - docNames[match[0]], - fullname, - "#" + anchor, - descr, - score, - filenames[match[0]], - SearchResultKind.object, - ]); - }; - Object.keys(objects).forEach((prefix) => - objects[prefix].forEach((array) => - objectSearchCallback(prefix, array) - ) - ); - return results; - }, - - /** - * search for full-text terms in the index - */ - performTermsSearch: (searchTerms, excludedTerms) => { - // prepare search - const terms = Search._index.terms; - const titleTerms = Search._index.titleterms; - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - - const scoreMap = new Map(); - const fileMap = new Map(); - - // perform the search on the required terms - searchTerms.forEach((word) => { - const files = []; - const arr = [ - { files: terms[word], score: Scorer.term }, - { files: titleTerms[word], score: Scorer.title }, - ]; - // add support for partial matches - if (word.length > 2) { - const escapedWord = _escapeRegExp(word); - if (!terms.hasOwnProperty(word)) { - Object.keys(terms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: terms[term], score: Scorer.partialTerm }); - }); - } - if (!titleTerms.hasOwnProperty(word)) { - Object.keys(titleTerms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); - }); - } - } - - // no match but word was a required one - if (arr.every((record) => record.files === undefined)) return; - - // found search word in contents - arr.forEach((record) => { - if (record.files === undefined) return; - - let recordFiles = record.files; - if (recordFiles.length === undefined) recordFiles = [recordFiles]; - files.push(...recordFiles); - - // set score for the word in each file - recordFiles.forEach((file) => { - if (!scoreMap.has(file)) scoreMap.set(file, {}); - scoreMap.get(file)[word] = record.score; - }); - }); - - // create the mapping - files.forEach((file) => { - if (!fileMap.has(file)) fileMap.set(file, [word]); - else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); - }); - }); - - // now check if the files don't contain excluded terms - const results = []; - for (const [file, wordList] of fileMap) { - // check if all requirements are matched - - // as search terms with length < 3 are discarded - const filteredTermCount = [...searchTerms].filter( - (term) => term.length > 2 - ).length; - if ( - wordList.length !== searchTerms.size && - wordList.length !== filteredTermCount - ) - continue; - - // ensure that none of the excluded terms is in the search result - if ( - [...excludedTerms].some( - (term) => - terms[term] === file || - titleTerms[term] === file || - (terms[term] || []).includes(file) || - (titleTerms[term] || []).includes(file) - ) - ) - break; - - // select one (max) score for the file. - const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); - // add result to the result list - results.push([ - docNames[file], - titles[file], - "", - null, - score, - filenames[file], - SearchResultKind.text, - ]); - } - return results; - }, - - /** - * helper function to return a node containing the - * search summary for a given text. keywords is a list - * of stemmed words. - */ - makeSearchSummary: (htmlText, keywords, anchor) => { - const text = Search.htmlToText(htmlText, anchor); - if (text === "") return null; - - const textLower = text.toLowerCase(); - const actualStartPosition = [...keywords] - .map((k) => textLower.indexOf(k.toLowerCase())) - .filter((i) => i > -1) - .slice(-1)[0]; - const startWithContext = Math.max(actualStartPosition - 120, 0); - - const top = startWithContext === 0 ? "" : "..."; - const tail = startWithContext + 240 < text.length ? "..." : ""; - - let summary = document.createElement("p"); - summary.classList.add("context"); - summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; - - return summary; - }, -}; - -_ready(Search.init); diff --git a/docs/1.0.5/_static/sphinx_highlight.js b/docs/1.0.5/_static/sphinx_highlight.js deleted file mode 100644 index 8a96c69a..00000000 --- a/docs/1.0.5/_static/sphinx_highlight.js +++ /dev/null @@ -1,154 +0,0 @@ -/* Highlighting utilities for Sphinx HTML documentation. */ -"use strict"; - -const SPHINX_HIGHLIGHT_ENABLED = true - -/** - * highlight a given string on a node by wrapping it in - * span elements with the given class name. - */ -const _highlight = (node, addItems, text, className) => { - if (node.nodeType === Node.TEXT_NODE) { - const val = node.nodeValue; - const parent = node.parentNode; - const pos = val.toLowerCase().indexOf(text); - if ( - pos >= 0 && - !parent.classList.contains(className) && - !parent.classList.contains("nohighlight") - ) { - let span; - - const closestNode = parent.closest("body, svg, foreignObject"); - const isInSVG = closestNode && closestNode.matches("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.classList.add(className); - } - - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - const rest = document.createTextNode(val.substr(pos + text.length)); - parent.insertBefore( - span, - parent.insertBefore( - rest, - node.nextSibling - ) - ); - node.nodeValue = val.substr(0, pos); - /* There may be more occurrences of search term in this node. So call this - * function recursively on the remaining fragment. - */ - _highlight(rest, addItems, text, className); - - if (isInSVG) { - const rect = document.createElementNS( - "http://www.w3.org/2000/svg", - "rect" - ); - const bbox = parent.getBBox(); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute("class", className); - addItems.push({ parent: parent, target: rect }); - } - } - } else if (node.matches && !node.matches("button, select, textarea")) { - node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); - } -}; -const _highlightText = (thisNode, text, className) => { - let addItems = []; - _highlight(thisNode, addItems, text, className); - addItems.forEach((obj) => - obj.parent.insertAdjacentElement("beforebegin", obj.target) - ); -}; - -/** - * Small JavaScript module for the documentation. - */ -const SphinxHighlight = { - - /** - * highlight the search words provided in localstorage in the text - */ - highlightSearchWords: () => { - if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight - - // get and clear terms from localstorage - const url = new URL(window.location); - const highlight = - localStorage.getItem("sphinx_highlight_terms") - || url.searchParams.get("highlight") - || ""; - localStorage.removeItem("sphinx_highlight_terms") - url.searchParams.delete("highlight"); - window.history.replaceState({}, "", url); - - // get individual terms from highlight string - const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); - if (terms.length === 0) return; // nothing to do - - // There should never be more than one element matching "div.body" - const divBody = document.querySelectorAll("div.body"); - const body = divBody.length ? divBody[0] : document.querySelector("body"); - window.setTimeout(() => { - terms.forEach((term) => _highlightText(body, term, "highlighted")); - }, 10); - - const searchBox = document.getElementById("searchbox"); - if (searchBox === null) return; - searchBox.appendChild( - document - .createRange() - .createContextualFragment( - '

' + - '' + - _("Hide Search Matches") + - "

" - ) - ); - }, - - /** - * helper function to hide the search marks again - */ - hideSearchWords: () => { - document - .querySelectorAll("#searchbox .highlight-link") - .forEach((el) => el.remove()); - document - .querySelectorAll("span.highlighted") - .forEach((el) => el.classList.remove("highlighted")); - localStorage.removeItem("sphinx_highlight_terms") - }, - - initEscapeListener: () => { - // only install a listener if it is really needed - if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; - - document.addEventListener("keydown", (event) => { - // bail for input elements - if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; - // bail with special keys - if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; - if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { - SphinxHighlight.hideSearchWords(); - event.preventDefault(); - } - }); - }, -}; - -_ready(() => { - /* Do not call highlightSearchWords() when we are on the search page. - * It will highlight words from the *previous* search query. - */ - if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); - SphinxHighlight.initEscapeListener(); -}); diff --git a/docs/1.0.5/autodoc/mmif.serialize.html b/docs/1.0.5/autodoc/mmif.serialize.html deleted file mode 100644 index cb02af24..00000000 --- a/docs/1.0.5/autodoc/mmif.serialize.html +++ /dev/null @@ -1,1271 +0,0 @@ - - - - - - - - - mmif.serialize module — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
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mmif.serialize module

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mmif.serialize.model module

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The model module contains the classes used to represent an -abstract MMIF object as a live Python object.

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The MmifObject class or one of its derivatives is subclassed by -all other classes defined in this SDK, except for MmifObjectEncoder.

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These objects are generally instantiated from JSON, either as a string -or as an already-loaded Python dictionary. This base class provides the -core functionality for deserializing MMIF JSON data into live objects -and serializing live objects into MMIF JSON data. Specialized behavior -for the different components of MMIF is added in the subclasses.

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-class mmif.serialize.model.DataDict(mmif_obj: bytes | str | dict | None = None)[source]
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Bases: MmifObject, Generic[T, S]

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-empty()[source]
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-get(key: T, default=None) → S | None[source]
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-items()[source]
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-keys()[source]
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-update(other, overwrite)[source]
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-values()[source]
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-class mmif.serialize.model.DataList(mmif_obj: bytes | str | list | None = None)[source]
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Bases: MmifObject, Generic[T]

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The DataList class is an abstraction that represents the -various lists found in a MMIF file, such as documents, subdocuments, -views, and annotations.

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Parameters:
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mmif_obj (Union[str, list]) – the data that the list contains

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-append(value, overwrite)[source]
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-deserialize(mmif_json: str | list) → None[source]
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Passes the input data into the internal deserializer.

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-empty()[source]
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-get(key: str) → T | None[source]
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Standard dictionary-style get() method, albeit with no default -parameter. Relies on the implementation of __getitem__.

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Will return None if the key is not found.

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Parameters:
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key – the key to search for

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Returns:
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the value matching that key

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-class mmif.serialize.model.MmifObject(mmif_obj: bytes | str | dict | None = None)[source]
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Bases: object

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Abstract superclass for MMIF related key-value pair objects.

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Any MMIF object can be initialized as an empty placeholder or -an actual representation with a JSON formatted string or equivalent -dict object argument.

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This superclass has four specially designed instance variables, and these -variable names cannot be used as attribute names for MMIF objects.

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  1. _unnamed_attributes: -Only can be either None or an empty dictionary. If it’s set to None, -it means the class won’t take any Additional Attributes in the JSON -schema sense. If it’s a dict, users can throw any k-v pairs to the -class, EXCEPT for the reserved two key names.

    2. -

  2. _attribute_classes: -This is a dict from a key name to a specific python class to use for -deserialize the value. Note that a key name in this dict does NOT -have to be a named attribute, but is recommended to be one.

    3. -

  3. _required_attributes: -This is a simple list of names of attributes that are required in the object. -When serialize, an object will skip its empty (e.g. zero-length, or None) -attributes unless they are in this list. Otherwise, the serialized JSON -string would have empty representations (e.g. "", []).

    4. -

  4. _exclude_from_diff: -This is a simple list of names of attributes that should be excluded from -the diff calculation in __eq__.

    5. -
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# TODO (krim @ 8/17/20): this dict is however, a duplicate with the type hints in the class definition. -Maybe there is a better way to utilize type hints (e.g. getting them as a programmatically), but for now -developers should be careful to add types to hints as well as to this dict.

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Also note that those special attributes MUST be set in the __init__() -before calling super method, otherwise deserialization will not work.

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And also, a subclass that has one or more named attributes, it must -set those attributes in the __init__() before calling super method. When -serializing a MmifObject, all empty attributes will be ignored, so for -optional named attributes, you must leave the values empty (len == 0), but -NOT None. Any None-valued named attributes will cause issues with current -implementation.

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Parameters:
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mmif_obj – JSON string or dict to initialize an object. -If not given, an empty object will be initialized, sometimes with -an ID value automatically generated, based on its parent object.

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-deserialize(mmif_json: str | dict) → None[source]
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Takes a JSON-formatted string or a simple dict that’s json-loaded from -such a string as an input and populates object’s fields with the values -specified in the input.

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Parameters:
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mmif_json – JSON-formatted string or dict from such a string -that represents a MMIF object

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-disallow_additional_properties() → None[source]
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Call this method in __init__() to prevent the insertion -of unnamed attributes after initialization.

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-static is_empty(obj) → bool[source]
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return True if the obj is None or “emtpy”. The emptiness first defined as -having zero length. But for objects that lack __len__ method, we need -additional check.

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-reserved_names: Set[str] = {'_attribute_classes', '_exclude_from_diff', '_required_attributes', '_unnamed_attributes', 'reserved_names'}[source]
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-serialize(pretty: bool = False) → str[source]
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Generates JSON representation of an object.

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Parameters:
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pretty – If True, returns string representation with indentation.

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Returns:
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JSON string of the object.

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-set_additional_property(key: str, value: Any) → None[source]
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Method to set values in _unnamed_attributes.

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Parameters:
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  • key – the attribute name

    • -

  • value – the desired value

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Returns:
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None

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Raise:
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AttributeError if additional properties are disallowed by disallow_additional_properties()

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-class mmif.serialize.model.MmifObjectEncoder(*, skipkeys=False, ensure_ascii=True, check_circular=True, allow_nan=True, sort_keys=False, indent=None, separators=None, default=None)[source]
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Bases: JSONEncoder

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Encoder class to define behaviors of de-/serialization

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-default(obj: MmifObject)[source]
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Overrides default encoding behavior to prioritize MmifObject.serialize().

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mmif.serialize.mmif module

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The mmif module contains the classes used to represent a full MMIF -file as a live Python object.

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See the specification docs and the JSON Schema file for more information.

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-class mmif.serialize.mmif.Mmif(mmif_obj: bytes | str | dict | None = None, *, validate: bool = True)[source]
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Bases: MmifObject

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MmifObject that represents a full MMIF file.

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Parameters:
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  • mmif_obj – the JSON data

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  • validate – whether to validate the data against the MMIF JSON schema.

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-add_document(document: Document, overwrite=False) → None[source]
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Appends a Document object to the documents list.

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Fails if there is already a document with the same ID in the MMIF object.

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Parameters:
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  • document – the Document object to add

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  • overwrite – if set to True, will overwrite -an existing view with the same ID

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Returns:
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None

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-add_view(view: View, overwrite=False) → None[source]
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Appends a View object to the views list.

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Fails if there is already a view with the same ID in the MMIF object.

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Parameters:
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  • view – the Document object to add

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  • overwrite – if set to True, will overwrite -an existing view with the same ID

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Returns:
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None

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-generate_capital_annotations()[source]
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Automatically convert any “pending” temporary properties from -Document objects to Annotation objects . The generated Annotation -objects are then added to the last View in the views lists.

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See https://github.com/clamsproject/mmif-python/issues/226 for rationale -behind this behavior and discussion.

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-get_alignments(at_type1: str | TypesBase, at_type2: str | TypesBase) → Dict[str, List[Annotation]][source]
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Finds views where alignments between two given annotation types occurred.

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Returns:
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a dict that keyed by view IDs (str) and has lists of alignment Annotation objects as values.

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-get_all_views_contain(at_types: TypesBase | str | List[str | TypesBase]) → List[View][source]
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Returns the list of all views in the MMIF if given types -are present in that view’s ‘contains’ metadata.

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Parameters:
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at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

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Returns:
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the list of views that contain the type

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-get_document_by_id(doc_id: str) → Document[source]
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Finds a Document object with the given ID.

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Parameters:
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doc_id – the ID to search for

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Returns:
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a reference to the corresponding document, if it exists

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Raises:
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KeyError – if there is no corresponding document

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-get_document_location(m_type: DocumentTypes | str, path_only=False) → str | None[source]
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Method to get the location of first document of given type.

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Parameters:
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m_type – the type to search for

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Returns:
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the value of the location field in the corresponding document

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-get_documents_by_app(app_id: str) → List[Document][source]
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Method to get all documents object queries by its originated app name.

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Parameters:
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app_id – the app name to search for

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Returns:
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a list of documents matching the requested app name, or an empty list if the app not found

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-get_documents_by_property(prop_key: str, prop_value: str) → List[Document][source]
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Method to retrieve documents by an arbitrary key-value pair in the document properties objects.

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Parameters:
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  • prop_key – the metadata key to search for

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  • prop_value – the metadata value to match

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Returns:
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a list of documents matching the requested metadata key-value pair

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-get_documents_by_type(doc_type: str | DocumentTypes) → List[Document][source]
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Method to get all documents where the type matches a particular document type, which should be one of the CLAMS document types.

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Parameters:
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doc_type – the type of documents to search for, must be one of Document type defined in the CLAMS vocabulary.

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Returns:
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a list of documents matching the requested type, or an empty list if none found.

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-get_documents_in_view(vid: str | None = None) → List[Document][source]
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Method to get all documents object queries by a view id.

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Parameters:
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vid – the source view ID to search for

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Returns:
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a list of documents matching the requested source view ID, or an empty list if the view not found

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-get_documents_locations(m_type: DocumentTypes | str, path_only=False) → List[str | None][source]
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This method returns the file paths of documents of given type. -Only top-level documents have locations, so we only check them.

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Parameters:
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m_type – the type to search for

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Returns:
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a list of the values of the location fields in the corresponding documents

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-get_view_by_id(req_view_id: str) → View[source]
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Finds a View object with the given ID.

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Parameters:
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req_view_id – the ID to search for

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Returns:
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a reference to the corresponding view, if it exists

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Raises:
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Exception – if there is no corresponding view

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-get_view_contains(at_types: TypesBase | str | List[str | TypesBase]) → View | None[source]
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Returns the last view appended that contains the given -types in its ‘contains’ metadata.

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Parameters:
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at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

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Returns:
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the view, or None if the type is not found

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-get_views_contain(at_types: TypesBase | str | List[str | TypesBase]) → List[View][source]
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An alias to get_all_views_contain method.

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-get_views_for_document(doc_id: str) → List[View][source]
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Returns the list of all views that have annotations anchored on a particular document. -Note that when the document is inside a view (generated during the pipeline’s running), -doc_id must be prefixed with the view_id.

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-id_delimiter: ClassVar[str] = ':'[source]
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-new_view() → View[source]
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Creates an empty view with a new ID and appends it to the views list.

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Returns:
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a reference to the new View object

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-new_view_id() → str[source]
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Fetches an ID for a new view.

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Returns:
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the ID

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-sanitize()[source]
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Sanitizes a Mmif object by running some safeguards. -Concretely, it performs the following before returning the JSON string.

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  1. validating output using built-in MMIF jsonschema

    2. -

  2. remove non-existing annotation types from contains metadata

    3. -
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-serialize(pretty: bool = False, sanitize: bool = False, autogenerate_capital_annotations=True) → str[source]
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Serializes the MMIF object to a JSON string.

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Parameters:
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  • sanitize – If True, performs some sanitization of before returning -the JSON string. See sanitize() for details.

    • -

  • autogenerate_capital_annotations – If True, automatically convert -any “pending” temporary properties from Document objects to -Annotation objects. See generate_capital_annotations() for -details.

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  • pretty – If True, returns string representation with indentation.

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Returns:
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JSON string of the MMIF object.

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-static validate(json_str: bytes | str | dict) → None[source]
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Validates a MMIF JSON object against the MMIF Schema. -Note that this method operates before processing by MmifObject._load_str, -so it expects @ and not _ for the JSON-LD @-keys.

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Raises:
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jsonschema.exceptions.ValidationError – if the input fails validation

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Parameters:
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json_str – a MMIF JSON dict or string

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Returns:
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None

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-view_prefix: ClassVar[str] = 'v_'[source]
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mmif.serialize.view module

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The view module contains the classes used to represent a MMIF view -as a live Python object.

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In MMIF, views are created by apps in a pipeline that are annotating -data that was previously present in the MMIF file.

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-class mmif.serialize.view.Contain(mmif_obj: bytes | str | dict | None = None)[source]
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Bases: DataDict[str, str]

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Contain object that represents the metadata of a single -annotation type in the contains metadata of a MMIF view.

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-class mmif.serialize.view.View(view_obj: bytes | str | dict | None = None)[source]
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Bases: MmifObject

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View object that represents a single view in a MMIF file.

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A view is identified by an ID, and contains certain metadata, -a list of annotations, and potentially a JSON-LD @context -IRI.

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If view_obj is not provided, an empty View will be generated.

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Parameters:
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view_obj – the JSON data that defines the view

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-add_annotation(annotation: Annotation, overwrite=False) → Annotation[source]
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Adds an annotation to the current view.

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Fails if there is already an annotation with the same ID -in the view, unless overwrite is set to True.

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Parameters:
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Raises:
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KeyError – if overwrite is set to False and -an annotation with the same ID exists -in the view

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Returns:
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the same Annotation object passed in as annotation

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-add_document(document: Document, overwrite=False) → Annotation[source]
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Appends a Document object to the annotations list.

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Fails if there is already a document with the same ID in the annotations list.

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Parameters:
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  • document – the Document object to add

    • -

  • overwrite – if set to True, will overwrite -an existing view with the same ID

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Returns:
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None

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-get_annotation_by_id(ann_id)[source]
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-get_annotations(at_type: str | TypesBase | None = None, **properties) → Generator[Annotation, None, None][source]
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Look for certain annotations in this view, specified by parameters

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Parameters:
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  • at_type – @type of the annotations to look for. When this is None, any @type will match.

    • -

  • properties – properties of the annotations to look for. When given more than one property, all properties must match. Note that annotation type metadata are specified in the contains view metadata, not in individual annotation objects.

    • -
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-get_document_by_id(doc_id) → Document[source]
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-get_documents() → List[Document][source]
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-new_annotation(at_type: str | TypesBase, aid: str | None = None, overwrite=False, **properties) → Annotation[source]
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Generates a new mmif.serialize.annotation.Annotation -object and adds it to the current view.

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Fails if there is already an annotation with the same ID -in the view, unless overwrite is set to True.

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Parameters:
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  • at_type – the desired @type of the annotation.

    • -

  • aid – the desired ID of the annotation, when not given, -the mmif SDK tries to automatically generate an ID based on -Annotation type and existing annotations in the view.

    • -

  • overwrite – if set to True, will overwrite an -existing annotation with the same ID.

    • -
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Raises:
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KeyError – if overwrite is set to False and -an annotation with the same ID exists -in the view.

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Returns:
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the generated mmif.serialize.annotation.Annotation

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-new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
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Adds a new element to the contains metadata.

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Parameters:
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  • at_type – the @type of the annotation type being added

    • -

  • contains_metadata – any metadata associated with the annotation type

    • -
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Returns:
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the generated Contain object

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-new_textdocument(text: str, lang: str = 'en', did: str | None = None, overwrite=False, **properties) → Document[source]
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Generates a new mmif.serialize.annotation.Document -object, particularly typed as TextDocument and adds it to the current view.

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Fails if there is already a text document with the same ID -in the view, unless overwrite is set to True.

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Parameters:
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  • text – text content of the new document

    • -

  • lang – ISO 639-1 code of the language used in the new document

    • -

  • did – the desired ID of the document, when not given, -the mmif SDK tries to automatically generate an ID based on -Annotation type and existing documents in the view.

    • -

  • overwrite – if set to True, will overwrite an -existing document with the same ID

    • -
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Raises:
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KeyError – if overwrite is set to False and -an document with the same ID exists -in the view

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Returns:
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the generated mmif.serialize.annotation.Document

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-set_error(err_message: str, err_trace: str) → None[source]
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-class mmif.serialize.view.ViewMetadata(viewmetadata_obj: bytes | str | dict | None = None)[source]
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Bases: MmifObject

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ViewMetadata object that represents the metadata object within a MMIF view.

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Parameters:
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viewmetadata_obj – the JSON data that defines the metadata

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-add_contain(contain: Contain, at_type: str | TypesBase)[source]
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-add_parameter(param_key, param_value)[source]
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-add_parameters(**runtime_params)[source]
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-add_warnings(*warnings: Warning)[source]
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-emtpy_warnings()[source]
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-get_parameter(param_key)[source]
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-new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
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Adds a new element to the contains dictionary.

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Parameters:
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    -

  • at_type – the @type of the annotation type being added

    • -

  • contains_metadata – any metadata associated with the annotation type

    • -
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Returns:
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the generated Contain object

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-set_error(message: str, stack_trace: str)[source]
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mmif.serialize.annotation module

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The annotation module contains the classes used to represent a -MMIF annotation as a live Python object.

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In MMIF, annotations are created by apps in a pipeline as a part -of a view. For documentation on how views are represented, see -mmif.serialize.view.

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-class mmif.serialize.annotation.Annotation(anno_obj: bytes | str | dict | None = None)[source]
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Bases: MmifObject

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MmifObject that represents an annotation in a MMIF view.

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-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]]) → None[source]
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Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

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- -
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-property at_type: TypesBase[source]
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- -
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-static check_prop_value_is_simple_enough(value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]])[source]
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- -
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-get(prop_name: str) → AnnotationProperties | str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]][source]
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A special getter for Annotation properties. This is to allow for -directly accessing properties without having to go through the -properties object.

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- -
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-get_property(prop_name: str) → AnnotationProperties | str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]][source]
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A special getter for Annotation properties. This is to allow for -directly accessing properties without having to go through the -properties object.

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- -
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-property id: str[source]
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- -
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-is_document()[source]
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- -
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-is_type(at_type: str | TypesBase) → bool[source]
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Check if the @type of this object matches.

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- -
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-property parent: str[source]
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- -
- -
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-class mmif.serialize.annotation.AnnotationProperties(mmif_obj: bytes | str | dict | None = None)[source]
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Bases: MmifObject, MutableMapping[str, T]

-

AnnotationProperties object that represents the -properties object within a MMIF annotation.

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Parameters:
-

mmif_obj – the JSON data that defines the properties

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- -
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-class mmif.serialize.annotation.Document(doc_obj: bytes | str | dict | None = None)[source]
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Bases: Annotation

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Document object that represents a single document in a MMIF file.

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A document is identified by an ID, and contains certain attributes -and potentially contains the contents of the document itself, -metadata about how the document was created, and/or a list of -subdocuments grouped together logically.

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If document_obj is not provided, an empty Document will be generated.

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Parameters:
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document_obj – the JSON data that defines the document

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-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None]) → None[source]
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Adds a property to the document’s properties.

-

Unlike the parent Annotation class, added properties of a -Document object can be lost during serialization unless it belongs -to somewhere in a Mmif object. This is because we want to keep -Document object as “read-only” as possible. Thus, if you want to add -a property to a Document object,

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    -

  • add the document to a Mmif object (either in the documents list or -in a view from the views list), or

    • -

  • directly write to Document.properties instead of using this method -(which is not recommended).

    • -
-

With the former method, the SDK will record the added property as a -Annotation annotation object, separate from the original Document -object. See Mmif.generate_capital_annotations() for more.

-

A few notes to keep in mind:

-
    -

  1. You can’t overwrite an existing property of a Document object.

    2. -

  2. A MMIF can have multiple Annotation objects with the same -property name but different values. When this happens, the SDK will -only keep the latest value (in order of appearances in views list) of -the property, effectively overwriting the previous values.

    3. -
-
- -
-
-get(prop_name)[source]
-

A special getter for Document properties. This is to allow for reading -the three properties in a specific order so that the latest value is -returned, in case there are multiple values for the same key.

-
- -
-
-get_property(prop_name)[source]
-

A special getter for Document properties. This is to allow for reading -the three properties in a specific order so that the latest value is -returned, in case there are multiple values for the same key.

-
- -
-
-property location: str | None[source]
-

location property must be a legitimate URI. That is, should the document be a local file -then the file:// scheme must be used. -Returns None when no location is set.

-
- -
-
-location_address() → str | None[source]
-

Retrieves the full address from the document location URI. -Returns None when no location is set.

-
- -
-
-location_path() → str | None[source]
-

Retrieves a path that’s resolved to a pathname in the local file system. -To obtain the original value of the “path” part in the location string -(before resolving), use properties.location_path_literal method. -Returns None when no location is set.

-
- -
-
-location_scheme() → str | None[source]
-

Retrieves URI scheme of the document location. -Returns None when no location is set.

-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.DocumentProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: AnnotationProperties

-

DocumentProperties object that represents the -properties object within a MMIF document.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
-
-property location: str | None[source]
-

location property must be a legitimate URI. That is, should the document be a local file -then the file:// scheme must be used. -Returns None when no location is set.

-
- -
-
-location_address() → str | None[source]
-

Retrieves the full address from the document location URI. -Returns None when no location is set.

-
- -
-
-location_path() → str | None[source]
-
- -
-
-location_path_literal() → str | None[source]
-

Retrieves only path name of the document location (hostname is ignored). -Returns None when no location is set.

-
- -
-
-location_path_resolved(nonexist_ok=True) → str | None[source]
-

Retrieves only path name of the document location (hostname is ignored), -and then try to resolve the path name in the local file system. -This method should be used when the document scheme is file or empty. -For other schemes, users should install mmif-locdoc-<scheme> plugin.

-

Returns None when no location is set. -Raise ValueError when no code found to resolve the given location scheme.

-
- -
-
-location_scheme() → str | None[source]
-

Retrieves URI scheme of the document location. -Returns None when no location is set.

-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.Text(text_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-
-
-property lang: str[source]
-
- -
-
-property value: str[source]
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- - - \ No newline at end of file diff --git a/docs/1.0.5/autodoc/mmif.vocabulary.html b/docs/1.0.5/autodoc/mmif.vocabulary.html deleted file mode 100644 index 86a36105..00000000 --- a/docs/1.0.5/autodoc/mmif.vocabulary.html +++ /dev/null @@ -1,325 +0,0 @@ - - - - - - - - - mmif.vocabulary module — mmif-python documentation - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.vocabulary module

-
-

mmif.vocabulary.annotation_types module

-
-
-class mmif.vocabulary.annotation_types.AnnotationTypes(type_uri, fuzzymode=True)[source]
-

Bases: AnnotationTypesBase

-

This class contains the CLAMS annotation types -defined in the spec version 1.1.0 as class variables.

-
-
-Alignment = http://mmif.clams.ai/vocabulary/Alignment/v1[source]
-
- -
-
-Annotation = http://mmif.clams.ai/vocabulary/Annotation/v6[source]
-
- -
-
-BoundingBox = http://mmif.clams.ai/vocabulary/BoundingBox/v5[source]
-
- -
-
-Chapter = http://mmif.clams.ai/vocabulary/Chapter/v6[source]
-
- -
-
-Interval = http://mmif.clams.ai/vocabulary/Interval/v5[source]
-
- -
-
-NamedEntity = http://mmif.clams.ai/vocabulary/NamedEntity/v1[source]
-
- -
-
-NounChunk = http://mmif.clams.ai/vocabulary/NounChunk/v1[source]
-
- -
-
-Paragraph = http://mmif.clams.ai/vocabulary/Paragraph/v1[source]
-
- -
-
-Polygon = http://mmif.clams.ai/vocabulary/Polygon/v5[source]
-
- -
-
-Region = http://mmif.clams.ai/vocabulary/Region/v5[source]
-
- -
-
-Relation = http://mmif.clams.ai/vocabulary/Relation/v5[source]
-
- -
-
-Sentence = http://mmif.clams.ai/vocabulary/Sentence/v1[source]
-
- -
-
-Span = http://mmif.clams.ai/vocabulary/Span/v5[source]
-
- -
-
-TimeFrame = http://mmif.clams.ai/vocabulary/TimeFrame/v6[source]
-
- -
-
-TimePoint = http://mmif.clams.ai/vocabulary/TimePoint/v5[source]
-
- -
-
-Token = http://mmif.clams.ai/vocabulary/Token/v1[source]
-
- -
-
-VerbChunk = http://mmif.clams.ai/vocabulary/VerbChunk/v1[source]
-
- -
-
-VideoObject = http://mmif.clams.ai/vocabulary/VideoObject/v5[source]
-
- -
-
-typevers = {'Alignment': 'v1', 'Annotation': 'v6', 'BoundingBox': 'v5', 'Chapter': 'v6', 'Interval': 'v5', 'NamedEntity': 'v1', 'NounChunk': 'v1', 'Paragraph': 'v1', 'Polygon': 'v5', 'Region': 'v5', 'Relation': 'v5', 'Sentence': 'v1', 'Span': 'v5', 'TimeFrame': 'v6', 'TimePoint': 'v5', 'Token': 'v1', 'VerbChunk': 'v1', 'VideoObject': 'v5'}[source]
-
- -
- -
-
-

mmif.vocabulary.document_types module

-
-
-class mmif.vocabulary.document_types.DocumentTypes(type_uri, fuzzymode=True)[source]
-

Bases: DocumentTypesBase

-

This class contains the CLAMS document types -defined in the spec version 1.1.0 as class variables.

-
-
-AudioDocument = http://mmif.clams.ai/vocabulary/AudioDocument/v1[source]
-
- -
-
-Document = http://mmif.clams.ai/vocabulary/Document/v1[source]
-
- -
-
-ImageDocument = http://mmif.clams.ai/vocabulary/ImageDocument/v1[source]
-
- -
-
-TextDocument = http://mmif.clams.ai/vocabulary/TextDocument/v1[source]
-
- -
-
-VideoDocument = http://mmif.clams.ai/vocabulary/VideoDocument/v1[source]
-
- -
-
-typevers = {'AudioDocument': 'v1', 'Document': 'v1', 'ImageDocument': 'v1', 'TextDocument': 'v1', 'VideoDocument': 'v1'}[source]
-
- -
- -
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 1.0.5 - - -
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0.3.2
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0.3.3
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0.3.4
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- - - \ No newline at end of file diff --git a/docs/1.0.5/consumer-tutorial.html b/docs/1.0.5/consumer-tutorial.html deleted file mode 100644 index 03cca014..00000000 --- a/docs/1.0.5/consumer-tutorial.html +++ /dev/null @@ -1,171 +0,0 @@ - - - - - - - - - MMIF consumer — mmif-python documentation - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • MMIF consumer
    • -
  • -
    • -
-
-
-
-
- -
-

MMIF consumer

-

A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the appliance documentation to learn more about the appliance.

-

MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance.

-
    -

  1. The code must be hosted on a public git repository (e.g. Github, Gitlab, …)

    2. -

  2. Must listen to 5000 port.

    3. -

  3. Must expose /display route .

    4. -

  4. /display router should response to GET requests.

    5. -

  5. In the GET request, a public URL of the input MMIF file is passed via file URL parameter.

    6. -

  6. On the codebase root, there must be a Dockerfile that can build a docker image that runs the web app.

    7. -
-

We provide an example consumer at https://github.com/clamsproject/mmif-visualizer.

-
- - -
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- -
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- -
- - Other Versions - v: 1.0.5 - - -
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- - -
- -
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    -
    • -
  • Index
    • -
  • -
    • -
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Index

- -
- A - | B - | C - | D - | E - | G - | I - | K - | L - | M - | N - | P - | R - | S - | T - | U - | V - -
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A

- - - -
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B

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- - -
- -
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    • -
  • Welcome to mmif-python’s documentation!
    • -
  • -
    • -
-
-
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- -
-

Welcome to mmif-python’s documentation!

-
-

MultiMedia Interchange Format

-

MMIF is a JSON(-LD)-based data format designed for transferring annotation data between computational analysis applications in CLAMS project.

-
-

Contents

- -
-
-

API documentation:

- -
-
-
-
-

Indices and tables

- -
- - -
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- - -
- -
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  • Getting Started
    • -
  • -
    • -
-
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-
- -
-

Getting Started

-
-

Overview

-

MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for reproducibility, transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF website. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects.

-
-
-

Prerequisites

-
    -

  • Python: the latest mmif-python requires Python 3.8 or newer. We have no plan to support Python 2.7.

    • -
-
-
-

Installation

-

Package mmif-python is distributed via the official PyPI. Users are supposed to pip-install to get latest release.

-
pip install mmif-python
-
-
-

This will install a package mmif to local python.

-

The MMIF format and specification is evolving over time, and mmif-python package will be updated along with the changes in MMIF format.

-
-

Note

-

MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and mmif-python versions, please take time to read our decision on the subject here. If you need to know which python SDK supports which specification version, see Target MMIF Versions page.

-
-
-
-

MMIF Serialization

-

mmif.serialize.mmif.Mmif represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of mmif.serialize.model.MmifObject, including the mmif.serialize.mmif.Mmif. To start with an existing MMIF str, simple initiate a new Mmif object with the file.

-
import mmif
-from mmif import Mmif
-
-mmif_str = """{
-"metadata": {
-  "mmif": "http://mmif.clams.ai/1.0.0"
-},
-"documents": [
-  {
-    "@type": "http://mmif.clams.ai/vocabulary/VideoDocument/v1",
-    "properties": {
-      "id": "m1",
-      "mime": "video/mp4",
-      "location": "file:///var/archive/video-0012.mp4"
-    }
-  },
-  {
-    "@type": "http://mmif.clams.ai/vocabulary/TextDocument/v1",
-    "properties": {
-      "id": "m2",
-      "mime": "text/plain",
-      "location": "file:///var/archive/video-0012-transcript.txt"
-    }
-  }
-],
-"views": []}"""
-mmif_obj = Mmif(mmif_str)
-
-
-

Few notes;

-
    -

  1. MMIF does not carry the primary source files in it.

    2. -

  2. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version mmif-python implementation of the MMIF might not be able to load an unsupported version of MMIF string.

    3. -
-

When serializing back to str, call mmif.serialize.model.MmifObject.serialize() on the object.

-

To get subcomponents, you can use various getters implemented in subclasses. For example;

-
from mmif.vocabulary.document_types import DocumentTypes
-
-for video in mmif_obj.Mmif.get_documents_by_type(DocumentTypes.VideoDocument):
-  with open(video.location_path(), 'b') as in_video:
-    # do something with the video file
-
-
-

For a full list of available helper methods, please refer to the API documentation.

-
-
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- -
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- - Other Versions - v: 1.0.5 - - -
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- - - \ No newline at end of file diff --git a/docs/1.0.5/modules.html b/docs/1.0.5/modules.html deleted file mode 100644 index cfb4d35e..00000000 --- a/docs/1.0.5/modules.html +++ /dev/null @@ -1,349 +0,0 @@ - - - - - - - - - mmif package — mmif-python documentation - - - - - - - - - - - - - - - - - -
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  • mmif package
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  • -
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mmif package

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- - - \ No newline at end of file diff --git a/docs/1.0.5/objects.inv b/docs/1.0.5/objects.inv deleted file mode 100644 index 1436ca2e..00000000 Binary files a/docs/1.0.5/objects.inv and /dev/null differ diff --git a/docs/1.0.5/plugins.html b/docs/1.0.5/plugins.html deleted file mode 100644 index f6c5025a..00000000 --- a/docs/1.0.5/plugins.html +++ /dev/null @@ -1,227 +0,0 @@ - - - - - - - - - Developing plugins for MMIF Python SDK — mmif-python documentation - - - - - - - - - - - - - - - - - -
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  • Developing plugins for MMIF Python SDK
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Developing plugins for MMIF Python SDK

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Overview

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As MMIF JSON files can carry information about media document files without actually carrying file contents, file accessing modules in mmif Python package (distributed as mmif-python on PyPI) are designed to be lightweight and flexible so that it can work with additional “plugin” Python packages that can handle concrete file access.

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This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF website. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects.

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Developer can write simple plugins that can provide additional functionalities to mmif-python. For example, mmif-python does not provide any file access functionality beyond a local file system (with file scheme), but it can be extended with a plugin that can handle file access over different protocols (e.g. http, s3, ftp, etc).

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This document contains information about how to write plugins for mmif-python.

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Document Location Scheme Plugins

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mmif.serialize.annotation.Document class has various methods to access parts of location property of the document. The location is in URI/IRI format (SCHEME://HOSTNAME/PATH, in a nutshell) and it has to be resolved to a local file for CLAMS Apps to process the local file to analyze and extract information about the media and its contents. The core mmif-python distribution only provides a default implementation that can handle file scheme URIs.

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To add a document location handler plugin, you need to implement a Python “package” (do not confuse with PYPI distribution), that meets these requirements;

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  1. the package must be named mmif_docloc_<SCHEME>. For example, to implement a handler for s3 scheme, the package name must be mmif_docloc_s3. The prefix is important as it’s used in the plugin discovery process from the core mmif-python modules.

    2. -

  2. the top module of the package must have a function named resolve. The function must take a single argument, which is a str of the document location URI. The function must return a str of the local file path. For example, if the document location is s3://mybucket/myfile.mp4, a Python user should be able to to something like this;

    3. -
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import mmif_docloc_s3
-resolved = mmif_docloc_s3.resolve('s3://mybucket/myfile.mp4')
-# then resolved must be a local file path that can be used to open the file
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Here’s a minimal example codebase that you refer to when you develop a docloc plugin.

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(However, before you start writing your own plugin for a specific URI scheme, checking if there’s already a PyPI distribution for the scheme might be a good idea.)

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$ tree .
-.
-├── mmif_docloc_dummy
-│   └── __init__.py
-├── pyproject.toml
-└── setup.cfg
-
- $ cat pyproject.toml
-[build-system]
-requires = ["setuptools"]
-build-backend = "setuptools.build_meta"
-
-$ cat setup.cfg
-[metadata]
-name = mmif_docloc_dummy  # this name is IMPORTANT
-version = 0.0.1
-description = a plugin to mmif-pyhon to handle `dummy` location scheme
-
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And the plugin code.

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# mmif_docloc_dummy/__init__.py
-doc_types = {'video': 'mp4'}
-
-def resolve(docloc):
-    scheme = 'dummy'
-    if docloc.startswith(f'{scheme}://'):
-        doc_id, doc_type = docloc.split('.')
-        return f'/path/to/{doc_id}.{doc_types[doc_type]}'
-    else:
-        raise ValueError(f'cannot handle document location scheme: {docloc}')
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Python Module Index

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- - - - - - - - \ No newline at end of file diff --git a/docs/1.0.5/searchindex.js b/docs/1.0.5/searchindex.js deleted file mode 100644 index 028638e0..00000000 --- a/docs/1.0.5/searchindex.js +++ /dev/null @@ -1 +0,0 @@ -Search.setIndex({"alltitles": {"API documentation:": [[3, null]], "Contents": [[3, null]], "Developing plugins for MMIF Python SDK": [[6, null]], "Document Location Scheme Plugins": [[6, "document-location-scheme-plugins"]], "Getting Started": [[4, null]], "Indices and tables": [[3, "indices-and-tables"]], "Installation": [[4, "installation"]], "MMIF Serialization": [[4, "mmif-serialization"]], "MMIF consumer": [[2, null]], "MultiMedia Interchange Format": [[3, "multimedia-interchange-format"]], "Overview": [[4, "overview"], [6, "overview"]], "Prerequisites": [[4, "prerequisites"]], "Target MMIF Versions": [[7, null]], "Target Specification Versions": [[7, "id1"]], "Welcome to mmif-python\u2019s documentation!": [[3, null]], "mmif package": [[5, null]], 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[0, 4, 6], "when": [0, 4, 6], "where": 0, "whether": 0, "which": [0, 4, 6], "within": 0, "without": [0, 6], "won": 0, "work": [0, 6], "workflow": 4, "would": 0, "write": [0, 6], "you": [0, 4, 6], "your": 6, "zero": 0}, "titles": ["mmif.serialize module", "mmif.vocabulary module", "MMIF consumer", "Welcome to mmif-python\u2019s documentation!", "Getting Started", "mmif package", "Developing plugins for MMIF Python SDK", "Target MMIF Versions"], "titleterms": {"": 3, "annot": 0, "annotation_typ": 1, "api": 3, "consum": 2, "content": 3, "develop": 6, "document": [3, 6], "document_typ": 1, "format": 3, "get": 4, "indic": 3, "instal": 4, "interchang": 3, "locat": 6, "mmif": [0, 1, 2, 3, 4, 5, 6, 7], "model": 0, "modul": [0, 1], "multimedia": 3, "overview": [4, 6], "packag": 5, "plugin": 6, "prerequisit": 4, "python": [3, 6], "scheme": 6, "sdk": 6, "serial": [0, 4], "specif": 7, "start": 4, "tabl": 3, "target": 7, "version": 7, "view": 0, "vocabulari": 1, "welcom": 3}}) \ No newline at end of file diff --git a/docs/1.0.5/target-versions.html b/docs/1.0.5/target-versions.html deleted file mode 100644 index 8f68c072..00000000 --- a/docs/1.0.5/target-versions.html +++ /dev/null @@ -1,257 +0,0 @@ - - - - - - - - - Target MMIF Versions — mmif-python documentation - - - - - - - - - - - - - - - - - -
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Target MMIF Versions

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This article provides targeting MMIF specification versions of different versions of mmif-python SDK.

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Target Specification Versions

mmif-python version

Target MMIF Specification

1.0.5

1.1.0

1.0.4

1.0.0

1.0.3

1.0.0

1.0.2

1.0.0

1.0.1

1.0.0

1.0.0

0.5.0

0.5.2

0.5.0

0.5.1

0.5.0

0.5.0

0.5.0

0.4.8

0.4.2

0.4.7

0.4.1

0.4.6

0.4.0

0.4.5

0.4.0

0.4.4

0.4.0

0.4.3

0.4.0

0.4.2

0.4.0

0.4.1

0.4.0

0.4.0

0.4.0

0.3.5

0.3.1

0.3.4

0.3.1

0.3.3

0.3.1

0.3.2

0.3.1

0.3.1

0.3.0

0.3.0

0.3.0

0.2.2

0.2.1

0.2.1

0.2.1

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0.2.1

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0.3.3
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0.3.4
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0.3.5
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0.4.0
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0.4.1
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0.4.2
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0.4.3
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0.4.4
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0.4.5
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0.4.6
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0.4.7
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0.4.8
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0.5.0
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0.5.1
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0.5.2
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1.0.0
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1.0.1
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1.0.10
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1.0.11
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1.0.12
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1.0.13
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1.0.14
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1.0.15
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1.0.16
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1.0.17
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1.0.18
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1.0.19
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1.0.2
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1.0.3
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1.0.4
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1.0.5
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1.0.6
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1.0.8
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1.0.9
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The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the `appliance documentation `_ to learn more about the appliance. - -MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance. - -#. The code must be hosted on a public git repository (e.g. Github, Gitlab, ...) -#. Must listen to ``5000`` port. -#. Must expose ``/display`` route . -#. ``/display`` router should response to ``GET`` requests. -#. In the ``GET`` request, a public URL of the input MMIF file is passed via ``file`` URL parameter. -#. On the codebase root, there must be a ``Dockerfile`` that can build a `docker `_ image that runs the web app. - -We provide an example consumer at https://github.com/clamsproject/mmif-visualizer. diff --git a/docs/1.0.6/_sources/index.rst.txt b/docs/1.0.6/_sources/index.rst.txt deleted file mode 100644 index beb56aae..00000000 --- a/docs/1.0.6/_sources/index.rst.txt +++ /dev/null @@ -1,26 +0,0 @@ -Welcome to mmif-python's documentation! -======================================= - -.. mdinclude:: ../README.md - -.. toctree:: - :maxdepth: 2 - :caption: Contents - - introduction - plugins - target-versions - -.. toctree:: - :maxdepth: 2 - :caption: API documentation: - - modules - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/docs/1.0.6/_sources/introduction.rst.txt b/docs/1.0.6/_sources/introduction.rst.txt deleted file mode 100644 index cfd9eaf7..00000000 --- a/docs/1.0.6/_sources/introduction.rst.txt +++ /dev/null @@ -1,89 +0,0 @@ -.. _introduction: - -Getting Started -=============== - - -Overview ---------- - -MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for reproducibility, transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF website `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects. - -Prerequisites -------------- - -* `Python `_: the latest ``mmif-python`` requires Python 3.8 or newer. We have no plan to support `Python 2.7 `_. - -Installation ---------------- - -Package ``mmif-python`` is distributed via the official PyPI. Users are supposed to pip-install to get latest release. - -.. code-block:: bash - - pip install mmif-python - -This will install a package `mmif` to local python. - -The MMIF format and specification is evolving over time, and ``mmif-python`` package will be updated along with the changes in MMIF format. - -.. note:: MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and ``mmif-python`` versions, please take time to read our decision on the subject `here `_. If you need to know which python SDK supports which specification version, see :ref:`target-versions` page. - -MMIF Serialization ---------------------------- - -:class:`mmif.serialize.mmif.Mmif` represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of :class:`mmif.serialize.model.MmifObject`, including the :class:`mmif.serialize.mmif.Mmif`. To start with an existing MMIF :class:`str`, simple initiate a new ``Mmif`` object with the file. - -.. code-block:: python - - import mmif - from mmif import Mmif - - mmif_str = """{ - "metadata": { - "mmif": "http://mmif.clams.ai/1.0.0" - }, - "documents": [ - { - "@type": "http://mmif.clams.ai/vocabulary/VideoDocument/v1", - "properties": { - "id": "m1", - "mime": "video/mp4", - "location": "file:///var/archive/video-0012.mp4" - } - }, - { - "@type": "http://mmif.clams.ai/vocabulary/TextDocument/v1", - "properties": { - "id": "m2", - "mime": "text/plain", - "location": "file:///var/archive/video-0012-transcript.txt" - } - } - ], - "views": []}""" - mmif_obj = Mmif(mmif_str) - - -Few notes; - -#. MMIF does not carry the primary source files in it. -#. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version ``mmif-python`` implementation of the MMIF might not be able to load an unsupported version of MMIF string. - -When serializing back to :class:`str`, call :meth:`mmif.serialize.model.MmifObject.serialize` on the object. - -To get subcomponents, you can use various getters implemented in subclasses. For example; - -.. code-block:: python - - from mmif.vocabulary.document_types import DocumentTypes - - for video in mmif_obj.Mmif.get_documents_by_type(DocumentTypes.VideoDocument): - with open(video.location_path(), 'b') as in_video: - # do something with the video file - - -For a full list of available helper methods, please refer to :ref:`the API documentation `. - diff --git a/docs/1.0.6/_sources/modules.rst.txt b/docs/1.0.6/_sources/modules.rst.txt deleted file mode 100644 index e4269c6d..00000000 --- a/docs/1.0.6/_sources/modules.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _apidoc: - -mmif package -============ - -.. toctree:: - :maxdepth: 4 - - autodoc/mmif.serialize - autodoc/mmif.vocabulary diff --git a/docs/1.0.6/_sources/plugins.rst.txt b/docs/1.0.6/_sources/plugins.rst.txt deleted file mode 100644 index 9e1505e9..00000000 --- a/docs/1.0.6/_sources/plugins.rst.txt +++ /dev/null @@ -1,75 +0,0 @@ -.. _plugins: - -Developing plugins for MMIF Python SDK -====================================== - - -Overview --------- - -As MMIF JSON files can carry information about media document files without actually carrying file contents, file accessing modules in ``mmif`` Python package (distributed as ``mmif-python`` on PyPI) are designed to be lightweight and flexible so that it can work with additional "plugin" Python packages that can handle concrete file access. - - -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF website `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects. - -Developer can write simple plugins that can provide additional functionalities to ``mmif-python``. For example, ``mmif-python`` does not provide any file access functionality beyond a local file system (with ``file`` scheme), but it can be extended with a plugin that can handle file access over different protocols (e.g. ``http``, ``s3``, ``ftp``, etc). - -This document contains information about how to write plugins for ``mmif-python``. - -Document Location Scheme Plugins -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -:class:`mmif.serialize.annotation.Document` class has various methods to access parts of ``location`` property of the document. The location is in `URI/IRI format `_ (``SCHEME://HOSTNAME/PATH``, in a nutshell) and it has to be resolved to a local file for CLAMS Apps to process the local file to analyze and extract information about the media and its contents. The core ``mmif-python`` distribution only provides a default implementation that can handle ``file`` scheme URIs. - -To add a document location handler plugin, you need to implement a Python `"package" `_ (do not confuse with PYPI distribution), that meets these requirements; - -#. the package must be named ``mmif_docloc_``. For example, to implement a handler for ``s3`` scheme, the package name must be ``mmif_docloc_s3``. The prefix is important as it's used in the plugin discovery process from the core ``mmif-python`` modules. -#. the top module of the package must have a function named ``resolve``. The function must take a single argument, which is a :class:`str` of the document location URI. The function must return a :class:`str` of the local file path. For example, if the document location is ``s3://mybucket/myfile.mp4``, a Python user should be able to to something like this; - -.. code-block:: python - - import mmif_docloc_s3 - resolved = mmif_docloc_s3.resolve('s3://mybucket/myfile.mp4') - # then resolved must be a local file path that can be used to open the file - - -Here's a minimal example codebase that you refer to when you develop a ``docloc`` plugin. - -(However, before you start writing your own plugin for a specific URI scheme, checking `if there's already a PyPI distribution `_ for the scheme might be a good idea.) - -.. code-block:: sh - - $ tree . - . - ├── mmif_docloc_dummy - │ └── __init__.py - ├── pyproject.toml - └── setup.cfg - - $ cat pyproject.toml - [build-system] - requires = ["setuptools"] - build-backend = "setuptools.build_meta" - - $ cat setup.cfg - [metadata] - name = mmif_docloc_dummy # this name is IMPORTANT - version = 0.0.1 - description = a plugin to mmif-pyhon to handle `dummy` location scheme - - -And the plugin code. - -.. code-block:: python - - # mmif_docloc_dummy/__init__.py - doc_types = {'video': 'mp4'} - - def resolve(docloc): - scheme = 'dummy' - if docloc.startswith(f'{scheme}://'): - doc_id, doc_type = docloc.split('.') - return f'/path/to/{doc_id}.{doc_types[doc_type]}' - else: - raise ValueError(f'cannot handle document location scheme: {docloc}') diff --git a/docs/1.0.6/_sources/target-versions.rst.txt b/docs/1.0.6/_sources/target-versions.rst.txt deleted file mode 100644 index 34216d3e..00000000 --- a/docs/1.0.6/_sources/target-versions.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _target-versions: - -Target MMIF Versions -==================== - -This article provides targeting MMIF specification versions of different versions of ``mmif-python`` SDK. - -.. csv-table:: Target Specification Versions - :file: target-versions.csv - :header-rows: 1 diff --git a/docs/1.0.6/_static/_sphinx_javascript_frameworks_compat.js b/docs/1.0.6/_static/_sphinx_javascript_frameworks_compat.js deleted file mode 100644 index 81415803..00000000 --- a/docs/1.0.6/_static/_sphinx_javascript_frameworks_compat.js +++ /dev/null @@ -1,123 +0,0 @@ -/* Compatability shim for jQuery and underscores.js. - * - * Copyright Sphinx contributors - * Released under the two clause BSD licence - */ - -/** - * small helper function to urldecode strings - * - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL - */ -jQuery.urldecode = function(x) { - if (!x) { - return x - } - return decodeURIComponent(x.replace(/\+/g, ' ')); -}; - -/** - * small helper function to urlencode strings - */ -jQuery.urlencode = encodeURIComponent; - -/** - * This function returns the parsed url parameters of the - * current request. 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span; - var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.className = className; - } - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - node.parentNode.insertBefore(span, node.parentNode.insertBefore( - document.createTextNode(val.substr(pos + text.length)), - node.nextSibling)); - node.nodeValue = val.substr(0, pos); - if (isInSVG) { - var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect"); - var bbox = node.parentElement.getBBox(); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute('class', className); - addItems.push({ - "parent": node.parentNode, - "target": rect}); - } - } - } - else if (!jQuery(node).is("button, select, textarea")) { - 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- -/** - * Simple result scoring code. - */ -if (typeof Scorer === "undefined") { - var Scorer = { - // Implement the following function to further tweak the score for each result - // The function takes a result array [docname, title, anchor, descr, score, filename] - // and returns the new score. - /* - score: result => { - const [docname, title, anchor, descr, score, filename, kind] = result - return score - }, - */ - - // query matches the full name of an object - objNameMatch: 11, - // or matches in the last dotted part of the object name - objPartialMatch: 6, - // Additive scores depending on the priority of the object - objPrio: { - 0: 15, // used to be importantResults - 1: 5, // used to be objectResults - 2: -5, // used to be unimportantResults - }, - // Used when the priority is not in the mapping. - objPrioDefault: 0, - - // query found in title - title: 15, - partialTitle: 7, - // query found in terms - term: 5, - partialTerm: 2, - }; -} - -// Global search result kind enum, used by themes to style search results. -class SearchResultKind { - static get index() { return "index"; } - static get object() { return "object"; } - static get text() { return "text"; } - static get title() { return "title"; } -} - -const _removeChildren = (element) => { - while (element && element.lastChild) element.removeChild(element.lastChild); -}; - -/** - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping - */ -const _escapeRegExp = (string) => - string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string - -const _displayItem = (item, searchTerms, highlightTerms) => { - const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; - const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; - const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; - const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; - const contentRoot = document.documentElement.dataset.content_root; - - const [docName, title, anchor, descr, score, _filename, kind] = item; - - let listItem = document.createElement("li"); - // Add a class representing the item's type: - // can be used by a theme's CSS selector for styling - // See SearchResultKind for the class names. - listItem.classList.add(`kind-${kind}`); - let requestUrl; - let linkUrl; - if (docBuilder === "dirhtml") { - // dirhtml builder - let dirname = docName + "/"; - if (dirname.match(/\/index\/$/)) - dirname = dirname.substring(0, dirname.length - 6); - else if (dirname === "index/") dirname = ""; - requestUrl = contentRoot + dirname; - linkUrl = requestUrl; - } else { - // normal html builders - requestUrl = contentRoot + docName + docFileSuffix; - linkUrl = docName + docLinkSuffix; - } - let linkEl = listItem.appendChild(document.createElement("a")); - linkEl.href = linkUrl + anchor; - linkEl.dataset.score = score; - linkEl.innerHTML = title; - if (descr) { - listItem.appendChild(document.createElement("span")).innerHTML = - " (" + descr + ")"; - // highlight search terms in the description - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - } - else if (showSearchSummary) - fetch(requestUrl) - .then((responseData) => responseData.text()) - .then((data) => { - if (data) - listItem.appendChild( - Search.makeSearchSummary(data, searchTerms, anchor) - ); - // highlight search terms in the summary - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - }); - Search.output.appendChild(listItem); -}; -const _finishSearch = (resultCount) => { - Search.stopPulse(); - Search.title.innerText = _("Search Results"); - if (!resultCount) - Search.status.innerText = Documentation.gettext( - "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." - ); - else - Search.status.innerText = Documentation.ngettext( - "Search finished, found one page matching the search query.", - "Search finished, found ${resultCount} pages matching the search query.", - resultCount, - ).replace('${resultCount}', resultCount); -}; -const _displayNextItem = ( - results, - resultCount, - searchTerms, - highlightTerms, -) => { - // results left, load the summary and display it - // this is intended to be dynamic (don't sub resultsCount) - if (results.length) { - _displayItem(results.pop(), searchTerms, highlightTerms); - setTimeout( - () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), - 5 - ); - } - // search finished, update title and status message - else _finishSearch(resultCount); -}; -// Helper function used by query() to order search results. -// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. -// Order the results by score (in opposite order of appearance, since the -// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. -const _orderResultsByScoreThenName = (a, b) => { - const leftScore = a[4]; - const rightScore = b[4]; - if (leftScore === rightScore) { - // same score: sort alphabetically - const leftTitle = a[1].toLowerCase(); - const rightTitle = b[1].toLowerCase(); - if (leftTitle === rightTitle) return 0; - return leftTitle > rightTitle ? -1 : 1; // inverted is intentional - } - return leftScore > rightScore ? 1 : -1; -}; - -/** - * Default splitQuery function. Can be overridden in ``sphinx.search`` with a - * custom function per language. - * - * The regular expression works by splitting the string on consecutive characters - * that are not Unicode letters, numbers, underscores, or emoji characters. - * This is the same as ``\W+`` in Python, preserving the surrogate pair area. - */ -if (typeof splitQuery === "undefined") { - var splitQuery = (query) => query - .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) - .filter(term => term) // remove remaining empty strings -} - -/** - * Search Module - */ -const Search = { - _index: null, - _queued_query: null, - _pulse_status: -1, - - htmlToText: (htmlString, anchor) => { - const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - for (const removalQuery of [".headerlink", "script", "style"]) { - htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); - } - if (anchor) { - const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); - if (anchorContent) return anchorContent.textContent; - - console.warn( - `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` - ); - } - - // if anchor not specified or not found, fall back to main content - const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent) return docContent.textContent; - - console.warn( - "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." - ); - return ""; - }, - - init: () => { - const query = new URLSearchParams(window.location.search).get("q"); - document - .querySelectorAll('input[name="q"]') - .forEach((el) => (el.value = query)); - if (query) Search.performSearch(query); - }, - - loadIndex: (url) => - (document.body.appendChild(document.createElement("script")).src = url), - - setIndex: (index) => { - Search._index = index; - if (Search._queued_query !== null) { - const query = Search._queued_query; - Search._queued_query = null; - Search.query(query); - } - }, - - hasIndex: () => Search._index !== null, - - deferQuery: (query) => (Search._queued_query = query), - - stopPulse: () => (Search._pulse_status = -1), - - startPulse: () => { - if (Search._pulse_status >= 0) return; - - const pulse = () => { - Search._pulse_status = (Search._pulse_status + 1) % 4; - Search.dots.innerText = ".".repeat(Search._pulse_status); - if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); - }; - pulse(); - }, - - /** - * perform a search for something (or wait until index is loaded) - */ - performSearch: (query) => { - // create the required interface elements - const searchText = document.createElement("h2"); - searchText.textContent = _("Searching"); - const searchSummary = document.createElement("p"); - searchSummary.classList.add("search-summary"); - searchSummary.innerText = ""; - const searchList = document.createElement("ul"); - searchList.setAttribute("role", "list"); - searchList.classList.add("search"); - - const out = document.getElementById("search-results"); - Search.title = out.appendChild(searchText); - Search.dots = Search.title.appendChild(document.createElement("span")); - Search.status = out.appendChild(searchSummary); - Search.output = out.appendChild(searchList); - - const searchProgress = document.getElementById("search-progress"); - // Some themes don't use the search progress node - if (searchProgress) { - searchProgress.innerText = _("Preparing search..."); - } - Search.startPulse(); - - // index already loaded, the browser was quick! - if (Search.hasIndex()) Search.query(query); - else Search.deferQuery(query); - }, - - _parseQuery: (query) => { - // stem the search terms and add them to the correct list - const stemmer = new Stemmer(); - const searchTerms = new Set(); - const excludedTerms = new Set(); - const highlightTerms = new Set(); - const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); - splitQuery(query.trim()).forEach((queryTerm) => { - const queryTermLower = queryTerm.toLowerCase(); - - // maybe skip this "word" - // stopwords array is from language_data.js - if ( - stopwords.indexOf(queryTermLower) !== -1 || - queryTerm.match(/^\d+$/) - ) - return; - - // stem the word - let word = stemmer.stemWord(queryTermLower); - // select the correct list - if (word[0] === "-") excludedTerms.add(word.substr(1)); - else { - searchTerms.add(word); - highlightTerms.add(queryTermLower); - } - }); - - if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js - localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) - } - - // console.debug("SEARCH: searching for:"); - // console.info("required: ", [...searchTerms]); - // console.info("excluded: ", [...excludedTerms]); - - return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; - }, - - /** - * execute search (requires search index to be loaded) - */ - _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - - // Collect multiple result groups to be sorted separately and then ordered. - // Each is an array of [docname, title, anchor, descr, score, filename, kind]. - const normalResults = []; - const nonMainIndexResults = []; - - _removeChildren(document.getElementById("search-progress")); - - const queryLower = query.toLowerCase().trim(); - for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { - for (const [file, id] of foundTitles) { - const score = Math.round(Scorer.title * queryLower.length / title.length); - const boost = titles[file] === title ? 1 : 0; // add a boost for document titles - normalResults.push([ - docNames[file], - titles[file] !== title ? `${titles[file]} > ${title}` : title, - id !== null ? "#" + id : "", - null, - score + boost, - filenames[file], - SearchResultKind.title, - ]); - } - } - } - - // search for explicit entries in index directives - for (const [entry, foundEntries] of Object.entries(indexEntries)) { - if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id, isMain] of foundEntries) { - const score = Math.round(100 * queryLower.length / entry.length); - const result = [ - docNames[file], - titles[file], - id ? "#" + id : "", - null, - score, - filenames[file], - SearchResultKind.index, - ]; - if (isMain) { - normalResults.push(result); - } else { - nonMainIndexResults.push(result); - } - } - } - } - - // lookup as object - objectTerms.forEach((term) => - normalResults.push(...Search.performObjectSearch(term, objectTerms)) - ); - - // lookup as search terms in fulltext - normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); - - // let the scorer override scores with a custom scoring function - if (Scorer.score) { - normalResults.forEach((item) => (item[4] = Scorer.score(item))); - nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); - } - - // Sort each group of results by score and then alphabetically by name. - normalResults.sort(_orderResultsByScoreThenName); - nonMainIndexResults.sort(_orderResultsByScoreThenName); - - // Combine the result groups in (reverse) order. - // Non-main index entries are typically arbitrary cross-references, - // so display them after other results. - let results = [...nonMainIndexResults, ...normalResults]; - - // remove duplicate search results - // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept - let seen = new Set(); - results = results.reverse().reduce((acc, result) => { - let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); - if (!seen.has(resultStr)) { - acc.push(result); - seen.add(resultStr); - } - return acc; - }, []); - - return results.reverse(); - }, - - query: (query) => { - const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); - const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); - - // for debugging - //Search.lastresults = results.slice(); // a copy - // console.info("search results:", Search.lastresults); - - // print the results - _displayNextItem(results, results.length, searchTerms, highlightTerms); - }, - - /** - * search for object names - */ - performObjectSearch: (object, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const objects = Search._index.objects; - const objNames = Search._index.objnames; - const titles = Search._index.titles; - - const results = []; - - const objectSearchCallback = (prefix, match) => { - const name = match[4] - const fullname = (prefix ? prefix + "." : "") + name; - const fullnameLower = fullname.toLowerCase(); - if (fullnameLower.indexOf(object) < 0) return; - - let score = 0; - const parts = fullnameLower.split("."); - - // check for different match types: exact matches of full name or - // "last name" (i.e. last dotted part) - if (fullnameLower === object || parts.slice(-1)[0] === object) - score += Scorer.objNameMatch; - else if (parts.slice(-1)[0].indexOf(object) > -1) - score += Scorer.objPartialMatch; // matches in last name - - const objName = objNames[match[1]][2]; - const title = titles[match[0]]; - - // If more than one term searched for, we require other words to be - // found in the name/title/description - const otherTerms = new Set(objectTerms); - otherTerms.delete(object); - if (otherTerms.size > 0) { - const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); - if ( - [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) - ) - return; - } - - let anchor = match[3]; - if (anchor === "") anchor = fullname; - else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; - - const descr = objName + _(", in ") + title; - - // add custom score for some objects according to scorer - if (Scorer.objPrio.hasOwnProperty(match[2])) - score += Scorer.objPrio[match[2]]; - else score += Scorer.objPrioDefault; - - results.push([ - docNames[match[0]], - fullname, - "#" + anchor, - descr, - score, - filenames[match[0]], - SearchResultKind.object, - ]); - }; - Object.keys(objects).forEach((prefix) => - objects[prefix].forEach((array) => - objectSearchCallback(prefix, array) - ) - ); - return results; - }, - - /** - * search for full-text terms in the index - */ - performTermsSearch: (searchTerms, excludedTerms) => { - // prepare search - const terms = Search._index.terms; - const titleTerms = Search._index.titleterms; - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - - const scoreMap = new Map(); - const fileMap = new Map(); - - // perform the search on the required terms - searchTerms.forEach((word) => { - const files = []; - const arr = [ - { files: terms[word], score: Scorer.term }, - { files: titleTerms[word], score: Scorer.title }, - ]; - // add support for partial matches - if (word.length > 2) { - const escapedWord = _escapeRegExp(word); - if (!terms.hasOwnProperty(word)) { - Object.keys(terms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: terms[term], score: Scorer.partialTerm }); - }); - } - if (!titleTerms.hasOwnProperty(word)) { - Object.keys(titleTerms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); - }); - } - } - - // no match but word was a required one - if (arr.every((record) => record.files === undefined)) return; - - // found search word in contents - arr.forEach((record) => { - if (record.files === undefined) return; - - let recordFiles = record.files; - if (recordFiles.length === undefined) recordFiles = [recordFiles]; - files.push(...recordFiles); - - // set score for the word in each file - recordFiles.forEach((file) => { - if (!scoreMap.has(file)) scoreMap.set(file, {}); - scoreMap.get(file)[word] = record.score; - }); - }); - - // create the mapping - files.forEach((file) => { - if (!fileMap.has(file)) fileMap.set(file, [word]); - else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); - }); - }); - - // now check if the files don't contain excluded terms - const results = []; - for (const [file, wordList] of fileMap) { - // check if all requirements are matched - - // as search terms with length < 3 are discarded - const filteredTermCount = [...searchTerms].filter( - (term) => term.length > 2 - ).length; - if ( - wordList.length !== searchTerms.size && - wordList.length !== filteredTermCount - ) - continue; - - // ensure that none of the excluded terms is in the search result - if ( - [...excludedTerms].some( - (term) => - terms[term] === file || - titleTerms[term] === file || - (terms[term] || []).includes(file) || - (titleTerms[term] || []).includes(file) - ) - ) - break; - - // select one (max) score for the file. - const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); - // add result to the result list - results.push([ - docNames[file], - titles[file], - "", - null, - score, - filenames[file], - SearchResultKind.text, - ]); - } - return results; - }, - - /** - * helper function to return a node containing the - * search summary for a given text. keywords is a list - * of stemmed words. - */ - makeSearchSummary: (htmlText, keywords, anchor) => { - const text = Search.htmlToText(htmlText, anchor); - if (text === "") return null; - - const textLower = text.toLowerCase(); - const actualStartPosition = [...keywords] - .map((k) => textLower.indexOf(k.toLowerCase())) - .filter((i) => i > -1) - .slice(-1)[0]; - const startWithContext = Math.max(actualStartPosition - 120, 0); - - const top = startWithContext === 0 ? "" : "..."; - const tail = startWithContext + 240 < text.length ? "..." : ""; - - let summary = document.createElement("p"); - summary.classList.add("context"); - summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; - - return summary; - }, -}; - -_ready(Search.init); diff --git a/docs/1.0.6/_static/sphinx_highlight.js b/docs/1.0.6/_static/sphinx_highlight.js deleted file mode 100644 index 8a96c69a..00000000 --- a/docs/1.0.6/_static/sphinx_highlight.js +++ /dev/null @@ -1,154 +0,0 @@ -/* Highlighting utilities for Sphinx HTML documentation. */ -"use strict"; - -const SPHINX_HIGHLIGHT_ENABLED = true - -/** - * highlight a given string on a node by wrapping it in - * span elements with the given class name. - */ -const _highlight = (node, addItems, text, className) => { - if (node.nodeType === Node.TEXT_NODE) { - const val = node.nodeValue; - const parent = node.parentNode; - const pos = val.toLowerCase().indexOf(text); - if ( - pos >= 0 && - !parent.classList.contains(className) && - !parent.classList.contains("nohighlight") - ) { - let span; - - const closestNode = parent.closest("body, svg, foreignObject"); - const isInSVG = closestNode && closestNode.matches("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.classList.add(className); - } - - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - const rest = document.createTextNode(val.substr(pos + text.length)); - parent.insertBefore( - span, - parent.insertBefore( - rest, - node.nextSibling - ) - ); - node.nodeValue = val.substr(0, pos); - /* There may be more occurrences of search term in this node. So call this - * function recursively on the remaining fragment. - */ - _highlight(rest, addItems, text, className); - - if (isInSVG) { - const rect = document.createElementNS( - "http://www.w3.org/2000/svg", - "rect" - ); - const bbox = parent.getBBox(); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute("class", className); - addItems.push({ parent: parent, target: rect }); - } - } - } else if (node.matches && !node.matches("button, select, textarea")) { - node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); - } -}; -const _highlightText = (thisNode, text, className) => { - let addItems = []; - _highlight(thisNode, addItems, text, className); - addItems.forEach((obj) => - obj.parent.insertAdjacentElement("beforebegin", obj.target) - ); -}; - -/** - * Small JavaScript module for the documentation. - */ -const SphinxHighlight = { - - /** - * highlight the search words provided in localstorage in the text - */ - highlightSearchWords: () => { - if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight - - // get and clear terms from localstorage - const url = new URL(window.location); - const highlight = - localStorage.getItem("sphinx_highlight_terms") - || url.searchParams.get("highlight") - || ""; - localStorage.removeItem("sphinx_highlight_terms") - url.searchParams.delete("highlight"); - window.history.replaceState({}, "", url); - - // get individual terms from highlight string - const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); - if (terms.length === 0) return; // nothing to do - - // There should never be more than one element matching "div.body" - const divBody = document.querySelectorAll("div.body"); - const body = divBody.length ? divBody[0] : document.querySelector("body"); - window.setTimeout(() => { - terms.forEach((term) => _highlightText(body, term, "highlighted")); - }, 10); - - const searchBox = document.getElementById("searchbox"); - if (searchBox === null) return; - searchBox.appendChild( - document - .createRange() - .createContextualFragment( - '

' + - '' + - _("Hide Search Matches") + - "

" - ) - ); - }, - - /** - * helper function to hide the search marks again - */ - hideSearchWords: () => { - document - .querySelectorAll("#searchbox .highlight-link") - .forEach((el) => el.remove()); - document - .querySelectorAll("span.highlighted") - .forEach((el) => el.classList.remove("highlighted")); - localStorage.removeItem("sphinx_highlight_terms") - }, - - initEscapeListener: () => { - // only install a listener if it is really needed - if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; - - document.addEventListener("keydown", (event) => { - // bail for input elements - if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; - // bail with special keys - if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; - if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { - SphinxHighlight.hideSearchWords(); - event.preventDefault(); - } - }); - }, -}; - -_ready(() => { - /* Do not call highlightSearchWords() when we are on the search page. - * It will highlight words from the *previous* search query. - */ - if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); - SphinxHighlight.initEscapeListener(); -}); diff --git a/docs/1.0.6/autodoc/mmif.serialize.html b/docs/1.0.6/autodoc/mmif.serialize.html deleted file mode 100644 index 76a1e205..00000000 --- a/docs/1.0.6/autodoc/mmif.serialize.html +++ /dev/null @@ -1,1271 +0,0 @@ - - - - - - - - - mmif.serialize module — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
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mmif.serialize module

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mmif.serialize.model module

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The model module contains the classes used to represent an -abstract MMIF object as a live Python object.

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The MmifObject class or one of its derivatives is subclassed by -all other classes defined in this SDK, except for MmifObjectEncoder.

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These objects are generally instantiated from JSON, either as a string -or as an already-loaded Python dictionary. This base class provides the -core functionality for deserializing MMIF JSON data into live objects -and serializing live objects into MMIF JSON data. Specialized behavior -for the different components of MMIF is added in the subclasses.

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-class mmif.serialize.model.DataDict(mmif_obj: bytes | str | dict | None = None)[source]
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Bases: MmifObject, Generic[T, S]

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-empty()[source]
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-get(key: T, default=None) → S | None[source]
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-items()[source]
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-keys()[source]
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-update(other, overwrite)[source]
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-values()[source]
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-class mmif.serialize.model.DataList(mmif_obj: bytes | str | list | None = None)[source]
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Bases: MmifObject, Generic[T]

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The DataList class is an abstraction that represents the -various lists found in a MMIF file, such as documents, subdocuments, -views, and annotations.

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Parameters:
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mmif_obj (Union[str, list]) – the data that the list contains

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-append(value, overwrite)[source]
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-deserialize(mmif_json: str | list) → None[source]
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Passes the input data into the internal deserializer.

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-empty()[source]
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-get(key: str) → T | None[source]
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Standard dictionary-style get() method, albeit with no default -parameter. Relies on the implementation of __getitem__.

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Will return None if the key is not found.

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Parameters:
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key – the key to search for

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Returns:
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the value matching that key

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-class mmif.serialize.model.MmifObject(mmif_obj: bytes | str | dict | None = None)[source]
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Bases: object

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Abstract superclass for MMIF related key-value pair objects.

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Any MMIF object can be initialized as an empty placeholder or -an actual representation with a JSON formatted string or equivalent -dict object argument.

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This superclass has four specially designed instance variables, and these -variable names cannot be used as attribute names for MMIF objects.

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  1. _unnamed_attributes: -Only can be either None or an empty dictionary. If it’s set to None, -it means the class won’t take any Additional Attributes in the JSON -schema sense. If it’s a dict, users can throw any k-v pairs to the -class, EXCEPT for the reserved two key names.

    2. -

  2. _attribute_classes: -This is a dict from a key name to a specific python class to use for -deserialize the value. Note that a key name in this dict does NOT -have to be a named attribute, but is recommended to be one.

    3. -

  3. _required_attributes: -This is a simple list of names of attributes that are required in the object. -When serialize, an object will skip its empty (e.g. zero-length, or None) -attributes unless they are in this list. Otherwise, the serialized JSON -string would have empty representations (e.g. "", []).

    4. -

  4. _exclude_from_diff: -This is a simple list of names of attributes that should be excluded from -the diff calculation in __eq__.

    5. -
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# TODO (krim @ 8/17/20): this dict is however, a duplicate with the type hints in the class definition. -Maybe there is a better way to utilize type hints (e.g. getting them as a programmatically), but for now -developers should be careful to add types to hints as well as to this dict.

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Also note that those special attributes MUST be set in the __init__() -before calling super method, otherwise deserialization will not work.

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And also, a subclass that has one or more named attributes, it must -set those attributes in the __init__() before calling super method. When -serializing a MmifObject, all empty attributes will be ignored, so for -optional named attributes, you must leave the values empty (len == 0), but -NOT None. Any None-valued named attributes will cause issues with current -implementation.

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Parameters:
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mmif_obj – JSON string or dict to initialize an object. -If not given, an empty object will be initialized, sometimes with -an ID value automatically generated, based on its parent object.

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-deserialize(mmif_json: str | dict) → None[source]
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Takes a JSON-formatted string or a simple dict that’s json-loaded from -such a string as an input and populates object’s fields with the values -specified in the input.

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Parameters:
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mmif_json – JSON-formatted string or dict from such a string -that represents a MMIF object

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-disallow_additional_properties() → None[source]
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Call this method in __init__() to prevent the insertion -of unnamed attributes after initialization.

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-static is_empty(obj) → bool[source]
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return True if the obj is None or “emtpy”. The emptiness first defined as -having zero length. But for objects that lack __len__ method, we need -additional check.

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-reserved_names: Set[str] = {'_attribute_classes', '_exclude_from_diff', '_required_attributes', '_unnamed_attributes', 'reserved_names'}[source]
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-serialize(pretty: bool = False) → str[source]
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Generates JSON representation of an object.

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Parameters:
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pretty – If True, returns string representation with indentation.

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Returns:
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JSON string of the object.

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-set_additional_property(key: str, value: Any) → None[source]
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Method to set values in _unnamed_attributes.

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Parameters:
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  • key – the attribute name

    • -

  • value – the desired value

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Returns:
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None

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Raise:
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AttributeError if additional properties are disallowed by disallow_additional_properties()

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-class mmif.serialize.model.MmifObjectEncoder(*, skipkeys=False, ensure_ascii=True, check_circular=True, allow_nan=True, sort_keys=False, indent=None, separators=None, default=None)[source]
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Bases: JSONEncoder

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Encoder class to define behaviors of de-/serialization

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-default(obj: MmifObject)[source]
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Overrides default encoding behavior to prioritize MmifObject.serialize().

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mmif.serialize.mmif module

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The mmif module contains the classes used to represent a full MMIF -file as a live Python object.

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See the specification docs and the JSON Schema file for more information.

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-class mmif.serialize.mmif.Mmif(mmif_obj: bytes | str | dict | None = None, *, validate: bool = True)[source]
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Bases: MmifObject

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MmifObject that represents a full MMIF file.

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Parameters:
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  • mmif_obj – the JSON data

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  • validate – whether to validate the data against the MMIF JSON schema.

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-add_document(document: Document, overwrite=False) → None[source]
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Appends a Document object to the documents list.

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Fails if there is already a document with the same ID in the MMIF object.

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Parameters:
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  • document – the Document object to add

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  • overwrite – if set to True, will overwrite -an existing view with the same ID

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Returns:
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None

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-add_view(view: View, overwrite=False) → None[source]
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Appends a View object to the views list.

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Fails if there is already a view with the same ID in the MMIF object.

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Parameters:
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  • view – the Document object to add

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  • overwrite – if set to True, will overwrite -an existing view with the same ID

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Returns:
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None

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-generate_capital_annotations()[source]
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Automatically convert any “pending” temporary properties from -Document objects to Annotation objects . The generated Annotation -objects are then added to the last View in the views lists.

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See https://github.com/clamsproject/mmif-python/issues/226 for rationale -behind this behavior and discussion.

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-get_alignments(at_type1: str | TypesBase, at_type2: str | TypesBase) → Dict[str, List[Annotation]][source]
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Finds views where alignments between two given annotation types occurred.

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Returns:
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a dict that keyed by view IDs (str) and has lists of alignment Annotation objects as values.

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-get_all_views_contain(at_types: TypesBase | str | List[str | TypesBase]) → List[View][source]
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Returns the list of all views in the MMIF if given types -are present in that view’s ‘contains’ metadata.

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Parameters:
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at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

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Returns:
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the list of views that contain the type

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-get_document_by_id(doc_id: str) → Document[source]
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Finds a Document object with the given ID.

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Parameters:
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doc_id – the ID to search for

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Returns:
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a reference to the corresponding document, if it exists

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Raises:
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KeyError – if there is no corresponding document

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-get_document_location(m_type: DocumentTypes | str, path_only=False) → str | None[source]
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Method to get the location of first document of given type.

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Parameters:
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m_type – the type to search for

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Returns:
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the value of the location field in the corresponding document

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-get_documents_by_app(app_id: str) → List[Document][source]
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Method to get all documents object queries by its originated app name.

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Parameters:
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app_id – the app name to search for

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Returns:
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a list of documents matching the requested app name, or an empty list if the app not found

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-get_documents_by_property(prop_key: str, prop_value: str) → List[Document][source]
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Method to retrieve documents by an arbitrary key-value pair in the document properties objects.

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Parameters:
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  • prop_key – the metadata key to search for

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  • prop_value – the metadata value to match

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Returns:
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a list of documents matching the requested metadata key-value pair

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-get_documents_by_type(doc_type: str | DocumentTypes) → List[Document][source]
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Method to get all documents where the type matches a particular document type, which should be one of the CLAMS document types.

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Parameters:
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doc_type – the type of documents to search for, must be one of Document type defined in the CLAMS vocabulary.

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Returns:
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a list of documents matching the requested type, or an empty list if none found.

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-get_documents_in_view(vid: str | None = None) → List[Document][source]
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Method to get all documents object queries by a view id.

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Parameters:
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vid – the source view ID to search for

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Returns:
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a list of documents matching the requested source view ID, or an empty list if the view not found

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-get_documents_locations(m_type: DocumentTypes | str, path_only=False) → List[str | None][source]
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This method returns the file paths of documents of given type. -Only top-level documents have locations, so we only check them.

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Parameters:
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m_type – the type to search for

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Returns:
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a list of the values of the location fields in the corresponding documents

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-get_view_by_id(req_view_id: str) → View[source]
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Finds a View object with the given ID.

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Parameters:
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req_view_id – the ID to search for

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Returns:
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a reference to the corresponding view, if it exists

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Raises:
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Exception – if there is no corresponding view

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-get_view_contains(at_types: TypesBase | str | List[str | TypesBase]) → View | None[source]
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Returns the last view appended that contains the given -types in its ‘contains’ metadata.

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Parameters:
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at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

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Returns:
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the view, or None if the type is not found

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-get_views_contain(at_types: TypesBase | str | List[str | TypesBase]) → List[View][source]
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An alias to get_all_views_contain method.

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-get_views_for_document(doc_id: str) → List[View][source]
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Returns the list of all views that have annotations anchored on a particular document. -Note that when the document is inside a view (generated during the pipeline’s running), -doc_id must be prefixed with the view_id.

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-id_delimiter: ClassVar[str] = ':'[source]
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-new_view() → View[source]
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Creates an empty view with a new ID and appends it to the views list.

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Returns:
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a reference to the new View object

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-new_view_id() → str[source]
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Fetches an ID for a new view.

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Returns:
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the ID

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-sanitize()[source]
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Sanitizes a Mmif object by running some safeguards. -Concretely, it performs the following before returning the JSON string.

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  1. validating output using built-in MMIF jsonschema

    2. -

  2. remove non-existing annotation types from contains metadata

    3. -
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-serialize(pretty: bool = False, sanitize: bool = False, autogenerate_capital_annotations=True) → str[source]
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Serializes the MMIF object to a JSON string.

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Parameters:
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  • sanitize – If True, performs some sanitization of before returning -the JSON string. See sanitize() for details.

    • -

  • autogenerate_capital_annotations – If True, automatically convert -any “pending” temporary properties from Document objects to -Annotation objects. See generate_capital_annotations() for -details.

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  • pretty – If True, returns string representation with indentation.

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Returns:
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JSON string of the MMIF object.

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-static validate(json_str: bytes | str | dict) → None[source]
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Validates a MMIF JSON object against the MMIF Schema. -Note that this method operates before processing by MmifObject._load_str, -so it expects @ and not _ for the JSON-LD @-keys.

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Raises:
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jsonschema.exceptions.ValidationError – if the input fails validation

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Parameters:
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json_str – a MMIF JSON dict or string

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Returns:
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None

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-view_prefix: ClassVar[str] = 'v_'[source]
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mmif.serialize.view module

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The view module contains the classes used to represent a MMIF view -as a live Python object.

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In MMIF, views are created by apps in a pipeline that are annotating -data that was previously present in the MMIF file.

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-class mmif.serialize.view.Contain(mmif_obj: bytes | str | dict | None = None)[source]
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Bases: DataDict[str, str]

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Contain object that represents the metadata of a single -annotation type in the contains metadata of a MMIF view.

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-class mmif.serialize.view.View(view_obj: bytes | str | dict | None = None)[source]
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Bases: MmifObject

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View object that represents a single view in a MMIF file.

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A view is identified by an ID, and contains certain metadata, -a list of annotations, and potentially a JSON-LD @context -IRI.

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If view_obj is not provided, an empty View will be generated.

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Parameters:
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view_obj – the JSON data that defines the view

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-add_annotation(annotation: Annotation, overwrite=False) → Annotation[source]
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Adds an annotation to the current view.

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Fails if there is already an annotation with the same ID -in the view, unless overwrite is set to True.

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Parameters:
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Raises:
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KeyError – if overwrite is set to False and -an annotation with the same ID exists -in the view

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Returns:
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the same Annotation object passed in as annotation

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-add_document(document: Document, overwrite=False) → Annotation[source]
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Appends a Document object to the annotations list.

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Fails if there is already a document with the same ID in the annotations list.

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Parameters:
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  • document – the Document object to add

    • -

  • overwrite – if set to True, will overwrite -an existing view with the same ID

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Returns:
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None

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-get_annotation_by_id(ann_id)[source]
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-get_annotations(at_type: str | TypesBase | None = None, **properties) → Generator[Annotation, None, None][source]
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Look for certain annotations in this view, specified by parameters

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Parameters:
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  • at_type – @type of the annotations to look for. When this is None, any @type will match.

    • -

  • properties – properties of the annotations to look for. When given more than one property, all properties must match. Note that annotation type metadata are specified in the contains view metadata, not in individual annotation objects.

    • -
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-get_document_by_id(doc_id) → Document[source]
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-get_documents() → List[Document][source]
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-new_annotation(at_type: str | TypesBase, aid: str | None = None, overwrite=False, **properties) → Annotation[source]
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Generates a new mmif.serialize.annotation.Annotation -object and adds it to the current view.

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Fails if there is already an annotation with the same ID -in the view, unless overwrite is set to True.

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Parameters:
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  • at_type – the desired @type of the annotation.

    • -

  • aid – the desired ID of the annotation, when not given, -the mmif SDK tries to automatically generate an ID based on -Annotation type and existing annotations in the view.

    • -

  • overwrite – if set to True, will overwrite an -existing annotation with the same ID.

    • -
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Raises:
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KeyError – if overwrite is set to False and -an annotation with the same ID exists -in the view.

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Returns:
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the generated mmif.serialize.annotation.Annotation

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-new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
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Adds a new element to the contains metadata.

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Parameters:
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  • at_type – the @type of the annotation type being added

    • -

  • contains_metadata – any metadata associated with the annotation type

    • -
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Returns:
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the generated Contain object

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-new_textdocument(text: str, lang: str = 'en', did: str | None = None, overwrite=False, **properties) → Document[source]
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Generates a new mmif.serialize.annotation.Document -object, particularly typed as TextDocument and adds it to the current view.

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Fails if there is already a text document with the same ID -in the view, unless overwrite is set to True.

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Parameters:
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  • text – text content of the new document

    • -

  • lang – ISO 639-1 code of the language used in the new document

    • -

  • did – the desired ID of the document, when not given, -the mmif SDK tries to automatically generate an ID based on -Annotation type and existing documents in the view.

    • -

  • overwrite – if set to True, will overwrite an -existing document with the same ID

    • -
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Raises:
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KeyError – if overwrite is set to False and -an document with the same ID exists -in the view

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Returns:
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the generated mmif.serialize.annotation.Document

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-set_error(err_message: str, err_trace: str) → None[source]
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-class mmif.serialize.view.ViewMetadata(viewmetadata_obj: bytes | str | dict | None = None)[source]
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Bases: MmifObject

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ViewMetadata object that represents the metadata object within a MMIF view.

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Parameters:
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viewmetadata_obj – the JSON data that defines the metadata

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-add_contain(contain: Contain, at_type: str | TypesBase)[source]
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-add_parameter(param_key, param_value)[source]
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-add_parameters(**runtime_params)[source]
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-add_warnings(*warnings: Warning)[source]
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-emtpy_warnings()[source]
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-get_parameter(param_key)[source]
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-new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
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Adds a new element to the contains dictionary.

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Parameters:
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    -

  • at_type – the @type of the annotation type being added

    • -

  • contains_metadata – any metadata associated with the annotation type

    • -
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Returns:
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the generated Contain object

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-set_error(message: str, stack_trace: str)[source]
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mmif.serialize.annotation module

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The annotation module contains the classes used to represent a -MMIF annotation as a live Python object.

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In MMIF, annotations are created by apps in a pipeline as a part -of a view. For documentation on how views are represented, see -mmif.serialize.view.

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-class mmif.serialize.annotation.Annotation(anno_obj: bytes | str | dict | None = None)[source]
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Bases: MmifObject

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MmifObject that represents an annotation in a MMIF view.

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-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]]) → None[source]
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Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

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- -
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-property at_type: TypesBase[source]
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- -
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-static check_prop_value_is_simple_enough(value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]])[source]
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- -
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-get(prop_name: str) → AnnotationProperties | str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]][source]
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A special getter for Annotation properties. This is to allow for -directly accessing properties without having to go through the -properties object.

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- -
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-get_property(prop_name: str) → AnnotationProperties | str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]][source]
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A special getter for Annotation properties. This is to allow for -directly accessing properties without having to go through the -properties object.

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- -
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-property id: str[source]
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- -
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-is_document()[source]
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- -
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-is_type(at_type: str | TypesBase) → bool[source]
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Check if the @type of this object matches.

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- -
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-property parent: str[source]
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- -
- -
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-class mmif.serialize.annotation.AnnotationProperties(mmif_obj: bytes | str | dict | None = None)[source]
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Bases: MmifObject, MutableMapping[str, T]

-

AnnotationProperties object that represents the -properties object within a MMIF annotation.

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Parameters:
-

mmif_obj – the JSON data that defines the properties

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- -
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-class mmif.serialize.annotation.Document(doc_obj: bytes | str | dict | None = None)[source]
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Bases: Annotation

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Document object that represents a single document in a MMIF file.

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A document is identified by an ID, and contains certain attributes -and potentially contains the contents of the document itself, -metadata about how the document was created, and/or a list of -subdocuments grouped together logically.

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If document_obj is not provided, an empty Document will be generated.

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Parameters:
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document_obj – the JSON data that defines the document

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-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None]) → None[source]
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Adds a property to the document’s properties.

-

Unlike the parent Annotation class, added properties of a -Document object can be lost during serialization unless it belongs -to somewhere in a Mmif object. This is because we want to keep -Document object as “read-only” as possible. Thus, if you want to add -a property to a Document object,

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    -

  • add the document to a Mmif object (either in the documents list or -in a view from the views list), or

    • -

  • directly write to Document.properties instead of using this method -(which is not recommended).

    • -
-

With the former method, the SDK will record the added property as a -Annotation annotation object, separate from the original Document -object. See Mmif.generate_capital_annotations() for more.

-

A few notes to keep in mind:

-
    -

  1. You can’t overwrite an existing property of a Document object.

    2. -

  2. A MMIF can have multiple Annotation objects with the same -property name but different values. When this happens, the SDK will -only keep the latest value (in order of appearances in views list) of -the property, effectively overwriting the previous values.

    3. -
-
- -
-
-get(prop_name)[source]
-

A special getter for Document properties. This is to allow for reading -the three properties in a specific order so that the latest value is -returned, in case there are multiple values for the same key.

-
- -
-
-get_property(prop_name)[source]
-

A special getter for Document properties. This is to allow for reading -the three properties in a specific order so that the latest value is -returned, in case there are multiple values for the same key.

-
- -
-
-property location: str | None[source]
-

location property must be a legitimate URI. That is, should the document be a local file -then the file:// scheme must be used. -Returns None when no location is set.

-
- -
-
-location_address() → str | None[source]
-

Retrieves the full address from the document location URI. -Returns None when no location is set.

-
- -
-
-location_path() → str | None[source]
-

Retrieves a path that’s resolved to a pathname in the local file system. -To obtain the original value of the “path” part in the location string -(before resolving), use properties.location_path_literal method. -Returns None when no location is set.

-
- -
-
-location_scheme() → str | None[source]
-

Retrieves URI scheme of the document location. -Returns None when no location is set.

-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.DocumentProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: AnnotationProperties

-

DocumentProperties object that represents the -properties object within a MMIF document.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
-
-property location: str | None[source]
-

location property must be a legitimate URI. That is, should the document be a local file -then the file:// scheme must be used. -Returns None when no location is set.

-
- -
-
-location_address() → str | None[source]
-

Retrieves the full address from the document location URI. -Returns None when no location is set.

-
- -
-
-location_path() → str | None[source]
-
- -
-
-location_path_literal() → str | None[source]
-

Retrieves only path name of the document location (hostname is ignored). -Returns None when no location is set.

-
- -
-
-location_path_resolved(nonexist_ok=True) → str | None[source]
-

Retrieves only path name of the document location (hostname is ignored), -and then try to resolve the path name in the local file system. -This method should be used when the document scheme is file or empty. -For other schemes, users should install mmif-locdoc-<scheme> plugin.

-

Returns None when no location is set. -Raise ValueError when no code found to resolve the given location scheme.

-
- -
-
-location_scheme() → str | None[source]
-

Retrieves URI scheme of the document location. -Returns None when no location is set.

-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.Text(text_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-
-
-property lang: str[source]
-
- -
-
-property value: str[source]
-
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- - - \ No newline at end of file diff --git a/docs/1.0.6/autodoc/mmif.vocabulary.html b/docs/1.0.6/autodoc/mmif.vocabulary.html deleted file mode 100644 index 22526b0e..00000000 --- a/docs/1.0.6/autodoc/mmif.vocabulary.html +++ /dev/null @@ -1,325 +0,0 @@ - - - - - - - - - mmif.vocabulary module — mmif-python documentation - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.vocabulary module

-
-

mmif.vocabulary.annotation_types module

-
-
-class mmif.vocabulary.annotation_types.AnnotationTypes(type_uri, fuzzymode=True)[source]
-

Bases: AnnotationTypesBase

-

This class contains the CLAMS annotation types -defined in the spec version 1.1.0 as class variables.

-
-
-Alignment = http://mmif.clams.ai/vocabulary/Alignment/v1[source]
-
- -
-
-Annotation = http://mmif.clams.ai/vocabulary/Annotation/v6[source]
-
- -
-
-BoundingBox = http://mmif.clams.ai/vocabulary/BoundingBox/v5[source]
-
- -
-
-Chapter = http://mmif.clams.ai/vocabulary/Chapter/v6[source]
-
- -
-
-Interval = http://mmif.clams.ai/vocabulary/Interval/v5[source]
-
- -
-
-NamedEntity = http://mmif.clams.ai/vocabulary/NamedEntity/v1[source]
-
- -
-
-NounChunk = http://mmif.clams.ai/vocabulary/NounChunk/v1[source]
-
- -
-
-Paragraph = http://mmif.clams.ai/vocabulary/Paragraph/v1[source]
-
- -
-
-Polygon = http://mmif.clams.ai/vocabulary/Polygon/v5[source]
-
- -
-
-Region = http://mmif.clams.ai/vocabulary/Region/v5[source]
-
- -
-
-Relation = http://mmif.clams.ai/vocabulary/Relation/v5[source]
-
- -
-
-Sentence = http://mmif.clams.ai/vocabulary/Sentence/v1[source]
-
- -
-
-Span = http://mmif.clams.ai/vocabulary/Span/v5[source]
-
- -
-
-TimeFrame = http://mmif.clams.ai/vocabulary/TimeFrame/v6[source]
-
- -
-
-TimePoint = http://mmif.clams.ai/vocabulary/TimePoint/v5[source]
-
- -
-
-Token = http://mmif.clams.ai/vocabulary/Token/v1[source]
-
- -
-
-VerbChunk = http://mmif.clams.ai/vocabulary/VerbChunk/v1[source]
-
- -
-
-VideoObject = http://mmif.clams.ai/vocabulary/VideoObject/v5[source]
-
- -
-
-typevers = {'Alignment': 'v1', 'Annotation': 'v6', 'BoundingBox': 'v5', 'Chapter': 'v6', 'Interval': 'v5', 'NamedEntity': 'v1', 'NounChunk': 'v1', 'Paragraph': 'v1', 'Polygon': 'v5', 'Region': 'v5', 'Relation': 'v5', 'Sentence': 'v1', 'Span': 'v5', 'TimeFrame': 'v6', 'TimePoint': 'v5', 'Token': 'v1', 'VerbChunk': 'v1', 'VideoObject': 'v5'}[source]
-
- -
- -
-
-

mmif.vocabulary.document_types module

-
-
-class mmif.vocabulary.document_types.DocumentTypes(type_uri, fuzzymode=True)[source]
-

Bases: DocumentTypesBase

-

This class contains the CLAMS document types -defined in the spec version 1.1.0 as class variables.

-
-
-AudioDocument = http://mmif.clams.ai/vocabulary/AudioDocument/v1[source]
-
- -
-
-Document = http://mmif.clams.ai/vocabulary/Document/v1[source]
-
- -
-
-ImageDocument = http://mmif.clams.ai/vocabulary/ImageDocument/v1[source]
-
- -
-
-TextDocument = http://mmif.clams.ai/vocabulary/TextDocument/v1[source]
-
- -
-
-VideoDocument = http://mmif.clams.ai/vocabulary/VideoDocument/v1[source]
-
- -
-
-typevers = {'AudioDocument': 'v1', 'Document': 'v1', 'ImageDocument': 'v1', 'TextDocument': 'v1', 'VideoDocument': 'v1'}[source]
-
- -
- -
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 1.0.6 - - -
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0.3.3
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0.3.4
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- - - \ No newline at end of file diff --git a/docs/1.0.6/consumer-tutorial.html b/docs/1.0.6/consumer-tutorial.html deleted file mode 100644 index 417ef92b..00000000 --- a/docs/1.0.6/consumer-tutorial.html +++ /dev/null @@ -1,171 +0,0 @@ - - - - - - - - - MMIF consumer — mmif-python documentation - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • MMIF consumer
    • -
  • -
    • -
-
-
-
-
- -
-

MMIF consumer

-

A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the appliance documentation to learn more about the appliance.

-

MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance.

-
    -

  1. The code must be hosted on a public git repository (e.g. Github, Gitlab, …)

    2. -

  2. Must listen to 5000 port.

    3. -

  3. Must expose /display route .

    4. -

  4. /display router should response to GET requests.

    5. -

  5. In the GET request, a public URL of the input MMIF file is passed via file URL parameter.

    6. -

  6. On the codebase root, there must be a Dockerfile that can build a docker image that runs the web app.

    7. -
-

We provide an example consumer at https://github.com/clamsproject/mmif-visualizer.

-
- - -
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- -
-
-
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- -
- - Other Versions - v: 1.0.6 - - -
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- - -
- -
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    -
    • -
  • Index
    • -
  • -
    • -
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Index

- -
- A - | B - | C - | D - | E - | G - | I - | K - | L - | M - | N - | P - | R - | S - | T - | U - | V - -
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A

- - - -
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B

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D

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- - -
- -
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  • Welcome to mmif-python’s documentation!
    • -
  • -
    • -
-
-
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- -
-

Welcome to mmif-python’s documentation!

-
-

MultiMedia Interchange Format

-

MMIF is a JSON(-LD)-based data format designed for transferring annotation data between computational analysis applications in CLAMS project.

-
-

Contents

- -
-
-

API documentation:

- -
-
-
-
-

Indices and tables

- -
- - -
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- - Other Versions - v: 1.0.6 - - -
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- - -
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  • Getting Started
    • -
  • -
    • -
-
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-
- -
-

Getting Started

-
-

Overview

-

MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for reproducibility, transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF website. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects.

-
-
-

Prerequisites

-
    -

  • Python: the latest mmif-python requires Python 3.8 or newer. We have no plan to support Python 2.7.

    • -
-
-
-

Installation

-

Package mmif-python is distributed via the official PyPI. Users are supposed to pip-install to get latest release.

-
pip install mmif-python
-
-
-

This will install a package mmif to local python.

-

The MMIF format and specification is evolving over time, and mmif-python package will be updated along with the changes in MMIF format.

-
-

Note

-

MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and mmif-python versions, please take time to read our decision on the subject here. If you need to know which python SDK supports which specification version, see Target MMIF Versions page.

-
-
-
-

MMIF Serialization

-

mmif.serialize.mmif.Mmif represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of mmif.serialize.model.MmifObject, including the mmif.serialize.mmif.Mmif. To start with an existing MMIF str, simple initiate a new Mmif object with the file.

-
import mmif
-from mmif import Mmif
-
-mmif_str = """{
-"metadata": {
-  "mmif": "http://mmif.clams.ai/1.0.0"
-},
-"documents": [
-  {
-    "@type": "http://mmif.clams.ai/vocabulary/VideoDocument/v1",
-    "properties": {
-      "id": "m1",
-      "mime": "video/mp4",
-      "location": "file:///var/archive/video-0012.mp4"
-    }
-  },
-  {
-    "@type": "http://mmif.clams.ai/vocabulary/TextDocument/v1",
-    "properties": {
-      "id": "m2",
-      "mime": "text/plain",
-      "location": "file:///var/archive/video-0012-transcript.txt"
-    }
-  }
-],
-"views": []}"""
-mmif_obj = Mmif(mmif_str)
-
-
-

Few notes;

-
    -

  1. MMIF does not carry the primary source files in it.

    2. -

  2. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version mmif-python implementation of the MMIF might not be able to load an unsupported version of MMIF string.

    3. -
-

When serializing back to str, call mmif.serialize.model.MmifObject.serialize() on the object.

-

To get subcomponents, you can use various getters implemented in subclasses. For example;

-
from mmif.vocabulary.document_types import DocumentTypes
-
-for video in mmif_obj.Mmif.get_documents_by_type(DocumentTypes.VideoDocument):
-  with open(video.location_path(), 'b') as in_video:
-    # do something with the video file
-
-
-

For a full list of available helper methods, please refer to the API documentation.

-
-
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- -
-
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- - Other Versions - v: 1.0.6 - - -
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  • mmif package
    • -
  • -
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mmif package

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- - - \ No newline at end of file diff --git a/docs/1.0.6/objects.inv b/docs/1.0.6/objects.inv deleted file mode 100644 index aaac0c73..00000000 Binary files a/docs/1.0.6/objects.inv and /dev/null differ diff --git a/docs/1.0.6/plugins.html b/docs/1.0.6/plugins.html deleted file mode 100644 index fcfd15de..00000000 --- a/docs/1.0.6/plugins.html +++ /dev/null @@ -1,227 +0,0 @@ - - - - - - - - - Developing plugins for MMIF Python SDK — mmif-python documentation - - - - - - - - - - - - - - - - - -
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  • Developing plugins for MMIF Python SDK
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Developing plugins for MMIF Python SDK

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Overview

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As MMIF JSON files can carry information about media document files without actually carrying file contents, file accessing modules in mmif Python package (distributed as mmif-python on PyPI) are designed to be lightweight and flexible so that it can work with additional “plugin” Python packages that can handle concrete file access.

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This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF website. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects.

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Developer can write simple plugins that can provide additional functionalities to mmif-python. For example, mmif-python does not provide any file access functionality beyond a local file system (with file scheme), but it can be extended with a plugin that can handle file access over different protocols (e.g. http, s3, ftp, etc).

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This document contains information about how to write plugins for mmif-python.

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Document Location Scheme Plugins

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mmif.serialize.annotation.Document class has various methods to access parts of location property of the document. The location is in URI/IRI format (SCHEME://HOSTNAME/PATH, in a nutshell) and it has to be resolved to a local file for CLAMS Apps to process the local file to analyze and extract information about the media and its contents. The core mmif-python distribution only provides a default implementation that can handle file scheme URIs.

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To add a document location handler plugin, you need to implement a Python “package” (do not confuse with PYPI distribution), that meets these requirements;

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  1. the package must be named mmif_docloc_<SCHEME>. For example, to implement a handler for s3 scheme, the package name must be mmif_docloc_s3. The prefix is important as it’s used in the plugin discovery process from the core mmif-python modules.

    2. -

  2. the top module of the package must have a function named resolve. The function must take a single argument, which is a str of the document location URI. The function must return a str of the local file path. For example, if the document location is s3://mybucket/myfile.mp4, a Python user should be able to to something like this;

    3. -
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import mmif_docloc_s3
-resolved = mmif_docloc_s3.resolve('s3://mybucket/myfile.mp4')
-# then resolved must be a local file path that can be used to open the file
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Here’s a minimal example codebase that you refer to when you develop a docloc plugin.

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(However, before you start writing your own plugin for a specific URI scheme, checking if there’s already a PyPI distribution for the scheme might be a good idea.)

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$ tree .
-.
-├── mmif_docloc_dummy
-│   └── __init__.py
-├── pyproject.toml
-└── setup.cfg
-
- $ cat pyproject.toml
-[build-system]
-requires = ["setuptools"]
-build-backend = "setuptools.build_meta"
-
-$ cat setup.cfg
-[metadata]
-name = mmif_docloc_dummy  # this name is IMPORTANT
-version = 0.0.1
-description = a plugin to mmif-pyhon to handle `dummy` location scheme
-
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And the plugin code.

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# mmif_docloc_dummy/__init__.py
-doc_types = {'video': 'mp4'}
-
-def resolve(docloc):
-    scheme = 'dummy'
-    if docloc.startswith(f'{scheme}://'):
-        doc_id, doc_type = docloc.split('.')
-        return f'/path/to/{doc_id}.{doc_types[doc_type]}'
-    else:
-        raise ValueError(f'cannot handle document location scheme: {docloc}')
-
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Python Module Index

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- - - - - - - - \ No newline at end of file diff --git a/docs/1.0.6/searchindex.js b/docs/1.0.6/searchindex.js deleted file mode 100644 index 028638e0..00000000 --- a/docs/1.0.6/searchindex.js +++ /dev/null @@ -1 +0,0 @@ -Search.setIndex({"alltitles": {"API documentation:": [[3, null]], "Contents": [[3, null]], "Developing plugins for MMIF Python SDK": [[6, null]], "Document Location Scheme Plugins": [[6, "document-location-scheme-plugins"]], "Getting Started": [[4, null]], "Indices and tables": [[3, "indices-and-tables"]], "Installation": [[4, "installation"]], "MMIF Serialization": [[4, "mmif-serialization"]], "MMIF consumer": [[2, null]], "MultiMedia Interchange Format": [[3, "multimedia-interchange-format"]], "Overview": [[4, "overview"], [6, "overview"]], "Prerequisites": [[4, "prerequisites"]], "Target MMIF Versions": [[7, null]], "Target Specification Versions": [[7, "id1"]], "Welcome to mmif-python\u2019s documentation!": [[3, null]], "mmif package": [[5, null]], 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[0, 4, 6], "when": [0, 4, 6], "where": 0, "whether": 0, "which": [0, 4, 6], "within": 0, "without": [0, 6], "won": 0, "work": [0, 6], "workflow": 4, "would": 0, "write": [0, 6], "you": [0, 4, 6], "your": 6, "zero": 0}, "titles": ["mmif.serialize module", "mmif.vocabulary module", "MMIF consumer", "Welcome to mmif-python\u2019s documentation!", "Getting Started", "mmif package", "Developing plugins for MMIF Python SDK", "Target MMIF Versions"], "titleterms": {"": 3, "annot": 0, "annotation_typ": 1, "api": 3, "consum": 2, "content": 3, "develop": 6, "document": [3, 6], "document_typ": 1, "format": 3, "get": 4, "indic": 3, "instal": 4, "interchang": 3, "locat": 6, "mmif": [0, 1, 2, 3, 4, 5, 6, 7], "model": 0, "modul": [0, 1], "multimedia": 3, "overview": [4, 6], "packag": 5, "plugin": 6, "prerequisit": 4, "python": [3, 6], "scheme": 6, "sdk": 6, "serial": [0, 4], "specif": 7, "start": 4, "tabl": 3, "target": 7, "version": 7, "view": 0, "vocabulari": 1, "welcom": 3}}) \ No newline at end of file diff --git a/docs/1.0.6/target-versions.html b/docs/1.0.6/target-versions.html deleted file mode 100644 index e52db963..00000000 --- a/docs/1.0.6/target-versions.html +++ /dev/null @@ -1,260 +0,0 @@ - - - - - - - - - Target MMIF Versions — mmif-python documentation - - - - - - - - - - - - - - - - - -
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Target MMIF Versions

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This article provides targeting MMIF specification versions of different versions of mmif-python SDK.

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Target Specification Versions

mmif-python version

Target MMIF Specification

1.0.6

1.1.0

1.0.5

1.0.0

1.0.4

1.0.0

1.0.3

1.0.0

1.0.2

1.0.0

1.0.1

1.0.0

1.0.0

0.5.0

0.5.2

0.5.0

0.5.1

0.5.0

0.5.0

0.5.0

0.4.8

0.4.2

0.4.7

0.4.1

0.4.6

0.4.0

0.4.5

0.4.0

0.4.4

0.4.0

0.4.3

0.4.0

0.4.2

0.4.0

0.4.1

0.4.0

0.4.0

0.4.0

0.3.5

0.3.1

0.3.4

0.3.1

0.3.3

0.3.1

0.3.2

0.3.1

0.3.1

0.3.0

0.3.0

0.3.0

0.2.2

0.2.1

0.2.1

0.2.1

0.2.0

0.2.1

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0.3.0
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0.3.1
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0.3.2
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0.3.3
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0.3.4
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0.3.5
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0.4.0
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0.4.1
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0.4.2
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0.4.3
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0.4.4
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0.4.5
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0.4.6
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0.4.7
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0.4.8
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0.5.0
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0.5.1
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0.5.2
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1.0.0
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1.0.1
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1.0.10
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1.0.11
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1.0.12
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1.0.13
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1.0.14
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1.0.15
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1.0.16
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1.0.17
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1.0.18
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1.0.19
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1.0.2
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1.0.3
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1.0.4
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1.0.5
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1.0.6
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1.0.7
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1.0.8
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1.0.9
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1.1.0
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The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the `appliance documentation `_ to learn more about the appliance. - -MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance. - -#. The code must be hosted on a public git repository (e.g. Github, Gitlab, ...) -#. Must listen to ``5000`` port. -#. Must expose ``/display`` route . -#. ``/display`` router should response to ``GET`` requests. -#. In the ``GET`` request, a public URL of the input MMIF file is passed via ``file`` URL parameter. -#. On the codebase root, there must be a ``Dockerfile`` that can build a `docker `_ image that runs the web app. - -We provide an example consumer at https://github.com/clamsproject/mmif-visualizer. diff --git a/docs/1.0.7/_sources/index.rst.txt b/docs/1.0.7/_sources/index.rst.txt deleted file mode 100644 index beb56aae..00000000 --- a/docs/1.0.7/_sources/index.rst.txt +++ /dev/null @@ -1,26 +0,0 @@ -Welcome to mmif-python's documentation! -======================================= - -.. mdinclude:: ../README.md - -.. toctree:: - :maxdepth: 2 - :caption: Contents - - introduction - plugins - target-versions - -.. toctree:: - :maxdepth: 2 - :caption: API documentation: - - modules - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/docs/1.0.7/_sources/introduction.rst.txt b/docs/1.0.7/_sources/introduction.rst.txt deleted file mode 100644 index cfd9eaf7..00000000 --- a/docs/1.0.7/_sources/introduction.rst.txt +++ /dev/null @@ -1,89 +0,0 @@ -.. _introduction: - -Getting Started -=============== - - -Overview ---------- - -MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for reproducibility, transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF website `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects. - -Prerequisites -------------- - -* `Python `_: the latest ``mmif-python`` requires Python 3.8 or newer. We have no plan to support `Python 2.7 `_. - -Installation ---------------- - -Package ``mmif-python`` is distributed via the official PyPI. Users are supposed to pip-install to get latest release. - -.. code-block:: bash - - pip install mmif-python - -This will install a package `mmif` to local python. - -The MMIF format and specification is evolving over time, and ``mmif-python`` package will be updated along with the changes in MMIF format. - -.. note:: MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and ``mmif-python`` versions, please take time to read our decision on the subject `here `_. If you need to know which python SDK supports which specification version, see :ref:`target-versions` page. - -MMIF Serialization ---------------------------- - -:class:`mmif.serialize.mmif.Mmif` represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of :class:`mmif.serialize.model.MmifObject`, including the :class:`mmif.serialize.mmif.Mmif`. To start with an existing MMIF :class:`str`, simple initiate a new ``Mmif`` object with the file. - -.. code-block:: python - - import mmif - from mmif import Mmif - - mmif_str = """{ - "metadata": { - "mmif": "http://mmif.clams.ai/1.0.0" - }, - "documents": [ - { - "@type": "http://mmif.clams.ai/vocabulary/VideoDocument/v1", - "properties": { - "id": "m1", - "mime": "video/mp4", - "location": "file:///var/archive/video-0012.mp4" - } - }, - { - "@type": "http://mmif.clams.ai/vocabulary/TextDocument/v1", - "properties": { - "id": "m2", - "mime": "text/plain", - "location": "file:///var/archive/video-0012-transcript.txt" - } - } - ], - "views": []}""" - mmif_obj = Mmif(mmif_str) - - -Few notes; - -#. MMIF does not carry the primary source files in it. -#. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version ``mmif-python`` implementation of the MMIF might not be able to load an unsupported version of MMIF string. - -When serializing back to :class:`str`, call :meth:`mmif.serialize.model.MmifObject.serialize` on the object. - -To get subcomponents, you can use various getters implemented in subclasses. For example; - -.. code-block:: python - - from mmif.vocabulary.document_types import DocumentTypes - - for video in mmif_obj.Mmif.get_documents_by_type(DocumentTypes.VideoDocument): - with open(video.location_path(), 'b') as in_video: - # do something with the video file - - -For a full list of available helper methods, please refer to :ref:`the API documentation `. - diff --git a/docs/1.0.7/_sources/modules.rst.txt b/docs/1.0.7/_sources/modules.rst.txt deleted file mode 100644 index e4269c6d..00000000 --- a/docs/1.0.7/_sources/modules.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _apidoc: - -mmif package -============ - -.. toctree:: - :maxdepth: 4 - - autodoc/mmif.serialize - autodoc/mmif.vocabulary diff --git a/docs/1.0.7/_sources/plugins.rst.txt b/docs/1.0.7/_sources/plugins.rst.txt deleted file mode 100644 index 9e1505e9..00000000 --- a/docs/1.0.7/_sources/plugins.rst.txt +++ /dev/null @@ -1,75 +0,0 @@ -.. _plugins: - -Developing plugins for MMIF Python SDK -====================================== - - -Overview --------- - -As MMIF JSON files can carry information about media document files without actually carrying file contents, file accessing modules in ``mmif`` Python package (distributed as ``mmif-python`` on PyPI) are designed to be lightweight and flexible so that it can work with additional "plugin" Python packages that can handle concrete file access. - - -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF website `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects. - -Developer can write simple plugins that can provide additional functionalities to ``mmif-python``. For example, ``mmif-python`` does not provide any file access functionality beyond a local file system (with ``file`` scheme), but it can be extended with a plugin that can handle file access over different protocols (e.g. ``http``, ``s3``, ``ftp``, etc). - -This document contains information about how to write plugins for ``mmif-python``. - -Document Location Scheme Plugins -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -:class:`mmif.serialize.annotation.Document` class has various methods to access parts of ``location`` property of the document. The location is in `URI/IRI format `_ (``SCHEME://HOSTNAME/PATH``, in a nutshell) and it has to be resolved to a local file for CLAMS Apps to process the local file to analyze and extract information about the media and its contents. The core ``mmif-python`` distribution only provides a default implementation that can handle ``file`` scheme URIs. - -To add a document location handler plugin, you need to implement a Python `"package" `_ (do not confuse with PYPI distribution), that meets these requirements; - -#. the package must be named ``mmif_docloc_``. For example, to implement a handler for ``s3`` scheme, the package name must be ``mmif_docloc_s3``. The prefix is important as it's used in the plugin discovery process from the core ``mmif-python`` modules. -#. the top module of the package must have a function named ``resolve``. The function must take a single argument, which is a :class:`str` of the document location URI. The function must return a :class:`str` of the local file path. For example, if the document location is ``s3://mybucket/myfile.mp4``, a Python user should be able to to something like this; - -.. code-block:: python - - import mmif_docloc_s3 - resolved = mmif_docloc_s3.resolve('s3://mybucket/myfile.mp4') - # then resolved must be a local file path that can be used to open the file - - -Here's a minimal example codebase that you refer to when you develop a ``docloc`` plugin. - -(However, before you start writing your own plugin for a specific URI scheme, checking `if there's already a PyPI distribution `_ for the scheme might be a good idea.) - -.. code-block:: sh - - $ tree . - . - ├── mmif_docloc_dummy - │ └── __init__.py - ├── pyproject.toml - └── setup.cfg - - $ cat pyproject.toml - [build-system] - requires = ["setuptools"] - build-backend = "setuptools.build_meta" - - $ cat setup.cfg - [metadata] - name = mmif_docloc_dummy # this name is IMPORTANT - version = 0.0.1 - description = a plugin to mmif-pyhon to handle `dummy` location scheme - - -And the plugin code. - -.. code-block:: python - - # mmif_docloc_dummy/__init__.py - doc_types = {'video': 'mp4'} - - def resolve(docloc): - scheme = 'dummy' - if docloc.startswith(f'{scheme}://'): - doc_id, doc_type = docloc.split('.') - return f'/path/to/{doc_id}.{doc_types[doc_type]}' - else: - raise ValueError(f'cannot handle document location scheme: {docloc}') diff --git a/docs/1.0.7/_sources/target-versions.rst.txt b/docs/1.0.7/_sources/target-versions.rst.txt deleted file mode 100644 index 34216d3e..00000000 --- a/docs/1.0.7/_sources/target-versions.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _target-versions: - -Target MMIF Versions -==================== - -This article provides targeting MMIF specification versions of different versions of ``mmif-python`` SDK. - -.. csv-table:: Target Specification Versions - :file: target-versions.csv - :header-rows: 1 diff --git a/docs/1.0.7/_static/_sphinx_javascript_frameworks_compat.js b/docs/1.0.7/_static/_sphinx_javascript_frameworks_compat.js deleted file mode 100644 index 81415803..00000000 --- a/docs/1.0.7/_static/_sphinx_javascript_frameworks_compat.js +++ /dev/null @@ -1,123 +0,0 @@ -/* Compatability shim for jQuery and underscores.js. - * - * Copyright Sphinx contributors - * Released under the two clause BSD licence - */ - -/** - * small helper function to urldecode strings - * - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL - */ -jQuery.urldecode = function(x) { - if (!x) { - return x - } - return decodeURIComponent(x.replace(/\+/g, ' ')); -}; - -/** - * small helper function to urlencode strings - */ -jQuery.urlencode = encodeURIComponent; - -/** - * This function returns the parsed url parameters of the - * current request. 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span; - var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.className = className; - } - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - node.parentNode.insertBefore(span, node.parentNode.insertBefore( - document.createTextNode(val.substr(pos + text.length)), - node.nextSibling)); - node.nodeValue = val.substr(0, pos); - if (isInSVG) { - var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect"); - var bbox = node.parentElement.getBBox(); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute('class', className); - addItems.push({ - "parent": node.parentNode, - "target": rect}); - } - } - } - else if (!jQuery(node).is("button, select, textarea")) { - jQuery.each(node.childNodes, function() { - highlight(this, addItems); - }); - } - } - var addItems = []; - var result = this.each(function() { - highlight(this, addItems); - }); - for (var i = 0; i < addItems.length; ++i) { - jQuery(addItems[i].parent).before(addItems[i].target); - } - return result; -}; - -/* - * backward compatibility for jQuery.browser - * This will be supported until firefox bug is fixed. - */ -if (!jQuery.browser) { - jQuery.uaMatch = function(ua) { - ua = ua.toLowerCase(); - - var match = /(chrome)[ \/]([\w.]+)/.exec(ua) || - /(webkit)[ \/]([\w.]+)/.exec(ua) || - /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) || - /(msie) ([\w.]+)/.exec(ua) || - ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) || - []; - - return { - browser: match[ 1 ] || "", - version: match[ 2 ] || "0" - }; - }; - jQuery.browser = {}; - jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true; -} diff --git a/docs/1.0.7/_static/basic.css 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- -/** - * Simple result scoring code. - */ -if (typeof Scorer === "undefined") { - var Scorer = { - // Implement the following function to further tweak the score for each result - // The function takes a result array [docname, title, anchor, descr, score, filename] - // and returns the new score. - /* - score: result => { - const [docname, title, anchor, descr, score, filename, kind] = result - return score - }, - */ - - // query matches the full name of an object - objNameMatch: 11, - // or matches in the last dotted part of the object name - objPartialMatch: 6, - // Additive scores depending on the priority of the object - objPrio: { - 0: 15, // used to be importantResults - 1: 5, // used to be objectResults - 2: -5, // used to be unimportantResults - }, - // Used when the priority is not in the mapping. - objPrioDefault: 0, - - // query found in title - title: 15, - partialTitle: 7, - // query found in terms - term: 5, - partialTerm: 2, - }; -} - -// Global search result kind enum, used by themes to style search results. -class SearchResultKind { - static get index() { return "index"; } - static get object() { return "object"; } - static get text() { return "text"; } - static get title() { return "title"; } -} - -const _removeChildren = (element) => { - while (element && element.lastChild) element.removeChild(element.lastChild); -}; - -/** - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping - */ -const _escapeRegExp = (string) => - string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string - -const _displayItem = (item, searchTerms, highlightTerms) => { - const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; - const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; - const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; - const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; - const contentRoot = document.documentElement.dataset.content_root; - - const [docName, title, anchor, descr, score, _filename, kind] = item; - - let listItem = document.createElement("li"); - // Add a class representing the item's type: - // can be used by a theme's CSS selector for styling - // See SearchResultKind for the class names. - listItem.classList.add(`kind-${kind}`); - let requestUrl; - let linkUrl; - if (docBuilder === "dirhtml") { - // dirhtml builder - let dirname = docName + "/"; - if (dirname.match(/\/index\/$/)) - dirname = dirname.substring(0, dirname.length - 6); - else if (dirname === "index/") dirname = ""; - requestUrl = contentRoot + dirname; - linkUrl = requestUrl; - } else { - // normal html builders - requestUrl = contentRoot + docName + docFileSuffix; - linkUrl = docName + docLinkSuffix; - } - let linkEl = listItem.appendChild(document.createElement("a")); - linkEl.href = linkUrl + anchor; - linkEl.dataset.score = score; - linkEl.innerHTML = title; - if (descr) { - listItem.appendChild(document.createElement("span")).innerHTML = - " (" + descr + ")"; - // highlight search terms in the description - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - } - else if (showSearchSummary) - fetch(requestUrl) - .then((responseData) => responseData.text()) - .then((data) => { - if (data) - listItem.appendChild( - Search.makeSearchSummary(data, searchTerms, anchor) - ); - // highlight search terms in the summary - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - }); - Search.output.appendChild(listItem); -}; -const _finishSearch = (resultCount) => { - Search.stopPulse(); - Search.title.innerText = _("Search Results"); - if (!resultCount) - Search.status.innerText = Documentation.gettext( - "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." - ); - else - Search.status.innerText = Documentation.ngettext( - "Search finished, found one page matching the search query.", - "Search finished, found ${resultCount} pages matching the search query.", - resultCount, - ).replace('${resultCount}', resultCount); -}; -const _displayNextItem = ( - results, - resultCount, - searchTerms, - highlightTerms, -) => { - // results left, load the summary and display it - // this is intended to be dynamic (don't sub resultsCount) - if (results.length) { - _displayItem(results.pop(), searchTerms, highlightTerms); - setTimeout( - () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), - 5 - ); - } - // search finished, update title and status message - else _finishSearch(resultCount); -}; -// Helper function used by query() to order search results. -// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. -// Order the results by score (in opposite order of appearance, since the -// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. -const _orderResultsByScoreThenName = (a, b) => { - const leftScore = a[4]; - const rightScore = b[4]; - if (leftScore === rightScore) { - // same score: sort alphabetically - const leftTitle = a[1].toLowerCase(); - const rightTitle = b[1].toLowerCase(); - if (leftTitle === rightTitle) return 0; - return leftTitle > rightTitle ? -1 : 1; // inverted is intentional - } - return leftScore > rightScore ? 1 : -1; -}; - -/** - * Default splitQuery function. Can be overridden in ``sphinx.search`` with a - * custom function per language. - * - * The regular expression works by splitting the string on consecutive characters - * that are not Unicode letters, numbers, underscores, or emoji characters. - * This is the same as ``\W+`` in Python, preserving the surrogate pair area. - */ -if (typeof splitQuery === "undefined") { - var splitQuery = (query) => query - .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) - .filter(term => term) // remove remaining empty strings -} - -/** - * Search Module - */ -const Search = { - _index: null, - _queued_query: null, - _pulse_status: -1, - - htmlToText: (htmlString, anchor) => { - const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - for (const removalQuery of [".headerlink", "script", "style"]) { - htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); - } - if (anchor) { - const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); - if (anchorContent) return anchorContent.textContent; - - console.warn( - `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` - ); - } - - // if anchor not specified or not found, fall back to main content - const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent) return docContent.textContent; - - console.warn( - "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." - ); - return ""; - }, - - init: () => { - const query = new URLSearchParams(window.location.search).get("q"); - document - .querySelectorAll('input[name="q"]') - .forEach((el) => (el.value = query)); - if (query) Search.performSearch(query); - }, - - loadIndex: (url) => - (document.body.appendChild(document.createElement("script")).src = url), - - setIndex: (index) => { - Search._index = index; - if (Search._queued_query !== null) { - const query = Search._queued_query; - Search._queued_query = null; - Search.query(query); - } - }, - - hasIndex: () => Search._index !== null, - - deferQuery: (query) => (Search._queued_query = query), - - stopPulse: () => (Search._pulse_status = -1), - - startPulse: () => { - if (Search._pulse_status >= 0) return; - - const pulse = () => { - Search._pulse_status = (Search._pulse_status + 1) % 4; - Search.dots.innerText = ".".repeat(Search._pulse_status); - if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); - }; - pulse(); - }, - - /** - * perform a search for something (or wait until index is loaded) - */ - performSearch: (query) => { - // create the required interface elements - const searchText = document.createElement("h2"); - searchText.textContent = _("Searching"); - const searchSummary = document.createElement("p"); - searchSummary.classList.add("search-summary"); - searchSummary.innerText = ""; - const searchList = document.createElement("ul"); - searchList.setAttribute("role", "list"); - searchList.classList.add("search"); - - const out = document.getElementById("search-results"); - Search.title = out.appendChild(searchText); - Search.dots = Search.title.appendChild(document.createElement("span")); - Search.status = out.appendChild(searchSummary); - Search.output = out.appendChild(searchList); - - const searchProgress = document.getElementById("search-progress"); - // Some themes don't use the search progress node - if (searchProgress) { - searchProgress.innerText = _("Preparing search..."); - } - Search.startPulse(); - - // index already loaded, the browser was quick! - if (Search.hasIndex()) Search.query(query); - else Search.deferQuery(query); - }, - - _parseQuery: (query) => { - // stem the search terms and add them to the correct list - const stemmer = new Stemmer(); - const searchTerms = new Set(); - const excludedTerms = new Set(); - const highlightTerms = new Set(); - const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); - splitQuery(query.trim()).forEach((queryTerm) => { - const queryTermLower = queryTerm.toLowerCase(); - - // maybe skip this "word" - // stopwords array is from language_data.js - if ( - stopwords.indexOf(queryTermLower) !== -1 || - queryTerm.match(/^\d+$/) - ) - return; - - // stem the word - let word = stemmer.stemWord(queryTermLower); - // select the correct list - if (word[0] === "-") excludedTerms.add(word.substr(1)); - else { - searchTerms.add(word); - highlightTerms.add(queryTermLower); - } - }); - - if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js - localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) - } - - // console.debug("SEARCH: searching for:"); - // console.info("required: ", [...searchTerms]); - // console.info("excluded: ", [...excludedTerms]); - - return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; - }, - - /** - * execute search (requires search index to be loaded) - */ - _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - - // Collect multiple result groups to be sorted separately and then ordered. - // Each is an array of [docname, title, anchor, descr, score, filename, kind]. - const normalResults = []; - const nonMainIndexResults = []; - - _removeChildren(document.getElementById("search-progress")); - - const queryLower = query.toLowerCase().trim(); - for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { - for (const [file, id] of foundTitles) { - const score = Math.round(Scorer.title * queryLower.length / title.length); - const boost = titles[file] === title ? 1 : 0; // add a boost for document titles - normalResults.push([ - docNames[file], - titles[file] !== title ? `${titles[file]} > ${title}` : title, - id !== null ? "#" + id : "", - null, - score + boost, - filenames[file], - SearchResultKind.title, - ]); - } - } - } - - // search for explicit entries in index directives - for (const [entry, foundEntries] of Object.entries(indexEntries)) { - if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id, isMain] of foundEntries) { - const score = Math.round(100 * queryLower.length / entry.length); - const result = [ - docNames[file], - titles[file], - id ? "#" + id : "", - null, - score, - filenames[file], - SearchResultKind.index, - ]; - if (isMain) { - normalResults.push(result); - } else { - nonMainIndexResults.push(result); - } - } - } - } - - // lookup as object - objectTerms.forEach((term) => - normalResults.push(...Search.performObjectSearch(term, objectTerms)) - ); - - // lookup as search terms in fulltext - normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); - - // let the scorer override scores with a custom scoring function - if (Scorer.score) { - normalResults.forEach((item) => (item[4] = Scorer.score(item))); - nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); - } - - // Sort each group of results by score and then alphabetically by name. - normalResults.sort(_orderResultsByScoreThenName); - nonMainIndexResults.sort(_orderResultsByScoreThenName); - - // Combine the result groups in (reverse) order. - // Non-main index entries are typically arbitrary cross-references, - // so display them after other results. - let results = [...nonMainIndexResults, ...normalResults]; - - // remove duplicate search results - // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept - let seen = new Set(); - results = results.reverse().reduce((acc, result) => { - let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); - if (!seen.has(resultStr)) { - acc.push(result); - seen.add(resultStr); - } - return acc; - }, []); - - return results.reverse(); - }, - - query: (query) => { - const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); - const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); - - // for debugging - //Search.lastresults = results.slice(); // a copy - // console.info("search results:", Search.lastresults); - - // print the results - _displayNextItem(results, results.length, searchTerms, highlightTerms); - }, - - /** - * search for object names - */ - performObjectSearch: (object, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const objects = Search._index.objects; - const objNames = Search._index.objnames; - const titles = Search._index.titles; - - const results = []; - - const objectSearchCallback = (prefix, match) => { - const name = match[4] - const fullname = (prefix ? prefix + "." : "") + name; - const fullnameLower = fullname.toLowerCase(); - if (fullnameLower.indexOf(object) < 0) return; - - let score = 0; - const parts = fullnameLower.split("."); - - // check for different match types: exact matches of full name or - // "last name" (i.e. last dotted part) - if (fullnameLower === object || parts.slice(-1)[0] === object) - score += Scorer.objNameMatch; - else if (parts.slice(-1)[0].indexOf(object) > -1) - score += Scorer.objPartialMatch; // matches in last name - - const objName = objNames[match[1]][2]; - const title = titles[match[0]]; - - // If more than one term searched for, we require other words to be - // found in the name/title/description - const otherTerms = new Set(objectTerms); - otherTerms.delete(object); - if (otherTerms.size > 0) { - const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); - if ( - [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) - ) - return; - } - - let anchor = match[3]; - if (anchor === "") anchor = fullname; - else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; - - const descr = objName + _(", in ") + title; - - // add custom score for some objects according to scorer - if (Scorer.objPrio.hasOwnProperty(match[2])) - score += Scorer.objPrio[match[2]]; - else score += Scorer.objPrioDefault; - - results.push([ - docNames[match[0]], - fullname, - "#" + anchor, - descr, - score, - filenames[match[0]], - SearchResultKind.object, - ]); - }; - Object.keys(objects).forEach((prefix) => - objects[prefix].forEach((array) => - objectSearchCallback(prefix, array) - ) - ); - return results; - }, - - /** - * search for full-text terms in the index - */ - performTermsSearch: (searchTerms, excludedTerms) => { - // prepare search - const terms = Search._index.terms; - const titleTerms = Search._index.titleterms; - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - - const scoreMap = new Map(); - const fileMap = new Map(); - - // perform the search on the required terms - searchTerms.forEach((word) => { - const files = []; - const arr = [ - { files: terms[word], score: Scorer.term }, - { files: titleTerms[word], score: Scorer.title }, - ]; - // add support for partial matches - if (word.length > 2) { - const escapedWord = _escapeRegExp(word); - if (!terms.hasOwnProperty(word)) { - Object.keys(terms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: terms[term], score: Scorer.partialTerm }); - }); - } - if (!titleTerms.hasOwnProperty(word)) { - Object.keys(titleTerms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); - }); - } - } - - // no match but word was a required one - if (arr.every((record) => record.files === undefined)) return; - - // found search word in contents - arr.forEach((record) => { - if (record.files === undefined) return; - - let recordFiles = record.files; - if (recordFiles.length === undefined) recordFiles = [recordFiles]; - files.push(...recordFiles); - - // set score for the word in each file - recordFiles.forEach((file) => { - if (!scoreMap.has(file)) scoreMap.set(file, {}); - scoreMap.get(file)[word] = record.score; - }); - }); - - // create the mapping - files.forEach((file) => { - if (!fileMap.has(file)) fileMap.set(file, [word]); - else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); - }); - }); - - // now check if the files don't contain excluded terms - const results = []; - for (const [file, wordList] of fileMap) { - // check if all requirements are matched - - // as search terms with length < 3 are discarded - const filteredTermCount = [...searchTerms].filter( - (term) => term.length > 2 - ).length; - if ( - wordList.length !== searchTerms.size && - wordList.length !== filteredTermCount - ) - continue; - - // ensure that none of the excluded terms is in the search result - if ( - [...excludedTerms].some( - (term) => - terms[term] === file || - titleTerms[term] === file || - (terms[term] || []).includes(file) || - (titleTerms[term] || []).includes(file) - ) - ) - break; - - // select one (max) score for the file. - const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); - // add result to the result list - results.push([ - docNames[file], - titles[file], - "", - null, - score, - filenames[file], - SearchResultKind.text, - ]); - } - return results; - }, - - /** - * helper function to return a node containing the - * search summary for a given text. keywords is a list - * of stemmed words. - */ - makeSearchSummary: (htmlText, keywords, anchor) => { - const text = Search.htmlToText(htmlText, anchor); - if (text === "") return null; - - const textLower = text.toLowerCase(); - const actualStartPosition = [...keywords] - .map((k) => textLower.indexOf(k.toLowerCase())) - .filter((i) => i > -1) - .slice(-1)[0]; - const startWithContext = Math.max(actualStartPosition - 120, 0); - - const top = startWithContext === 0 ? "" : "..."; - const tail = startWithContext + 240 < text.length ? "..." : ""; - - let summary = document.createElement("p"); - summary.classList.add("context"); - summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; - - return summary; - }, -}; - -_ready(Search.init); diff --git a/docs/1.0.7/_static/sphinx_highlight.js b/docs/1.0.7/_static/sphinx_highlight.js deleted file mode 100644 index 8a96c69a..00000000 --- a/docs/1.0.7/_static/sphinx_highlight.js +++ /dev/null @@ -1,154 +0,0 @@ -/* Highlighting utilities for Sphinx HTML documentation. */ -"use strict"; - -const SPHINX_HIGHLIGHT_ENABLED = true - -/** - * highlight a given string on a node by wrapping it in - * span elements with the given class name. - */ -const _highlight = (node, addItems, text, className) => { - if (node.nodeType === Node.TEXT_NODE) { - const val = node.nodeValue; - const parent = node.parentNode; - const pos = val.toLowerCase().indexOf(text); - if ( - pos >= 0 && - !parent.classList.contains(className) && - !parent.classList.contains("nohighlight") - ) { - let span; - - const closestNode = parent.closest("body, svg, foreignObject"); - const isInSVG = closestNode && closestNode.matches("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.classList.add(className); - } - - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - const rest = document.createTextNode(val.substr(pos + text.length)); - parent.insertBefore( - span, - parent.insertBefore( - rest, - node.nextSibling - ) - ); - node.nodeValue = val.substr(0, pos); - /* There may be more occurrences of search term in this node. So call this - * function recursively on the remaining fragment. - */ - _highlight(rest, addItems, text, className); - - if (isInSVG) { - const rect = document.createElementNS( - "http://www.w3.org/2000/svg", - "rect" - ); - const bbox = parent.getBBox(); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute("class", className); - addItems.push({ parent: parent, target: rect }); - } - } - } else if (node.matches && !node.matches("button, select, textarea")) { - node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); - } -}; -const _highlightText = (thisNode, text, className) => { - let addItems = []; - _highlight(thisNode, addItems, text, className); - addItems.forEach((obj) => - obj.parent.insertAdjacentElement("beforebegin", obj.target) - ); -}; - -/** - * Small JavaScript module for the documentation. - */ -const SphinxHighlight = { - - /** - * highlight the search words provided in localstorage in the text - */ - highlightSearchWords: () => { - if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight - - // get and clear terms from localstorage - const url = new URL(window.location); - const highlight = - localStorage.getItem("sphinx_highlight_terms") - || url.searchParams.get("highlight") - || ""; - localStorage.removeItem("sphinx_highlight_terms") - url.searchParams.delete("highlight"); - window.history.replaceState({}, "", url); - - // get individual terms from highlight string - const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); - if (terms.length === 0) return; // nothing to do - - // There should never be more than one element matching "div.body" - const divBody = document.querySelectorAll("div.body"); - const body = divBody.length ? divBody[0] : document.querySelector("body"); - window.setTimeout(() => { - terms.forEach((term) => _highlightText(body, term, "highlighted")); - }, 10); - - const searchBox = document.getElementById("searchbox"); - if (searchBox === null) return; - searchBox.appendChild( - document - .createRange() - .createContextualFragment( - '

' + - '' + - _("Hide Search Matches") + - "

" - ) - ); - }, - - /** - * helper function to hide the search marks again - */ - hideSearchWords: () => { - document - .querySelectorAll("#searchbox .highlight-link") - .forEach((el) => el.remove()); - document - .querySelectorAll("span.highlighted") - .forEach((el) => el.classList.remove("highlighted")); - localStorage.removeItem("sphinx_highlight_terms") - }, - - initEscapeListener: () => { - // only install a listener if it is really needed - if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; - - document.addEventListener("keydown", (event) => { - // bail for input elements - if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; - // bail with special keys - if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; - if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { - SphinxHighlight.hideSearchWords(); - event.preventDefault(); - } - }); - }, -}; - -_ready(() => { - /* Do not call highlightSearchWords() when we are on the search page. - * It will highlight words from the *previous* search query. - */ - if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); - SphinxHighlight.initEscapeListener(); -}); diff --git a/docs/1.0.7/autodoc/mmif.serialize.html b/docs/1.0.7/autodoc/mmif.serialize.html deleted file mode 100644 index 7d53797b..00000000 --- a/docs/1.0.7/autodoc/mmif.serialize.html +++ /dev/null @@ -1,1271 +0,0 @@ - - - - - - - - - mmif.serialize module — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
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mmif.serialize module

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mmif.serialize.model module

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The model module contains the classes used to represent an -abstract MMIF object as a live Python object.

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The MmifObject class or one of its derivatives is subclassed by -all other classes defined in this SDK, except for MmifObjectEncoder.

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These objects are generally instantiated from JSON, either as a string -or as an already-loaded Python dictionary. This base class provides the -core functionality for deserializing MMIF JSON data into live objects -and serializing live objects into MMIF JSON data. Specialized behavior -for the different components of MMIF is added in the subclasses.

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-class mmif.serialize.model.DataDict(mmif_obj: bytes | str | dict | None = None)[source]
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Bases: MmifObject, Generic[T, S]

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-empty()[source]
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-get(key: T, default=None) → S | None[source]
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-items()[source]
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-keys()[source]
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-update(other, overwrite)[source]
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-values()[source]
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-class mmif.serialize.model.DataList(mmif_obj: bytes | str | list | None = None)[source]
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Bases: MmifObject, Generic[T]

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The DataList class is an abstraction that represents the -various lists found in a MMIF file, such as documents, subdocuments, -views, and annotations.

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Parameters:
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mmif_obj (Union[str, list]) – the data that the list contains

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-append(value, overwrite)[source]
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-deserialize(mmif_json: str | list) → None[source]
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Passes the input data into the internal deserializer.

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-empty()[source]
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-get(key: str) → T | None[source]
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Standard dictionary-style get() method, albeit with no default -parameter. Relies on the implementation of __getitem__.

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Will return None if the key is not found.

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Parameters:
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key – the key to search for

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Returns:
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the value matching that key

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-class mmif.serialize.model.MmifObject(mmif_obj: bytes | str | dict | None = None)[source]
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Bases: object

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Abstract superclass for MMIF related key-value pair objects.

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Any MMIF object can be initialized as an empty placeholder or -an actual representation with a JSON formatted string or equivalent -dict object argument.

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This superclass has four specially designed instance variables, and these -variable names cannot be used as attribute names for MMIF objects.

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  1. _unnamed_attributes: -Only can be either None or an empty dictionary. If it’s set to None, -it means the class won’t take any Additional Attributes in the JSON -schema sense. If it’s a dict, users can throw any k-v pairs to the -class, EXCEPT for the reserved two key names.

    2. -

  2. _attribute_classes: -This is a dict from a key name to a specific python class to use for -deserialize the value. Note that a key name in this dict does NOT -have to be a named attribute, but is recommended to be one.

    3. -

  3. _required_attributes: -This is a simple list of names of attributes that are required in the object. -When serialize, an object will skip its empty (e.g. zero-length, or None) -attributes unless they are in this list. Otherwise, the serialized JSON -string would have empty representations (e.g. "", []).

    4. -

  4. _exclude_from_diff: -This is a simple list of names of attributes that should be excluded from -the diff calculation in __eq__.

    5. -
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# TODO (krim @ 8/17/20): this dict is however, a duplicate with the type hints in the class definition. -Maybe there is a better way to utilize type hints (e.g. getting them as a programmatically), but for now -developers should be careful to add types to hints as well as to this dict.

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Also note that those special attributes MUST be set in the __init__() -before calling super method, otherwise deserialization will not work.

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And also, a subclass that has one or more named attributes, it must -set those attributes in the __init__() before calling super method. When -serializing a MmifObject, all empty attributes will be ignored, so for -optional named attributes, you must leave the values empty (len == 0), but -NOT None. Any None-valued named attributes will cause issues with current -implementation.

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Parameters:
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mmif_obj – JSON string or dict to initialize an object. -If not given, an empty object will be initialized, sometimes with -an ID value automatically generated, based on its parent object.

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-deserialize(mmif_json: str | dict) → None[source]
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Takes a JSON-formatted string or a simple dict that’s json-loaded from -such a string as an input and populates object’s fields with the values -specified in the input.

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Parameters:
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mmif_json – JSON-formatted string or dict from such a string -that represents a MMIF object

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-disallow_additional_properties() → None[source]
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Call this method in __init__() to prevent the insertion -of unnamed attributes after initialization.

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-static is_empty(obj) → bool[source]
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return True if the obj is None or “emtpy”. The emptiness first defined as -having zero length. But for objects that lack __len__ method, we need -additional check.

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-reserved_names: Set[str] = {'_attribute_classes', '_exclude_from_diff', '_required_attributes', '_unnamed_attributes', 'reserved_names'}[source]
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-serialize(pretty: bool = False) → str[source]
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Generates JSON representation of an object.

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Parameters:
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pretty – If True, returns string representation with indentation.

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Returns:
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JSON string of the object.

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-set_additional_property(key: str, value: Any) → None[source]
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Method to set values in _unnamed_attributes.

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Parameters:
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  • key – the attribute name

    • -

  • value – the desired value

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Returns:
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None

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Raise:
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AttributeError if additional properties are disallowed by disallow_additional_properties()

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-class mmif.serialize.model.MmifObjectEncoder(*, skipkeys=False, ensure_ascii=True, check_circular=True, allow_nan=True, sort_keys=False, indent=None, separators=None, default=None)[source]
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Bases: JSONEncoder

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Encoder class to define behaviors of de-/serialization

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-default(obj: MmifObject)[source]
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Overrides default encoding behavior to prioritize MmifObject.serialize().

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mmif.serialize.mmif module

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The mmif module contains the classes used to represent a full MMIF -file as a live Python object.

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See the specification docs and the JSON Schema file for more information.

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-class mmif.serialize.mmif.Mmif(mmif_obj: bytes | str | dict | None = None, *, validate: bool = True)[source]
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Bases: MmifObject

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MmifObject that represents a full MMIF file.

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Parameters:
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  • mmif_obj – the JSON data

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  • validate – whether to validate the data against the MMIF JSON schema.

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-add_document(document: Document, overwrite=False) → None[source]
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Appends a Document object to the documents list.

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Fails if there is already a document with the same ID in the MMIF object.

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Parameters:
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  • document – the Document object to add

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  • overwrite – if set to True, will overwrite -an existing view with the same ID

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Returns:
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None

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-add_view(view: View, overwrite=False) → None[source]
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Appends a View object to the views list.

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Fails if there is already a view with the same ID in the MMIF object.

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Parameters:
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  • view – the Document object to add

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  • overwrite – if set to True, will overwrite -an existing view with the same ID

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Returns:
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None

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-generate_capital_annotations()[source]
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Automatically convert any “pending” temporary properties from -Document objects to Annotation objects . The generated Annotation -objects are then added to the last View in the views lists.

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See https://github.com/clamsproject/mmif-python/issues/226 for rationale -behind this behavior and discussion.

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-get_alignments(at_type1: str | TypesBase, at_type2: str | TypesBase) → Dict[str, List[Annotation]][source]
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Finds views where alignments between two given annotation types occurred.

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Returns:
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a dict that keyed by view IDs (str) and has lists of alignment Annotation objects as values.

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-get_all_views_contain(at_types: TypesBase | str | List[str | TypesBase]) → List[View][source]
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Returns the list of all views in the MMIF if given types -are present in that view’s ‘contains’ metadata.

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Parameters:
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at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

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Returns:
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the list of views that contain the type

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-get_document_by_id(doc_id: str) → Document[source]
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Finds a Document object with the given ID.

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Parameters:
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doc_id – the ID to search for

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Returns:
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a reference to the corresponding document, if it exists

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Raises:
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KeyError – if there is no corresponding document

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-get_document_location(m_type: DocumentTypes | str, path_only=False) → str | None[source]
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Method to get the location of first document of given type.

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Parameters:
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m_type – the type to search for

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Returns:
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the value of the location field in the corresponding document

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-get_documents_by_app(app_id: str) → List[Document][source]
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Method to get all documents object queries by its originated app name.

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Parameters:
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app_id – the app name to search for

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Returns:
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a list of documents matching the requested app name, or an empty list if the app not found

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-get_documents_by_property(prop_key: str, prop_value: str) → List[Document][source]
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Method to retrieve documents by an arbitrary key-value pair in the document properties objects.

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Parameters:
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  • prop_key – the metadata key to search for

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  • prop_value – the metadata value to match

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Returns:
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a list of documents matching the requested metadata key-value pair

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-get_documents_by_type(doc_type: str | DocumentTypes) → List[Document][source]
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Method to get all documents where the type matches a particular document type, which should be one of the CLAMS document types.

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Parameters:
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doc_type – the type of documents to search for, must be one of Document type defined in the CLAMS vocabulary.

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Returns:
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a list of documents matching the requested type, or an empty list if none found.

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-get_documents_in_view(vid: str | None = None) → List[Document][source]
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Method to get all documents object queries by a view id.

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Parameters:
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vid – the source view ID to search for

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Returns:
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a list of documents matching the requested source view ID, or an empty list if the view not found

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-get_documents_locations(m_type: DocumentTypes | str, path_only=False) → List[str | None][source]
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This method returns the file paths of documents of given type. -Only top-level documents have locations, so we only check them.

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Parameters:
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m_type – the type to search for

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Returns:
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a list of the values of the location fields in the corresponding documents

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-get_view_by_id(req_view_id: str) → View[source]
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Finds a View object with the given ID.

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Parameters:
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req_view_id – the ID to search for

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Returns:
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a reference to the corresponding view, if it exists

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Raises:
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Exception – if there is no corresponding view

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-get_view_contains(at_types: TypesBase | str | List[str | TypesBase]) → View | None[source]
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Returns the last view appended that contains the given -types in its ‘contains’ metadata.

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Parameters:
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at_types – a list of types or just a type to check for. When given more than one types, all types must be found.

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Returns:
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the view, or None if the type is not found

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-get_views_contain(at_types: TypesBase | str | List[str | TypesBase]) → List[View][source]
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An alias to get_all_views_contain method.

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-get_views_for_document(doc_id: str) → List[View][source]
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Returns the list of all views that have annotations anchored on a particular document. -Note that when the document is inside a view (generated during the pipeline’s running), -doc_id must be prefixed with the view_id.

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-id_delimiter: ClassVar[str] = ':'[source]
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-new_view() → View[source]
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Creates an empty view with a new ID and appends it to the views list.

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Returns:
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a reference to the new View object

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-new_view_id() → str[source]
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Fetches an ID for a new view.

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Returns:
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the ID

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-sanitize()[source]
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Sanitizes a Mmif object by running some safeguards. -Concretely, it performs the following before returning the JSON string.

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  1. validating output using built-in MMIF jsonschema

    2. -

  2. remove non-existing annotation types from contains metadata

    3. -
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-serialize(pretty: bool = False, sanitize: bool = False, autogenerate_capital_annotations=True) → str[source]
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Serializes the MMIF object to a JSON string.

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Parameters:
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  • sanitize – If True, performs some sanitization of before returning -the JSON string. See sanitize() for details.

    • -

  • autogenerate_capital_annotations – If True, automatically convert -any “pending” temporary properties from Document objects to -Annotation objects. See generate_capital_annotations() for -details.

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  • pretty – If True, returns string representation with indentation.

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Returns:
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JSON string of the MMIF object.

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-static validate(json_str: bytes | str | dict) → None[source]
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Validates a MMIF JSON object against the MMIF Schema. -Note that this method operates before processing by MmifObject._load_str, -so it expects @ and not _ for the JSON-LD @-keys.

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Raises:
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jsonschema.exceptions.ValidationError – if the input fails validation

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Parameters:
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json_str – a MMIF JSON dict or string

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Returns:
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None

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-view_prefix: ClassVar[str] = 'v_'[source]
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mmif.serialize.view module

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The view module contains the classes used to represent a MMIF view -as a live Python object.

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In MMIF, views are created by apps in a pipeline that are annotating -data that was previously present in the MMIF file.

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-class mmif.serialize.view.Contain(mmif_obj: bytes | str | dict | None = None)[source]
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Bases: DataDict[str, str]

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Contain object that represents the metadata of a single -annotation type in the contains metadata of a MMIF view.

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-class mmif.serialize.view.View(view_obj: bytes | str | dict | None = None)[source]
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Bases: MmifObject

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View object that represents a single view in a MMIF file.

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A view is identified by an ID, and contains certain metadata, -a list of annotations, and potentially a JSON-LD @context -IRI.

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If view_obj is not provided, an empty View will be generated.

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Parameters:
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view_obj – the JSON data that defines the view

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-add_annotation(annotation: Annotation, overwrite=False) → Annotation[source]
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Adds an annotation to the current view.

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Fails if there is already an annotation with the same ID -in the view, unless overwrite is set to True.

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Parameters:
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Raises:
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KeyError – if overwrite is set to False and -an annotation with the same ID exists -in the view

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Returns:
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the same Annotation object passed in as annotation

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-add_document(document: Document, overwrite=False) → Annotation[source]
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Appends a Document object to the annotations list.

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Fails if there is already a document with the same ID in the annotations list.

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Parameters:
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  • document – the Document object to add

    • -

  • overwrite – if set to True, will overwrite -an existing view with the same ID

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Returns:
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None

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-get_annotation_by_id(ann_id)[source]
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-get_annotations(at_type: str | TypesBase | None = None, **properties) → Generator[Annotation, None, None][source]
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Look for certain annotations in this view, specified by parameters

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Parameters:
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  • at_type – @type of the annotations to look for. When this is None, any @type will match.

    • -

  • properties – properties of the annotations to look for. When given more than one property, all properties must match. Note that annotation type metadata are specified in the contains view metadata, not in individual annotation objects.

    • -
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-get_document_by_id(doc_id) → Document[source]
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-get_documents() → List[Document][source]
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-new_annotation(at_type: str | TypesBase, aid: str | None = None, overwrite=False, **properties) → Annotation[source]
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Generates a new mmif.serialize.annotation.Annotation -object and adds it to the current view.

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Fails if there is already an annotation with the same ID -in the view, unless overwrite is set to True.

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Parameters:
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  • at_type – the desired @type of the annotation.

    • -

  • aid – the desired ID of the annotation, when not given, -the mmif SDK tries to automatically generate an ID based on -Annotation type and existing annotations in the view.

    • -

  • overwrite – if set to True, will overwrite an -existing annotation with the same ID.

    • -
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Raises:
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KeyError – if overwrite is set to False and -an annotation with the same ID exists -in the view.

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Returns:
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the generated mmif.serialize.annotation.Annotation

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-new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
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Adds a new element to the contains metadata.

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Parameters:
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  • at_type – the @type of the annotation type being added

    • -

  • contains_metadata – any metadata associated with the annotation type

    • -
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Returns:
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the generated Contain object

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-new_textdocument(text: str, lang: str = 'en', did: str | None = None, overwrite=False, **properties) → Document[source]
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Generates a new mmif.serialize.annotation.Document -object, particularly typed as TextDocument and adds it to the current view.

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Fails if there is already a text document with the same ID -in the view, unless overwrite is set to True.

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Parameters:
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  • text – text content of the new document

    • -

  • lang – ISO 639-1 code of the language used in the new document

    • -

  • did – the desired ID of the document, when not given, -the mmif SDK tries to automatically generate an ID based on -Annotation type and existing documents in the view.

    • -

  • overwrite – if set to True, will overwrite an -existing document with the same ID

    • -
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Raises:
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KeyError – if overwrite is set to False and -an document with the same ID exists -in the view

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Returns:
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the generated mmif.serialize.annotation.Document

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-set_error(err_message: str, err_trace: str) → None[source]
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-class mmif.serialize.view.ViewMetadata(viewmetadata_obj: bytes | str | dict | None = None)[source]
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Bases: MmifObject

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ViewMetadata object that represents the metadata object within a MMIF view.

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Parameters:
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viewmetadata_obj – the JSON data that defines the metadata

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-add_contain(contain: Contain, at_type: str | TypesBase)[source]
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-add_parameter(param_key, param_value)[source]
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-add_parameters(**runtime_params)[source]
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-add_warnings(*warnings: Warning)[source]
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-emtpy_warnings()[source]
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-get_parameter(param_key)[source]
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-new_contain(at_type: str | TypesBase, **contains_metadata) → Contain | None[source]
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Adds a new element to the contains dictionary.

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Parameters:
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    -

  • at_type – the @type of the annotation type being added

    • -

  • contains_metadata – any metadata associated with the annotation type

    • -
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Returns:
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the generated Contain object

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-set_error(message: str, stack_trace: str)[source]
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mmif.serialize.annotation module

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The annotation module contains the classes used to represent a -MMIF annotation as a live Python object.

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In MMIF, annotations are created by apps in a pipeline as a part -of a view. For documentation on how views are represented, see -mmif.serialize.view.

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-class mmif.serialize.annotation.Annotation(anno_obj: bytes | str | dict | None = None)[source]
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Bases: MmifObject

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MmifObject that represents an annotation in a MMIF view.

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-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]]) → None[source]
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Adds a property to the annotation’s properties. -:param name: the name of the property -:param value: the property’s desired value -:return: None

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- -
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-property at_type: TypesBase[source]
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- -
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-static check_prop_value_is_simple_enough(value: str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]])[source]
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- -
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-get(prop_name: str) → AnnotationProperties | str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]][source]
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A special getter for Annotation properties. This is to allow for -directly accessing properties without having to go through the -properties object.

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- -
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-get_property(prop_name: str) → AnnotationProperties | str | int | float | bool | None | List[str | int | float | bool | None] | List[List[str | int | float | bool | None]][source]
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A special getter for Annotation properties. This is to allow for -directly accessing properties without having to go through the -properties object.

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- -
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-property id: str[source]
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- -
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-is_document()[source]
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- -
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-is_type(at_type: str | TypesBase) → bool[source]
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Check if the @type of this object matches.

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- -
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-property parent: str[source]
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- -
- -
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-class mmif.serialize.annotation.AnnotationProperties(mmif_obj: bytes | str | dict | None = None)[source]
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Bases: MmifObject, MutableMapping[str, T]

-

AnnotationProperties object that represents the -properties object within a MMIF annotation.

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Parameters:
-

mmif_obj – the JSON data that defines the properties

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- -
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-class mmif.serialize.annotation.Document(doc_obj: bytes | str | dict | None = None)[source]
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Bases: Annotation

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Document object that represents a single document in a MMIF file.

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A document is identified by an ID, and contains certain attributes -and potentially contains the contents of the document itself, -metadata about how the document was created, and/or a list of -subdocuments grouped together logically.

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If document_obj is not provided, an empty Document will be generated.

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Parameters:
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document_obj – the JSON data that defines the document

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-add_property(name: str, value: str | int | float | bool | None | List[str | int | float | bool | None]) → None[source]
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Adds a property to the document’s properties.

-

Unlike the parent Annotation class, added properties of a -Document object can be lost during serialization unless it belongs -to somewhere in a Mmif object. This is because we want to keep -Document object as “read-only” as possible. Thus, if you want to add -a property to a Document object,

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    -

  • add the document to a Mmif object (either in the documents list or -in a view from the views list), or

    • -

  • directly write to Document.properties instead of using this method -(which is not recommended).

    • -
-

With the former method, the SDK will record the added property as a -Annotation annotation object, separate from the original Document -object. See Mmif.generate_capital_annotations() for more.

-

A few notes to keep in mind:

-
    -

  1. You can’t overwrite an existing property of a Document object.

    2. -

  2. A MMIF can have multiple Annotation objects with the same -property name but different values. When this happens, the SDK will -only keep the latest value (in order of appearances in views list) of -the property, effectively overwriting the previous values.

    3. -
-
- -
-
-get(prop_name)[source]
-

A special getter for Document properties. This is to allow for reading -the three properties in a specific order so that the latest value is -returned, in case there are multiple values for the same key.

-
- -
-
-get_property(prop_name)[source]
-

A special getter for Document properties. This is to allow for reading -the three properties in a specific order so that the latest value is -returned, in case there are multiple values for the same key.

-
- -
-
-property location: str | None[source]
-

location property must be a legitimate URI. That is, should the document be a local file -then the file:// scheme must be used. -Returns None when no location is set.

-
- -
-
-location_address() → str | None[source]
-

Retrieves the full address from the document location URI. -Returns None when no location is set.

-
- -
-
-location_path() → str | None[source]
-

Retrieves a path that’s resolved to a pathname in the local file system. -To obtain the original value of the “path” part in the location string -(before resolving), use properties.location_path_literal method. -Returns None when no location is set.

-
- -
-
-location_scheme() → str | None[source]
-

Retrieves URI scheme of the document location. -Returns None when no location is set.

-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.DocumentProperties(mmif_obj: bytes | str | dict | None = None)[source]
-

Bases: AnnotationProperties

-

DocumentProperties object that represents the -properties object within a MMIF document.

-
-
Parameters:
-

mmif_obj – the JSON data that defines the properties

-
-
-
-
-property location: str | None[source]
-

location property must be a legitimate URI. That is, should the document be a local file -then the file:// scheme must be used. -Returns None when no location is set.

-
- -
-
-location_address() → str | None[source]
-

Retrieves the full address from the document location URI. -Returns None when no location is set.

-
- -
-
-location_path() → str | None[source]
-
- -
-
-location_path_literal() → str | None[source]
-

Retrieves only path name of the document location (hostname is ignored). -Returns None when no location is set.

-
- -
-
-location_path_resolved(nonexist_ok=True) → str | None[source]
-

Retrieves only path name of the document location (hostname is ignored), -and then try to resolve the path name in the local file system. -This method should be used when the document scheme is file or empty. -For other schemes, users should install mmif-locdoc-<scheme> plugin.

-

Returns None when no location is set. -Raise ValueError when no code found to resolve the given location scheme.

-
- -
-
-location_scheme() → str | None[source]
-

Retrieves URI scheme of the document location. -Returns None when no location is set.

-
- -
-
-property text_language: str[source]
-
- -
-
-property text_value: str[source]
-
- -
- -
-
-class mmif.serialize.annotation.Text(text_obj: bytes | str | dict | None = None)[source]
-

Bases: MmifObject

-
-
-property lang: str[source]
-
- -
-
-property value: str[source]
-
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- - - \ No newline at end of file diff --git a/docs/1.0.7/autodoc/mmif.vocabulary.html b/docs/1.0.7/autodoc/mmif.vocabulary.html deleted file mode 100644 index 522c2495..00000000 --- a/docs/1.0.7/autodoc/mmif.vocabulary.html +++ /dev/null @@ -1,325 +0,0 @@ - - - - - - - - - mmif.vocabulary module — mmif-python documentation - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

mmif.vocabulary module

-
-

mmif.vocabulary.annotation_types module

-
-
-class mmif.vocabulary.annotation_types.AnnotationTypes(type_uri, fuzzymode=True)[source]
-

Bases: AnnotationTypesBase

-

This class contains the CLAMS annotation types -defined in the spec version 1.1.0 as class variables.

-
-
-Alignment = http://mmif.clams.ai/vocabulary/Alignment/v1[source]
-
- -
-
-Annotation = http://mmif.clams.ai/vocabulary/Annotation/v6[source]
-
- -
-
-BoundingBox = http://mmif.clams.ai/vocabulary/BoundingBox/v5[source]
-
- -
-
-Chapter = http://mmif.clams.ai/vocabulary/Chapter/v6[source]
-
- -
-
-Interval = http://mmif.clams.ai/vocabulary/Interval/v5[source]
-
- -
-
-NamedEntity = http://mmif.clams.ai/vocabulary/NamedEntity/v1[source]
-
- -
-
-NounChunk = http://mmif.clams.ai/vocabulary/NounChunk/v1[source]
-
- -
-
-Paragraph = http://mmif.clams.ai/vocabulary/Paragraph/v1[source]
-
- -
-
-Polygon = http://mmif.clams.ai/vocabulary/Polygon/v5[source]
-
- -
-
-Region = http://mmif.clams.ai/vocabulary/Region/v5[source]
-
- -
-
-Relation = http://mmif.clams.ai/vocabulary/Relation/v5[source]
-
- -
-
-Sentence = http://mmif.clams.ai/vocabulary/Sentence/v1[source]
-
- -
-
-Span = http://mmif.clams.ai/vocabulary/Span/v5[source]
-
- -
-
-TimeFrame = http://mmif.clams.ai/vocabulary/TimeFrame/v6[source]
-
- -
-
-TimePoint = http://mmif.clams.ai/vocabulary/TimePoint/v5[source]
-
- -
-
-Token = http://mmif.clams.ai/vocabulary/Token/v1[source]
-
- -
-
-VerbChunk = http://mmif.clams.ai/vocabulary/VerbChunk/v1[source]
-
- -
-
-VideoObject = http://mmif.clams.ai/vocabulary/VideoObject/v5[source]
-
- -
-
-typevers = {'Alignment': 'v1', 'Annotation': 'v6', 'BoundingBox': 'v5', 'Chapter': 'v6', 'Interval': 'v5', 'NamedEntity': 'v1', 'NounChunk': 'v1', 'Paragraph': 'v1', 'Polygon': 'v5', 'Region': 'v5', 'Relation': 'v5', 'Sentence': 'v1', 'Span': 'v5', 'TimeFrame': 'v6', 'TimePoint': 'v5', 'Token': 'v1', 'VerbChunk': 'v1', 'VideoObject': 'v5'}[source]
-
- -
- -
-
-

mmif.vocabulary.document_types module

-
-
-class mmif.vocabulary.document_types.DocumentTypes(type_uri, fuzzymode=True)[source]
-

Bases: DocumentTypesBase

-

This class contains the CLAMS document types -defined in the spec version 1.1.0 as class variables.

-
-
-AudioDocument = http://mmif.clams.ai/vocabulary/AudioDocument/v1[source]
-
- -
-
-Document = http://mmif.clams.ai/vocabulary/Document/v1[source]
-
- -
-
-ImageDocument = http://mmif.clams.ai/vocabulary/ImageDocument/v1[source]
-
- -
-
-TextDocument = http://mmif.clams.ai/vocabulary/TextDocument/v1[source]
-
- -
-
-VideoDocument = http://mmif.clams.ai/vocabulary/VideoDocument/v1[source]
-
- -
-
-typevers = {'AudioDocument': 'v1', 'Document': 'v1', 'ImageDocument': 'v1', 'TextDocument': 'v1', 'VideoDocument': 'v1'}[source]
-
- -
- -
-
- - -
-
- -
-
-
-
- -
- - Other Versions - v: 1.0.7 - - -
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0.3.2
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0.3.3
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- - - \ No newline at end of file diff --git a/docs/1.0.7/consumer-tutorial.html b/docs/1.0.7/consumer-tutorial.html deleted file mode 100644 index 0497432a..00000000 --- a/docs/1.0.7/consumer-tutorial.html +++ /dev/null @@ -1,171 +0,0 @@ - - - - - - - - - MMIF consumer — mmif-python documentation - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • MMIF consumer
    • -
  • -
    • -
-
-
-
-
- -
-

MMIF consumer

-

A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the appliance documentation to learn more about the appliance.

-

MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance.

-
    -

  1. The code must be hosted on a public git repository (e.g. Github, Gitlab, …)

    2. -

  2. Must listen to 5000 port.

    3. -

  3. Must expose /display route .

    4. -

  4. /display router should response to GET requests.

    5. -

  5. In the GET request, a public URL of the input MMIF file is passed via file URL parameter.

    6. -

  6. On the codebase root, there must be a Dockerfile that can build a docker image that runs the web app.

    7. -
-

We provide an example consumer at https://github.com/clamsproject/mmif-visualizer.

-
- - -
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- -
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-
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- -
- - Other Versions - v: 1.0.7 - - -
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    • -
  • Index
    • -
  • -
    • -
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Index

- -
- A - | B - | C - | D - | E - | G - | I - | K - | L - | M - | N - | P - | R - | S - | T - | U - | V - -
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A

- - - -
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B

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- - -
- -
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  • Welcome to mmif-python’s documentation!
    • -
  • -
    • -
-
-
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- -
-

Welcome to mmif-python’s documentation!

-
-

MultiMedia Interchange Format

-

MMIF is a JSON(-LD)-based data format designed for transferring annotation data between computational analysis applications in CLAMS project.

-
-

Contents

- -
-
-

API documentation:

- -
-
-
-
-

Indices and tables

- -
- - -
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- - -
- -
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  • Getting Started
    • -
  • -
    • -
-
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-
- -
-

Getting Started

-
-

Overview

-

MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for reproducibility, transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF website. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects.

-
-
-

Prerequisites

-
    -

  • Python: the latest mmif-python requires Python 3.8 or newer. We have no plan to support Python 2.7.

    • -
-
-
-

Installation

-

Package mmif-python is distributed via the official PyPI. Users are supposed to pip-install to get latest release.

-
pip install mmif-python
-
-
-

This will install a package mmif to local python.

-

The MMIF format and specification is evolving over time, and mmif-python package will be updated along with the changes in MMIF format.

-
-

Note

-

MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and mmif-python versions, please take time to read our decision on the subject here. If you need to know which python SDK supports which specification version, see Target MMIF Versions page.

-
-
-
-

MMIF Serialization

-

mmif.serialize.mmif.Mmif represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of mmif.serialize.model.MmifObject, including the mmif.serialize.mmif.Mmif. To start with an existing MMIF str, simple initiate a new Mmif object with the file.

-
import mmif
-from mmif import Mmif
-
-mmif_str = """{
-"metadata": {
-  "mmif": "http://mmif.clams.ai/1.0.0"
-},
-"documents": [
-  {
-    "@type": "http://mmif.clams.ai/vocabulary/VideoDocument/v1",
-    "properties": {
-      "id": "m1",
-      "mime": "video/mp4",
-      "location": "file:///var/archive/video-0012.mp4"
-    }
-  },
-  {
-    "@type": "http://mmif.clams.ai/vocabulary/TextDocument/v1",
-    "properties": {
-      "id": "m2",
-      "mime": "text/plain",
-      "location": "file:///var/archive/video-0012-transcript.txt"
-    }
-  }
-],
-"views": []}"""
-mmif_obj = Mmif(mmif_str)
-
-
-

Few notes;

-
    -

  1. MMIF does not carry the primary source files in it.

    2. -

  2. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version mmif-python implementation of the MMIF might not be able to load an unsupported version of MMIF string.

    3. -
-

When serializing back to str, call mmif.serialize.model.MmifObject.serialize() on the object.

-

To get subcomponents, you can use various getters implemented in subclasses. For example;

-
from mmif.vocabulary.document_types import DocumentTypes
-
-for video in mmif_obj.Mmif.get_documents_by_type(DocumentTypes.VideoDocument):
-  with open(video.location_path(), 'b') as in_video:
-    # do something with the video file
-
-
-

For a full list of available helper methods, please refer to the API documentation.

-
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- -
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- - Other Versions - v: 1.0.7 - - -
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- - - \ No newline at end of file diff --git a/docs/1.0.7/modules.html b/docs/1.0.7/modules.html deleted file mode 100644 index 561bb2ac..00000000 --- a/docs/1.0.7/modules.html +++ /dev/null @@ -1,349 +0,0 @@ - - - - - - - - - mmif package — mmif-python documentation - - - - - - - - - - - - - - - - - -
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  • mmif package
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mmif package

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- - - \ No newline at end of file diff --git a/docs/1.0.7/objects.inv b/docs/1.0.7/objects.inv deleted file mode 100644 index 79aea03b..00000000 Binary files a/docs/1.0.7/objects.inv and /dev/null differ diff --git a/docs/1.0.7/plugins.html b/docs/1.0.7/plugins.html deleted file mode 100644 index 4ade60f9..00000000 --- a/docs/1.0.7/plugins.html +++ /dev/null @@ -1,227 +0,0 @@ - - - - - - - - - Developing plugins for MMIF Python SDK — mmif-python documentation - - - - - - - - - - - - - - - - - -
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  • Developing plugins for MMIF Python SDK
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Developing plugins for MMIF Python SDK

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Overview

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As MMIF JSON files can carry information about media document files without actually carrying file contents, file accessing modules in mmif Python package (distributed as mmif-python on PyPI) are designed to be lightweight and flexible so that it can work with additional “plugin” Python packages that can handle concrete file access.

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This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF website. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects.

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Developer can write simple plugins that can provide additional functionalities to mmif-python. For example, mmif-python does not provide any file access functionality beyond a local file system (with file scheme), but it can be extended with a plugin that can handle file access over different protocols (e.g. http, s3, ftp, etc).

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This document contains information about how to write plugins for mmif-python.

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Document Location Scheme Plugins

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mmif.serialize.annotation.Document class has various methods to access parts of location property of the document. The location is in URI/IRI format (SCHEME://HOSTNAME/PATH, in a nutshell) and it has to be resolved to a local file for CLAMS Apps to process the local file to analyze and extract information about the media and its contents. The core mmif-python distribution only provides a default implementation that can handle file scheme URIs.

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To add a document location handler plugin, you need to implement a Python “package” (do not confuse with PYPI distribution), that meets these requirements;

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  1. the package must be named mmif_docloc_<SCHEME>. For example, to implement a handler for s3 scheme, the package name must be mmif_docloc_s3. The prefix is important as it’s used in the plugin discovery process from the core mmif-python modules.

    2. -

  2. the top module of the package must have a function named resolve. The function must take a single argument, which is a str of the document location URI. The function must return a str of the local file path. For example, if the document location is s3://mybucket/myfile.mp4, a Python user should be able to to something like this;

    3. -
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import mmif_docloc_s3
-resolved = mmif_docloc_s3.resolve('s3://mybucket/myfile.mp4')
-# then resolved must be a local file path that can be used to open the file
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Here’s a minimal example codebase that you refer to when you develop a docloc plugin.

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(However, before you start writing your own plugin for a specific URI scheme, checking if there’s already a PyPI distribution for the scheme might be a good idea.)

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$ tree .
-.
-├── mmif_docloc_dummy
-│   └── __init__.py
-├── pyproject.toml
-└── setup.cfg
-
- $ cat pyproject.toml
-[build-system]
-requires = ["setuptools"]
-build-backend = "setuptools.build_meta"
-
-$ cat setup.cfg
-[metadata]
-name = mmif_docloc_dummy  # this name is IMPORTANT
-version = 0.0.1
-description = a plugin to mmif-pyhon to handle `dummy` location scheme
-
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And the plugin code.

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# mmif_docloc_dummy/__init__.py
-doc_types = {'video': 'mp4'}
-
-def resolve(docloc):
-    scheme = 'dummy'
-    if docloc.startswith(f'{scheme}://'):
-        doc_id, doc_type = docloc.split('.')
-        return f'/path/to/{doc_id}.{doc_types[doc_type]}'
-    else:
-        raise ValueError(f'cannot handle document location scheme: {docloc}')
-
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Python Module Index

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- - - - - - - - \ No newline at end of file diff --git a/docs/1.0.7/searchindex.js b/docs/1.0.7/searchindex.js deleted file mode 100644 index 028638e0..00000000 --- a/docs/1.0.7/searchindex.js +++ /dev/null @@ -1 +0,0 @@ -Search.setIndex({"alltitles": {"API documentation:": [[3, null]], "Contents": [[3, null]], "Developing plugins for MMIF Python SDK": [[6, null]], "Document Location Scheme Plugins": [[6, "document-location-scheme-plugins"]], "Getting Started": [[4, null]], "Indices and tables": [[3, "indices-and-tables"]], "Installation": [[4, "installation"]], "MMIF Serialization": [[4, "mmif-serialization"]], "MMIF consumer": [[2, null]], "MultiMedia Interchange Format": [[3, "multimedia-interchange-format"]], "Overview": [[4, "overview"], [6, "overview"]], "Prerequisites": [[4, "prerequisites"]], "Target MMIF Versions": [[7, null]], "Target Specification Versions": [[7, "id1"]], "Welcome to mmif-python\u2019s documentation!": [[3, null]], "mmif package": [[5, null]], 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[0, 4, 6], "when": [0, 4, 6], "where": 0, "whether": 0, "which": [0, 4, 6], "within": 0, "without": [0, 6], "won": 0, "work": [0, 6], "workflow": 4, "would": 0, "write": [0, 6], "you": [0, 4, 6], "your": 6, "zero": 0}, "titles": ["mmif.serialize module", "mmif.vocabulary module", "MMIF consumer", "Welcome to mmif-python\u2019s documentation!", "Getting Started", "mmif package", "Developing plugins for MMIF Python SDK", "Target MMIF Versions"], "titleterms": {"": 3, "annot": 0, "annotation_typ": 1, "api": 3, "consum": 2, "content": 3, "develop": 6, "document": [3, 6], "document_typ": 1, "format": 3, "get": 4, "indic": 3, "instal": 4, "interchang": 3, "locat": 6, "mmif": [0, 1, 2, 3, 4, 5, 6, 7], "model": 0, "modul": [0, 1], "multimedia": 3, "overview": [4, 6], "packag": 5, "plugin": 6, "prerequisit": 4, "python": [3, 6], "scheme": 6, "sdk": 6, "serial": [0, 4], "specif": 7, "start": 4, "tabl": 3, "target": 7, "version": 7, "view": 0, "vocabulari": 1, "welcom": 3}}) \ No newline at end of file diff --git a/docs/1.0.7/target-versions.html b/docs/1.0.7/target-versions.html deleted file mode 100644 index 7aca8557..00000000 --- a/docs/1.0.7/target-versions.html +++ /dev/null @@ -1,263 +0,0 @@ - - - - - - - - - Target MMIF Versions — mmif-python documentation - - - - - - - - - - - - - - - - - -
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Target MMIF Versions

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This article provides targeting MMIF specification versions of different versions of mmif-python SDK.

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Target Specification Versions

mmif-python version

Target MMIF Specification

1.0.7

1.1.0

1.0.6

1.0.0

1.0.5

1.0.0

1.0.4

1.0.0

1.0.3

1.0.0

1.0.2

1.0.0

1.0.1

1.0.0

1.0.0

0.5.0

0.5.2

0.5.0

0.5.1

0.5.0

0.5.0

0.5.0

0.4.8

0.4.2

0.4.7

0.4.1

0.4.6

0.4.0

0.4.5

0.4.0

0.4.4

0.4.0

0.4.3

0.4.0

0.4.2

0.4.0

0.4.1

0.4.0

0.4.0

0.4.0

0.3.5

0.3.1

0.3.4

0.3.1

0.3.3

0.3.1

0.3.2

0.3.1

0.3.1

0.3.0

0.3.0

0.3.0

0.2.2

0.2.1

0.2.1

0.2.1

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0.3.3
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0.3.4
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0.4.0
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0.4.1
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0.4.2
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0.4.4
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0.4.5
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0.4.6
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0.4.7
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0.4.8
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0.5.0
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0.5.1
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0.5.2
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1.0.0
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1.0.1
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1.0.10
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1.0.11
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1.0.12
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1.0.13
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1.0.14
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1.0.15
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1.0.16
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1.0.17
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1.0.18
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1.0.19
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1.0.2
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1.0.3
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1.0.4
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1.0.7
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1.0.8
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1.0.9
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1.1.0
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The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the `appliance documentation `_ to learn more about the appliance. - -MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance. - -#. The code must be hosted on a public git repository (e.g. Github, Gitlab, ...) -#. Must listen to ``5000`` port. -#. Must expose ``/display`` route . -#. ``/display`` router should response to ``GET`` requests. -#. In the ``GET`` request, a public URL of the input MMIF file is passed via ``file`` URL parameter. -#. On the codebase root, there must be a ``Dockerfile`` that can build a `docker `_ image that runs the web app. - -We provide an example consumer at https://github.com/clamsproject/mmif-visualizer. diff --git a/docs/1.0.8/_sources/index.rst.txt b/docs/1.0.8/_sources/index.rst.txt deleted file mode 100644 index beb56aae..00000000 --- a/docs/1.0.8/_sources/index.rst.txt +++ /dev/null @@ -1,26 +0,0 @@ -Welcome to mmif-python's documentation! -======================================= - -.. mdinclude:: ../README.md - -.. toctree:: - :maxdepth: 2 - :caption: Contents - - introduction - plugins - target-versions - -.. toctree:: - :maxdepth: 2 - :caption: API documentation: - - modules - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/docs/1.0.8/_sources/introduction.rst.txt b/docs/1.0.8/_sources/introduction.rst.txt deleted file mode 100644 index cfd9eaf7..00000000 --- a/docs/1.0.8/_sources/introduction.rst.txt +++ /dev/null @@ -1,89 +0,0 @@ -.. _introduction: - -Getting Started -=============== - - -Overview ---------- - -MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for reproducibility, transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF website `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects. - -Prerequisites -------------- - -* `Python `_: the latest ``mmif-python`` requires Python 3.8 or newer. We have no plan to support `Python 2.7 `_. - -Installation ---------------- - -Package ``mmif-python`` is distributed via the official PyPI. Users are supposed to pip-install to get latest release. - -.. code-block:: bash - - pip install mmif-python - -This will install a package `mmif` to local python. - -The MMIF format and specification is evolving over time, and ``mmif-python`` package will be updated along with the changes in MMIF format. - -.. note:: MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and ``mmif-python`` versions, please take time to read our decision on the subject `here `_. If you need to know which python SDK supports which specification version, see :ref:`target-versions` page. - -MMIF Serialization ---------------------------- - -:class:`mmif.serialize.mmif.Mmif` represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of :class:`mmif.serialize.model.MmifObject`, including the :class:`mmif.serialize.mmif.Mmif`. To start with an existing MMIF :class:`str`, simple initiate a new ``Mmif`` object with the file. - -.. code-block:: python - - import mmif - from mmif import Mmif - - mmif_str = """{ - "metadata": { - "mmif": "http://mmif.clams.ai/1.0.0" - }, - "documents": [ - { - "@type": "http://mmif.clams.ai/vocabulary/VideoDocument/v1", - "properties": { - "id": "m1", - "mime": "video/mp4", - "location": "file:///var/archive/video-0012.mp4" - } - }, - { - "@type": "http://mmif.clams.ai/vocabulary/TextDocument/v1", - "properties": { - "id": "m2", - "mime": "text/plain", - "location": "file:///var/archive/video-0012-transcript.txt" - } - } - ], - "views": []}""" - mmif_obj = Mmif(mmif_str) - - -Few notes; - -#. MMIF does not carry the primary source files in it. -#. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version ``mmif-python`` implementation of the MMIF might not be able to load an unsupported version of MMIF string. - -When serializing back to :class:`str`, call :meth:`mmif.serialize.model.MmifObject.serialize` on the object. - -To get subcomponents, you can use various getters implemented in subclasses. For example; - -.. code-block:: python - - from mmif.vocabulary.document_types import DocumentTypes - - for video in mmif_obj.Mmif.get_documents_by_type(DocumentTypes.VideoDocument): - with open(video.location_path(), 'b') as in_video: - # do something with the video file - - -For a full list of available helper methods, please refer to :ref:`the API documentation `. - diff --git a/docs/1.0.8/_sources/modules.rst.txt b/docs/1.0.8/_sources/modules.rst.txt deleted file mode 100644 index 956fe555..00000000 --- a/docs/1.0.8/_sources/modules.rst.txt +++ /dev/null @@ -1,12 +0,0 @@ -.. _apidoc: - -mmif package -============ - -.. toctree:: - :maxdepth: 4 - - autodoc/mmif.serialize - autodoc/mmif.vocabulary - autodoc/mmif.utils - diff --git a/docs/1.0.8/_sources/plugins.rst.txt b/docs/1.0.8/_sources/plugins.rst.txt deleted file mode 100644 index 9e1505e9..00000000 --- a/docs/1.0.8/_sources/plugins.rst.txt +++ /dev/null @@ -1,75 +0,0 @@ -.. _plugins: - -Developing plugins for MMIF Python SDK -====================================== - - -Overview --------- - -As MMIF JSON files can carry information about media document files without actually carrying file contents, file accessing modules in ``mmif`` Python package (distributed as ``mmif-python`` on PyPI) are designed to be lightweight and flexible so that it can work with additional "plugin" Python packages that can handle concrete file access. - - -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF website `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects. - -Developer can write simple plugins that can provide additional functionalities to ``mmif-python``. For example, ``mmif-python`` does not provide any file access functionality beyond a local file system (with ``file`` scheme), but it can be extended with a plugin that can handle file access over different protocols (e.g. ``http``, ``s3``, ``ftp``, etc). - -This document contains information about how to write plugins for ``mmif-python``. - -Document Location Scheme Plugins -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -:class:`mmif.serialize.annotation.Document` class has various methods to access parts of ``location`` property of the document. The location is in `URI/IRI format `_ (``SCHEME://HOSTNAME/PATH``, in a nutshell) and it has to be resolved to a local file for CLAMS Apps to process the local file to analyze and extract information about the media and its contents. The core ``mmif-python`` distribution only provides a default implementation that can handle ``file`` scheme URIs. - -To add a document location handler plugin, you need to implement a Python `"package" `_ (do not confuse with PYPI distribution), that meets these requirements; - -#. the package must be named ``mmif_docloc_``. For example, to implement a handler for ``s3`` scheme, the package name must be ``mmif_docloc_s3``. The prefix is important as it's used in the plugin discovery process from the core ``mmif-python`` modules. -#. the top module of the package must have a function named ``resolve``. The function must take a single argument, which is a :class:`str` of the document location URI. The function must return a :class:`str` of the local file path. For example, if the document location is ``s3://mybucket/myfile.mp4``, a Python user should be able to to something like this; - -.. code-block:: python - - import mmif_docloc_s3 - resolved = mmif_docloc_s3.resolve('s3://mybucket/myfile.mp4') - # then resolved must be a local file path that can be used to open the file - - -Here's a minimal example codebase that you refer to when you develop a ``docloc`` plugin. - -(However, before you start writing your own plugin for a specific URI scheme, checking `if there's already a PyPI distribution `_ for the scheme might be a good idea.) - -.. code-block:: sh - - $ tree . - . - ├── mmif_docloc_dummy - │ └── __init__.py - ├── pyproject.toml - └── setup.cfg - - $ cat pyproject.toml - [build-system] - requires = ["setuptools"] - build-backend = "setuptools.build_meta" - - $ cat setup.cfg - [metadata] - name = mmif_docloc_dummy # this name is IMPORTANT - version = 0.0.1 - description = a plugin to mmif-pyhon to handle `dummy` location scheme - - -And the plugin code. - -.. code-block:: python - - # mmif_docloc_dummy/__init__.py - doc_types = {'video': 'mp4'} - - def resolve(docloc): - scheme = 'dummy' - if docloc.startswith(f'{scheme}://'): - doc_id, doc_type = docloc.split('.') - return f'/path/to/{doc_id}.{doc_types[doc_type]}' - else: - raise ValueError(f'cannot handle document location scheme: {docloc}') diff --git a/docs/1.0.8/_sources/target-versions.rst.txt b/docs/1.0.8/_sources/target-versions.rst.txt deleted file mode 100644 index 34216d3e..00000000 --- a/docs/1.0.8/_sources/target-versions.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _target-versions: - -Target MMIF Versions -==================== - -This article provides targeting MMIF specification versions of different versions of ``mmif-python`` SDK. - -.. csv-table:: Target Specification Versions - :file: target-versions.csv - :header-rows: 1 diff --git a/docs/1.0.8/_static/_sphinx_javascript_frameworks_compat.js b/docs/1.0.8/_static/_sphinx_javascript_frameworks_compat.js deleted file mode 100644 index 81415803..00000000 --- a/docs/1.0.8/_static/_sphinx_javascript_frameworks_compat.js +++ /dev/null @@ -1,123 +0,0 @@ -/* Compatability shim for jQuery and underscores.js. - * - * Copyright Sphinx contributors - * Released under the two clause BSD licence - */ - -/** - * small helper function to urldecode strings - * - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL - */ -jQuery.urldecode = function(x) { - if (!x) { - return x - } - return decodeURIComponent(x.replace(/\+/g, ' ')); -}; - -/** - * small helper function to urlencode strings - */ -jQuery.urlencode = encodeURIComponent; - -/** - * This function returns the parsed url parameters of the - * current request. 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span; - var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.className = className; - } - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - node.parentNode.insertBefore(span, node.parentNode.insertBefore( - document.createTextNode(val.substr(pos + text.length)), - node.nextSibling)); - node.nodeValue = val.substr(0, pos); - if (isInSVG) { - var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect"); - var bbox = node.parentElement.getBBox(); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute('class', className); - addItems.push({ - "parent": node.parentNode, - "target": rect}); - } - } - } - else if (!jQuery(node).is("button, select, textarea")) { - 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- -/** - * Simple result scoring code. - */ -if (typeof Scorer === "undefined") { - var Scorer = { - // Implement the following function to further tweak the score for each result - // The function takes a result array [docname, title, anchor, descr, score, filename] - // and returns the new score. - /* - score: result => { - const [docname, title, anchor, descr, score, filename, kind] = result - return score - }, - */ - - // query matches the full name of an object - objNameMatch: 11, - // or matches in the last dotted part of the object name - objPartialMatch: 6, - // Additive scores depending on the priority of the object - objPrio: { - 0: 15, // used to be importantResults - 1: 5, // used to be objectResults - 2: -5, // used to be unimportantResults - }, - // Used when the priority is not in the mapping. - objPrioDefault: 0, - - // query found in title - title: 15, - partialTitle: 7, - // query found in terms - term: 5, - partialTerm: 2, - }; -} - -// Global search result kind enum, used by themes to style search results. -class SearchResultKind { - static get index() { return "index"; } - static get object() { return "object"; } - static get text() { return "text"; } - static get title() { return "title"; } -} - -const _removeChildren = (element) => { - while (element && element.lastChild) element.removeChild(element.lastChild); -}; - -/** - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping - */ -const _escapeRegExp = (string) => - string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string - -const _displayItem = (item, searchTerms, highlightTerms) => { - const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; - const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; - const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; - const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; - const contentRoot = document.documentElement.dataset.content_root; - - const [docName, title, anchor, descr, score, _filename, kind] = item; - - let listItem = document.createElement("li"); - // Add a class representing the item's type: - // can be used by a theme's CSS selector for styling - // See SearchResultKind for the class names. - listItem.classList.add(`kind-${kind}`); - let requestUrl; - let linkUrl; - if (docBuilder === "dirhtml") { - // dirhtml builder - let dirname = docName + "/"; - if (dirname.match(/\/index\/$/)) - dirname = dirname.substring(0, dirname.length - 6); - else if (dirname === "index/") dirname = ""; - requestUrl = contentRoot + dirname; - linkUrl = requestUrl; - } else { - // normal html builders - requestUrl = contentRoot + docName + docFileSuffix; - linkUrl = docName + docLinkSuffix; - } - let linkEl = listItem.appendChild(document.createElement("a")); - linkEl.href = linkUrl + anchor; - linkEl.dataset.score = score; - linkEl.innerHTML = title; - if (descr) { - listItem.appendChild(document.createElement("span")).innerHTML = - " (" + descr + ")"; - // highlight search terms in the description - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - } - else if (showSearchSummary) - fetch(requestUrl) - .then((responseData) => responseData.text()) - .then((data) => { - if (data) - listItem.appendChild( - Search.makeSearchSummary(data, searchTerms, anchor) - ); - // highlight search terms in the summary - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - }); - Search.output.appendChild(listItem); -}; -const _finishSearch = (resultCount) => { - Search.stopPulse(); - Search.title.innerText = _("Search Results"); - if (!resultCount) - Search.status.innerText = Documentation.gettext( - "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." - ); - else - Search.status.innerText = Documentation.ngettext( - "Search finished, found one page matching the search query.", - "Search finished, found ${resultCount} pages matching the search query.", - resultCount, - ).replace('${resultCount}', resultCount); -}; -const _displayNextItem = ( - results, - resultCount, - searchTerms, - highlightTerms, -) => { - // results left, load the summary and display it - // this is intended to be dynamic (don't sub resultsCount) - if (results.length) { - _displayItem(results.pop(), searchTerms, highlightTerms); - setTimeout( - () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), - 5 - ); - } - // search finished, update title and status message - else _finishSearch(resultCount); -}; -// Helper function used by query() to order search results. -// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. -// Order the results by score (in opposite order of appearance, since the -// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. -const _orderResultsByScoreThenName = (a, b) => { - const leftScore = a[4]; - const rightScore = b[4]; - if (leftScore === rightScore) { - // same score: sort alphabetically - const leftTitle = a[1].toLowerCase(); - const rightTitle = b[1].toLowerCase(); - if (leftTitle === rightTitle) return 0; - return leftTitle > rightTitle ? -1 : 1; // inverted is intentional - } - return leftScore > rightScore ? 1 : -1; -}; - -/** - * Default splitQuery function. Can be overridden in ``sphinx.search`` with a - * custom function per language. - * - * The regular expression works by splitting the string on consecutive characters - * that are not Unicode letters, numbers, underscores, or emoji characters. - * This is the same as ``\W+`` in Python, preserving the surrogate pair area. - */ -if (typeof splitQuery === "undefined") { - var splitQuery = (query) => query - .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) - .filter(term => term) // remove remaining empty strings -} - -/** - * Search Module - */ -const Search = { - _index: null, - _queued_query: null, - _pulse_status: -1, - - htmlToText: (htmlString, anchor) => { - const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - for (const removalQuery of [".headerlink", "script", "style"]) { - htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); - } - if (anchor) { - const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); - if (anchorContent) return anchorContent.textContent; - - console.warn( - `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` - ); - } - - // if anchor not specified or not found, fall back to main content - const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent) return docContent.textContent; - - console.warn( - "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." - ); - return ""; - }, - - init: () => { - const query = new URLSearchParams(window.location.search).get("q"); - document - .querySelectorAll('input[name="q"]') - .forEach((el) => (el.value = query)); - if (query) Search.performSearch(query); - }, - - loadIndex: (url) => - (document.body.appendChild(document.createElement("script")).src = url), - - setIndex: (index) => { - Search._index = index; - if (Search._queued_query !== null) { - const query = Search._queued_query; - Search._queued_query = null; - Search.query(query); - } - }, - - hasIndex: () => Search._index !== null, - - deferQuery: (query) => (Search._queued_query = query), - - stopPulse: () => (Search._pulse_status = -1), - - startPulse: () => { - if (Search._pulse_status >= 0) return; - - const pulse = () => { - Search._pulse_status = (Search._pulse_status + 1) % 4; - Search.dots.innerText = ".".repeat(Search._pulse_status); - if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); - }; - pulse(); - }, - - /** - * perform a search for something (or wait until index is loaded) - */ - performSearch: (query) => { - // create the required interface elements - const searchText = document.createElement("h2"); - searchText.textContent = _("Searching"); - const searchSummary = document.createElement("p"); - searchSummary.classList.add("search-summary"); - searchSummary.innerText = ""; - const searchList = document.createElement("ul"); - searchList.setAttribute("role", "list"); - searchList.classList.add("search"); - - const out = document.getElementById("search-results"); - Search.title = out.appendChild(searchText); - Search.dots = Search.title.appendChild(document.createElement("span")); - Search.status = out.appendChild(searchSummary); - Search.output = out.appendChild(searchList); - - const searchProgress = document.getElementById("search-progress"); - // Some themes don't use the search progress node - if (searchProgress) { - searchProgress.innerText = _("Preparing search..."); - } - Search.startPulse(); - - // index already loaded, the browser was quick! - if (Search.hasIndex()) Search.query(query); - else Search.deferQuery(query); - }, - - _parseQuery: (query) => { - // stem the search terms and add them to the correct list - const stemmer = new Stemmer(); - const searchTerms = new Set(); - const excludedTerms = new Set(); - const highlightTerms = new Set(); - const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); - splitQuery(query.trim()).forEach((queryTerm) => { - const queryTermLower = queryTerm.toLowerCase(); - - // maybe skip this "word" - // stopwords array is from language_data.js - if ( - stopwords.indexOf(queryTermLower) !== -1 || - queryTerm.match(/^\d+$/) - ) - return; - - // stem the word - let word = stemmer.stemWord(queryTermLower); - // select the correct list - if (word[0] === "-") excludedTerms.add(word.substr(1)); - else { - searchTerms.add(word); - highlightTerms.add(queryTermLower); - } - }); - - if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js - localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) - } - - // console.debug("SEARCH: searching for:"); - // console.info("required: ", [...searchTerms]); - // console.info("excluded: ", [...excludedTerms]); - - return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; - }, - - /** - * execute search (requires search index to be loaded) - */ - _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - - // Collect multiple result groups to be sorted separately and then ordered. - // Each is an array of [docname, title, anchor, descr, score, filename, kind]. - const normalResults = []; - const nonMainIndexResults = []; - - _removeChildren(document.getElementById("search-progress")); - - const queryLower = query.toLowerCase().trim(); - for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { - for (const [file, id] of foundTitles) { - const score = Math.round(Scorer.title * queryLower.length / title.length); - const boost = titles[file] === title ? 1 : 0; // add a boost for document titles - normalResults.push([ - docNames[file], - titles[file] !== title ? `${titles[file]} > ${title}` : title, - id !== null ? "#" + id : "", - null, - score + boost, - filenames[file], - SearchResultKind.title, - ]); - } - } - } - - // search for explicit entries in index directives - for (const [entry, foundEntries] of Object.entries(indexEntries)) { - if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id, isMain] of foundEntries) { - const score = Math.round(100 * queryLower.length / entry.length); - const result = [ - docNames[file], - titles[file], - id ? "#" + id : "", - null, - score, - filenames[file], - SearchResultKind.index, - ]; - if (isMain) { - normalResults.push(result); - } else { - nonMainIndexResults.push(result); - } - } - } - } - - // lookup as object - objectTerms.forEach((term) => - normalResults.push(...Search.performObjectSearch(term, objectTerms)) - ); - - // lookup as search terms in fulltext - normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); - - // let the scorer override scores with a custom scoring function - if (Scorer.score) { - normalResults.forEach((item) => (item[4] = Scorer.score(item))); - nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); - } - - // Sort each group of results by score and then alphabetically by name. - normalResults.sort(_orderResultsByScoreThenName); - nonMainIndexResults.sort(_orderResultsByScoreThenName); - - // Combine the result groups in (reverse) order. - // Non-main index entries are typically arbitrary cross-references, - // so display them after other results. - let results = [...nonMainIndexResults, ...normalResults]; - - // remove duplicate search results - // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept - let seen = new Set(); - results = results.reverse().reduce((acc, result) => { - let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); - if (!seen.has(resultStr)) { - acc.push(result); - seen.add(resultStr); - } - return acc; - }, []); - - return results.reverse(); - }, - - query: (query) => { - const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); - const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); - - // for debugging - //Search.lastresults = results.slice(); // a copy - // console.info("search results:", Search.lastresults); - - // print the results - _displayNextItem(results, results.length, searchTerms, highlightTerms); - }, - - /** - * search for object names - */ - performObjectSearch: (object, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const objects = Search._index.objects; - const objNames = Search._index.objnames; - const titles = Search._index.titles; - - const results = []; - - const objectSearchCallback = (prefix, match) => { - const name = match[4] - const fullname = (prefix ? prefix + "." : "") + name; - const fullnameLower = fullname.toLowerCase(); - if (fullnameLower.indexOf(object) < 0) return; - - let score = 0; - const parts = fullnameLower.split("."); - - // check for different match types: exact matches of full name or - // "last name" (i.e. last dotted part) - if (fullnameLower === object || parts.slice(-1)[0] === object) - score += Scorer.objNameMatch; - else if (parts.slice(-1)[0].indexOf(object) > -1) - score += Scorer.objPartialMatch; // matches in last name - - const objName = objNames[match[1]][2]; - const title = titles[match[0]]; - - // If more than one term searched for, we require other words to be - // found in the name/title/description - const otherTerms = new Set(objectTerms); - otherTerms.delete(object); - if (otherTerms.size > 0) { - const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); - if ( - [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) - ) - return; - } - - let anchor = match[3]; - if (anchor === "") anchor = fullname; - else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; - - const descr = objName + _(", in ") + title; - - // add custom score for some objects according to scorer - if (Scorer.objPrio.hasOwnProperty(match[2])) - score += Scorer.objPrio[match[2]]; - else score += Scorer.objPrioDefault; - - results.push([ - docNames[match[0]], - fullname, - "#" + anchor, - descr, - score, - filenames[match[0]], - SearchResultKind.object, - ]); - }; - Object.keys(objects).forEach((prefix) => - objects[prefix].forEach((array) => - objectSearchCallback(prefix, array) - ) - ); - return results; - }, - - /** - * search for full-text terms in the index - */ - performTermsSearch: (searchTerms, excludedTerms) => { - // prepare search - const terms = Search._index.terms; - const titleTerms = Search._index.titleterms; - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - - const scoreMap = new Map(); - const fileMap = new Map(); - - // perform the search on the required terms - searchTerms.forEach((word) => { - const files = []; - const arr = [ - { files: terms[word], score: Scorer.term }, - { files: titleTerms[word], score: Scorer.title }, - ]; - // add support for partial matches - if (word.length > 2) { - const escapedWord = _escapeRegExp(word); - if (!terms.hasOwnProperty(word)) { - Object.keys(terms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: terms[term], score: Scorer.partialTerm }); - }); - } - if (!titleTerms.hasOwnProperty(word)) { - Object.keys(titleTerms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); - }); - } - } - - // no match but word was a required one - if (arr.every((record) => record.files === undefined)) return; - - // found search word in contents - arr.forEach((record) => { - if (record.files === undefined) return; - - let recordFiles = record.files; - if (recordFiles.length === undefined) recordFiles = [recordFiles]; - files.push(...recordFiles); - - // set score for the word in each file - recordFiles.forEach((file) => { - if (!scoreMap.has(file)) scoreMap.set(file, {}); - scoreMap.get(file)[word] = record.score; - }); - }); - - // create the mapping - files.forEach((file) => { - if (!fileMap.has(file)) fileMap.set(file, [word]); - else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); - }); - }); - - // now check if the files don't contain excluded terms - const results = []; - for (const [file, wordList] of fileMap) { - // check if all requirements are matched - - // as search terms with length < 3 are discarded - const filteredTermCount = [...searchTerms].filter( - (term) => term.length > 2 - ).length; - if ( - wordList.length !== searchTerms.size && - wordList.length !== filteredTermCount - ) - continue; - - // ensure that none of the excluded terms is in the search result - if ( - [...excludedTerms].some( - (term) => - terms[term] === file || - titleTerms[term] === file || - (terms[term] || []).includes(file) || - (titleTerms[term] || []).includes(file) - ) - ) - break; - - // select one (max) score for the file. - const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); - // add result to the result list - results.push([ - docNames[file], - titles[file], - "", - null, - score, - filenames[file], - SearchResultKind.text, - ]); - } - return results; - }, - - /** - * helper function to return a node containing the - * search summary for a given text. keywords is a list - * of stemmed words. - */ - makeSearchSummary: (htmlText, keywords, anchor) => { - const text = Search.htmlToText(htmlText, anchor); - if (text === "") return null; - - const textLower = text.toLowerCase(); - const actualStartPosition = [...keywords] - .map((k) => textLower.indexOf(k.toLowerCase())) - .filter((i) => i > -1) - .slice(-1)[0]; - const startWithContext = Math.max(actualStartPosition - 120, 0); - - const top = startWithContext === 0 ? "" : "..."; - const tail = startWithContext + 240 < text.length ? "..." : ""; - - let summary = document.createElement("p"); - summary.classList.add("context"); - summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; - - return summary; - }, -}; - -_ready(Search.init); diff --git a/docs/1.0.8/_static/sphinx_highlight.js b/docs/1.0.8/_static/sphinx_highlight.js deleted file mode 100644 index 8a96c69a..00000000 --- a/docs/1.0.8/_static/sphinx_highlight.js +++ /dev/null @@ -1,154 +0,0 @@ -/* Highlighting utilities for Sphinx HTML documentation. */ -"use strict"; - -const SPHINX_HIGHLIGHT_ENABLED = true - -/** - * highlight a given string on a node by wrapping it in - * span elements with the given class name. - */ -const _highlight = (node, addItems, text, className) => { - if (node.nodeType === Node.TEXT_NODE) { - const val = node.nodeValue; - const parent = node.parentNode; - const pos = val.toLowerCase().indexOf(text); - if ( - pos >= 0 && - !parent.classList.contains(className) && - !parent.classList.contains("nohighlight") - ) { - let span; - - const closestNode = parent.closest("body, svg, foreignObject"); - const isInSVG = closestNode && closestNode.matches("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.classList.add(className); - } - - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - const rest = document.createTextNode(val.substr(pos + text.length)); - parent.insertBefore( - span, - parent.insertBefore( - rest, - node.nextSibling - ) - ); - node.nodeValue = val.substr(0, pos); - /* There may be more occurrences of search term in this node. So call this - * function recursively on the remaining fragment. - */ - _highlight(rest, addItems, text, className); - - if (isInSVG) { - const rect = document.createElementNS( - "http://www.w3.org/2000/svg", - "rect" - ); - const bbox = parent.getBBox(); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute("class", className); - addItems.push({ parent: parent, target: rect }); - } - } - } else if (node.matches && !node.matches("button, select, textarea")) { - node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); - } -}; -const _highlightText = (thisNode, text, className) => { - let addItems = []; - _highlight(thisNode, addItems, text, className); - addItems.forEach((obj) => - obj.parent.insertAdjacentElement("beforebegin", obj.target) - ); -}; - -/** - * Small JavaScript module for the documentation. - */ -const SphinxHighlight = { - - /** - * highlight the search words provided in localstorage in the text - */ - highlightSearchWords: () => { - if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight - - // get and clear terms from localstorage - const url = new URL(window.location); - const highlight = - localStorage.getItem("sphinx_highlight_terms") - || url.searchParams.get("highlight") - || ""; - localStorage.removeItem("sphinx_highlight_terms") - url.searchParams.delete("highlight"); - window.history.replaceState({}, "", url); - - // get individual terms from highlight string - const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); - if (terms.length === 0) return; // nothing to do - - // There should never be more than one element matching "div.body" - const divBody = document.querySelectorAll("div.body"); - const body = divBody.length ? divBody[0] : document.querySelector("body"); - window.setTimeout(() => { - terms.forEach((term) => _highlightText(body, term, "highlighted")); - }, 10); - - const searchBox = document.getElementById("searchbox"); - if (searchBox === null) return; - searchBox.appendChild( - document - .createRange() - .createContextualFragment( - '

' + - '' + - _("Hide Search Matches") + - "

" - ) - ); - }, - - /** - * helper function to hide the search marks again - */ - hideSearchWords: () => { - document - .querySelectorAll("#searchbox .highlight-link") - .forEach((el) => el.remove()); - document - .querySelectorAll("span.highlighted") - .forEach((el) => el.classList.remove("highlighted")); - localStorage.removeItem("sphinx_highlight_terms") - }, - - initEscapeListener: () => { - // only install a listener if it is really needed - if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; - - document.addEventListener("keydown", (event) => { - // bail for input elements - if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; - // bail with special keys - if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; - if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { - SphinxHighlight.hideSearchWords(); - event.preventDefault(); - } - }); - }, -}; - -_ready(() => { - /* Do not call highlightSearchWords() when we are on the search page. - * It will highlight words from the *previous* search query. - */ - if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); - SphinxHighlight.initEscapeListener(); -}); diff --git a/docs/1.0.8/autodoc/mmif.serialize.html b/docs/1.0.8/autodoc/mmif.serialize.html deleted file mode 100644 index 1caf6ff6..00000000 --- a/docs/1.0.8/autodoc/mmif.serialize.html +++ /dev/null @@ -1,189 +0,0 @@ - - - - - - - - - mmif.serialize module — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
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MMIF consumer

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A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the appliance documentation to learn more about the appliance.

-

MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance.

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    -

  1. The code must be hosted on a public git repository (e.g. Github, Gitlab, …)

    2. -

  2. Must listen to 5000 port.

    3. -

  3. Must expose /display route .

    4. -

  4. /display router should response to GET requests.

    5. -

  5. In the GET request, a public URL of the input MMIF file is passed via file URL parameter.

    6. -

  6. On the codebase root, there must be a Dockerfile that can build a docker image that runs the web app.

    7. -
-

We provide an example consumer at https://github.com/clamsproject/mmif-visualizer.

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  • Welcome to mmif-python’s documentation!
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Welcome to mmif-python’s documentation!

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MultiMedia Interchange Format

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MMIF is a JSON(-LD)-based data format designed for transferring annotation data between computational analysis applications in CLAMS project.

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Contents

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API documentation:

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Indices and tables

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Getting Started

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Overview

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MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for reproducibility, transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF website. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects.

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Prerequisites

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  • Python: the latest mmif-python requires Python 3.8 or newer. We have no plan to support Python 2.7.

    • -
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Installation

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Package mmif-python is distributed via the official PyPI. Users are supposed to pip-install to get latest release.

-
pip install mmif-python
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This will install a package mmif to local python.

-

The MMIF format and specification is evolving over time, and mmif-python package will be updated along with the changes in MMIF format.

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Note

-

MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and mmif-python versions, please take time to read our decision on the subject here. If you need to know which python SDK supports which specification version, see Target MMIF Versions page.

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MMIF Serialization

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mmif.serialize.mmif.Mmif represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of mmif.serialize.model.MmifObject, including the mmif.serialize.mmif.Mmif. To start with an existing MMIF str, simple initiate a new Mmif object with the file.

-
import mmif
-from mmif import Mmif
-
-mmif_str = """{
-"metadata": {
-  "mmif": "http://mmif.clams.ai/1.0.0"
-},
-"documents": [
-  {
-    "@type": "http://mmif.clams.ai/vocabulary/VideoDocument/v1",
-    "properties": {
-      "id": "m1",
-      "mime": "video/mp4",
-      "location": "file:///var/archive/video-0012.mp4"
-    }
-  },
-  {
-    "@type": "http://mmif.clams.ai/vocabulary/TextDocument/v1",
-    "properties": {
-      "id": "m2",
-      "mime": "text/plain",
-      "location": "file:///var/archive/video-0012-transcript.txt"
-    }
-  }
-],
-"views": []}"""
-mmif_obj = Mmif(mmif_str)
-
-
-

Few notes;

-
    -

  1. MMIF does not carry the primary source files in it.

    2. -

  2. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version mmif-python implementation of the MMIF might not be able to load an unsupported version of MMIF string.

    3. -
-

When serializing back to str, call mmif.serialize.model.MmifObject.serialize() on the object.

-

To get subcomponents, you can use various getters implemented in subclasses. For example;

-
from mmif.vocabulary.document_types import DocumentTypes
-
-for video in mmif_obj.Mmif.get_documents_by_type(DocumentTypes.VideoDocument):
-  with open(video.location_path(), 'b') as in_video:
-    # do something with the video file
-
-
-

For a full list of available helper methods, please refer to the API documentation.

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- - - \ No newline at end of file diff --git a/docs/1.0.8/objects.inv b/docs/1.0.8/objects.inv deleted file mode 100644 index 51b6249d..00000000 --- a/docs/1.0.8/objects.inv +++ /dev/null @@ -1,8 +0,0 @@ -# Sphinx inventory version 2 -# Project: mmif-python -# Version: 1.0.8 -# The remainder of this file is compressed using zlib. -xڍAN0E)b˺UR"X4pȞTz&v -v3杬`7XuZS -lem+7p{4d3Vr%? -c'pPQ*w +K|+na$!&F[!SY3ػ@.3(Ҁ|s$S&7P´};#14(h)1尩O(u-B}=Җngwq|+pFLKA<=( 3[cm|\l=0Ә v/jZ)[bC-x֡vjdS'0D  \ No newline at end of file diff --git a/docs/1.0.8/plugins.html b/docs/1.0.8/plugins.html deleted file mode 100644 index 757147a0..00000000 --- a/docs/1.0.8/plugins.html +++ /dev/null @@ -1,227 +0,0 @@ - - - - - - - - - Developing plugins for MMIF Python SDK — mmif-python documentation - - - - - - - - - - - - - - - - - -
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  • Developing plugins for MMIF Python SDK
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Developing plugins for MMIF Python SDK

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Overview

-

As MMIF JSON files can carry information about media document files without actually carrying file contents, file accessing modules in mmif Python package (distributed as mmif-python on PyPI) are designed to be lightweight and flexible so that it can work with additional “plugin” Python packages that can handle concrete file access.

-

This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF website. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects.

-

Developer can write simple plugins that can provide additional functionalities to mmif-python. For example, mmif-python does not provide any file access functionality beyond a local file system (with file scheme), but it can be extended with a plugin that can handle file access over different protocols (e.g. http, s3, ftp, etc).

-

This document contains information about how to write plugins for mmif-python.

-
-

Document Location Scheme Plugins

-

mmif.serialize.annotation.Document class has various methods to access parts of location property of the document. The location is in URI/IRI format (SCHEME://HOSTNAME/PATH, in a nutshell) and it has to be resolved to a local file for CLAMS Apps to process the local file to analyze and extract information about the media and its contents. The core mmif-python distribution only provides a default implementation that can handle file scheme URIs.

-

To add a document location handler plugin, you need to implement a Python “package” (do not confuse with PYPI distribution), that meets these requirements;

-
    -

  1. the package must be named mmif_docloc_<SCHEME>. For example, to implement a handler for s3 scheme, the package name must be mmif_docloc_s3. The prefix is important as it’s used in the plugin discovery process from the core mmif-python modules.

    2. -

  2. the top module of the package must have a function named resolve. The function must take a single argument, which is a str of the document location URI. The function must return a str of the local file path. For example, if the document location is s3://mybucket/myfile.mp4, a Python user should be able to to something like this;

    3. -
-
import mmif_docloc_s3
-resolved = mmif_docloc_s3.resolve('s3://mybucket/myfile.mp4')
-# then resolved must be a local file path that can be used to open the file
-
-
-

Here’s a minimal example codebase that you refer to when you develop a docloc plugin.

-

(However, before you start writing your own plugin for a specific URI scheme, checking if there’s already a PyPI distribution for the scheme might be a good idea.)

-
$ tree .
-.
-├── mmif_docloc_dummy
-│   └── __init__.py
-├── pyproject.toml
-└── setup.cfg
-
- $ cat pyproject.toml
-[build-system]
-requires = ["setuptools"]
-build-backend = "setuptools.build_meta"
-
-$ cat setup.cfg
-[metadata]
-name = mmif_docloc_dummy  # this name is IMPORTANT
-version = 0.0.1
-description = a plugin to mmif-pyhon to handle `dummy` location scheme
-
-
-

And the plugin code.

-
# mmif_docloc_dummy/__init__.py
-doc_types = {'video': 'mp4'}
-
-def resolve(docloc):
-    scheme = 'dummy'
-    if docloc.startswith(f'{scheme}://'):
-        doc_id, doc_type = docloc.split('.')
-        return f'/path/to/{doc_id}.{doc_types[doc_type]}'
-    else:
-        raise ValueError(f'cannot handle document location scheme: {docloc}')
-
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"tabl": 4, "target": 8, "util": 1, "version": 8, "video_document_help": 1, "view": 0, "vocabulari": 2, "welcom": 4}}) \ No newline at end of file diff --git a/docs/1.0.8/target-versions.html b/docs/1.0.8/target-versions.html deleted file mode 100644 index 66bde886..00000000 --- a/docs/1.0.8/target-versions.html +++ /dev/null @@ -1,263 +0,0 @@ - - - - - - - - - Target MMIF Versions — mmif-python documentation - - - - - - - - - - - - - - - - - -
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This article provides targeting MMIF specification versions of different versions of mmif-python SDK.

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mmif-python version

Target MMIF Specification

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-mmif.serialize.model module ---------------------------- - -.. automodule:: mmif.serialize.model - :members: - :undoc-members: - :show-inheritance: - -mmif.serialize.mmif module --------------------------- - -.. automodule:: mmif.serialize.mmif - :members: - :undoc-members: - :show-inheritance: - -mmif.serialize.view module --------------------------- - -.. automodule:: mmif.serialize.view - :members: - :undoc-members: - :show-inheritance: - -mmif.serialize.annotation module --------------------------------- - -.. automodule:: mmif.serialize.annotation - :members: - :undoc-members: - :show-inheritance: - diff --git a/docs/1.0.9/_sources/autodoc/mmif.utils.rst.txt b/docs/1.0.9/_sources/autodoc/mmif.utils.rst.txt deleted file mode 100644 index 64195e45..00000000 --- a/docs/1.0.9/_sources/autodoc/mmif.utils.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -mmif.utils module -================= - -mmif.utils.video_document_helper module ----------------------------------------- - -.. automodule:: mmif.utils.video_document_helper - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/1.0.9/_sources/autodoc/mmif.vocabulary.rst.txt b/docs/1.0.9/_sources/autodoc/mmif.vocabulary.rst.txt deleted file mode 100644 index d250c6a3..00000000 --- a/docs/1.0.9/_sources/autodoc/mmif.vocabulary.rst.txt +++ /dev/null @@ -1,18 +0,0 @@ -mmif.vocabulary module -====================== - -mmif.vocabulary.annotation\_types module ----------------------------------------- - -.. automodule:: mmif.vocabulary.annotation_types - :members: - :undoc-members: - :show-inheritance: - -mmif.vocabulary.document\_types module --------------------------------------- - -.. automodule:: mmif.vocabulary.document_types - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/1.0.9/_sources/autodoc/mmif_docloc_http.rst.txt b/docs/1.0.9/_sources/autodoc/mmif_docloc_http.rst.txt deleted file mode 100644 index b76c8df5..00000000 --- a/docs/1.0.9/_sources/autodoc/mmif_docloc_http.rst.txt +++ /dev/null @@ -1,11 +0,0 @@ -mmif_docloc_http package -======================== - -MMIF document location helper module for `http` and `https` schemes. -If you want to write your own docloc scheme handler, please use the source code of this module as a reference. -See this :ref:`plug-in section ` for more information. - -.. automodule:: mmif_docloc_http - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/1.0.9/_sources/consumer-tutorial.rst.txt b/docs/1.0.9/_sources/consumer-tutorial.rst.txt deleted file mode 100644 index c54634e2..00000000 --- a/docs/1.0.9/_sources/consumer-tutorial.rst.txt +++ /dev/null @@ -1,17 +0,0 @@ -.. _consumer-tutorial: - -MMIF consumer -================================= - -A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the `appliance documentation `_ to learn more about the appliance. - -MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance. - -#. The code must be hosted on a public git repository (e.g. Github, Gitlab, ...) -#. Must listen to ``5000`` port. -#. Must expose ``/display`` route . -#. ``/display`` router should response to ``GET`` requests. -#. In the ``GET`` request, a public URL of the input MMIF file is passed via ``file`` URL parameter. -#. On the codebase root, there must be a ``Dockerfile`` that can build a `docker `_ image that runs the web app. - -We provide an example consumer at https://github.com/clamsproject/mmif-visualizer. diff --git a/docs/1.0.9/_sources/index.rst.txt b/docs/1.0.9/_sources/index.rst.txt deleted file mode 100644 index beb56aae..00000000 --- a/docs/1.0.9/_sources/index.rst.txt +++ /dev/null @@ -1,26 +0,0 @@ -Welcome to mmif-python's documentation! -======================================= - -.. mdinclude:: ../README.md - -.. toctree:: - :maxdepth: 2 - :caption: Contents - - introduction - plugins - target-versions - -.. toctree:: - :maxdepth: 2 - :caption: API documentation: - - modules - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/docs/1.0.9/_sources/introduction.rst.txt b/docs/1.0.9/_sources/introduction.rst.txt deleted file mode 100644 index cfd9eaf7..00000000 --- a/docs/1.0.9/_sources/introduction.rst.txt +++ /dev/null @@ -1,89 +0,0 @@ -.. _introduction: - -Getting Started -=============== - - -Overview ---------- - -MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for reproducibility, transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF website `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects. - -Prerequisites -------------- - -* `Python `_: the latest ``mmif-python`` requires Python 3.8 or newer. We have no plan to support `Python 2.7 `_. - -Installation ---------------- - -Package ``mmif-python`` is distributed via the official PyPI. Users are supposed to pip-install to get latest release. - -.. code-block:: bash - - pip install mmif-python - -This will install a package `mmif` to local python. - -The MMIF format and specification is evolving over time, and ``mmif-python`` package will be updated along with the changes in MMIF format. - -.. note:: MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and ``mmif-python`` versions, please take time to read our decision on the subject `here `_. If you need to know which python SDK supports which specification version, see :ref:`target-versions` page. - -MMIF Serialization ---------------------------- - -:class:`mmif.serialize.mmif.Mmif` represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of :class:`mmif.serialize.model.MmifObject`, including the :class:`mmif.serialize.mmif.Mmif`. To start with an existing MMIF :class:`str`, simple initiate a new ``Mmif`` object with the file. - -.. code-block:: python - - import mmif - from mmif import Mmif - - mmif_str = """{ - "metadata": { - "mmif": "http://mmif.clams.ai/1.0.0" - }, - "documents": [ - { - "@type": "http://mmif.clams.ai/vocabulary/VideoDocument/v1", - "properties": { - "id": "m1", - "mime": "video/mp4", - "location": "file:///var/archive/video-0012.mp4" - } - }, - { - "@type": "http://mmif.clams.ai/vocabulary/TextDocument/v1", - "properties": { - "id": "m2", - "mime": "text/plain", - "location": "file:///var/archive/video-0012-transcript.txt" - } - } - ], - "views": []}""" - mmif_obj = Mmif(mmif_str) - - -Few notes; - -#. MMIF does not carry the primary source files in it. -#. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version ``mmif-python`` implementation of the MMIF might not be able to load an unsupported version of MMIF string. - -When serializing back to :class:`str`, call :meth:`mmif.serialize.model.MmifObject.serialize` on the object. - -To get subcomponents, you can use various getters implemented in subclasses. For example; - -.. code-block:: python - - from mmif.vocabulary.document_types import DocumentTypes - - for video in mmif_obj.Mmif.get_documents_by_type(DocumentTypes.VideoDocument): - with open(video.location_path(), 'b') as in_video: - # do something with the video file - - -For a full list of available helper methods, please refer to :ref:`the API documentation `. - diff --git a/docs/1.0.9/_sources/modules.rst.txt b/docs/1.0.9/_sources/modules.rst.txt deleted file mode 100644 index 4bb9307d..00000000 --- a/docs/1.0.9/_sources/modules.rst.txt +++ /dev/null @@ -1,20 +0,0 @@ -.. _apidoc: - -mmif package -============ - -.. toctree:: - :maxdepth: 4 - - autodoc/mmif.serialize - autodoc/mmif.vocabulary - autodoc/mmif.utils - -mmif_docloc_http package -======================== - -.. toctree:: - :maxdepth: 2 - - autodoc/mmif_docloc_http - diff --git a/docs/1.0.9/_sources/plugins.rst.txt b/docs/1.0.9/_sources/plugins.rst.txt deleted file mode 100644 index 9907c495..00000000 --- a/docs/1.0.9/_sources/plugins.rst.txt +++ /dev/null @@ -1,83 +0,0 @@ -.. _plugins: - -Developing plugins for MMIF Python SDK -====================================== - - -Overview --------- - -As MMIF JSON files can carry information about media document files without actually carrying file contents, file accessing modules in ``mmif`` Python package (distributed as ``mmif-python`` on PyPI) are designed to be lightweight and flexible so that it can work with additional "plugin" Python packages that can handle concrete file access. - - -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF website `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects. - -Developer can write simple plugins that can provide additional functionalities to ``mmif-python``. For example, ``mmif-python`` does not provide any file access functionality beyond a local file system (with ``file`` scheme), but it can be extended with a plugin that can handle file access over different protocols (e.g. ``http``, ``s3``, ``ftp``, etc). - -This document contains information about how to write plugins for ``mmif-python``. - -.. _docloc_plugin: - -Document Location Scheme Plugins -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -:class:`mmif.serialize.annotation.Document` class has various methods to access parts of ``location`` property of the document. The location is in `URI/IRI format `_ (``SCHEME://HOSTNAME/PATH``, in a nutshell) and it has to be resolved to a local file for CLAMS Apps to process the local file to analyze and extract information about the media and its contents. The core ``mmif-python`` distribution only provides a default implementation that can handle ``file`` scheme URIs. - -To add a document location handler plugin, you need to implement a Python `"package" `_ (do not confuse with PYPI distribution), that meets these requirements; - -#. the package must be named ``mmif_docloc_``. For example, to implement a handler for ``s3`` scheme, the package name must be ``mmif_docloc_s3``. The prefix is important as it's used in the plugin discovery process from the core ``mmif-python`` modules. -#. the top module of the package must have a function named ``resolve``. The function must take a single argument, which is a :class:`str` of the document location URI. The function must return a :class:`str` of the local file path. For example, if the document location is ``s3://mybucket/myfile.mp4``, a Python user should be able to to something like this; - -.. code-block:: python - - import mmif_docloc_s3 - resolved = mmif_docloc_s3.resolve('s3://mybucket/myfile.mp4') - # then resolved must be a local file path that can be used to open the file - - -Here's a minimal example codebase that you refer to when you develop a ``docloc`` plugin. - -(However, before you start writing your own plugin for a specific URI scheme, checking `if there's already a PyPI distribution `_ for the scheme might be a good idea.) - -.. code-block:: sh - - $ tree . - . - ├── mmif_docloc_dummy - │ └── __init__.py - ├── pyproject.toml - └── setup.cfg - - $ cat pyproject.toml - [build-system] - requires = ["setuptools"] - build-backend = "setuptools.build_meta" - - $ cat setup.cfg - [metadata] - name = mmif_docloc_dummy # this name is IMPORTANT - version = 0.0.1 - description = a plugin to mmif-pyhon to handle `dummy` location scheme - - -And the plugin code. - -.. code-block:: python - - # mmif_docloc_dummy/__init__.py - doc_types = {'video': 'mp4'} - - def resolve(docloc): - scheme = 'dummy' - if docloc.startswith(f'{scheme}://'): - doc_id, doc_type = docloc.split('.') - return f'/path/to/{doc_id}.{doc_types[doc_type]}' - else: - raise ValueError(f'cannot handle document location scheme: {docloc}') - -Bulit-in Document Location Scheme Plugins -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -At the moment, ``mmif-python`` PyPI distribution ships a built-in *docloc* plugin that support both ``http`` and ``https`` schemes. -Take a look at :mod:`mmif_docloc_http` module for details. diff --git a/docs/1.0.9/_sources/target-versions.rst.txt b/docs/1.0.9/_sources/target-versions.rst.txt deleted file mode 100644 index 34216d3e..00000000 --- a/docs/1.0.9/_sources/target-versions.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _target-versions: - -Target MMIF Versions -==================== - -This article provides targeting MMIF specification versions of different versions of ``mmif-python`` SDK. - -.. csv-table:: Target Specification Versions - :file: target-versions.csv - :header-rows: 1 diff --git a/docs/1.0.9/_static/_sphinx_javascript_frameworks_compat.js b/docs/1.0.9/_static/_sphinx_javascript_frameworks_compat.js deleted file mode 100644 index 81415803..00000000 --- a/docs/1.0.9/_static/_sphinx_javascript_frameworks_compat.js +++ /dev/null @@ -1,123 +0,0 @@ -/* Compatability shim for jQuery and underscores.js. - * - * Copyright Sphinx contributors - * Released under the two clause BSD licence - */ - -/** - * small helper function to urldecode strings - * - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL - */ -jQuery.urldecode = function(x) { - if (!x) { - return x - } - return decodeURIComponent(x.replace(/\+/g, ' ')); -}; - -/** - * small helper function to urlencode strings - */ -jQuery.urlencode = encodeURIComponent; - -/** - * This function returns the parsed url parameters of the - * current request. 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- -/** - * Simple result scoring code. - */ -if (typeof Scorer === "undefined") { - var Scorer = { - // Implement the following function to further tweak the score for each result - // The function takes a result array [docname, title, anchor, descr, score, filename] - // and returns the new score. - /* - score: result => { - const [docname, title, anchor, descr, score, filename, kind] = result - return score - }, - */ - - // query matches the full name of an object - objNameMatch: 11, - // or matches in the last dotted part of the object name - objPartialMatch: 6, - // Additive scores depending on the priority of the object - objPrio: { - 0: 15, // used to be importantResults - 1: 5, // used to be objectResults - 2: -5, // used to be unimportantResults - }, - // Used when the priority is not in the mapping. - objPrioDefault: 0, - - // query found in title - title: 15, - partialTitle: 7, - // query found in terms - term: 5, - partialTerm: 2, - }; -} - -// Global search result kind enum, used by themes to style search results. -class SearchResultKind { - static get index() { return "index"; } - static get object() { return "object"; } - static get text() { return "text"; } - static get title() { return "title"; } -} - -const _removeChildren = (element) => { - while (element && element.lastChild) element.removeChild(element.lastChild); -}; - -/** - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping - */ -const _escapeRegExp = (string) => - string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string - -const _displayItem = (item, searchTerms, highlightTerms) => { - const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; - const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; - const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; - const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; - const contentRoot = document.documentElement.dataset.content_root; - - const [docName, title, anchor, descr, score, _filename, kind] = item; - - let listItem = document.createElement("li"); - // Add a class representing the item's type: - // can be used by a theme's CSS selector for styling - // See SearchResultKind for the class names. - listItem.classList.add(`kind-${kind}`); - let requestUrl; - let linkUrl; - if (docBuilder === "dirhtml") { - // dirhtml builder - let dirname = docName + "/"; - if (dirname.match(/\/index\/$/)) - dirname = dirname.substring(0, dirname.length - 6); - else if (dirname === "index/") dirname = ""; - requestUrl = contentRoot + dirname; - linkUrl = requestUrl; - } else { - // normal html builders - requestUrl = contentRoot + docName + docFileSuffix; - linkUrl = docName + docLinkSuffix; - } - let linkEl = listItem.appendChild(document.createElement("a")); - linkEl.href = linkUrl + anchor; - linkEl.dataset.score = score; - linkEl.innerHTML = title; - if (descr) { - listItem.appendChild(document.createElement("span")).innerHTML = - " (" + descr + ")"; - // highlight search terms in the description - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - } - else if (showSearchSummary) - fetch(requestUrl) - .then((responseData) => responseData.text()) - .then((data) => { - if (data) - listItem.appendChild( - Search.makeSearchSummary(data, searchTerms, anchor) - ); - // highlight search terms in the summary - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - }); - Search.output.appendChild(listItem); -}; -const _finishSearch = (resultCount) => { - Search.stopPulse(); - Search.title.innerText = _("Search Results"); - if (!resultCount) - Search.status.innerText = Documentation.gettext( - "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." - ); - else - Search.status.innerText = Documentation.ngettext( - "Search finished, found one page matching the search query.", - "Search finished, found ${resultCount} pages matching the search query.", - resultCount, - ).replace('${resultCount}', resultCount); -}; -const _displayNextItem = ( - results, - resultCount, - searchTerms, - highlightTerms, -) => { - // results left, load the summary and display it - // this is intended to be dynamic (don't sub resultsCount) - if (results.length) { - _displayItem(results.pop(), searchTerms, highlightTerms); - setTimeout( - () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), - 5 - ); - } - // search finished, update title and status message - else _finishSearch(resultCount); -}; -// Helper function used by query() to order search results. -// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. -// Order the results by score (in opposite order of appearance, since the -// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. -const _orderResultsByScoreThenName = (a, b) => { - const leftScore = a[4]; - const rightScore = b[4]; - if (leftScore === rightScore) { - // same score: sort alphabetically - const leftTitle = a[1].toLowerCase(); - const rightTitle = b[1].toLowerCase(); - if (leftTitle === rightTitle) return 0; - return leftTitle > rightTitle ? -1 : 1; // inverted is intentional - } - return leftScore > rightScore ? 1 : -1; -}; - -/** - * Default splitQuery function. Can be overridden in ``sphinx.search`` with a - * custom function per language. - * - * The regular expression works by splitting the string on consecutive characters - * that are not Unicode letters, numbers, underscores, or emoji characters. - * This is the same as ``\W+`` in Python, preserving the surrogate pair area. - */ -if (typeof splitQuery === "undefined") { - var splitQuery = (query) => query - .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) - .filter(term => term) // remove remaining empty strings -} - -/** - * Search Module - */ -const Search = { - _index: null, - _queued_query: null, - _pulse_status: -1, - - htmlToText: (htmlString, anchor) => { - const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - for (const removalQuery of [".headerlink", "script", "style"]) { - htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); - } - if (anchor) { - const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); - if (anchorContent) return anchorContent.textContent; - - console.warn( - `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` - ); - } - - // if anchor not specified or not found, fall back to main content - const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent) return docContent.textContent; - - console.warn( - "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." - ); - return ""; - }, - - init: () => { - const query = new URLSearchParams(window.location.search).get("q"); - document - .querySelectorAll('input[name="q"]') - .forEach((el) => (el.value = query)); - if (query) Search.performSearch(query); - }, - - loadIndex: (url) => - (document.body.appendChild(document.createElement("script")).src = url), - - setIndex: (index) => { - Search._index = index; - if (Search._queued_query !== null) { - const query = Search._queued_query; - Search._queued_query = null; - Search.query(query); - } - }, - - hasIndex: () => Search._index !== null, - - deferQuery: (query) => (Search._queued_query = query), - - stopPulse: () => (Search._pulse_status = -1), - - startPulse: () => { - if (Search._pulse_status >= 0) return; - - const pulse = () => { - Search._pulse_status = (Search._pulse_status + 1) % 4; - Search.dots.innerText = ".".repeat(Search._pulse_status); - if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); - }; - pulse(); - }, - - /** - * perform a search for something (or wait until index is loaded) - */ - performSearch: (query) => { - // create the required interface elements - const searchText = document.createElement("h2"); - searchText.textContent = _("Searching"); - const searchSummary = document.createElement("p"); - searchSummary.classList.add("search-summary"); - searchSummary.innerText = ""; - const searchList = document.createElement("ul"); - searchList.setAttribute("role", "list"); - searchList.classList.add("search"); - - const out = document.getElementById("search-results"); - Search.title = out.appendChild(searchText); - Search.dots = Search.title.appendChild(document.createElement("span")); - Search.status = out.appendChild(searchSummary); - Search.output = out.appendChild(searchList); - - const searchProgress = document.getElementById("search-progress"); - // Some themes don't use the search progress node - if (searchProgress) { - searchProgress.innerText = _("Preparing search..."); - } - Search.startPulse(); - - // index already loaded, the browser was quick! - if (Search.hasIndex()) Search.query(query); - else Search.deferQuery(query); - }, - - _parseQuery: (query) => { - // stem the search terms and add them to the correct list - const stemmer = new Stemmer(); - const searchTerms = new Set(); - const excludedTerms = new Set(); - const highlightTerms = new Set(); - const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); - splitQuery(query.trim()).forEach((queryTerm) => { - const queryTermLower = queryTerm.toLowerCase(); - - // maybe skip this "word" - // stopwords array is from language_data.js - if ( - stopwords.indexOf(queryTermLower) !== -1 || - queryTerm.match(/^\d+$/) - ) - return; - - // stem the word - let word = stemmer.stemWord(queryTermLower); - // select the correct list - if (word[0] === "-") excludedTerms.add(word.substr(1)); - else { - searchTerms.add(word); - highlightTerms.add(queryTermLower); - } - }); - - if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js - localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) - } - - // console.debug("SEARCH: searching for:"); - // console.info("required: ", [...searchTerms]); - // console.info("excluded: ", [...excludedTerms]); - - return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; - }, - - /** - * execute search (requires search index to be loaded) - */ - _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - - // Collect multiple result groups to be sorted separately and then ordered. - // Each is an array of [docname, title, anchor, descr, score, filename, kind]. - const normalResults = []; - const nonMainIndexResults = []; - - _removeChildren(document.getElementById("search-progress")); - - const queryLower = query.toLowerCase().trim(); - for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { - for (const [file, id] of foundTitles) { - const score = Math.round(Scorer.title * queryLower.length / title.length); - const boost = titles[file] === title ? 1 : 0; // add a boost for document titles - normalResults.push([ - docNames[file], - titles[file] !== title ? `${titles[file]} > ${title}` : title, - id !== null ? "#" + id : "", - null, - score + boost, - filenames[file], - SearchResultKind.title, - ]); - } - } - } - - // search for explicit entries in index directives - for (const [entry, foundEntries] of Object.entries(indexEntries)) { - if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id, isMain] of foundEntries) { - const score = Math.round(100 * queryLower.length / entry.length); - const result = [ - docNames[file], - titles[file], - id ? "#" + id : "", - null, - score, - filenames[file], - SearchResultKind.index, - ]; - if (isMain) { - normalResults.push(result); - } else { - nonMainIndexResults.push(result); - } - } - } - } - - // lookup as object - objectTerms.forEach((term) => - normalResults.push(...Search.performObjectSearch(term, objectTerms)) - ); - - // lookup as search terms in fulltext - normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); - - // let the scorer override scores with a custom scoring function - if (Scorer.score) { - normalResults.forEach((item) => (item[4] = Scorer.score(item))); - nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); - } - - // Sort each group of results by score and then alphabetically by name. - normalResults.sort(_orderResultsByScoreThenName); - nonMainIndexResults.sort(_orderResultsByScoreThenName); - - // Combine the result groups in (reverse) order. - // Non-main index entries are typically arbitrary cross-references, - // so display them after other results. - let results = [...nonMainIndexResults, ...normalResults]; - - // remove duplicate search results - // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept - let seen = new Set(); - results = results.reverse().reduce((acc, result) => { - let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); - if (!seen.has(resultStr)) { - acc.push(result); - seen.add(resultStr); - } - return acc; - }, []); - - return results.reverse(); - }, - - query: (query) => { - const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); - const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); - - // for debugging - //Search.lastresults = results.slice(); // a copy - // console.info("search results:", Search.lastresults); - - // print the results - _displayNextItem(results, results.length, searchTerms, highlightTerms); - }, - - /** - * search for object names - */ - performObjectSearch: (object, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const objects = Search._index.objects; - const objNames = Search._index.objnames; - const titles = Search._index.titles; - - const results = []; - - const objectSearchCallback = (prefix, match) => { - const name = match[4] - const fullname = (prefix ? prefix + "." : "") + name; - const fullnameLower = fullname.toLowerCase(); - if (fullnameLower.indexOf(object) < 0) return; - - let score = 0; - const parts = fullnameLower.split("."); - - // check for different match types: exact matches of full name or - // "last name" (i.e. last dotted part) - if (fullnameLower === object || parts.slice(-1)[0] === object) - score += Scorer.objNameMatch; - else if (parts.slice(-1)[0].indexOf(object) > -1) - score += Scorer.objPartialMatch; // matches in last name - - const objName = objNames[match[1]][2]; - const title = titles[match[0]]; - - // If more than one term searched for, we require other words to be - // found in the name/title/description - const otherTerms = new Set(objectTerms); - otherTerms.delete(object); - if (otherTerms.size > 0) { - const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); - if ( - [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) - ) - return; - } - - let anchor = match[3]; - if (anchor === "") anchor = fullname; - else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; - - const descr = objName + _(", in ") + title; - - // add custom score for some objects according to scorer - if (Scorer.objPrio.hasOwnProperty(match[2])) - score += Scorer.objPrio[match[2]]; - else score += Scorer.objPrioDefault; - - results.push([ - docNames[match[0]], - fullname, - "#" + anchor, - descr, - score, - filenames[match[0]], - SearchResultKind.object, - ]); - }; - Object.keys(objects).forEach((prefix) => - objects[prefix].forEach((array) => - objectSearchCallback(prefix, array) - ) - ); - return results; - }, - - /** - * search for full-text terms in the index - */ - performTermsSearch: (searchTerms, excludedTerms) => { - // prepare search - const terms = Search._index.terms; - const titleTerms = Search._index.titleterms; - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - - const scoreMap = new Map(); - const fileMap = new Map(); - - // perform the search on the required terms - searchTerms.forEach((word) => { - const files = []; - const arr = [ - { files: terms[word], score: Scorer.term }, - { files: titleTerms[word], score: Scorer.title }, - ]; - // add support for partial matches - if (word.length > 2) { - const escapedWord = _escapeRegExp(word); - if (!terms.hasOwnProperty(word)) { - Object.keys(terms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: terms[term], score: Scorer.partialTerm }); - }); - } - if (!titleTerms.hasOwnProperty(word)) { - Object.keys(titleTerms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); - }); - } - } - - // no match but word was a required one - if (arr.every((record) => record.files === undefined)) return; - - // found search word in contents - arr.forEach((record) => { - if (record.files === undefined) return; - - let recordFiles = record.files; - if (recordFiles.length === undefined) recordFiles = [recordFiles]; - files.push(...recordFiles); - - // set score for the word in each file - recordFiles.forEach((file) => { - if (!scoreMap.has(file)) scoreMap.set(file, {}); - scoreMap.get(file)[word] = record.score; - }); - }); - - // create the mapping - files.forEach((file) => { - if (!fileMap.has(file)) fileMap.set(file, [word]); - else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); - }); - }); - - // now check if the files don't contain excluded terms - const results = []; - for (const [file, wordList] of fileMap) { - // check if all requirements are matched - - // as search terms with length < 3 are discarded - const filteredTermCount = [...searchTerms].filter( - (term) => term.length > 2 - ).length; - if ( - wordList.length !== searchTerms.size && - wordList.length !== filteredTermCount - ) - continue; - - // ensure that none of the excluded terms is in the search result - if ( - [...excludedTerms].some( - (term) => - terms[term] === file || - titleTerms[term] === file || - (terms[term] || []).includes(file) || - (titleTerms[term] || []).includes(file) - ) - ) - break; - - // select one (max) score for the file. - const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); - // add result to the result list - results.push([ - docNames[file], - titles[file], - "", - null, - score, - filenames[file], - SearchResultKind.text, - ]); - } - return results; - }, - - /** - * helper function to return a node containing the - * search summary for a given text. keywords is a list - * of stemmed words. - */ - makeSearchSummary: (htmlText, keywords, anchor) => { - const text = Search.htmlToText(htmlText, anchor); - if (text === "") return null; - - const textLower = text.toLowerCase(); - const actualStartPosition = [...keywords] - .map((k) => textLower.indexOf(k.toLowerCase())) - .filter((i) => i > -1) - .slice(-1)[0]; - const startWithContext = Math.max(actualStartPosition - 120, 0); - - const top = startWithContext === 0 ? "" : "..."; - const tail = startWithContext + 240 < text.length ? "..." : ""; - - let summary = document.createElement("p"); - summary.classList.add("context"); - summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; - - return summary; - }, -}; - -_ready(Search.init); diff --git a/docs/1.0.9/_static/sphinx_highlight.js b/docs/1.0.9/_static/sphinx_highlight.js deleted file mode 100644 index 8a96c69a..00000000 --- a/docs/1.0.9/_static/sphinx_highlight.js +++ /dev/null @@ -1,154 +0,0 @@ -/* Highlighting utilities for Sphinx HTML documentation. */ -"use strict"; - -const SPHINX_HIGHLIGHT_ENABLED = true - -/** - * highlight a given string on a node by wrapping it in - * span elements with the given class name. - */ -const _highlight = (node, addItems, text, className) => { - if (node.nodeType === Node.TEXT_NODE) { - const val = node.nodeValue; - const parent = node.parentNode; - const pos = val.toLowerCase().indexOf(text); - if ( - pos >= 0 && - !parent.classList.contains(className) && - !parent.classList.contains("nohighlight") - ) { - let span; - - const closestNode = parent.closest("body, svg, foreignObject"); - const isInSVG = closestNode && closestNode.matches("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.classList.add(className); - } - - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - const rest = document.createTextNode(val.substr(pos + text.length)); - parent.insertBefore( - span, - parent.insertBefore( - rest, - node.nextSibling - ) - ); - node.nodeValue = val.substr(0, pos); - /* There may be more occurrences of search term in this node. So call this - * function recursively on the remaining fragment. - */ - _highlight(rest, addItems, text, className); - - if (isInSVG) { - const rect = document.createElementNS( - "http://www.w3.org/2000/svg", - "rect" - ); - const bbox = parent.getBBox(); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute("class", className); - addItems.push({ parent: parent, target: rect }); - } - } - } else if (node.matches && !node.matches("button, select, textarea")) { - node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); - } -}; -const _highlightText = (thisNode, text, className) => { - let addItems = []; - _highlight(thisNode, addItems, text, className); - addItems.forEach((obj) => - obj.parent.insertAdjacentElement("beforebegin", obj.target) - ); -}; - -/** - * Small JavaScript module for the documentation. - */ -const SphinxHighlight = { - - /** - * highlight the search words provided in localstorage in the text - */ - highlightSearchWords: () => { - if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight - - // get and clear terms from localstorage - const url = new URL(window.location); - const highlight = - localStorage.getItem("sphinx_highlight_terms") - || url.searchParams.get("highlight") - || ""; - localStorage.removeItem("sphinx_highlight_terms") - url.searchParams.delete("highlight"); - window.history.replaceState({}, "", url); - - // get individual terms from highlight string - const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); - if (terms.length === 0) return; // nothing to do - - // There should never be more than one element matching "div.body" - const divBody = document.querySelectorAll("div.body"); - const body = divBody.length ? divBody[0] : document.querySelector("body"); - window.setTimeout(() => { - terms.forEach((term) => _highlightText(body, term, "highlighted")); - }, 10); - - const searchBox = document.getElementById("searchbox"); - if (searchBox === null) return; - searchBox.appendChild( - document - .createRange() - .createContextualFragment( - '

' + - '' + - _("Hide Search Matches") + - "

" - ) - ); - }, - - /** - * helper function to hide the search marks again - */ - hideSearchWords: () => { - document - .querySelectorAll("#searchbox .highlight-link") - .forEach((el) => el.remove()); - document - .querySelectorAll("span.highlighted") - .forEach((el) => el.classList.remove("highlighted")); - localStorage.removeItem("sphinx_highlight_terms") - }, - - initEscapeListener: () => { - // only install a listener if it is really needed - if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; - - document.addEventListener("keydown", (event) => { - // bail for input elements - if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; - // bail with special keys - if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; - if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { - SphinxHighlight.hideSearchWords(); - event.preventDefault(); - } - }); - }, -}; - -_ready(() => { - /* Do not call highlightSearchWords() when we are on the search page. - * It will highlight words from the *previous* search query. - */ - if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); - SphinxHighlight.initEscapeListener(); -}); diff --git a/docs/1.0.9/autodoc/mmif.serialize.html b/docs/1.0.9/autodoc/mmif.serialize.html deleted file mode 100644 index a94decde..00000000 --- a/docs/1.0.9/autodoc/mmif.serialize.html +++ /dev/null @@ -1,190 +0,0 @@ - - - - - - - - - mmif.serialize module — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
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- -
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mmif.serialize module

-
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mmif.serialize.model module

-
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mmif.serialize.mmif module

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mmif.serialize.view module

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mmif.serialize.annotation module

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- - -
- -
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mmif.utils module

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mmif.utils.video_document_helper module

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- - -
- -
-
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- -
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mmif.vocabulary module

-
-

mmif.vocabulary.annotation_types module

-
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mmif.vocabulary.document_types module

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- - - \ No newline at end of file diff --git a/docs/1.0.9/autodoc/mmif_docloc_http.html b/docs/1.0.9/autodoc/mmif_docloc_http.html deleted file mode 100644 index 844e2132..00000000 --- a/docs/1.0.9/autodoc/mmif_docloc_http.html +++ /dev/null @@ -1,179 +0,0 @@ - - - - - - - - - mmif_docloc_http package — mmif-python documentation - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
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- -
-

mmif_docloc_http package

-

MMIF document location helper module for http and https schemes. -If you want to write your own docloc scheme handler, please use the source code of this module as a reference. -See this plug-in section for more information.

-
-
-mmif_docloc_http.resolve(docloc)[source]
-
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- - - \ No newline at end of file diff --git a/docs/1.0.9/consumer-tutorial.html b/docs/1.0.9/consumer-tutorial.html deleted file mode 100644 index 30937c34..00000000 --- a/docs/1.0.9/consumer-tutorial.html +++ /dev/null @@ -1,172 +0,0 @@ - - - - - - - - - MMIF consumer — mmif-python documentation - - - - - - - - - - - - - - - -
- - -
- -
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  • MMIF consumer
    • -
  • -
    • -
-
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- -
-

MMIF consumer

-

A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the appliance documentation to learn more about the appliance.

-

MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance.

-
    -

  1. The code must be hosted on a public git repository (e.g. Github, Gitlab, …)

    2. -

  2. Must listen to 5000 port.

    3. -

  3. Must expose /display route .

    4. -

  4. /display router should response to GET requests.

    5. -

  5. In the GET request, a public URL of the input MMIF file is passed via file URL parameter.

    6. -

  6. On the codebase root, there must be a Dockerfile that can build a docker image that runs the web app.

    7. -
-

We provide an example consumer at https://github.com/clamsproject/mmif-visualizer.

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  • Index
    • -
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Index

- -
- M - | R - -
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- - - -
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- - -
- -
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  • Welcome to mmif-python’s documentation!
    • -
  • -
    • -
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- -
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Welcome to mmif-python’s documentation!

-
-

MultiMedia Interchange Format

-

MMIF is a JSON(-LD)-based data format designed for transferring annotation data between computational analysis applications in CLAMS project.

-
-

Contents

- -
-
-

API documentation:

- -
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Indices and tables

- -
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- - -
- -
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    • -
  • Getting Started
    • -
  • -
    • -
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Getting Started

-
-

Overview

-

MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for reproducibility, transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF website. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects.

-
-
-

Prerequisites

-
    -

  • Python: the latest mmif-python requires Python 3.8 or newer. We have no plan to support Python 2.7.

    • -
-
-
-

Installation

-

Package mmif-python is distributed via the official PyPI. Users are supposed to pip-install to get latest release.

-
pip install mmif-python
-
-
-

This will install a package mmif to local python.

-

The MMIF format and specification is evolving over time, and mmif-python package will be updated along with the changes in MMIF format.

-
-

Note

-

MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and mmif-python versions, please take time to read our decision on the subject here. If you need to know which python SDK supports which specification version, see Target MMIF Versions page.

-
-
-
-

MMIF Serialization

-

mmif.serialize.mmif.Mmif represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of mmif.serialize.model.MmifObject, including the mmif.serialize.mmif.Mmif. To start with an existing MMIF str, simple initiate a new Mmif object with the file.

-
import mmif
-from mmif import Mmif
-
-mmif_str = """{
-"metadata": {
-  "mmif": "http://mmif.clams.ai/1.0.0"
-},
-"documents": [
-  {
-    "@type": "http://mmif.clams.ai/vocabulary/VideoDocument/v1",
-    "properties": {
-      "id": "m1",
-      "mime": "video/mp4",
-      "location": "file:///var/archive/video-0012.mp4"
-    }
-  },
-  {
-    "@type": "http://mmif.clams.ai/vocabulary/TextDocument/v1",
-    "properties": {
-      "id": "m2",
-      "mime": "text/plain",
-      "location": "file:///var/archive/video-0012-transcript.txt"
-    }
-  }
-],
-"views": []}"""
-mmif_obj = Mmif(mmif_str)
-
-
-

Few notes;

-
    -

  1. MMIF does not carry the primary source files in it.

    2. -

  2. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version mmif-python implementation of the MMIF might not be able to load an unsupported version of MMIF string.

    3. -
-

When serializing back to str, call mmif.serialize.model.MmifObject.serialize() on the object.

-

To get subcomponents, you can use various getters implemented in subclasses. For example;

-
from mmif.vocabulary.document_types import DocumentTypes
-
-for video in mmif_obj.Mmif.get_documents_by_type(DocumentTypes.VideoDocument):
-  with open(video.location_path(), 'b') as in_video:
-    # do something with the video file
-
-
-

For a full list of available helper methods, please refer to the API documentation.

-
-
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- - Other Versions - v: 1.0.9 - - -
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- - - \ No newline at end of file diff --git a/docs/1.0.9/objects.inv b/docs/1.0.9/objects.inv deleted file mode 100644 index e4d91247..00000000 Binary files a/docs/1.0.9/objects.inv and /dev/null differ diff --git a/docs/1.0.9/plugins.html b/docs/1.0.9/plugins.html deleted file mode 100644 index 873193fb..00000000 --- a/docs/1.0.9/plugins.html +++ /dev/null @@ -1,234 +0,0 @@ - - - - - - - - - Developing plugins for MMIF Python SDK — mmif-python documentation - - - - - - - - - - - - - - - - - -
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Developing plugins for MMIF Python SDK

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Overview

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As MMIF JSON files can carry information about media document files without actually carrying file contents, file accessing modules in mmif Python package (distributed as mmif-python on PyPI) are designed to be lightweight and flexible so that it can work with additional “plugin” Python packages that can handle concrete file access.

-

This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF website. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects.

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Developer can write simple plugins that can provide additional functionalities to mmif-python. For example, mmif-python does not provide any file access functionality beyond a local file system (with file scheme), but it can be extended with a plugin that can handle file access over different protocols (e.g. http, s3, ftp, etc).

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This document contains information about how to write plugins for mmif-python.

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Document Location Scheme Plugins

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mmif.serialize.annotation.Document class has various methods to access parts of location property of the document. The location is in URI/IRI format (SCHEME://HOSTNAME/PATH, in a nutshell) and it has to be resolved to a local file for CLAMS Apps to process the local file to analyze and extract information about the media and its contents. The core mmif-python distribution only provides a default implementation that can handle file scheme URIs.

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To add a document location handler plugin, you need to implement a Python “package” (do not confuse with PYPI distribution), that meets these requirements;

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  1. the package must be named mmif_docloc_<SCHEME>. For example, to implement a handler for s3 scheme, the package name must be mmif_docloc_s3. The prefix is important as it’s used in the plugin discovery process from the core mmif-python modules.

    2. -

  2. the top module of the package must have a function named resolve. The function must take a single argument, which is a str of the document location URI. The function must return a str of the local file path. For example, if the document location is s3://mybucket/myfile.mp4, a Python user should be able to to something like this;

    3. -
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import mmif_docloc_s3
-resolved = mmif_docloc_s3.resolve('s3://mybucket/myfile.mp4')
-# then resolved must be a local file path that can be used to open the file
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Here’s a minimal example codebase that you refer to when you develop a docloc plugin.

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(However, before you start writing your own plugin for a specific URI scheme, checking if there’s already a PyPI distribution for the scheme might be a good idea.)

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$ tree .
-.
-├── mmif_docloc_dummy
-│   └── __init__.py
-├── pyproject.toml
-└── setup.cfg
-
- $ cat pyproject.toml
-[build-system]
-requires = ["setuptools"]
-build-backend = "setuptools.build_meta"
-
-$ cat setup.cfg
-[metadata]
-name = mmif_docloc_dummy  # this name is IMPORTANT
-version = 0.0.1
-description = a plugin to mmif-pyhon to handle `dummy` location scheme
-
-
-

And the plugin code.

-
# mmif_docloc_dummy/__init__.py
-doc_types = {'video': 'mp4'}
-
-def resolve(docloc):
-    scheme = 'dummy'
-    if docloc.startswith(f'{scheme}://'):
-        doc_id, doc_type = docloc.split('.')
-        return f'/path/to/{doc_id}.{doc_types[doc_type]}'
-    else:
-        raise ValueError(f'cannot handle document location scheme: {docloc}')
-
-
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-

Bulit-in Document Location Scheme Plugins

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At the moment, mmif-python PyPI distribution ships a built-in docloc plugin that support both http and https schemes. -Take a look at mmif_docloc_http module for details.

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- - - - - - - - \ No newline at end of file diff --git a/docs/1.0.9/searchindex.js b/docs/1.0.9/searchindex.js deleted file mode 100644 index 01ff21db..00000000 --- a/docs/1.0.9/searchindex.js +++ /dev/null @@ -1 +0,0 @@ -Search.setIndex({"alltitles": {"API documentation:": [[5, null]], "Bulit-in Document Location Scheme Plugins": [[8, "bulit-in-document-location-scheme-plugins"]], "Contents": [[5, null]], "Developing plugins for MMIF Python SDK": [[8, null]], "Document Location Scheme Plugins": [[8, "document-location-scheme-plugins"]], "Getting Started": [[6, null]], "Indices and tables": [[5, "indices-and-tables"]], "Installation": [[6, "installation"]], "MMIF Serialization": [[6, "mmif-serialization"]], "MMIF consumer": [[4, null]], "MultiMedia Interchange Format": [[5, "multimedia-interchange-format"]], "Overview": [[6, "overview"], [8, "overview"]], "Prerequisites": [[6, "prerequisites"]], "Target MMIF Versions": [[9, null]], "Target Specification Versions": [[9, "id1"]], 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"video_document_help": 1, "view": 0, "vocabulari": 2, "welcom": 5}}) \ No newline at end of file diff --git a/docs/1.0.9/target-versions.html b/docs/1.0.9/target-versions.html deleted file mode 100644 index ba776024..00000000 --- a/docs/1.0.9/target-versions.html +++ /dev/null @@ -1,267 +0,0 @@ - - - - - - - - - Target MMIF Versions — mmif-python documentation - - - - - - - - - - - - - - - - - -
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- -
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    -
    • -
  • Target MMIF Versions
    • -
  • -
    • -
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Target MMIF Versions

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This article provides targeting MMIF specification versions of different versions of mmif-python SDK.

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Target Specification Versions

mmif-python version

Target MMIF Specification

1.0.8

1.0.0

1.0.7

1.0.0

1.0.6

1.0.0

1.0.5

1.0.0

1.0.4

1.0.0

1.0.3

1.0.0

1.0.2

1.0.0

1.0.1

1.0.0

1.0.0

0.5.0

0.5.2

0.5.0

0.5.1

0.5.0

0.5.0

0.5.0

0.4.8

0.4.2

0.4.7

0.4.1

0.4.6

0.4.0

0.4.5

0.4.0

0.4.4

0.4.0

0.4.3

0.4.0

0.4.2

0.4.0

0.4.1

0.4.0

0.4.0

0.4.0

0.3.5

0.3.1

0.3.4

0.3.1

0.3.3

0.3.1

0.3.2

0.3.1

0.3.1

0.3.0

0.3.0

0.3.0

0.2.2

0.2.1

0.2.1

0.2.1

0.2.0

0.2.1

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0.3.0
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0.4.0
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0.4.3
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0.4.4
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0.4.5
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0.4.6
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0.4.7
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0.4.8
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0.5.0
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0.5.1
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0.5.2
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1.0.0
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1.0.1
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1.0.10
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1.0.11
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1.0.12
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1.0.13
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1.0.14
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1.0.15
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1.0.16
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1.0.17
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1.0.18
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1.0.19
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1.0.2
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1.0.3
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1.0.4
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1.0.7
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1.0.8
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1.0.9
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1.1.0
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-Core package to provide serialization and deserialization of MMIF format. - -``model`` module ---------------------------- - -.. automodule:: mmif.serialize.model - :members: - :undoc-members: - :show-inheritance: - -``mmif`` module --------------------------- - -.. automodule:: mmif.serialize.mmif - :members: - :undoc-members: - :show-inheritance: - -``view`` module --------------------------- - -.. automodule:: mmif.serialize.view - :members: - :undoc-members: - :show-inheritance: - -``annotation`` module --------------------------------- - -.. automodule:: mmif.serialize.annotation - :members: - :undoc-members: - :show-inheritance: - diff --git a/docs/1.1.0/_sources/autodoc/mmif.utils.rst.txt b/docs/1.1.0/_sources/autodoc/mmif.utils.rst.txt deleted file mode 100644 index a9275023..00000000 --- a/docs/1.1.0/_sources/autodoc/mmif.utils.rst.txt +++ /dev/null @@ -1,39 +0,0 @@ -mmif.utils package -================== - -Package containing utility modules for handling different types of source -documents, and general implementation of common data structures and -algorithms. - -``video_document_helper`` module ----------------------------------------- - -.. automodule:: mmif.utils.video_document_helper - :members: - :undoc-members: - :show-inheritance: - -``text_document_helper`` module ---------------------------------- - -.. automodule:: mmif.utils.sequence_helper - :members: - :undoc-members: - :show-inheritance: - -``sequence_helper`` module ---------------------------------- - -.. automodule:: mmif.utils.sequence_helper - :members: - :undoc-members: - :show-inheritance: - -``sequence_helper`` module ---------------------------------- - -.. automodule:: mmif.utils.sequence_helper - :members: - :undoc-members: - :show-inheritance: - diff --git a/docs/1.1.0/_sources/autodoc/mmif.vocabulary.rst.txt b/docs/1.1.0/_sources/autodoc/mmif.vocabulary.rst.txt deleted file mode 100644 index 0eb985b5..00000000 --- a/docs/1.1.0/_sources/autodoc/mmif.vocabulary.rst.txt +++ /dev/null @@ -1,28 +0,0 @@ -mmif.vocabulary package -======================= - -Package contains Enum-like classes for CLAMS vocabulary. - -.. autoclass:: mmif.vocabulary.ThingTypesBase - :show-inheritance: -.. autoclass:: mmif.vocabulary.ThingType - :members: - :undoc-members: - :show-inheritance: - -.. autoclass:: mmif.vocabulary.ClamsTypesBase - :show-inheritance: -.. autoclass:: mmif.vocabulary.AnnotationTypesBase - :show-inheritance: -.. autoclass:: mmif.vocabulary.DocumentTypesBase - :show-inheritance: - -.. autoclass:: mmif.vocabulary.AnnotationTypes - :members: - :undoc-members: - :show-inheritance: - -.. autoclass:: mmif.vocabulary.DocumentTypes - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/1.1.0/_sources/autodoc/mmif_docloc_http.rst.txt b/docs/1.1.0/_sources/autodoc/mmif_docloc_http.rst.txt deleted file mode 100644 index b76c8df5..00000000 --- a/docs/1.1.0/_sources/autodoc/mmif_docloc_http.rst.txt +++ /dev/null @@ -1,11 +0,0 @@ -mmif_docloc_http package -======================== - -MMIF document location helper module for `http` and `https` schemes. -If you want to write your own docloc scheme handler, please use the source code of this module as a reference. -See this :ref:`plug-in section ` for more information. - -.. automodule:: mmif_docloc_http - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/1.1.0/_sources/consumer-tutorial.rst.txt b/docs/1.1.0/_sources/consumer-tutorial.rst.txt deleted file mode 100644 index c54634e2..00000000 --- a/docs/1.1.0/_sources/consumer-tutorial.rst.txt +++ /dev/null @@ -1,17 +0,0 @@ -.. _consumer-tutorial: - -MMIF consumer -================================= - -A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the `appliance documentation `_ to learn more about the appliance. - -MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance. - -#. The code must be hosted on a public git repository (e.g. Github, Gitlab, ...) -#. Must listen to ``5000`` port. -#. Must expose ``/display`` route . -#. ``/display`` router should response to ``GET`` requests. -#. In the ``GET`` request, a public URL of the input MMIF file is passed via ``file`` URL parameter. -#. On the codebase root, there must be a ``Dockerfile`` that can build a `docker `_ image that runs the web app. - -We provide an example consumer at https://github.com/clamsproject/mmif-visualizer. diff --git a/docs/1.1.0/_sources/index.rst.txt b/docs/1.1.0/_sources/index.rst.txt deleted file mode 100644 index beb56aae..00000000 --- a/docs/1.1.0/_sources/index.rst.txt +++ /dev/null @@ -1,26 +0,0 @@ -Welcome to mmif-python's documentation! -======================================= - -.. mdinclude:: ../README.md - -.. toctree:: - :maxdepth: 2 - :caption: Contents - - introduction - plugins - target-versions - -.. toctree:: - :maxdepth: 2 - :caption: API documentation: - - modules - - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/docs/1.1.0/_sources/introduction.rst.txt b/docs/1.1.0/_sources/introduction.rst.txt deleted file mode 100644 index cfd9eaf7..00000000 --- a/docs/1.1.0/_sources/introduction.rst.txt +++ /dev/null @@ -1,89 +0,0 @@ -.. _introduction: - -Getting Started -=============== - - -Overview ---------- - -MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for reproducibility, transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF website `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects. - -Prerequisites -------------- - -* `Python `_: the latest ``mmif-python`` requires Python 3.8 or newer. We have no plan to support `Python 2.7 `_. - -Installation ---------------- - -Package ``mmif-python`` is distributed via the official PyPI. Users are supposed to pip-install to get latest release. - -.. code-block:: bash - - pip install mmif-python - -This will install a package `mmif` to local python. - -The MMIF format and specification is evolving over time, and ``mmif-python`` package will be updated along with the changes in MMIF format. - -.. note:: MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and ``mmif-python`` versions, please take time to read our decision on the subject `here `_. If you need to know which python SDK supports which specification version, see :ref:`target-versions` page. - -MMIF Serialization ---------------------------- - -:class:`mmif.serialize.mmif.Mmif` represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of :class:`mmif.serialize.model.MmifObject`, including the :class:`mmif.serialize.mmif.Mmif`. To start with an existing MMIF :class:`str`, simple initiate a new ``Mmif`` object with the file. - -.. code-block:: python - - import mmif - from mmif import Mmif - - mmif_str = """{ - "metadata": { - "mmif": "http://mmif.clams.ai/1.0.0" - }, - "documents": [ - { - "@type": "http://mmif.clams.ai/vocabulary/VideoDocument/v1", - "properties": { - "id": "m1", - "mime": "video/mp4", - "location": "file:///var/archive/video-0012.mp4" - } - }, - { - "@type": "http://mmif.clams.ai/vocabulary/TextDocument/v1", - "properties": { - "id": "m2", - "mime": "text/plain", - "location": "file:///var/archive/video-0012-transcript.txt" - } - } - ], - "views": []}""" - mmif_obj = Mmif(mmif_str) - - -Few notes; - -#. MMIF does not carry the primary source files in it. -#. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version ``mmif-python`` implementation of the MMIF might not be able to load an unsupported version of MMIF string. - -When serializing back to :class:`str`, call :meth:`mmif.serialize.model.MmifObject.serialize` on the object. - -To get subcomponents, you can use various getters implemented in subclasses. For example; - -.. code-block:: python - - from mmif.vocabulary.document_types import DocumentTypes - - for video in mmif_obj.Mmif.get_documents_by_type(DocumentTypes.VideoDocument): - with open(video.location_path(), 'b') as in_video: - # do something with the video file - - -For a full list of available helper methods, please refer to :ref:`the API documentation `. - diff --git a/docs/1.1.0/_sources/modules.rst.txt b/docs/1.1.0/_sources/modules.rst.txt deleted file mode 100644 index 4bb9307d..00000000 --- a/docs/1.1.0/_sources/modules.rst.txt +++ /dev/null @@ -1,20 +0,0 @@ -.. _apidoc: - -mmif package -============ - -.. toctree:: - :maxdepth: 4 - - autodoc/mmif.serialize - autodoc/mmif.vocabulary - autodoc/mmif.utils - -mmif_docloc_http package -======================== - -.. toctree:: - :maxdepth: 2 - - autodoc/mmif_docloc_http - diff --git a/docs/1.1.0/_sources/plugins.rst.txt b/docs/1.1.0/_sources/plugins.rst.txt deleted file mode 100644 index 1af39426..00000000 --- a/docs/1.1.0/_sources/plugins.rst.txt +++ /dev/null @@ -1,89 +0,0 @@ -.. _plugins: - -Developing plugins for MMIF Python SDK -====================================== - - -Overview --------- - -As MMIF JSON files can carry information about media document files without actually carrying file contents, file accessing modules in ``mmif`` Python package (distributed as ``mmif-python`` on PyPI) are designed to be lightweight and flexible so that it can work with additional "plugin" Python packages that can handle concrete file access. - - -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the `MMIF website `_. -``mmif-python`` is a public, open source implementation of the MMIF data format. ``mmif-python`` supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects. - -Developer can write simple plugins that can provide additional functionalities to ``mmif-python``. For example, ``mmif-python`` does not provide any file access functionality beyond a local file system (with ``file`` scheme), but it can be extended with a plugin that can handle file access over different protocols (e.g. ``http``, ``s3``, ``ftp``, etc). - -This document contains information about how to write plugins for ``mmif-python``. - -.. _docloc_plugin: - -Document Location Scheme Plugins -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -:class:`mmif.serialize.annotation.Document` class has various methods to access parts of ``location`` property of the document. The location is in `URI/IRI format `_ (``SCHEME://HOSTNAME/PATH``, in a nutshell) and it has to be resolved to a local file for CLAMS Apps to process the local file to analyze and extract information about the media and its contents. The core ``mmif-python`` distribution only provides a default implementation that can handle ``file`` scheme URIs. - -To add a document location handler plugin, you need to implement a Python `"package" `_ (do not confuse with PYPI distribution), that meets these requirements; - -#. the package must be named ``mmif_docloc_``. For example, to implement a handler for ``s3`` scheme, the package name must be ``mmif_docloc_s3``. The prefix is important as it's used in the plugin discovery process from the core ``mmif-python`` modules. -#. the top module of the package must have a function named ``resolve``. The function must take a single argument, which is a :class:`str` of the document location URI. The function must return a :class:`str` of the local file path. For example, if the document location is ``s3://mybucket/myfile.mp4``, a Python user should be able to to something like this; -#. Optionally (but highly recommended), the top module also can provide another function named ``help``. The function must take no arguments and return a :class:`str` that explains how the input string to the ``resolve`` function should be formatted. - -.. code-block:: python - - import mmif_docloc_s3 - resolved = mmif_docloc_s3.resolve('s3://mybucket/myfile.mp4') - # then resolved must be a local file path that can be used to open the file - - -Here's a minimal example codebase that you refer to when you develop a ``docloc`` plugin. - -(However, before you start writing your own plugin for a specific URI scheme, checking `if there's already a PyPI distribution `_ for the scheme might be a good idea.) - -.. code-block:: sh - - $ tree . - . - ├── mmif_docloc_dummy - │ └── __init__.py - ├── pyproject.toml - └── setup.cfg - - $ cat pyproject.toml - [build-system] - requires = ["setuptools"] - build-backend = "setuptools.build_meta" - - $ cat setup.cfg - [metadata] - name = mmif_docloc_dummy # this name is IMPORTANT - version = 0.0.1 - description = a plugin to mmif-pyhon to handle `dummy` location scheme - - -And the plugin code. - -.. code-block:: python - - # mmif_docloc_dummy/__init__.py - doc_types = {'video': 'mp4'} - - def resolve(docloc): - scheme = 'dummy' - if docloc.startswith(f'{scheme}://'): - doc_id, doc_type = docloc.split('.') - return f'/path/to/{doc_id}.{doc_types[doc_type]}' - else: - raise ValueError(f'cannot handle document location scheme: {docloc}') - - def help(): - return "location format: `.video`" - - - -Bulit-in Document Location Scheme Plugins -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -At the moment, ``mmif-python`` PyPI distribution ships a built-in *docloc* plugin that support both ``http`` and ``https`` schemes. -Take a look at :mod:`mmif_docloc_http` module for details. diff --git a/docs/1.1.0/_sources/target-versions.rst.txt b/docs/1.1.0/_sources/target-versions.rst.txt deleted file mode 100644 index 34216d3e..00000000 --- a/docs/1.1.0/_sources/target-versions.rst.txt +++ /dev/null @@ -1,10 +0,0 @@ -.. _target-versions: - -Target MMIF Versions -==================== - -This article provides targeting MMIF specification versions of different versions of ``mmif-python`` SDK. - -.. csv-table:: Target Specification Versions - :file: target-versions.csv - :header-rows: 1 diff --git a/docs/1.1.0/_static/_sphinx_javascript_frameworks_compat.js b/docs/1.1.0/_static/_sphinx_javascript_frameworks_compat.js deleted file mode 100644 index 81415803..00000000 --- a/docs/1.1.0/_static/_sphinx_javascript_frameworks_compat.js +++ /dev/null @@ -1,123 +0,0 @@ -/* Compatability shim for jQuery and underscores.js. - * - * Copyright Sphinx contributors - * Released under the two clause BSD licence - */ - -/** - * small helper function to urldecode strings - * - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL - */ -jQuery.urldecode = function(x) { - if (!x) { - return x - } - return decodeURIComponent(x.replace(/\+/g, ' ')); -}; - -/** - * small helper function to urlencode strings - */ -jQuery.urlencode = encodeURIComponent; - -/** - * This function returns the parsed url parameters of the - * current request. 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- -/** - * Simple result scoring code. - */ -if (typeof Scorer === "undefined") { - var Scorer = { - // Implement the following function to further tweak the score for each result - // The function takes a result array [docname, title, anchor, descr, score, filename] - // and returns the new score. - /* - score: result => { - const [docname, title, anchor, descr, score, filename, kind] = result - return score - }, - */ - - // query matches the full name of an object - objNameMatch: 11, - // or matches in the last dotted part of the object name - objPartialMatch: 6, - // Additive scores depending on the priority of the object - objPrio: { - 0: 15, // used to be importantResults - 1: 5, // used to be objectResults - 2: -5, // used to be unimportantResults - }, - // Used when the priority is not in the mapping. - objPrioDefault: 0, - - // query found in title - title: 15, - partialTitle: 7, - // query found in terms - term: 5, - partialTerm: 2, - }; -} - -// Global search result kind enum, used by themes to style search results. -class SearchResultKind { - static get index() { return "index"; } - static get object() { return "object"; } - static get text() { return "text"; } - static get title() { return "title"; } -} - -const _removeChildren = (element) => { - while (element && element.lastChild) element.removeChild(element.lastChild); -}; - -/** - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Guide/Regular_Expressions#escaping - */ -const _escapeRegExp = (string) => - string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string - -const _displayItem = (item, searchTerms, highlightTerms) => { - const docBuilder = DOCUMENTATION_OPTIONS.BUILDER; - const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX; - const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX; - const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY; - const contentRoot = document.documentElement.dataset.content_root; - - const [docName, title, anchor, descr, score, _filename, kind] = item; - - let listItem = document.createElement("li"); - // Add a class representing the item's type: - // can be used by a theme's CSS selector for styling - // See SearchResultKind for the class names. - listItem.classList.add(`kind-${kind}`); - let requestUrl; - let linkUrl; - if (docBuilder === "dirhtml") { - // dirhtml builder - let dirname = docName + "/"; - if (dirname.match(/\/index\/$/)) - dirname = dirname.substring(0, dirname.length - 6); - else if (dirname === "index/") dirname = ""; - requestUrl = contentRoot + dirname; - linkUrl = requestUrl; - } else { - // normal html builders - requestUrl = contentRoot + docName + docFileSuffix; - linkUrl = docName + docLinkSuffix; - } - let linkEl = listItem.appendChild(document.createElement("a")); - linkEl.href = linkUrl + anchor; - linkEl.dataset.score = score; - linkEl.innerHTML = title; - if (descr) { - listItem.appendChild(document.createElement("span")).innerHTML = - " (" + descr + ")"; - // highlight search terms in the description - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - } - else if (showSearchSummary) - fetch(requestUrl) - .then((responseData) => responseData.text()) - .then((data) => { - if (data) - listItem.appendChild( - Search.makeSearchSummary(data, searchTerms, anchor) - ); - // highlight search terms in the summary - if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js - highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted")); - }); - Search.output.appendChild(listItem); -}; -const _finishSearch = (resultCount) => { - Search.stopPulse(); - Search.title.innerText = _("Search Results"); - if (!resultCount) - Search.status.innerText = Documentation.gettext( - "Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories." - ); - else - Search.status.innerText = Documentation.ngettext( - "Search finished, found one page matching the search query.", - "Search finished, found ${resultCount} pages matching the search query.", - resultCount, - ).replace('${resultCount}', resultCount); -}; -const _displayNextItem = ( - results, - resultCount, - searchTerms, - highlightTerms, -) => { - // results left, load the summary and display it - // this is intended to be dynamic (don't sub resultsCount) - if (results.length) { - _displayItem(results.pop(), searchTerms, highlightTerms); - setTimeout( - () => _displayNextItem(results, resultCount, searchTerms, highlightTerms), - 5 - ); - } - // search finished, update title and status message - else _finishSearch(resultCount); -}; -// Helper function used by query() to order search results. -// Each input is an array of [docname, title, anchor, descr, score, filename, kind]. -// Order the results by score (in opposite order of appearance, since the -// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically. -const _orderResultsByScoreThenName = (a, b) => { - const leftScore = a[4]; - const rightScore = b[4]; - if (leftScore === rightScore) { - // same score: sort alphabetically - const leftTitle = a[1].toLowerCase(); - const rightTitle = b[1].toLowerCase(); - if (leftTitle === rightTitle) return 0; - return leftTitle > rightTitle ? -1 : 1; // inverted is intentional - } - return leftScore > rightScore ? 1 : -1; -}; - -/** - * Default splitQuery function. Can be overridden in ``sphinx.search`` with a - * custom function per language. - * - * The regular expression works by splitting the string on consecutive characters - * that are not Unicode letters, numbers, underscores, or emoji characters. - * This is the same as ``\W+`` in Python, preserving the surrogate pair area. - */ -if (typeof splitQuery === "undefined") { - var splitQuery = (query) => query - .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) - .filter(term => term) // remove remaining empty strings -} - -/** - * Search Module - */ -const Search = { - _index: null, - _queued_query: null, - _pulse_status: -1, - - htmlToText: (htmlString, anchor) => { - const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - for (const removalQuery of [".headerlink", "script", "style"]) { - htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); - } - if (anchor) { - const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`); - if (anchorContent) return anchorContent.textContent; - - console.warn( - `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.` - ); - } - - // if anchor not specified or not found, fall back to main content - const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent) return docContent.textContent; - - console.warn( - "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template." - ); - return ""; - }, - - init: () => { - const query = new URLSearchParams(window.location.search).get("q"); - document - .querySelectorAll('input[name="q"]') - .forEach((el) => (el.value = query)); - if (query) Search.performSearch(query); - }, - - loadIndex: (url) => - (document.body.appendChild(document.createElement("script")).src = url), - - setIndex: (index) => { - Search._index = index; - if (Search._queued_query !== null) { - const query = Search._queued_query; - Search._queued_query = null; - Search.query(query); - } - }, - - hasIndex: () => Search._index !== null, - - deferQuery: (query) => (Search._queued_query = query), - - stopPulse: () => (Search._pulse_status = -1), - - startPulse: () => { - if (Search._pulse_status >= 0) return; - - const pulse = () => { - Search._pulse_status = (Search._pulse_status + 1) % 4; - Search.dots.innerText = ".".repeat(Search._pulse_status); - if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); - }; - pulse(); - }, - - /** - * perform a search for something (or wait until index is loaded) - */ - performSearch: (query) => { - // create the required interface elements - const searchText = document.createElement("h2"); - searchText.textContent = _("Searching"); - const searchSummary = document.createElement("p"); - searchSummary.classList.add("search-summary"); - searchSummary.innerText = ""; - const searchList = document.createElement("ul"); - searchList.setAttribute("role", "list"); - searchList.classList.add("search"); - - const out = document.getElementById("search-results"); - Search.title = out.appendChild(searchText); - Search.dots = Search.title.appendChild(document.createElement("span")); - Search.status = out.appendChild(searchSummary); - Search.output = out.appendChild(searchList); - - const searchProgress = document.getElementById("search-progress"); - // Some themes don't use the search progress node - if (searchProgress) { - searchProgress.innerText = _("Preparing search..."); - } - Search.startPulse(); - - // index already loaded, the browser was quick! - if (Search.hasIndex()) Search.query(query); - else Search.deferQuery(query); - }, - - _parseQuery: (query) => { - // stem the search terms and add them to the correct list - const stemmer = new Stemmer(); - const searchTerms = new Set(); - const excludedTerms = new Set(); - const highlightTerms = new Set(); - const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); - splitQuery(query.trim()).forEach((queryTerm) => { - const queryTermLower = queryTerm.toLowerCase(); - - // maybe skip this "word" - // stopwords array is from language_data.js - if ( - stopwords.indexOf(queryTermLower) !== -1 || - queryTerm.match(/^\d+$/) - ) - return; - - // stem the word - let word = stemmer.stemWord(queryTermLower); - // select the correct list - if (word[0] === "-") excludedTerms.add(word.substr(1)); - else { - searchTerms.add(word); - highlightTerms.add(queryTermLower); - } - }); - - if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js - localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) - } - - // console.debug("SEARCH: searching for:"); - // console.info("required: ", [...searchTerms]); - // console.info("excluded: ", [...excludedTerms]); - - return [query, searchTerms, excludedTerms, highlightTerms, objectTerms]; - }, - - /** - * execute search (requires search index to be loaded) - */ - _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - - // Collect multiple result groups to be sorted separately and then ordered. - // Each is an array of [docname, title, anchor, descr, score, filename, kind]. - const normalResults = []; - const nonMainIndexResults = []; - - _removeChildren(document.getElementById("search-progress")); - - const queryLower = query.toLowerCase().trim(); - for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { - for (const [file, id] of foundTitles) { - const score = Math.round(Scorer.title * queryLower.length / title.length); - const boost = titles[file] === title ? 1 : 0; // add a boost for document titles - normalResults.push([ - docNames[file], - titles[file] !== title ? `${titles[file]} > ${title}` : title, - id !== null ? "#" + id : "", - null, - score + boost, - filenames[file], - SearchResultKind.title, - ]); - } - } - } - - // search for explicit entries in index directives - for (const [entry, foundEntries] of Object.entries(indexEntries)) { - if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id, isMain] of foundEntries) { - const score = Math.round(100 * queryLower.length / entry.length); - const result = [ - docNames[file], - titles[file], - id ? "#" + id : "", - null, - score, - filenames[file], - SearchResultKind.index, - ]; - if (isMain) { - normalResults.push(result); - } else { - nonMainIndexResults.push(result); - } - } - } - } - - // lookup as object - objectTerms.forEach((term) => - normalResults.push(...Search.performObjectSearch(term, objectTerms)) - ); - - // lookup as search terms in fulltext - normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms)); - - // let the scorer override scores with a custom scoring function - if (Scorer.score) { - normalResults.forEach((item) => (item[4] = Scorer.score(item))); - nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item))); - } - - // Sort each group of results by score and then alphabetically by name. - normalResults.sort(_orderResultsByScoreThenName); - nonMainIndexResults.sort(_orderResultsByScoreThenName); - - // Combine the result groups in (reverse) order. - // Non-main index entries are typically arbitrary cross-references, - // so display them after other results. - let results = [...nonMainIndexResults, ...normalResults]; - - // remove duplicate search results - // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept - let seen = new Set(); - results = results.reverse().reduce((acc, result) => { - let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); - if (!seen.has(resultStr)) { - acc.push(result); - seen.add(resultStr); - } - return acc; - }, []); - - return results.reverse(); - }, - - query: (query) => { - const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query); - const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms); - - // for debugging - //Search.lastresults = results.slice(); // a copy - // console.info("search results:", Search.lastresults); - - // print the results - _displayNextItem(results, results.length, searchTerms, highlightTerms); - }, - - /** - * search for object names - */ - performObjectSearch: (object, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const objects = Search._index.objects; - const objNames = Search._index.objnames; - const titles = Search._index.titles; - - const results = []; - - const objectSearchCallback = (prefix, match) => { - const name = match[4] - const fullname = (prefix ? prefix + "." : "") + name; - const fullnameLower = fullname.toLowerCase(); - if (fullnameLower.indexOf(object) < 0) return; - - let score = 0; - const parts = fullnameLower.split("."); - - // check for different match types: exact matches of full name or - // "last name" (i.e. last dotted part) - if (fullnameLower === object || parts.slice(-1)[0] === object) - score += Scorer.objNameMatch; - else if (parts.slice(-1)[0].indexOf(object) > -1) - score += Scorer.objPartialMatch; // matches in last name - - const objName = objNames[match[1]][2]; - const title = titles[match[0]]; - - // If more than one term searched for, we require other words to be - // found in the name/title/description - const otherTerms = new Set(objectTerms); - otherTerms.delete(object); - if (otherTerms.size > 0) { - const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); - if ( - [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) - ) - return; - } - - let anchor = match[3]; - if (anchor === "") anchor = fullname; - else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; - - const descr = objName + _(", in ") + title; - - // add custom score for some objects according to scorer - if (Scorer.objPrio.hasOwnProperty(match[2])) - score += Scorer.objPrio[match[2]]; - else score += Scorer.objPrioDefault; - - results.push([ - docNames[match[0]], - fullname, - "#" + anchor, - descr, - score, - filenames[match[0]], - SearchResultKind.object, - ]); - }; - Object.keys(objects).forEach((prefix) => - objects[prefix].forEach((array) => - objectSearchCallback(prefix, array) - ) - ); - return results; - }, - - /** - * search for full-text terms in the index - */ - performTermsSearch: (searchTerms, excludedTerms) => { - // prepare search - const terms = Search._index.terms; - const titleTerms = Search._index.titleterms; - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - - const scoreMap = new Map(); - const fileMap = new Map(); - - // perform the search on the required terms - searchTerms.forEach((word) => { - const files = []; - const arr = [ - { files: terms[word], score: Scorer.term }, - { files: titleTerms[word], score: Scorer.title }, - ]; - // add support for partial matches - if (word.length > 2) { - const escapedWord = _escapeRegExp(word); - if (!terms.hasOwnProperty(word)) { - Object.keys(terms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: terms[term], score: Scorer.partialTerm }); - }); - } - if (!titleTerms.hasOwnProperty(word)) { - Object.keys(titleTerms).forEach((term) => { - if (term.match(escapedWord)) - arr.push({ files: titleTerms[term], score: Scorer.partialTitle }); - }); - } - } - - // no match but word was a required one - if (arr.every((record) => record.files === undefined)) return; - - // found search word in contents - arr.forEach((record) => { - if (record.files === undefined) return; - - let recordFiles = record.files; - if (recordFiles.length === undefined) recordFiles = [recordFiles]; - files.push(...recordFiles); - - // set score for the word in each file - recordFiles.forEach((file) => { - if (!scoreMap.has(file)) scoreMap.set(file, {}); - scoreMap.get(file)[word] = record.score; - }); - }); - - // create the mapping - files.forEach((file) => { - if (!fileMap.has(file)) fileMap.set(file, [word]); - else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word); - }); - }); - - // now check if the files don't contain excluded terms - const results = []; - for (const [file, wordList] of fileMap) { - // check if all requirements are matched - - // as search terms with length < 3 are discarded - const filteredTermCount = [...searchTerms].filter( - (term) => term.length > 2 - ).length; - if ( - wordList.length !== searchTerms.size && - wordList.length !== filteredTermCount - ) - continue; - - // ensure that none of the excluded terms is in the search result - if ( - [...excludedTerms].some( - (term) => - terms[term] === file || - titleTerms[term] === file || - (terms[term] || []).includes(file) || - (titleTerms[term] || []).includes(file) - ) - ) - break; - - // select one (max) score for the file. - const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); - // add result to the result list - results.push([ - docNames[file], - titles[file], - "", - null, - score, - filenames[file], - SearchResultKind.text, - ]); - } - return results; - }, - - /** - * helper function to return a node containing the - * search summary for a given text. keywords is a list - * of stemmed words. - */ - makeSearchSummary: (htmlText, keywords, anchor) => { - const text = Search.htmlToText(htmlText, anchor); - if (text === "") return null; - - const textLower = text.toLowerCase(); - const actualStartPosition = [...keywords] - .map((k) => textLower.indexOf(k.toLowerCase())) - .filter((i) => i > -1) - .slice(-1)[0]; - const startWithContext = Math.max(actualStartPosition - 120, 0); - - const top = startWithContext === 0 ? "" : "..."; - const tail = startWithContext + 240 < text.length ? "..." : ""; - - let summary = document.createElement("p"); - summary.classList.add("context"); - summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; - - return summary; - }, -}; - -_ready(Search.init); diff --git a/docs/1.1.0/_static/sphinx_highlight.js b/docs/1.1.0/_static/sphinx_highlight.js deleted file mode 100644 index 8a96c69a..00000000 --- a/docs/1.1.0/_static/sphinx_highlight.js +++ /dev/null @@ -1,154 +0,0 @@ -/* Highlighting utilities for Sphinx HTML documentation. */ -"use strict"; - -const SPHINX_HIGHLIGHT_ENABLED = true - -/** - * highlight a given string on a node by wrapping it in - * span elements with the given class name. - */ -const _highlight = (node, addItems, text, className) => { - if (node.nodeType === Node.TEXT_NODE) { - const val = node.nodeValue; - const parent = node.parentNode; - const pos = val.toLowerCase().indexOf(text); - if ( - pos >= 0 && - !parent.classList.contains(className) && - !parent.classList.contains("nohighlight") - ) { - let span; - - const closestNode = parent.closest("body, svg, foreignObject"); - const isInSVG = closestNode && closestNode.matches("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.classList.add(className); - } - - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - const rest = document.createTextNode(val.substr(pos + text.length)); - parent.insertBefore( - span, - parent.insertBefore( - rest, - node.nextSibling - ) - ); - node.nodeValue = val.substr(0, pos); - /* There may be more occurrences of search term in this node. So call this - * function recursively on the remaining fragment. - */ - _highlight(rest, addItems, text, className); - - if (isInSVG) { - const rect = document.createElementNS( - "http://www.w3.org/2000/svg", - "rect" - ); - const bbox = parent.getBBox(); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute("class", className); - addItems.push({ parent: parent, target: rect }); - } - } - } else if (node.matches && !node.matches("button, select, textarea")) { - node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); - } -}; -const _highlightText = (thisNode, text, className) => { - let addItems = []; - _highlight(thisNode, addItems, text, className); - addItems.forEach((obj) => - obj.parent.insertAdjacentElement("beforebegin", obj.target) - ); -}; - -/** - * Small JavaScript module for the documentation. - */ -const SphinxHighlight = { - - /** - * highlight the search words provided in localstorage in the text - */ - highlightSearchWords: () => { - if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight - - // get and clear terms from localstorage - const url = new URL(window.location); - const highlight = - localStorage.getItem("sphinx_highlight_terms") - || url.searchParams.get("highlight") - || ""; - localStorage.removeItem("sphinx_highlight_terms") - url.searchParams.delete("highlight"); - window.history.replaceState({}, "", url); - - // get individual terms from highlight string - const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); - if (terms.length === 0) return; // nothing to do - - // There should never be more than one element matching "div.body" - const divBody = document.querySelectorAll("div.body"); - const body = divBody.length ? divBody[0] : document.querySelector("body"); - window.setTimeout(() => { - terms.forEach((term) => _highlightText(body, term, "highlighted")); - }, 10); - - const searchBox = document.getElementById("searchbox"); - if (searchBox === null) return; - searchBox.appendChild( - document - .createRange() - .createContextualFragment( - '

' + - '' + - _("Hide Search Matches") + - "

" - ) - ); - }, - - /** - * helper function to hide the search marks again - */ - hideSearchWords: () => { - document - .querySelectorAll("#searchbox .highlight-link") - .forEach((el) => el.remove()); - document - .querySelectorAll("span.highlighted") - .forEach((el) => el.classList.remove("highlighted")); - localStorage.removeItem("sphinx_highlight_terms") - }, - - initEscapeListener: () => { - // only install a listener if it is really needed - if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; - - document.addEventListener("keydown", (event) => { - // bail for input elements - if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; - // bail with special keys - if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; - if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { - SphinxHighlight.hideSearchWords(); - event.preventDefault(); - } - }); - }, -}; - -_ready(() => { - /* Do not call highlightSearchWords() when we are on the search page. - * It will highlight words from the *previous* search query. - */ - if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords(); - SphinxHighlight.initEscapeListener(); -}); diff --git a/docs/1.1.0/autodoc/mmif.serialize.html b/docs/1.1.0/autodoc/mmif.serialize.html deleted file mode 100644 index 78497e82..00000000 --- a/docs/1.1.0/autodoc/mmif.serialize.html +++ /dev/null @@ -1,191 +0,0 @@ - - - - - - - - - mmif.serialize package — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
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Core package to provide serialization and deserialization of MMIF format.

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model module

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mmif module

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view module

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annotation module

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mmif.utils package

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Package containing utility modules for handling different types of source -documents, and general implementation of common data structures and -algorithms.

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video_document_helper module

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text_document_helper module

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sequence_helper module

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mmif.vocabulary package

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Package contains Enum-like classes for CLAMS vocabulary.

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mmif_docloc_http package

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MMIF document location helper module for http and https schemes. -If you want to write your own docloc scheme handler, please use the source code of this module as a reference. -See this plug-in section for more information.

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-mmif_docloc_http.help()[source]
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-mmif_docloc_http.resolve(docloc)[source]
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  • MMIF consumer
    • -
  • -
    • -
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MMIF consumer

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A MMIF consumer discuss in this document is a web application that is designed for CLAMS appliance integration. The CLAMS appliance provides a turn-key installation of CLAMS-Galaxy instance. Please refer to the appliance documentation to learn more about the appliance.

-

MMIF consumer can be implemented with any language. However a MMIF consumer must meet these requirements to be compatible with the CLAMS appliance.

-
    -

  1. The code must be hosted on a public git repository (e.g. Github, Gitlab, …)

    2. -

  2. Must listen to 5000 port.

    3. -

  3. Must expose /display route .

    4. -

  4. /display router should response to GET requests.

    5. -

  5. In the GET request, a public URL of the input MMIF file is passed via file URL parameter.

    6. -

  6. On the codebase root, there must be a Dockerfile that can build a docker image that runs the web app.

    7. -
-

We provide an example consumer at https://github.com/clamsproject/mmif-visualizer.

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  • Welcome to mmif-python’s documentation!
    • -
  • -
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Welcome to mmif-python’s documentation!

-
-

MultiMedia Interchange Format

-

MMIF is a JSON(-LD)-based data format designed for transferring annotation data between computational analysis applications in CLAMS project.

-
-
-

mmif-python

-

mmif-python is a Python implementation of the MMIF data format. -mmif-python provides various helper classes and functions to handle MMIF JSON in Python, -including ;

-
    -

  1. de-/serialization of MMIF internal data structures to/from JSON

    2. -

  2. validation of MMIF JSON

    3. -

  3. handling of CLAMS vocabulary types

    4. -

  4. navigation of MMIF object via various “search” methods (e.g. mmif.get_all_views_contain(vocab_type)))

    5. -
-
-
-

For more …

- -
-

Contents

- -
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-

API documentation:

- -
-
-
-
-

Indices and tables

- -
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- - -
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  • Getting Started
    • -
  • -
    • -
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Getting Started

-
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Overview

-

MultiMedia Interchange Format (MMIF) is a JSON(-LD)-based data format designed for reproducibility, transparency and interoperability for customized computational analysis application workflows. -This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF website. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects.

-
-
-

Prerequisites

-
    -

  • Python: the latest mmif-python requires Python 3.8 or newer. We have no plan to support Python 2.7.

    • -
-
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Installation

-

Package mmif-python is distributed via the official PyPI. Users are supposed to pip-install to get latest release.

-
pip install mmif-python
-
-
-

This will install a package mmif to local python.

-

The MMIF format and specification is evolving over time, and mmif-python package will be updated along with the changes in MMIF format.

-
-

Note

-

MMIF format is not always backward-compatible. To find out more about relations between MMIF specification versions and mmif-python versions, please take time to read our decision on the subject here. If you need to know which python SDK supports which specification version, see Target MMIF Versions page.

-
-
-
-

MMIF Serialization

-

mmif.serialize.mmif.Mmif represents the top-level MMIF object. For subcomponents of the MMIF (view objects, annotation objects, metadata for each object) are all subclass of mmif.serialize.model.MmifObject, including the mmif.serialize.mmif.Mmif. To start with an existing MMIF str, simple initiate a new Mmif object with the file.

-
import mmif
-from mmif import Mmif
-
-mmif_str = """{
-"metadata": {
-  "mmif": "http://mmif.clams.ai/1.0.0"
-},
-"documents": [
-  {
-    "@type": "http://mmif.clams.ai/vocabulary/VideoDocument/v1",
-    "properties": {
-      "id": "m1",
-      "mime": "video/mp4",
-      "location": "file:///var/archive/video-0012.mp4"
-    }
-  },
-  {
-    "@type": "http://mmif.clams.ai/vocabulary/TextDocument/v1",
-    "properties": {
-      "id": "m2",
-      "mime": "text/plain",
-      "location": "file:///var/archive/video-0012-transcript.txt"
-    }
-  }
-],
-"views": []}"""
-mmif_obj = Mmif(mmif_str)
-
-
-

Few notes;

-
    -

  1. MMIF does not carry the primary source files in it.

    2. -

  2. MMIF encode the specification version at the top. As not all MMIF versions are backward-compatible, a version mmif-python implementation of the MMIF might not be able to load an unsupported version of MMIF string.

    3. -
-

When serializing back to str, call mmif.serialize.model.MmifObject.serialize() on the object.

-

To get subcomponents, you can use various getters implemented in subclasses. For example;

-
from mmif.vocabulary.document_types import DocumentTypes
-
-for video in mmif_obj.Mmif.get_documents_by_type(DocumentTypes.VideoDocument):
-  with open(video.location_path(), 'b') as in_video:
-    # do something with the video file
-
-
-

For a full list of available helper methods, please refer to the API documentation.

-
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- - Other Versions - v: 1.1.0 - - -
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- - - \ No newline at end of file diff --git a/docs/1.1.0/modules.html b/docs/1.1.0/modules.html deleted file mode 100644 index f5801062..00000000 --- a/docs/1.1.0/modules.html +++ /dev/null @@ -1,205 +0,0 @@ - - - - - - - - - mmif package — mmif-python documentation - - - - - - - - - - - - - - - - - -
- - -
- -
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  • mmif package
    • -
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- - - \ No newline at end of file diff --git a/docs/1.1.0/objects.inv b/docs/1.1.0/objects.inv deleted file mode 100644 index 19227435..00000000 Binary files a/docs/1.1.0/objects.inv and /dev/null differ diff --git a/docs/1.1.0/plugins.html b/docs/1.1.0/plugins.html deleted file mode 100644 index 5625272e..00000000 --- a/docs/1.1.0/plugins.html +++ /dev/null @@ -1,238 +0,0 @@ - - - - - - - - - Developing plugins for MMIF Python SDK — mmif-python documentation - - - - - - - - - - - - - - - - - -
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  • Developing plugins for MMIF Python SDK
    • -
  • -
    • -
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Developing plugins for MMIF Python SDK

-
-

Overview

-

As MMIF JSON files can carry information about media document files without actually carrying file contents, file accessing modules in mmif Python package (distributed as mmif-python on PyPI) are designed to be lightweight and flexible so that it can work with additional “plugin” Python packages that can handle concrete file access.

-

This documentation focuses on Python implementation of the MMIF. To learn more about the data format specification, please visit the MMIF website. -mmif-python is a public, open source implementation of the MMIF data format. mmif-python supports serialization/deserialization of MMIF objects from/to Python objects, as well as many navigation and manipulation helpers for MMIF objects.

-

Developer can write simple plugins that can provide additional functionalities to mmif-python. For example, mmif-python does not provide any file access functionality beyond a local file system (with file scheme), but it can be extended with a plugin that can handle file access over different protocols (e.g. http, s3, ftp, etc).

-

This document contains information about how to write plugins for mmif-python.

-
-

Document Location Scheme Plugins

-

mmif.serialize.annotation.Document class has various methods to access parts of location property of the document. The location is in URI/IRI format (SCHEME://HOSTNAME/PATH, in a nutshell) and it has to be resolved to a local file for CLAMS Apps to process the local file to analyze and extract information about the media and its contents. The core mmif-python distribution only provides a default implementation that can handle file scheme URIs.

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To add a document location handler plugin, you need to implement a Python “package” (do not confuse with PYPI distribution), that meets these requirements;

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  1. the package must be named mmif_docloc_<SCHEME>. For example, to implement a handler for s3 scheme, the package name must be mmif_docloc_s3. The prefix is important as it’s used in the plugin discovery process from the core mmif-python modules.

    2. -

  2. the top module of the package must have a function named resolve. The function must take a single argument, which is a str of the document location URI. The function must return a str of the local file path. For example, if the document location is s3://mybucket/myfile.mp4, a Python user should be able to to something like this;

    3. -

  3. Optionally (but highly recommended), the top module also can provide another function named help. The function must take no arguments and return a str that explains how the input string to the resolve function should be formatted.

    4. -
-
import mmif_docloc_s3
-resolved = mmif_docloc_s3.resolve('s3://mybucket/myfile.mp4')
-# then resolved must be a local file path that can be used to open the file
-
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Here’s a minimal example codebase that you refer to when you develop a docloc plugin.

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(However, before you start writing your own plugin for a specific URI scheme, checking if there’s already a PyPI distribution for the scheme might be a good idea.)

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$ tree .
-.
-├── mmif_docloc_dummy
-│   └── __init__.py
-├── pyproject.toml
-└── setup.cfg
-
- $ cat pyproject.toml
-[build-system]
-requires = ["setuptools"]
-build-backend = "setuptools.build_meta"
-
-$ cat setup.cfg
-[metadata]
-name = mmif_docloc_dummy  # this name is IMPORTANT
-version = 0.0.1
-description = a plugin to mmif-pyhon to handle `dummy` location scheme
-
-
-

And the plugin code.

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# mmif_docloc_dummy/__init__.py
-doc_types = {'video': 'mp4'}
-
-def resolve(docloc):
-    scheme = 'dummy'
-    if docloc.startswith(f'{scheme}://'):
-        doc_id, doc_type = docloc.split('.')
-        return f'/path/to/{doc_id}.{doc_types[doc_type]}'
-    else:
-        raise ValueError(f'cannot handle document location scheme: {docloc}')
-
-def help():
-    return "location format: `<DOCUMENT_ID>.video`"
-
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Bulit-in Document Location Scheme Plugins

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At the moment, mmif-python PyPI distribution ships a built-in docloc plugin that support both http and https schemes. -Take a look at mmif_docloc_http module for details.

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- - - \ No newline at end of file diff --git a/docs/1.1.0/py-modindex.html b/docs/1.1.0/py-modindex.html deleted file mode 100644 index 9481d0fc..00000000 --- a/docs/1.1.0/py-modindex.html +++ /dev/null @@ -1,181 +0,0 @@ - - - - - - - - Python Module Index — mmif-python documentation - - - - - - - - - - - - - - - - - - - - -
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- - - \ No newline at end of file diff --git a/docs/1.1.0/search.html b/docs/1.1.0/search.html deleted file mode 100644 index 887bd70d..00000000 --- a/docs/1.1.0/search.html +++ /dev/null @@ -1,178 +0,0 @@ - - - - - - - - Search — mmif-python documentation - - - - - - - - - - - - - - - - - - -
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- - - - - - - - \ No newline at end of file diff --git a/docs/1.1.0/searchindex.js b/docs/1.1.0/searchindex.js deleted file mode 100644 index 89cebc52..00000000 --- a/docs/1.1.0/searchindex.js +++ /dev/null @@ -1 +0,0 @@ -Search.setIndex({"alltitles": {"API documentation:": [[5, null]], "Bulit-in Document Location Scheme Plugins": [[8, "bulit-in-document-location-scheme-plugins"]], "Contents": [[5, null]], "Developing plugins for MMIF Python SDK": [[8, null]], "Document Location Scheme Plugins": [[8, "document-location-scheme-plugins"]], "For more \u2026": [[5, "for-more"]], "Getting Started": [[6, null]], "Indices and tables": [[5, "indices-and-tables"]], "Installation": [[6, "installation"]], "MMIF Serialization": [[6, "mmif-serialization"]], "MMIF consumer": [[4, null]], "MultiMedia Interchange Format": [[5, "multimedia-interchange-format"]], "Overview": [[6, "overview"], [8, "overview"]], "Prerequisites": [[6, "prerequisites"]], "Target MMIF Versions": [[9, null]], "Target Specification Versions": [[9, "id1"]], "Welcome to mmif-python\u2019s documentation!": [[5, null]], "annotation module": [[0, "annotation-module"]], "mmif module": [[0, "mmif-module"]], "mmif package": [[7, null]], "mmif-python": [[5, "mmif-python"]], "mmif.serialize package": [[0, null]], "mmif.utils package": [[1, null]], "mmif.vocabulary package": [[2, null]], "mmif_docloc_http package": [[3, null], [7, "mmif-docloc-http-package"]], "model module": [[0, "model-module"]], "sequence_helper module": [[1, "sequence-helper-module"], [1, "id1"]], "text_document_helper module": [[1, "text-document-helper-module"]], "video_document_helper module": [[1, "video-document-helper-module"]], "view module": [[0, "view-module"]]}, "docnames": ["autodoc/mmif.serialize", "autodoc/mmif.utils", "autodoc/mmif.vocabulary", "autodoc/mmif_docloc_http", "consumer-tutorial", "index", "introduction", "modules", "plugins", "target-versions"], "envversion": {"sphinx": 64, "sphinx.domains.c": 3, 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"call": 6, "can": [4, 6, 8], "cannot": 8, "carri": [6, 8], "cat": 8, "cfg": 8, "chang": 6, "check": 8, "clam": [2, 4, 5, 6, 8], "clamsproject": 4, "class": [2, 5, 8], "code": [3, 4, 8], "codebas": [4, 8], "com": 4, "common": 1, "compat": [4, 6], "comput": [5, 6], "concret": 8, "confus": 8, "contain": [1, 2, 8], "content": 8, "core": [0, 8], "custom": 6, "data": [1, 5, 6, 8], "de": 5, "decis": 6, "def": 8, "default": 8, "descript": 8, "deseri": [0, 6, 8], "design": [4, 5, 6, 8], "detail": 8, "develop": 5, "differ": [1, 8, 9], "discoveri": 8, "discuss": 4, "displai": 4, "distribut": [6, 8], "do": [6, 8], "doc_id": 8, "doc_typ": 8, "docker": 4, "dockerfil": 4, "docloc": [3, 8], "document": [1, 3, 4, 6], "document_id": 8, "document_typ": 6, "documenttyp": 6, "doe": [6, 8], "dummi": 8, "e": [4, 5, 8], "each": 6, "els": 8, "encod": 6, "enum": 2, "etc": 8, "evolv": 6, "exampl": [4, 6, 8], "exist": 6, "explain": 8, "expos": 4, "extend": 8, "extract": 8, "f": 8, "few": 6, "file": [4, 6, 8], 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"titleterms": {"": 5, "For": 5, "annot": 0, "api": 5, "bulit": 8, "consum": 4, "content": 5, "develop": 8, "document": [5, 8], "format": 5, "get": 6, "indic": 5, "instal": 6, "interchang": 5, "locat": 8, "mmif": [0, 1, 2, 4, 5, 6, 7, 8, 9], "mmif_docloc_http": [3, 7], "model": 0, "modul": [0, 1], "more": 5, "multimedia": 5, "overview": [6, 8], "packag": [0, 1, 2, 3, 7], "plugin": 8, "prerequisit": 6, "python": [5, 8], "scheme": 8, "sdk": 8, "sequence_help": 1, "serial": [0, 6], "specif": 9, "start": 6, "tabl": 5, "target": 9, "text_document_help": 1, "util": 1, "version": 9, "video_document_help": 1, "view": 0, "vocabulari": 2, "welcom": 5}}) \ No newline at end of file diff --git a/docs/1.1.0/target-versions.html b/docs/1.1.0/target-versions.html deleted file mode 100644 index 81722db8..00000000 --- a/docs/1.1.0/target-versions.html +++ /dev/null @@ -1,300 +0,0 @@ - - - - - - - - - Target MMIF Versions — mmif-python documentation - - - - - - - - - - - - - - - - - -
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Target MMIF Versions

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This article provides targeting MMIF specification versions of different versions of mmif-python SDK.

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Target Specification Versions

mmif-python version

Target MMIF Specification

1.0.19

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1.0.16

1.0.4

1.0.15

1.0.4

1.0.14

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0.3.1

0.3.2

0.3.1

0.3.1

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0.2.1

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1.0.3
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1.0.4
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1.0.6
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1.1.0
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- - - \ No newline at end of file diff --git a/docs/index.html b/docs/index.html deleted file mode 100644 index e56f8e02..00000000 --- a/docs/index.html +++ /dev/null @@ -1 +0,0 @@ - Redirect to latest version diff --git a/docs/latest b/docs/latest deleted file mode 120000 index 1cc5f657..00000000 --- a/docs/latest +++ /dev/null @@ -1 +0,0 @@ -1.1.0 \ No newline at end of file diff --git a/documentation/conf.py b/documentation/conf.py index ad8e4e05..2b8a027d 100644 --- a/documentation/conf.py +++ b/documentation/conf.py @@ -1,141 +1,176 @@ # Configuration file for the Sphinx documentation builder. -# -# This file only contains a selection of the most common options. For a full -# list see the documentation: +# For the full list of built-in configuration values, see the documentation: # https://www.sphinx-doc.org/en/master/usage/configuration.html import datetime +import inspect import textwrap - -# -- Path setup -------------------------------------------------------------- - -# If extensions (or modules to document with autodoc) are in another directory, -# add these directories to sys.path here. If the directory is relative to the -# documentation root, use os.path.abspath to make it absolute, like shown here. -# import os -from pathlib import Path import sys -doc_src_dir = Path(os.getenv("SPHINX_MULTIVERSION_SOURCEDIR", default=__file__)) -proj_root_dir = doc_src_dir.parent.parent if doc_src_dir.is_file() else doc_src_dir.parent -sys.path.insert(0, proj_root_dir.as_posix()) +from pathlib import Path +# -- Path setup -------------------------------------------------------------- +# Add project root to sys.path so that autodoc can find the mmif package. +proj_root_dir = Path(__file__).parent.parent +sys.path.insert(0, str(proj_root_dir.absolute())) + +# At this point, `pip install -e .` should have been run, so mmif is importable +import mmif # -- Project information ----------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information project = 'mmif-python' +blob_base_url = f'https://github.com/clamsproject/{project}/blob' copyright = f'{datetime.date.today().year}, Brandeis LLC' author = 'Brandeis LLC' -version = open(proj_root_dir / 'VERSION').read().strip() - - -# The full version, including alpha/beta/rc tags -# release = '0.1.0' - +try: + version = open(proj_root_dir / 'VERSION').read().strip() +except FileNotFoundError: + print("WARNING: VERSION file not found, using 'dev' as version.") + version = 'dev' +release = version # -- General configuration --------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration -# Add any Sphinx extension module names here, as strings. They can be -# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom -# ones. extensions = [ - 'sphinx.ext.autodoc', - 'sphinx_rtd_theme', - 'sphinx.ext.linkcode', - 'm2r2', + 'sphinx.ext.autodoc', + 'sphinx.ext.linkcode', + 'm2r2', ] -try: - import sphinx_multiversion - extensions.append('sphinx_multiversion') -except ImportError: - pass -source_suffix = ['.rst', '.md'] -# Add any paths that contain templates here, relative to this directory. templates_path = ['_templates'] - -# List of patterns, relative to source directory, that match files and -# directories to ignore when looking for source files. -# This pattern also affects html_static_path and html_extra_path. exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] - +# dynamically generated files +exclude_patterns.extend(['cli_help.rst', 'whatsnew.md']) +# WIP files +exclude_patterns.extend(['consumer-tutorial.rst']) +source_suffix = ['.rst', '.md'] # -- Options for HTML output ------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output + +html_theme = 'furo' +html_static_path = [] # No static path for now, can be created if needed +html_show_sourcelink = True # Furo handles this well, no need to hide + +# Theme options for visual consistency with CLAMS branding +html_theme_options = { + # "light_logo": "logo.png", # TODO: Add logo files if available + # "dark_logo": "logo.png", + "sidebar_hide_name": False, + "navigation_with_keys": True, + "source_repository": "https://github.com/clamsproject/mmif-python", + "source_branch": "main", # Default branch for "Edit on GitHub" links + "source_directory": "documentation/", + + # CLAMS brand colors + "light_css_variables": { + "color-brand-primary": "#008AFF", + "color-brand-content": "#0085A1", + "color-link": "#008AFF", + "color-link-hover": "#0085A1", + }, + # Dark mode variables can be added here if needed +} + + +# -- Options for linkcode extension --------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/extensions/linkcode.html -# The theme to use for HTML and HTML Help pages. See the documentation for -# a list of builtin themes. -# -# html_theme = 'alabaster' -html_theme = 'sphinx_rtd_theme' +def linkcode_resolve(domain, info): + if domain != 'py' or not info.get('module'): + return None -# Add any paths that contain custom static files (such as style sheets) here, -# relative to this directory. They are copied after the builtin static files, -# so a file named "default.css" will overwrite the builtin "default.css". -# html_static_path = ['_static'] + try: + # Find the Python object + obj = sys.modules.get(info['module']) + if obj is None: return None + for part in info['fullname'].split('.'): + obj = getattr(obj, part) + + # Get the source file and line numbers + # Use inspect.unwrap to handle decorated objects + unwrapped_obj = inspect.unwrap(obj) + filename = inspect.getsourcefile(unwrapped_obj) + if not filename: return None + + lines, start_lineno = inspect.getsourcelines(unwrapped_obj) + end_lineno = start_lineno + len(lines) - 1 + + # Get git ref (tag or branch) + # GITHUB_REF_NAME is set by GitHub Actions (e.g., 'main', 'v1.2.0') + git_ref = os.environ.get("GITHUB_REF_NAME") or version + if not git_ref or 'dev' in git_ref: + git_ref = 'main' # Fallback for local builds or dev versions + + # Get file path relative to repository root + repo_root = Path(__file__).parent.parent + rel_path = Path(filename).relative_to(repo_root) + + return f"{blob_base_url}/{git_ref}/{rel_path}#L{start_lineno}-L{end_lineno}" + + except Exception: + # Don't fail the entire build if one link fails, just return None + return None -# hide document source view link at the top -html_show_sourcelink = False +def update_target_versions(app): + """ + Update documentation/target-versions.csv with the current version and spec version. + This replaces the old logic in setup.py. + """ + # Check if we have __specver__ (it might not be there if not installed via setup.py develop) + if not hasattr(mmif, '__specver__'): + return + + current_ver = mmif.__version__ + spec_ver = mmif.__specver__ + + csv_path = proj_root_dir / 'documentation' / 'target-versions.csv' + if not csv_path.exists(): + return + + # Read existing content + with open(csv_path, 'r') as f: + lines = f.readlines() + + # Check if current version is already in the file (first data line) + # lines[0] is header, lines[1] is latest version + if len(lines) > 1 and lines[1].startswith(f'{current_ver},'): + return + + # Insert new version + print(f"Updating target-versions.csv: {current_ver} -> {spec_ver}") + lines.insert(1, f'{current_ver},"{spec_ver}"\n') + + with open(csv_path, 'w') as f: + f.writelines(lines) -# function used by `linkcode` extension -def linkcode_resolve(domain, info): - if domain != 'py': - return None - if not info['module']: - return None - filename = info['module'].replace('.', '/') - # TODO (krim): it's not trivial to recover the file path from a module name - try: - return f"https://github.com/clamsproject/mmif-python/tree/{version}/{filename}.py" - except: - return f"https://github.com/clamsproject/mmif-python/tree/main/{filename}.py" - - - -# configuration for multiversion extension -# Whitelist pattern for tags (set to None to ignore all tags) -smv_tag_whitelist = r'^[0-9]+\.[0-9]+\.[0-9]+.*$' -# Whitelist pattern for branches (set to None to ignore all branches) -smv_branch_whitelist = None -# Whitelist pattern for remotes (set to None to use local branches only) -smv_remote_whitelist = 'origin' -# Pattern for released versions -smv_released_pattern = r'^tags/[0-9]+\.[0-9]+\.[0-9]+.*$' -# Format for versioned output directories inside the build directory -smv_outputdir_format = '{ref.name}' -# Determines whether remote or local git branches/tags are preferred if their output dirs conflict -smv_prefer_remote_refs = True - -# TODO (krim @ 6/13/21): maybe there's a way to re-write what I wrote in the -# fork of sphinx-multiversion here in conf.py. Issues I can think of as of now; -# 1. sphinx-mv/main.py know current version of the library by git tag, -# but conf.py has no way to know that... -# 2. target-versions.csv file can be read once and used in the for loop -# ... (previous content) def generate_cli_rst(app): - import mmif from mmif import prep_argparser_and_subcmds, find_all_modules - + # Generate main help os.environ['COLUMNS'] = '100' parser, subparsers = prep_argparser_and_subcmds() help_text = parser.format_help() - + content = [] - + content.append('Main Command\n') content.append('------------\n\n') content.append('.. code-block:: text\n\n') content.append(textwrap.indent(help_text, ' ')) content.append('\n\n') - + # Generate subcommand help for cli_module in find_all_modules('mmif.utils.cli'): cli_module_name = cli_module.__name__.rsplit('.')[-1] subparser = cli_module.prep_argparser(prog=f'mmif {cli_module_name}') sub_help = subparser.format_help() - + content.append(f'{cli_module_name}\n') content.append('-' * len(cli_module_name) + '\n\n') content.append('.. code-block:: text\n\n') @@ -146,5 +181,55 @@ def generate_cli_rst(app): f.write(''.join(content)) +def generate_whatsnew_rst(app): + changelog_path = proj_root_dir / 'CHANGELOG.md' + output_path = proj_root_dir / 'documentation' / 'whatsnew.md' + if not changelog_path.exists(): + print(f"WARNING: CHANGELOG.md not found at {changelog_path}") + with open(output_path, 'w') as f: + f.write("") + return + + import re + + content = [] + found_version = False + version_header_re = re.compile(r'^## releasing\s+([^\s]+)\s*(\(.*\))?') + + print(f"DEBUG: Looking for version '{version}' in CHANGELOG.md") + + with open(changelog_path, 'r') as f: + lines = f.readlines() + + for line in lines: + match = version_header_re.match(line) + if match: + header_version = match.group(1) + if header_version == version: + found_version = True + # We don't include the header line itself in the content we want to wrap + continue + elif found_version: + break + + if found_version: + content.append(line) + + if not found_version: + print(f"NOTE: No changelog entry found for version {version}") + with open(output_path, 'w') as f: + f.write("") + else: + # Dump matched markdown content directly to whatsnew.md + with open(output_path, 'w') as f: + f.write(f"## What's New in {version}\n\n(Full changelog available in the [CHANGELOG.md]({blob_base_url}/main/CHANGELOG.md))\n") + f.writelines(content) + + def setup(app): - app.connect('builder-inited', generate_cli_rst) + try: + app.connect('builder-inited', update_target_versions) + app.connect('builder-inited', generate_cli_rst) + app.connect('builder-inited', generate_whatsnew_rst) + except ImportError: + print("WARNING: 'mmif' package not found. Skipping dynamic generation of parts of documentation.") diff --git a/documentation/index.rst b/documentation/index.rst index 2648277c..ddbf0691 100644 --- a/documentation/index.rst +++ b/documentation/index.rst @@ -3,6 +3,12 @@ Welcome to mmif-python's documentation! .. mdinclude:: ../README.md +---- + +.. mdinclude:: whatsnew.md + +---- + .. toctree:: :maxdepth: 2 :caption: Contents diff --git a/requirements.dev b/requirements.dev index ec6113f7..caeb31ca 100644 --- a/requirements.dev +++ b/requirements.dev @@ -6,11 +6,5 @@ pytype pyyaml bs4 lxml -sphinx -autodoc -sphinx-rtd-theme -sphinx-autobuild -git+https://github.com/clamsproject/sphinx-multiversion.git@master twine -m2r2 setuptools>=70 # arbitrarily recent version \ No newline at end of file diff --git a/setup.py b/setup.py index 48e0056d..92eefff9 100644 --- a/setup.py +++ b/setup.py @@ -77,46 +77,6 @@ def generate_vocab_enum(spec_version, clams_types_vers, mod_name) -> str: return string_out -def update_target_spec(target_vers_csv, specver): - """ - Function to record target spec version at build time. - This will update ``documentation/target-versions.csv`` file. - And in the github action for publication (``.github/workflow/publish.yml``) - the csv fill will be committed as a part of documentation publication. - The csv file is used for - - #. Public website for ``mmif-python`` API - #. ``sphinx-multiversion`` to generate ``ver`` package for older versions - - Unlike ``clams-python`` where this function is placed in ``documentation/conf.py`` - (because the file is a part of documentation? ), - I put this function here in ``setup.py`` mainly because it is easier to access - ``version`` and ``specver`` variables in the ``setup.py``. - - Also note that there are two make goals for documentation generation. - - #. ``doc``: generated a single-versioned documentation from current work tree - * Uses vanilla ``sphinx-build`` command. - * Vanilla ``sphinx-build`` does not invoke ``setup.py`` at all. - * Thus, running vanilla cmd without sdist ran before will fail (e.g. ``ver`` package not found). - #. ``docs``: generated multi-version documentation from git tags - * Uses our fork of ``sphinx-multiversion`` (https://github.com/clamsproject/sphinx-multiversion) - * This will invoke ``setup.py sdist`` for each version to make sure all source dist content is generated. - - Finally, when this function is needed to be moved to conf.py (I think that's a more proper place), - use this code snippet to import local ``mmif`` package and use __version__ and __specver__ - sys.path.append("..") - import mmif - """ - with open(target_vers_csv) as in_f, open(f'{target_vers_csv}.new', 'w') as out_f: - lines = in_f.readlines() - if not lines[1].startswith(version): - lines.insert(1, f'{version},"{specver}"\n') - for line in lines: - out_f.write(line) - shutil.move(out_f.name, in_f.name) - - def generate_vocabulary(spec_version, clams_types_vers): """ :param spec_version: @@ -220,7 +180,7 @@ def mod_run(self): # the following will generate a new version value based on VERSION file generate_subpack(mmif_name, mmif_ver_pkg, f'__version__ = "{version}"\n__specver__ = "{spec_version}"') - update_target_spec('documentation/target-versions.csv', spec_version) + # and write resource files for res_name, res_oriname in [(mmif_schema_res_name, mmif_schema_res_oriname), (mmif_vocab_res_name, mmif_vocab_res_oriname)]: