diff --git a/.dockerignore b/.dockerignore index e5f70c591..143424bfb 100644 --- a/.dockerignore +++ b/.dockerignore @@ -1,4 +1,6 @@ .git +.venv +__pycache__ virt_* docs *.pyc diff --git a/clients/xnat/README.md b/clients/xnat/README.md index 21f6a408c..78b3e40f4 100644 --- a/clients/xnat/README.md +++ b/clients/xnat/README.md @@ -2,5 +2,5 @@ ## Generate an OpenAPI client from the xnat spec 1. Run the openapi generator tool: ```shell -docker run --rm -v $(pwd):/local openapitools/openapi-generator-cli:v7.4.0 generate -i /local/spec/xnat-api.yaml -g python -o /local/generated +docker run --rm -v $(pwd):/local openapitools/openapi-generator-cli:v7.18.0 generate -i /local/spec/xnat-api.yaml -g python -o /local/generated ``` diff --git a/clients/xnat/generated/.github/workflows/python.yml b/clients/xnat/generated/.github/workflows/python.yml index f128ba25e..02a097ebb 100644 --- a/clients/xnat/generated/.github/workflows/python.yml +++ b/clients/xnat/generated/.github/workflows/python.yml @@ -7,16 +7,19 @@ name: openapi_client Python package on: [push, pull_request] +permissions: + contents: read + jobs: build: runs-on: ubuntu-latest strategy: matrix: - python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"] + python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"] steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v4 with: @@ -24,15 +27,8 @@ jobs: - name: Install dependencies run: | python -m pip install --upgrade pip - pip install flake8 pytest - if [ -f requirements.txt ]; then pip install -r requirements.txt; fi - if [ -f test-requirements.txt ]; then pip install -r test-requirements.txt; fi - - name: Lint with flake8 - run: | - # stop the build if there are Python syntax errors or undefined names - flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics - # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide - flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics + pip install -r requirements.txt + pip install -r test-requirements.txt - name: Test with pytest run: | - pytest + pytest --cov=openapi_client diff --git a/clients/xnat/generated/.gitlab-ci.yml b/clients/xnat/generated/.gitlab-ci.yml index 29da72111..6b9641eb6 100644 --- a/clients/xnat/generated/.gitlab-ci.yml +++ b/clients/xnat/generated/.gitlab-ci.yml @@ -14,12 +14,6 @@ stages: - pip install -r test-requirements.txt - pytest --cov=openapi_client -pytest-3.7: - extends: .pytest - image: python:3.7-alpine -pytest-3.8: - extends: .pytest - image: python:3.8-alpine pytest-3.9: extends: .pytest image: python:3.9-alpine @@ -29,3 +23,9 @@ pytest-3.10: pytest-3.11: extends: .pytest image: python:3.11-alpine +pytest-3.12: + extends: .pytest + image: python:3.12-alpine +pytest-3.13: + extends: .pytest + image: python:3.13-alpine diff --git a/clients/xnat/generated/.openapi-generator/FILES b/clients/xnat/generated/.openapi-generator/FILES index b7d4f35aa..4a761d983 100644 --- a/clients/xnat/generated/.openapi-generator/FILES +++ b/clients/xnat/generated/.openapi-generator/FILES @@ -1,7 +1,6 @@ .github/workflows/python.yml .gitignore .gitlab-ci.yml -.openapi-generator-ignore .travis.yml README.md docs/DataExperimentsExperimentIdScansGet200Response.md @@ -34,11 +33,4 @@ setup.cfg setup.py test-requirements.txt test/__init__.py -test/test_data_experiments_experiment_id_scans_get200_response.py -test/test_data_experiments_experiment_id_scans_get200_response_result_set.py -test/test_data_experiments_experiment_id_scans_get200_response_result_set_result_inner.py -test/test_data_projects_project_id_subjects_subject_id_experiments_get200_response.py -test/test_data_projects_project_id_subjects_subject_id_experiments_get200_response_result_set.py -test/test_data_projects_project_id_subjects_subject_id_experiments_get200_response_result_set_result_inner.py -test/test_default_api.py tox.ini diff --git a/clients/xnat/generated/.openapi-generator/VERSION b/clients/xnat/generated/.openapi-generator/VERSION index ba7f754d0..1b2d969d1 100644 --- a/clients/xnat/generated/.openapi-generator/VERSION +++ b/clients/xnat/generated/.openapi-generator/VERSION @@ -1 +1 @@ -7.4.0 +7.18.0 diff --git a/clients/xnat/generated/.travis.yml b/clients/xnat/generated/.travis.yml index fd888f75d..a3e4200d4 100644 --- a/clients/xnat/generated/.travis.yml +++ b/clients/xnat/generated/.travis.yml @@ -1,13 +1,13 @@ # ref: https://docs.travis-ci.com/user/languages/python language: python python: - - "3.7" - - "3.8" - "3.9" - "3.10" - "3.11" + - "3.12" + - "3.13" # uncomment the following if needed - #- "3.11-dev" # 3.11 development branch + #- "3.13-dev" # 3.13 development branch #- "nightly" # nightly build # command to install dependencies install: diff --git a/clients/xnat/generated/README.md b/clients/xnat/generated/README.md index d9355bec8..f65042eb6 100644 --- a/clients/xnat/generated/README.md +++ b/clients/xnat/generated/README.md @@ -5,12 +5,12 @@ This Python package is automatically generated by the [OpenAPI Generator](https: - API version: 1.0.0 - Package version: 1.0.0 -- Generator version: 7.4.0 +- Generator version: 7.18.0 - Build package: org.openapitools.codegen.languages.PythonClientCodegen ## Requirements. -Python 3.7+ +Python 3.9+ ## Installation & Usage ### pip install diff --git a/clients/xnat/generated/docs/DataExperimentsExperimentIdScansGet200Response.md b/clients/xnat/generated/docs/DataExperimentsExperimentIdScansGet200Response.md index fb2994791..2ccafea00 100644 --- a/clients/xnat/generated/docs/DataExperimentsExperimentIdScansGet200Response.md +++ b/clients/xnat/generated/docs/DataExperimentsExperimentIdScansGet200Response.md @@ -22,7 +22,7 @@ print(DataExperimentsExperimentIdScansGet200Response.to_json()) # convert the object into a dict data_experiments_experiment_id_scans_get200_response_dict = data_experiments_experiment_id_scans_get200_response_instance.to_dict() # create an instance of DataExperimentsExperimentIdScansGet200Response from a dict -data_experiments_experiment_id_scans_get200_response_form_dict = data_experiments_experiment_id_scans_get200_response.from_dict(data_experiments_experiment_id_scans_get200_response_dict) +data_experiments_experiment_id_scans_get200_response_from_dict = DataExperimentsExperimentIdScansGet200Response.from_dict(data_experiments_experiment_id_scans_get200_response_dict) ``` [[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/clients/xnat/generated/docs/DataExperimentsExperimentIdScansGet200ResponseResultSet.md b/clients/xnat/generated/docs/DataExperimentsExperimentIdScansGet200ResponseResultSet.md index c41054e98..3da9c8cba 100644 --- a/clients/xnat/generated/docs/DataExperimentsExperimentIdScansGet200ResponseResultSet.md +++ b/clients/xnat/generated/docs/DataExperimentsExperimentIdScansGet200ResponseResultSet.md @@ -23,7 +23,7 @@ print(DataExperimentsExperimentIdScansGet200ResponseResultSet.to_json()) # convert the object into a dict data_experiments_experiment_id_scans_get200_response_result_set_dict = data_experiments_experiment_id_scans_get200_response_result_set_instance.to_dict() # create an instance of DataExperimentsExperimentIdScansGet200ResponseResultSet from a dict -data_experiments_experiment_id_scans_get200_response_result_set_form_dict = data_experiments_experiment_id_scans_get200_response_result_set.from_dict(data_experiments_experiment_id_scans_get200_response_result_set_dict) +data_experiments_experiment_id_scans_get200_response_result_set_from_dict = DataExperimentsExperimentIdScansGet200ResponseResultSet.from_dict(data_experiments_experiment_id_scans_get200_response_result_set_dict) ``` [[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/clients/xnat/generated/docs/DataExperimentsExperimentIdScansGet200ResponseResultSetResultInner.md b/clients/xnat/generated/docs/DataExperimentsExperimentIdScansGet200ResponseResultSetResultInner.md index 15b575265..2513047d4 100644 --- a/clients/xnat/generated/docs/DataExperimentsExperimentIdScansGet200ResponseResultSetResultInner.md +++ b/clients/xnat/generated/docs/DataExperimentsExperimentIdScansGet200ResponseResultSetResultInner.md @@ -25,7 +25,7 @@ print(DataExperimentsExperimentIdScansGet200ResponseResultSetResultInner.to_json # convert the object into a dict data_experiments_experiment_id_scans_get200_response_result_set_result_inner_dict = data_experiments_experiment_id_scans_get200_response_result_set_result_inner_instance.to_dict() # create an instance of DataExperimentsExperimentIdScansGet200ResponseResultSetResultInner from a dict -data_experiments_experiment_id_scans_get200_response_result_set_result_inner_form_dict = data_experiments_experiment_id_scans_get200_response_result_set_result_inner.from_dict(data_experiments_experiment_id_scans_get200_response_result_set_result_inner_dict) +data_experiments_experiment_id_scans_get200_response_result_set_result_inner_from_dict = DataExperimentsExperimentIdScansGet200ResponseResultSetResultInner.from_dict(data_experiments_experiment_id_scans_get200_response_result_set_result_inner_dict) ``` [[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/clients/xnat/generated/docs/DataProjectsProjectIdSubjectsSubjectIdExperimentsGet200Response.md b/clients/xnat/generated/docs/DataProjectsProjectIdSubjectsSubjectIdExperimentsGet200Response.md index 879269818..b59df1c6b 100644 --- a/clients/xnat/generated/docs/DataProjectsProjectIdSubjectsSubjectIdExperimentsGet200Response.md +++ b/clients/xnat/generated/docs/DataProjectsProjectIdSubjectsSubjectIdExperimentsGet200Response.md @@ -22,7 +22,7 @@ print(DataProjectsProjectIdSubjectsSubjectIdExperimentsGet200Response.to_json()) # convert the object into a dict data_projects_project_id_subjects_subject_id_experiments_get200_response_dict = data_projects_project_id_subjects_subject_id_experiments_get200_response_instance.to_dict() # create an instance of DataProjectsProjectIdSubjectsSubjectIdExperimentsGet200Response from a dict -data_projects_project_id_subjects_subject_id_experiments_get200_response_form_dict = data_projects_project_id_subjects_subject_id_experiments_get200_response.from_dict(data_projects_project_id_subjects_subject_id_experiments_get200_response_dict) +data_projects_project_id_subjects_subject_id_experiments_get200_response_from_dict = DataProjectsProjectIdSubjectsSubjectIdExperimentsGet200Response.from_dict(data_projects_project_id_subjects_subject_id_experiments_get200_response_dict) ``` [[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/clients/xnat/generated/docs/DataProjectsProjectIdSubjectsSubjectIdExperimentsGet200ResponseResultSet.md b/clients/xnat/generated/docs/DataProjectsProjectIdSubjectsSubjectIdExperimentsGet200ResponseResultSet.md index 7f352b666..088bb1d29 100644 --- a/clients/xnat/generated/docs/DataProjectsProjectIdSubjectsSubjectIdExperimentsGet200ResponseResultSet.md +++ b/clients/xnat/generated/docs/DataProjectsProjectIdSubjectsSubjectIdExperimentsGet200ResponseResultSet.md @@ -23,7 +23,7 @@ print(DataProjectsProjectIdSubjectsSubjectIdExperimentsGet200ResponseResultSet.t # convert the object into a dict data_projects_project_id_subjects_subject_id_experiments_get200_response_result_set_dict = data_projects_project_id_subjects_subject_id_experiments_get200_response_result_set_instance.to_dict() # create an instance of DataProjectsProjectIdSubjectsSubjectIdExperimentsGet200ResponseResultSet from a dict -data_projects_project_id_subjects_subject_id_experiments_get200_response_result_set_form_dict = data_projects_project_id_subjects_subject_id_experiments_get200_response_result_set.from_dict(data_projects_project_id_subjects_subject_id_experiments_get200_response_result_set_dict) +data_projects_project_id_subjects_subject_id_experiments_get200_response_result_set_from_dict = DataProjectsProjectIdSubjectsSubjectIdExperimentsGet200ResponseResultSet.from_dict(data_projects_project_id_subjects_subject_id_experiments_get200_response_result_set_dict) ``` [[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/clients/xnat/generated/docs/DataProjectsProjectIdSubjectsSubjectIdExperimentsGet200ResponseResultSetResultInner.md b/clients/xnat/generated/docs/DataProjectsProjectIdSubjectsSubjectIdExperimentsGet200ResponseResultSetResultInner.md index 2e44cbfab..ebf69fa65 100644 --- a/clients/xnat/generated/docs/DataProjectsProjectIdSubjectsSubjectIdExperimentsGet200ResponseResultSetResultInner.md +++ b/clients/xnat/generated/docs/DataProjectsProjectIdSubjectsSubjectIdExperimentsGet200ResponseResultSetResultInner.md @@ -25,7 +25,7 @@ print(DataProjectsProjectIdSubjectsSubjectIdExperimentsGet200ResponseResultSetRe # convert the object into a dict data_projects_project_id_subjects_subject_id_experiments_get200_response_result_set_result_inner_dict = data_projects_project_id_subjects_subject_id_experiments_get200_response_result_set_result_inner_instance.to_dict() # create an instance of DataProjectsProjectIdSubjectsSubjectIdExperimentsGet200ResponseResultSetResultInner from a dict -data_projects_project_id_subjects_subject_id_experiments_get200_response_result_set_result_inner_form_dict = data_projects_project_id_subjects_subject_id_experiments_get200_response_result_set_result_inner.from_dict(data_projects_project_id_subjects_subject_id_experiments_get200_response_result_set_result_inner_dict) +data_projects_project_id_subjects_subject_id_experiments_get200_response_result_set_result_inner_from_dict = DataProjectsProjectIdSubjectsSubjectIdExperimentsGet200ResponseResultSetResultInner.from_dict(data_projects_project_id_subjects_subject_id_experiments_get200_response_result_set_result_inner_dict) ``` [[Back to Model list]](../README.md#documentation-for-models) [[Back to API list]](../README.md#documentation-for-api-endpoints) [[Back to README]](../README.md) diff --git a/clients/xnat/generated/docs/DefaultApi.md b/clients/xnat/generated/docs/DefaultApi.md index c42f4493f..dc79686ff 100644 --- a/clients/xnat/generated/docs/DefaultApi.md +++ b/clients/xnat/generated/docs/DefaultApi.md @@ -12,8 +12,6 @@ Method | HTTP request | Description # **data_experiments_experiment_id_scans_get** > DataExperimentsExperimentIdScansGet200Response data_experiments_experiment_id_scans_get(experiment_id, format=format) - - Get A Listing Of Scans From An Image Session ### Example @@ -92,8 +90,6 @@ Name | Type | Description | Notes # **data_projects_project_id_subjects_subject_id_experiments_get** > DataProjectsProjectIdSubjectsSubjectIdExperimentsGet200Response data_projects_project_id_subjects_subject_id_experiments_get(project_id, subject_id, format=format) - - Get a list of experiments ### Example @@ -174,8 +170,6 @@ Name | Type | Description | Notes # **data_services_auth_put** > data_services_auth_put() - - Logs in and returns the authentication cookie ### Example diff --git a/clients/xnat/generated/openapi_client/__init__.py b/clients/xnat/generated/openapi_client/__init__.py index 901a60a36..9ee5313b9 100644 --- a/clients/xnat/generated/openapi_client/__init__.py +++ b/clients/xnat/generated/openapi_client/__init__.py @@ -16,24 +16,45 @@ __version__ = "1.0.0" +# Define package exports +__all__ = [ + "DefaultApi", + "ApiResponse", + "ApiClient", + "Configuration", + "OpenApiException", + "ApiTypeError", + "ApiValueError", + "ApiKeyError", + "ApiAttributeError", + "ApiException", + "DataExperimentsExperimentIdScansGet200Response", + "DataExperimentsExperimentIdScansGet200ResponseResultSet", + "DataExperimentsExperimentIdScansGet200ResponseResultSetResultInner", + "DataProjectsProjectIdSubjectsSubjectIdExperimentsGet200Response", + "DataProjectsProjectIdSubjectsSubjectIdExperimentsGet200ResponseResultSet", + "DataProjectsProjectIdSubjectsSubjectIdExperimentsGet200ResponseResultSetResultInner", +] + # import apis into sdk package -from openapi_client.api.default_api import DefaultApi +from openapi_client.api.default_api import DefaultApi as DefaultApi # import ApiClient -from openapi_client.api_response import ApiResponse -from openapi_client.api_client import ApiClient -from openapi_client.configuration import Configuration -from openapi_client.exceptions import OpenApiException -from openapi_client.exceptions import ApiTypeError -from openapi_client.exceptions import ApiValueError -from openapi_client.exceptions import ApiKeyError -from openapi_client.exceptions import ApiAttributeError -from openapi_client.exceptions import ApiException +from openapi_client.api_response import ApiResponse as ApiResponse +from openapi_client.api_client import ApiClient as ApiClient +from openapi_client.configuration import Configuration as Configuration +from openapi_client.exceptions import OpenApiException as OpenApiException +from openapi_client.exceptions import ApiTypeError as ApiTypeError +from openapi_client.exceptions import ApiValueError as ApiValueError +from openapi_client.exceptions import ApiKeyError as ApiKeyError +from openapi_client.exceptions import ApiAttributeError as ApiAttributeError +from openapi_client.exceptions import ApiException as ApiException # import models into sdk package -from openapi_client.models.data_experiments_experiment_id_scans_get200_response import DataExperimentsExperimentIdScansGet200Response -from openapi_client.models.data_experiments_experiment_id_scans_get200_response_result_set import DataExperimentsExperimentIdScansGet200ResponseResultSet -from openapi_client.models.data_experiments_experiment_id_scans_get200_response_result_set_result_inner import DataExperimentsExperimentIdScansGet200ResponseResultSetResultInner -from openapi_client.models.data_projects_project_id_subjects_subject_id_experiments_get200_response import DataProjectsProjectIdSubjectsSubjectIdExperimentsGet200Response -from openapi_client.models.data_projects_project_id_subjects_subject_id_experiments_get200_response_result_set import DataProjectsProjectIdSubjectsSubjectIdExperimentsGet200ResponseResultSet -from openapi_client.models.data_projects_project_id_subjects_subject_id_experiments_get200_response_result_set_result_inner import DataProjectsProjectIdSubjectsSubjectIdExperimentsGet200ResponseResultSetResultInner +from openapi_client.models.data_experiments_experiment_id_scans_get200_response import DataExperimentsExperimentIdScansGet200Response as DataExperimentsExperimentIdScansGet200Response +from openapi_client.models.data_experiments_experiment_id_scans_get200_response_result_set import DataExperimentsExperimentIdScansGet200ResponseResultSet as DataExperimentsExperimentIdScansGet200ResponseResultSet +from openapi_client.models.data_experiments_experiment_id_scans_get200_response_result_set_result_inner import DataExperimentsExperimentIdScansGet200ResponseResultSetResultInner as DataExperimentsExperimentIdScansGet200ResponseResultSetResultInner +from openapi_client.models.data_projects_project_id_subjects_subject_id_experiments_get200_response import DataProjectsProjectIdSubjectsSubjectIdExperimentsGet200Response as DataProjectsProjectIdSubjectsSubjectIdExperimentsGet200Response +from openapi_client.models.data_projects_project_id_subjects_subject_id_experiments_get200_response_result_set import DataProjectsProjectIdSubjectsSubjectIdExperimentsGet200ResponseResultSet as DataProjectsProjectIdSubjectsSubjectIdExperimentsGet200ResponseResultSet +from openapi_client.models.data_projects_project_id_subjects_subject_id_experiments_get200_response_result_set_result_inner import DataProjectsProjectIdSubjectsSubjectIdExperimentsGet200ResponseResultSetResultInner as DataProjectsProjectIdSubjectsSubjectIdExperimentsGet200ResponseResultSetResultInner + diff --git a/clients/xnat/generated/openapi_client/api/default_api.py b/clients/xnat/generated/openapi_client/api/default_api.py index c0dc66e8c..2a9fa2ebc 100644 --- a/clients/xnat/generated/openapi_client/api/default_api.py +++ b/clients/xnat/generated/openapi_client/api/default_api.py @@ -268,7 +268,9 @@ def _data_experiments_experiment_id_scans_get_serialize( _query_params: List[Tuple[str, str]] = [] _header_params: Dict[str, Optional[str]] = _headers or {} _form_params: List[Tuple[str, str]] = [] - _files: Dict[str, str] = {} + _files: Dict[ + str, Union[str, bytes, List[str], List[bytes], List[Tuple[str, bytes]]] + ] = {} _body_params: Optional[bytes] = None # process the path parameters @@ -285,11 +287,12 @@ def _data_experiments_experiment_id_scans_get_serialize( # set the HTTP header `Accept` - _header_params['Accept'] = self.api_client.select_header_accept( - [ - 'application/json' - ] - ) + if 'Accept' not in _header_params: + _header_params['Accept'] = self.api_client.select_header_accept( + [ + 'application/json' + ] + ) # authentication setting @@ -556,7 +559,9 @@ def _data_projects_project_id_subjects_subject_id_experiments_get_serialize( _query_params: List[Tuple[str, str]] = [] _header_params: Dict[str, Optional[str]] = _headers or {} _form_params: List[Tuple[str, str]] = [] - _files: Dict[str, str] = {} + _files: Dict[ + str, Union[str, bytes, List[str], List[bytes], List[Tuple[str, bytes]]] + ] = {} _body_params: Optional[bytes] = None # process the path parameters @@ -575,11 +580,12 @@ def _data_projects_project_id_subjects_subject_id_experiments_get_serialize( # set the HTTP header `Accept` - _header_params['Accept'] = self.api_client.select_header_accept( - [ - 'application/json' - ] - ) + if 'Accept' not in _header_params: + _header_params['Accept'] = self.api_client.select_header_accept( + [ + 'application/json' + ] + ) # authentication setting @@ -807,7 +813,9 @@ def _data_services_auth_put_serialize( _query_params: List[Tuple[str, str]] = [] _header_params: Dict[str, Optional[str]] = _headers or {} _form_params: List[Tuple[str, str]] = [] - _files: Dict[str, str] = {} + _files: Dict[ + str, Union[str, bytes, List[str], List[bytes], List[Tuple[str, bytes]]] + ] = {} _body_params: Optional[bytes] = None # process the path parameters diff --git a/clients/xnat/generated/openapi_client/api_client.py b/clients/xnat/generated/openapi_client/api_client.py index b03fa098b..056f53c67 100644 --- a/clients/xnat/generated/openapi_client/api_client.py +++ b/clients/xnat/generated/openapi_client/api_client.py @@ -15,14 +15,17 @@ import datetime from dateutil.parser import parse from enum import Enum +import decimal import json import mimetypes import os import re import tempfile +import uuid from urllib.parse import quote -from typing import Tuple, Optional, List, Dict +from typing import Tuple, Optional, List, Dict, Union +from pydantic import SecretStr from openapi_client.configuration import Configuration from openapi_client.api_response import ApiResponse, T as ApiResponseT @@ -65,6 +68,7 @@ class ApiClient: 'bool': bool, 'date': datetime.date, 'datetime': datetime.datetime, + 'decimal': decimal.Decimal, 'object': object, } _pool = None @@ -207,7 +211,8 @@ def param_serialize( post_params, collection_formats ) - post_params.extend(self.files_parameters(files)) + if files: + post_params.extend(self.files_parameters(files)) # auth setting self.update_params_for_auth( @@ -225,7 +230,7 @@ def param_serialize( body = self.sanitize_for_serialization(body) # request url - if _host is None: + if _host is None or self.configuration.ignore_operation_servers: url = self.configuration.host + resource_path else: # use server/host defined in path or operation instead @@ -307,12 +312,12 @@ def response_deserialize( return_data = self.__deserialize_file(response_data) elif response_type is not None: match = None - content_type = response_data.getheader('content-type') + content_type = response_data.headers.get('content-type') if content_type is not None: match = re.search(r"charset=([a-zA-Z\-\d]+)[\s;]?", content_type) encoding = match.group(1) if match else "utf-8" response_text = response_data.data.decode(encoding) - return_data = self.deserialize(response_text, response_type) + return_data = self.deserialize(response_text, response_type, content_type) finally: if not 200 <= response_data.status <= 299: raise ApiException.from_response( @@ -324,7 +329,7 @@ def response_deserialize( return ApiResponse( status_code = response_data.status, data = return_data, - headers = response_data.getheaders(), + headers = response_data.headers, raw_data = response_data.data ) @@ -332,9 +337,11 @@ def sanitize_for_serialization(self, obj): """Builds a JSON POST object. If obj is None, return None. + If obj is SecretStr, return obj.get_secret_value() If obj is str, int, long, float, bool, return directly. If obj is datetime.datetime, datetime.date convert to string in iso8601 format. + If obj is decimal.Decimal return string representation. If obj is list, sanitize each element in the list. If obj is dict, return the dict. If obj is OpenAPI model, return the properties dict. @@ -344,8 +351,14 @@ def sanitize_for_serialization(self, obj): """ if obj is None: return None + elif isinstance(obj, Enum): + return obj.value + elif isinstance(obj, SecretStr): + return obj.get_secret_value() elif isinstance(obj, self.PRIMITIVE_TYPES): return obj + elif isinstance(obj, uuid.UUID): + return str(obj) elif isinstance(obj, list): return [ self.sanitize_for_serialization(sub_obj) for sub_obj in obj @@ -356,6 +369,8 @@ def sanitize_for_serialization(self, obj): ) elif isinstance(obj, (datetime.datetime, datetime.date)): return obj.isoformat() + elif isinstance(obj, decimal.Decimal): + return str(obj) elif isinstance(obj, dict): obj_dict = obj @@ -365,28 +380,49 @@ def sanitize_for_serialization(self, obj): # and attributes which value is not None. # Convert attribute name to json key in # model definition for request. - obj_dict = obj.to_dict() + if hasattr(obj, 'to_dict') and callable(getattr(obj, 'to_dict')): + obj_dict = obj.to_dict() + else: + obj_dict = obj.__dict__ + + if isinstance(obj_dict, list): + # here we handle instances that can either be a list or something else, and only became a real list by calling to_dict() + return self.sanitize_for_serialization(obj_dict) return { key: self.sanitize_for_serialization(val) for key, val in obj_dict.items() } - def deserialize(self, response_text, response_type): + def deserialize(self, response_text: str, response_type: str, content_type: Optional[str]): """Deserializes response into an object. :param response: RESTResponse object to be deserialized. :param response_type: class literal for deserialized object, or string of class name. + :param content_type: content type of response. :return: deserialized object. """ # fetch data from response object - try: - data = json.loads(response_text) - except ValueError: + if content_type is None: + try: + data = json.loads(response_text) + except ValueError: + data = response_text + elif re.match(r'^application/(json|[\w!#$&.+\-^_]+\+json)\s*(;|$)', content_type, re.IGNORECASE): + if response_text == "": + data = "" + else: + data = json.loads(response_text) + elif re.match(r'^text\/[a-z.+-]+\s*(;|$)', content_type, re.IGNORECASE): data = response_text + else: + raise ApiException( + status=0, + reason="Unsupported content type: {0}".format(content_type) + ) return self.__deserialize(data, response_type) @@ -424,12 +460,14 @@ def __deserialize(self, data, klass): if klass in self.PRIMITIVE_TYPES: return self.__deserialize_primitive(data, klass) - elif klass == object: + elif klass is object: return self.__deserialize_object(data) - elif klass == datetime.date: + elif klass is datetime.date: return self.__deserialize_date(data) - elif klass == datetime.datetime: + elif klass is datetime.datetime: return self.__deserialize_datetime(data) + elif klass is decimal.Decimal: + return decimal.Decimal(data) elif issubclass(klass, Enum): return self.__deserialize_enum(data, klass) else: @@ -486,7 +524,7 @@ def parameters_to_url_query(self, params, collection_formats): if k in collection_formats: collection_format = collection_formats[k] if collection_format == 'multi': - new_params.extend((k, str(value)) for value in v) + new_params.extend((k, quote(str(value))) for value in v) else: if collection_format == 'ssv': delimiter = ' ' @@ -504,31 +542,39 @@ def parameters_to_url_query(self, params, collection_formats): return "&".join(["=".join(map(str, item)) for item in new_params]) - def files_parameters(self, files=None): + def files_parameters( + self, + files: Dict[str, Union[str, bytes, List[str], List[bytes], Tuple[str, bytes]]], + ): """Builds form parameters. :param files: File parameters. :return: Form parameters with files. """ params = [] - - if files: - for k, v in files.items(): - if not v: - continue - file_names = v if type(v) is list else [v] - for n in file_names: - with open(n, 'rb') as f: - filename = os.path.basename(f.name) - filedata = f.read() - mimetype = ( - mimetypes.guess_type(filename)[0] - or 'application/octet-stream' - ) - params.append( - tuple([k, tuple([filename, filedata, mimetype])]) - ) - + for k, v in files.items(): + if isinstance(v, str): + with open(v, 'rb') as f: + filename = os.path.basename(f.name) + filedata = f.read() + elif isinstance(v, bytes): + filename = k + filedata = v + elif isinstance(v, tuple): + filename, filedata = v + elif isinstance(v, list): + for file_param in v: + params.extend(self.files_parameters({k: file_param})) + continue + else: + raise ValueError("Unsupported file value") + mimetype = ( + mimetypes.guess_type(filename)[0] + or 'application/octet-stream' + ) + params.append( + tuple([k, tuple([filename, filedata, mimetype])]) + ) return params def select_header_accept(self, accepts: List[str]) -> Optional[str]: @@ -655,7 +701,7 @@ def __deserialize_file(self, response): os.close(fd) os.remove(path) - content_disposition = response.getheader("Content-Disposition") + content_disposition = response.headers.get("Content-Disposition") if content_disposition: m = re.search( r'filename=[\'"]?([^\'"\s]+)[\'"]?', diff --git a/clients/xnat/generated/openapi_client/configuration.py b/clients/xnat/generated/openapi_client/configuration.py index 830c76d59..293e66a22 100644 --- a/clients/xnat/generated/openapi_client/configuration.py +++ b/clients/xnat/generated/openapi_client/configuration.py @@ -13,14 +13,16 @@ import copy +import http.client as httplib import logging from logging import FileHandler import multiprocessing import sys -from typing import Optional +from typing import Any, ClassVar, Dict, List, Literal, Optional, TypedDict, Union +from typing_extensions import NotRequired, Self + import urllib3 -import http.client as httplib JSON_SCHEMA_VALIDATION_KEYWORDS = { 'multipleOf', 'maximum', 'exclusiveMaximum', @@ -28,10 +30,115 @@ 'minLength', 'pattern', 'maxItems', 'minItems' } +ServerVariablesT = Dict[str, str] + +GenericAuthSetting = TypedDict( + "GenericAuthSetting", + { + "type": str, + "in": str, + "key": str, + "value": str, + }, +) + + +OAuth2AuthSetting = TypedDict( + "OAuth2AuthSetting", + { + "type": Literal["oauth2"], + "in": Literal["header"], + "key": Literal["Authorization"], + "value": str, + }, +) + + +APIKeyAuthSetting = TypedDict( + "APIKeyAuthSetting", + { + "type": Literal["api_key"], + "in": str, + "key": str, + "value": Optional[str], + }, +) + + +BasicAuthSetting = TypedDict( + "BasicAuthSetting", + { + "type": Literal["basic"], + "in": Literal["header"], + "key": Literal["Authorization"], + "value": Optional[str], + }, +) + + +BearerFormatAuthSetting = TypedDict( + "BearerFormatAuthSetting", + { + "type": Literal["bearer"], + "in": Literal["header"], + "format": Literal["JWT"], + "key": Literal["Authorization"], + "value": str, + }, +) + + +BearerAuthSetting = TypedDict( + "BearerAuthSetting", + { + "type": Literal["bearer"], + "in": Literal["header"], + "key": Literal["Authorization"], + "value": str, + }, +) + + +HTTPSignatureAuthSetting = TypedDict( + "HTTPSignatureAuthSetting", + { + "type": Literal["http-signature"], + "in": Literal["header"], + "key": Literal["Authorization"], + "value": None, + }, +) + + +AuthSettings = TypedDict( + "AuthSettings", + { + "basicAuth": BasicAuthSetting, + "cookieAuth": APIKeyAuthSetting, + }, + total=False, +) + + +class HostSettingVariable(TypedDict): + description: str + default_value: str + enum_values: List[str] + + +class HostSetting(TypedDict): + url: str + description: str + variables: NotRequired[Dict[str, HostSettingVariable]] + + class Configuration: """This class contains various settings of the API client. :param host: Base url. + :param ignore_operation_servers + Boolean to ignore operation servers for the API client. + Config will use `host` as the base url regardless of the operation servers. :param api_key: Dict to store API key(s). Each entry in the dict specifies an API key. The dict key is the name of the security scheme in the OAS specification. @@ -54,6 +161,11 @@ class Configuration: values before. :param ssl_ca_cert: str - the path to a file of concatenated CA certificates in PEM format. + :param retries: Number of retries for API requests. + :param ca_cert_data: verify the peer using concatenated CA certificate data + in PEM (str) or DER (bytes) format. + :param cert_file: the path to a client certificate file, for mTLS. + :param key_file: the path to a client key file, for mTLS. :Example: @@ -93,16 +205,29 @@ class Configuration: """ - _default = None - - def __init__(self, host=None, - api_key=None, api_key_prefix=None, - username=None, password=None, - access_token=None, - server_index=None, server_variables=None, - server_operation_index=None, server_operation_variables=None, - ssl_ca_cert=None, - ) -> None: + _default: ClassVar[Optional[Self]] = None + + def __init__( + self, + host: Optional[str]=None, + api_key: Optional[Dict[str, str]]=None, + api_key_prefix: Optional[Dict[str, str]]=None, + username: Optional[str]=None, + password: Optional[str]=None, + access_token: Optional[str]=None, + server_index: Optional[int]=None, + server_variables: Optional[ServerVariablesT]=None, + server_operation_index: Optional[Dict[int, int]]=None, + server_operation_variables: Optional[Dict[int, ServerVariablesT]]=None, + ignore_operation_servers: bool=False, + ssl_ca_cert: Optional[str]=None, + retries: Optional[int] = None, + ca_cert_data: Optional[Union[str, bytes]] = None, + cert_file: Optional[str]=None, + key_file: Optional[str]=None, + *, + debug: Optional[bool] = None, + ) -> None: """Constructor """ self._base_path = "http://localhost" if host is None else host @@ -116,6 +241,9 @@ def __init__(self, host=None, self.server_operation_variables = server_operation_variables or {} """Default server variables """ + self.ignore_operation_servers = ignore_operation_servers + """Ignore operation servers + """ self.temp_folder_path = None """Temp file folder for downloading files """ @@ -159,7 +287,10 @@ def __init__(self, host=None, self.logger_file = None """Debug file location """ - self.debug = False + if debug is not None: + self.debug = debug + else: + self.__debug = False """Debug switch """ @@ -171,10 +302,14 @@ def __init__(self, host=None, self.ssl_ca_cert = ssl_ca_cert """Set this to customize the certificate file to verify the peer. """ - self.cert_file = None + self.ca_cert_data = ca_cert_data + """Set this to verify the peer using PEM (str) or DER (bytes) + certificate data. + """ + self.cert_file = cert_file """client certificate file """ - self.key_file = None + self.key_file = key_file """client key file """ self.assert_hostname = None @@ -202,7 +337,7 @@ def __init__(self, host=None, self.safe_chars_for_path_param = '' """Safe chars for path_param """ - self.retries = None + self.retries = retries """Adding retries to override urllib3 default value 3 """ # Enable client side validation @@ -220,7 +355,7 @@ def __init__(self, host=None, """date format """ - def __deepcopy__(self, memo): + def __deepcopy__(self, memo: Dict[int, Any]) -> Self: cls = self.__class__ result = cls.__new__(cls) memo[id(self)] = result @@ -234,11 +369,11 @@ def __deepcopy__(self, memo): result.debug = self.debug return result - def __setattr__(self, name, value): + def __setattr__(self, name: str, value: Any) -> None: object.__setattr__(self, name, value) @classmethod - def set_default(cls, default): + def set_default(cls, default: Optional[Self]) -> None: """Set default instance of configuration. It stores default configuration, which can be @@ -249,7 +384,7 @@ def set_default(cls, default): cls._default = default @classmethod - def get_default_copy(cls): + def get_default_copy(cls) -> Self: """Deprecated. Please use `get_default` instead. Deprecated. Please use `get_default` instead. @@ -259,7 +394,7 @@ def get_default_copy(cls): return cls.get_default() @classmethod - def get_default(cls): + def get_default(cls) -> Self: """Return the default configuration. This method returns newly created, based on default constructor, @@ -269,11 +404,11 @@ def get_default(cls): :return: The configuration object. """ if cls._default is None: - cls._default = Configuration() + cls._default = cls() return cls._default @property - def logger_file(self): + def logger_file(self) -> Optional[str]: """The logger file. If the logger_file is None, then add stream handler and remove file @@ -285,7 +420,7 @@ def logger_file(self): return self.__logger_file @logger_file.setter - def logger_file(self, value): + def logger_file(self, value: Optional[str]) -> None: """The logger file. If the logger_file is None, then add stream handler and remove file @@ -304,7 +439,7 @@ def logger_file(self, value): logger.addHandler(self.logger_file_handler) @property - def debug(self): + def debug(self) -> bool: """Debug status :param value: The debug status, True or False. @@ -313,7 +448,7 @@ def debug(self): return self.__debug @debug.setter - def debug(self, value): + def debug(self, value: bool) -> None: """Debug status :param value: The debug status, True or False. @@ -335,7 +470,7 @@ def debug(self, value): httplib.HTTPConnection.debuglevel = 0 @property - def logger_format(self): + def logger_format(self) -> str: """The logger format. The logger_formatter will be updated when sets logger_format. @@ -346,7 +481,7 @@ def logger_format(self): return self.__logger_format @logger_format.setter - def logger_format(self, value): + def logger_format(self, value: str) -> None: """The logger format. The logger_formatter will be updated when sets logger_format. @@ -357,7 +492,7 @@ def logger_format(self, value): self.__logger_format = value self.logger_formatter = logging.Formatter(self.__logger_format) - def get_api_key_with_prefix(self, identifier, alias=None): + def get_api_key_with_prefix(self, identifier: str, alias: Optional[str]=None) -> Optional[str]: """Gets API key (with prefix if set). :param identifier: The identifier of apiKey. @@ -374,7 +509,9 @@ def get_api_key_with_prefix(self, identifier, alias=None): else: return key - def get_basic_auth_token(self): + return None + + def get_basic_auth_token(self) -> Optional[str]: """Gets HTTP basic authentication header (string). :return: The token for basic HTTP authentication. @@ -385,16 +522,17 @@ def get_basic_auth_token(self): password = "" if self.password is not None: password = self.password + return urllib3.util.make_headers( basic_auth=username + ':' + password ).get('authorization') - def auth_settings(self): + def auth_settings(self)-> AuthSettings: """Gets Auth Settings dict for api client. :return: The Auth Settings information dict. """ - auth = {} + auth: AuthSettings = {} if self.username is not None and self.password is not None: auth['basicAuth'] = { 'type': 'basic', @@ -413,7 +551,7 @@ def auth_settings(self): } return auth - def to_debug_report(self): + def to_debug_report(self) -> str: """Gets the essential information for debugging. :return: The report for debugging. @@ -425,7 +563,7 @@ def to_debug_report(self): "SDK Package Version: 1.0.0".\ format(env=sys.platform, pyversion=sys.version) - def get_host_settings(self): + def get_host_settings(self) -> List[HostSetting]: """Gets an array of host settings :return: An array of host settings @@ -437,7 +575,12 @@ def get_host_settings(self): } ] - def get_host_from_settings(self, index, variables=None, servers=None): + def get_host_from_settings( + self, + index: Optional[int], + variables: Optional[ServerVariablesT]=None, + servers: Optional[List[HostSetting]]=None, + ) -> str: """Gets host URL based on the index and variables :param index: array index of the host settings :param variables: hash of variable and the corresponding value @@ -465,6 +608,7 @@ def get_host_from_settings(self, index, variables=None, servers=None): variable_name, variable['default_value']) if 'enum_values' in variable \ + and variable['enum_values'] \ and used_value not in variable['enum_values']: raise ValueError( "The variable `{0}` in the host URL has invalid value " @@ -477,12 +621,12 @@ def get_host_from_settings(self, index, variables=None, servers=None): return url @property - def host(self): + def host(self) -> str: """Return generated host.""" return self.get_host_from_settings(self.server_index, variables=self.server_variables) @host.setter - def host(self, value): + def host(self, value: str) -> None: """Fix base path.""" self._base_path = value self.server_index = None diff --git a/clients/xnat/generated/openapi_client/exceptions.py b/clients/xnat/generated/openapi_client/exceptions.py index 30d9a5db3..32c84d28f 100644 --- a/clients/xnat/generated/openapi_client/exceptions.py +++ b/clients/xnat/generated/openapi_client/exceptions.py @@ -128,7 +128,7 @@ def __init__( self.body = http_resp.data.decode('utf-8') except Exception: pass - self.headers = http_resp.getheaders() + self.headers = http_resp.headers @classmethod def from_response( @@ -150,6 +150,13 @@ def from_response( if http_resp.status == 404: raise NotFoundException(http_resp=http_resp, body=body, data=data) + # Added new conditions for 409 and 422 + if http_resp.status == 409: + raise ConflictException(http_resp=http_resp, body=body, data=data) + + if http_resp.status == 422: + raise UnprocessableEntityException(http_resp=http_resp, body=body, data=data) + if 500 <= http_resp.status <= 599: raise ServiceException(http_resp=http_resp, body=body, data=data) raise ApiException(http_resp=http_resp, body=body, data=data) @@ -162,8 +169,11 @@ def __str__(self): error_message += "HTTP response headers: {0}\n".format( self.headers) - if self.data or self.body: - error_message += "HTTP response body: {0}\n".format(self.data or self.body) + if self.body: + error_message += "HTTP response body: {0}\n".format(self.body) + + if self.data: + error_message += "HTTP response data: {0}\n".format(self.data) return error_message @@ -188,6 +198,16 @@ class ServiceException(ApiException): pass +class ConflictException(ApiException): + """Exception for HTTP 409 Conflict.""" + pass + + +class UnprocessableEntityException(ApiException): + """Exception for HTTP 422 Unprocessable Entity.""" + pass + + def render_path(path_to_item): """Returns a string representation of a path""" result = "" diff --git a/clients/xnat/generated/openapi_client/models/__init__.py b/clients/xnat/generated/openapi_client/models/__init__.py index 4c37c2cfa..cca18d9b2 100644 --- a/clients/xnat/generated/openapi_client/models/__init__.py +++ b/clients/xnat/generated/openapi_client/models/__init__.py @@ -12,7 +12,6 @@ Do not edit the class manually. """ # noqa: E501 - # import models into model package from openapi_client.models.data_experiments_experiment_id_scans_get200_response import DataExperimentsExperimentIdScansGet200Response from openapi_client.models.data_experiments_experiment_id_scans_get200_response_result_set import DataExperimentsExperimentIdScansGet200ResponseResultSet @@ -20,3 +19,4 @@ from openapi_client.models.data_projects_project_id_subjects_subject_id_experiments_get200_response import DataProjectsProjectIdSubjectsSubjectIdExperimentsGet200Response from openapi_client.models.data_projects_project_id_subjects_subject_id_experiments_get200_response_result_set import DataProjectsProjectIdSubjectsSubjectIdExperimentsGet200ResponseResultSet from openapi_client.models.data_projects_project_id_subjects_subject_id_experiments_get200_response_result_set_result_inner import DataProjectsProjectIdSubjectsSubjectIdExperimentsGet200ResponseResultSetResultInner + diff --git a/clients/xnat/generated/openapi_client/models/data_experiments_experiment_id_scans_get200_response_result_set.py b/clients/xnat/generated/openapi_client/models/data_experiments_experiment_id_scans_get200_response_result_set.py index 80363b848..11257fc8f 100644 --- a/clients/xnat/generated/openapi_client/models/data_experiments_experiment_id_scans_get200_response_result_set.py +++ b/clients/xnat/generated/openapi_client/models/data_experiments_experiment_id_scans_get200_response_result_set.py @@ -73,9 +73,9 @@ def to_dict(self) -> Dict[str, Any]: # override the default output from pydantic by calling `to_dict()` of each item in result (list) _items = [] if self.result: - for _item in self.result: - if _item: - _items.append(_item.to_dict()) + for _item_result in self.result: + if _item_result: + _items.append(_item_result.to_dict()) _dict['Result'] = _items return _dict diff --git a/clients/xnat/generated/openapi_client/models/data_projects_project_id_subjects_subject_id_experiments_get200_response_result_set.py b/clients/xnat/generated/openapi_client/models/data_projects_project_id_subjects_subject_id_experiments_get200_response_result_set.py index 1bfd822e0..9777337b8 100644 --- a/clients/xnat/generated/openapi_client/models/data_projects_project_id_subjects_subject_id_experiments_get200_response_result_set.py +++ b/clients/xnat/generated/openapi_client/models/data_projects_project_id_subjects_subject_id_experiments_get200_response_result_set.py @@ -73,9 +73,9 @@ def to_dict(self) -> Dict[str, Any]: # override the default output from pydantic by calling `to_dict()` of each item in result (list) _items = [] if self.result: - for _item in self.result: - if _item: - _items.append(_item.to_dict()) + for _item_result in self.result: + if _item_result: + _items.append(_item_result.to_dict()) _dict['Result'] = _items return _dict diff --git a/clients/xnat/generated/openapi_client/rest.py b/clients/xnat/generated/openapi_client/rest.py index 966666995..ed8a4326f 100644 --- a/clients/xnat/generated/openapi_client/rest.py +++ b/clients/xnat/generated/openapi_client/rest.py @@ -48,12 +48,17 @@ def read(self): self.data = self.response.data return self.data + @property + def headers(self): + """Returns a dictionary of response headers.""" + return self.response.headers + def getheaders(self): - """Returns a dictionary of the response headers.""" + """Returns a dictionary of the response headers; use ``headers`` instead.""" return self.response.headers def getheader(self, name, default=None): - """Returns a given response header.""" + """Returns a given response header; use ``headers.get()`` instead.""" return self.response.headers.get(name, default) @@ -76,6 +81,7 @@ def __init__(self, configuration) -> None: "ca_certs": configuration.ssl_ca_cert, "cert_file": configuration.cert_file, "key_file": configuration.key_file, + "ca_cert_data": configuration.ca_cert_data, } if configuration.assert_hostname is not None: pool_args['assert_hostname'] = ( @@ -202,6 +208,8 @@ def request( # Content-Type which generated by urllib3 will be # overwritten. del headers['Content-Type'] + # Ensures that dict objects are serialized + post_params = [(a, json.dumps(b)) if isinstance(b, dict) else (a,b) for a, b in post_params] r = self.pool_manager.request( method, url, @@ -223,7 +231,7 @@ def request( headers=headers, preload_content=False ) - elif headers['Content-Type'] == 'text/plain' and isinstance(body, bool): + elif headers['Content-Type'].startswith('text/') and isinstance(body, bool): request_body = "true" if body else "false" r = self.pool_manager.request( method, diff --git a/clients/xnat/generated/pyproject.toml b/clients/xnat/generated/pyproject.toml index 2096bc99f..9847fa40e 100644 --- a/clients/xnat/generated/pyproject.toml +++ b/clients/xnat/generated/pyproject.toml @@ -1,28 +1,34 @@ -[tool.poetry] +[project] name = "openapi_client" version = "1.0.0" description = "XNAT REST API Translation" -authors = ["OpenAPI Generator Community "] -license = "NoLicense" +authors = [ + {name = "OpenAPI Generator Community",email = "team@openapitools.org"}, +] readme = "README.md" -repository = "https://github.com/GIT_USER_ID/GIT_REPO_ID" keywords = ["OpenAPI", "OpenAPI-Generator", "XNAT REST API Translation"] -include = ["openapi_client/py.typed"] +requires-python = ">=3.9" -[tool.poetry.dependencies] -python = "^3.7" +dependencies = [ + "urllib3 (>=2.1.0,<3.0.0)", + "python-dateutil (>=2.8.2)", + "pydantic (>=2)", + "typing-extensions (>=4.7.1)", +] -urllib3 = ">= 1.25.3" -python-dateutil = ">=2.8.2" -pydantic = ">=2" -typing-extensions = ">=4.7.1" +[project.urls] +Repository = "https://github.com/GIT_USER_ID/GIT_REPO_ID" -[tool.poetry.dev-dependencies] -pytest = ">=7.2.1" -tox = ">=3.9.0" -flake8 = ">=4.0.0" -types-python-dateutil = ">=2.8.19.14" -mypy = "1.4.1" +[tool.poetry] +requires-poetry = ">=2.0" + +[tool.poetry.group.dev.dependencies] +pytest = ">= 7.2.1" +pytest-cov = ">= 2.8.1" +tox = ">= 3.9.0" +flake8 = ">= 4.0.0" +types-python-dateutil = ">= 2.8.19.14" +mypy = ">= 1.5" [build-system] @@ -48,7 +54,7 @@ warn_unused_ignores = true ## Getting these passing should be easy strict_equality = true -strict_concatenate = true +extra_checks = true ## Strongly recommend enabling this one as soon as you can check_untyped_defs = true @@ -69,3 +75,20 @@ disallow_any_generics = true # ### This one can be tricky to get passing if you use a lot of untyped libraries #warn_return_any = true + +[[tool.mypy.overrides]] +module = [ + "openapi_client.configuration", +] +warn_unused_ignores = true +strict_equality = true +extra_checks = true +check_untyped_defs = true +disallow_subclassing_any = true +disallow_untyped_decorators = true +disallow_any_generics = true +disallow_untyped_calls = true +disallow_incomplete_defs = true +disallow_untyped_defs = true +no_implicit_reexport = true +warn_return_any = true diff --git a/clients/xnat/generated/requirements.txt b/clients/xnat/generated/requirements.txt index cc85509ec..6cbb2b98b 100644 --- a/clients/xnat/generated/requirements.txt +++ b/clients/xnat/generated/requirements.txt @@ -1,5 +1,4 @@ -python_dateutil >= 2.5.3 -setuptools >= 21.0.0 -urllib3 >= 1.25.3, < 2.1.0 +urllib3 >= 2.1.0, < 3.0.0 +python_dateutil >= 2.8.2 pydantic >= 2 typing-extensions >= 4.7.1 diff --git a/clients/xnat/generated/setup.py b/clients/xnat/generated/setup.py index 6f3312d81..bf2127aa3 100644 --- a/clients/xnat/generated/setup.py +++ b/clients/xnat/generated/setup.py @@ -22,10 +22,10 @@ # http://pypi.python.org/pypi/setuptools NAME = "openapi-client" VERSION = "1.0.0" -PYTHON_REQUIRES = ">=3.7" +PYTHON_REQUIRES = ">= 3.9" REQUIRES = [ - "urllib3 >= 1.25.3, < 2.1.0", - "python-dateutil", + "urllib3 >= 2.1.0, < 3.0.0", + "python-dateutil >= 2.8.2", "pydantic >= 2", "typing-extensions >= 4.7.1", ] @@ -46,4 +46,4 @@ REST API converted to Open API """, # noqa: E501 package_data={"openapi_client": ["py.typed"]}, -) +) \ No newline at end of file diff --git a/clients/xnat/generated/test-requirements.txt b/clients/xnat/generated/test-requirements.txt index 8e6d8cb13..e98555c11 100644 --- a/clients/xnat/generated/test-requirements.txt +++ b/clients/xnat/generated/test-requirements.txt @@ -1,5 +1,6 @@ -pytest~=7.1.3 -pytest-cov>=2.8.1 -pytest-randomly>=3.12.0 -mypy>=1.4.1 -types-python-dateutil>=2.8.19 +pytest >= 7.2.1 +pytest-cov >= 2.8.1 +tox >= 3.9.0 +flake8 >= 4.0.0 +types-python-dateutil >= 2.8.19.14 +mypy >= 1.5 diff --git a/docker-compose-aloe.yml b/docker-compose-aloe.yml index 9a57b6ca3..85d6d969c 100644 --- a/docker-compose-aloe.yml +++ b/docker-compose-aloe.yml @@ -1,5 +1,3 @@ -version: '3.7' - x-common-env-variables: &common-env-variables DEBUG: 0 TEST_WAIT: 10 diff --git a/docker-compose-selenium.yml b/docker-compose-selenium.yml index 71c9551c0..76e432b75 100644 --- a/docker-compose-selenium.yml +++ b/docker-compose-selenium.yml @@ -1,5 +1,3 @@ -version: '3.7' - services: hub: image: selenium/hub:3.141 diff --git a/docker-compose-teststack-base.yml b/docker-compose-teststack-base.yml index 4a795ddb1..beaf91607 100644 --- a/docker-compose-teststack-base.yml +++ b/docker-compose-teststack-base.yml @@ -1,5 +1,3 @@ -version: '3.7' - services: dbtest: image: "postgres:${POSTGRES_VERSION}" @@ -26,6 +24,6 @@ services: - "8443:8443" - "8080:8080" expose: - - "8080" + - "8080" volumes: - "./clients/xnat/mock:/home/wiremock" diff --git a/docker-compose-teststack-dev.yml b/docker-compose-teststack-dev.yml index b1678ab68..948759c66 100644 --- a/docker-compose-teststack-dev.yml +++ b/docker-compose-teststack-dev.yml @@ -1,5 +1,3 @@ -version: '3.7' - services: serverundertest: build: diff --git a/docker-compose.yml b/docker-compose.yml index 5f8da5165..a29eeb5f4 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -1,5 +1,3 @@ -version: "3.7" - volumes: dev_db_data: dev_clinicaldb_data: diff --git a/docker/dev/Dockerfile b/docker/dev/Dockerfile index 8d9d74ccc..a5a213144 100644 --- a/docker/dev/Dockerfile +++ b/docker/dev/Dockerfile @@ -1,10 +1,12 @@ -# FROM muccg/rdrf-builder -FROM python:3.13 as builder +# Builder stage +FROM python:3.13 AS builder -ENV PYTHONUNBUFFERED 1 +ENV PYTHONUNBUFFERED=1 + +# Install uv +COPY --from=ghcr.io/astral-sh/uv:latest /uv /uvx /bin/ RUN apt-get update && apt-get install -y --no-install-recommends \ - # TODO check if requirements are needed # Base gettext \ libpq5 \ @@ -22,43 +24,36 @@ RUN apt-get update && apt-get install -y --no-install-recommends \ zlib1g-dev \ && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* -RUN mkdir -p /requirements -WORKDIR /requirements - -# RUN env | sort - -# Add our python deps in multiple docker layers -# hgvs was failing due to lack of nose, hence the order - -COPY requirements/* ./ +WORKDIR /app +# Copy dependency files first for layer caching +COPY pyproject.toml uv.lock ./ COPY clients ./clients -RUN --mount=type=cache,target=/root/.cache/pip \ - pip install --upgrade pip setuptools && \ - pip install -r requirements.txt && \ - pip install -r dev-requirements.txt && \ - pip install -r test-requirements.txt +# Sync dependencies to /opt/venv (outside /app which gets volume-mounted in dev) +ENV UV_PROJECT_ENVIRONMENT=/opt/venv +ENV UV_LINK_MODE=copy +RUN --mount=type=cache,target=/root/.cache/uv \ + uv sync --locked --no-install-project --all-extras VOLUME ["/data"] +# Runtime stage FROM python:3.13-slim +# Install uv +COPY --from=ghcr.io/astral-sh/uv:latest /uv /uvx /bin/ + ENV PYTHONPATH="/app/rdrf/:${PYTHONPATH}" -ENV DJANGO_SETTINGS_MODULE rdrf.settings +ENV DJANGO_SETTINGS_MODULE=rdrf.settings ENV STATIC_ROOT="/data/static" ENV WRITABLE_DIRECTORY="/data/scratch" ENV LOCALE_PATHS="/app/translations/locale" ENV LOG_DIRECTORY="/data/log" ENV MEDIA_ROOT="/data/static/media" -# RUN apt-get update && apt-get install -y --no-install-recommends \ -# libxml2 \ -# && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* - RUN apt-get update && apt-get install -y --no-install-recommends \ # Base - # TODO check if requirements are needed gettext \ libpq5 \ media-types \ @@ -71,17 +66,23 @@ RUN apt-get update && apt-get install -y --no-install-recommends \ git \ && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* -RUN mkdir /requirements -WORKDIR /requirements +# Copy venv from builder to /opt/venv +COPY --from=builder /opt/venv /opt/venv -COPY --from=builder /requirements/ . +WORKDIR /app + +# Copy dependency files +COPY pyproject.toml uv.lock ./ +COPY clients ./clients -RUN --mount=type=cache,target=/root/.cache/pip \ - pip install -r requirements.txt && \ - pip install -r dev-requirements.txt && \ - pip install -r test-requirements.txt +# Finalize dependency install +ENV UV_PROJECT_ENVIRONMENT=/opt/venv +ENV UV_LINK_MODE=copy +RUN --mount=type=cache,target=/root/.cache/uv \ + uv sync --locked --all-extras -RUN rm -Rf /root/.cache +# Add venv to PATH +ENV PATH="/opt/venv/bin:$PATH" COPY docker/dev/docker-entrypoint.sh / RUN chmod +x /docker-entrypoint.sh @@ -91,7 +92,7 @@ RUN chmod +x /aws-lambda-rie VOLUME ["/app", "/data"] -ENV HOME /data +ENV HOME=/data WORKDIR /data EXPOSE 8000 diff --git a/docker/production/Dockerfile b/docker/production/Dockerfile index 68652cd8d..2008ee1ef 100644 --- a/docker/production/Dockerfile +++ b/docker/production/Dockerfile @@ -1,10 +1,12 @@ -# Container to build our prod image -FROM python:3.13 as builder +# Builder stage +FROM python:3.13 AS builder -ENV PYTHONUNBUFFERED 1 +ENV PYTHONUNBUFFERED=1 + +# Install uv +COPY --from=ghcr.io/astral-sh/uv:latest /uv /uvx /bin/ RUN apt-get update && apt-get install -y --no-install-recommends \ - # TODO check if requirements are needed # Base gettext \ libpq5 \ @@ -20,43 +22,40 @@ RUN apt-get update && apt-get install -y --no-install-recommends \ libyaml-dev \ unixodbc-dev \ zlib1g-dev \ - unixodbc-dev \ && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* -RUN mkdir -p /requirements -WORKDIR /requirements - -# RUN env | sort - -# Add our python deps in multiple docker layers -# hgvs was failing due to lack of nose, hence the order - -COPY requirements/* ./ +WORKDIR /app +# Copy dependency files first for layer caching +COPY pyproject.toml uv.lock ./ COPY clients ./clients -RUN pip install --upgrade setuptools pip -RUN pip install -r requirements.txt +# Sync production dependencies only +ENV UV_LINK_MODE=copy +RUN --mount=type=cache,target=/root/.cache/uv \ + uv sync --locked --no-install-project --no-dev -# Actual image we are building +# Runtime stage FROM python:3.13-slim -ENV PYTHONUNBUFFERED 1 +ENV PYTHONUNBUFFERED=1 + +# Install uv +COPY --from=ghcr.io/astral-sh/uv:latest /uv /uvx /bin/ ENV PYTHONPATH="/app/rdrf/" -ENV DJANGO_SETTINGS_MODULE rdrf.settings - -ENV PROJECT_NAME trrf -ENV PROJECT_SOURCE https://github.com/eresearchqut/trrf.git -ENV DEPLOYMENT prod -ENV PRODUCTION 1 -ENV DEBUG 0 -ENV STATIC_ROOT /data/static -ENV WRITABLE_DIRECTORY /data/scratch -ENV MEDIA_ROOT /data/static/media -ENV LOG_DIRECTORY /data/log -ENV LOCALE_PATHS /data/translations/locale -ENV DJANGO_SETTINGS_MODULE rdrf.settings +ENV DJANGO_SETTINGS_MODULE=rdrf.settings + +ENV PROJECT_NAME=trrf +ENV PROJECT_SOURCE=https://github.com/eresearchqut/trrf.git +ENV DEPLOYMENT=prod +ENV PRODUCTION=1 +ENV DEBUG=0 +ENV STATIC_ROOT=/data/static +ENV WRITABLE_DIRECTORY=/data/scratch +ENV MEDIA_ROOT=/data/static/media +ENV LOG_DIRECTORY=/data/log +ENV LOCALE_PATHS=/data/translations/locale RUN mkdir /app @@ -68,7 +67,6 @@ RUN addgroup --gid 1000 django \ RUN apt-get update && apt-get install -y --no-install-recommends \ # Base - # TODO check if requirements are needed git \ gettext \ libpq5 \ @@ -80,43 +78,43 @@ RUN apt-get update && apt-get install -y --no-install-recommends \ curl \ && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* -RUN mkdir /requirements -WORKDIR /requirements +WORKDIR /app -COPY --from=builder /root/.cache /root/.cache -COPY --from=builder /requirements/requirements.txt . +# Copy venv from builder +COPY --from=builder /app/.venv /app/.venv +# Copy dependency files +COPY pyproject.toml uv.lock ./ COPY clients ./clients -RUN pip install -r requirements.txt +# Finalize dependency install (production only) +ENV UV_LINK_MODE=copy +RUN --mount=type=cache,target=/root/.cache/uv \ + uv sync --locked --no-dev + +# Add venv to PATH +ENV PATH="/app/.venv/bin:$PATH" -# The generate snakeoil cert is valid for 10 years, but if you need to +# The generated snakeoil cert is valid for 10 years, but if you need to # re-generate it you can use: # RUN make-ssl-cert generate-default-snakeoil --force-overwrite RUN chgrp -R django /etc/ssl/private/ \ && chmod g+r /etc/ssl/private/ssl-cert-snakeoil.key -RUN rm -Rf /root/.cache - # Currently just using the dev entrypoint for prod as well -# TODO separate or move one level up COPY docker/dev/docker-entrypoint.sh / RUN chmod +x /docker-entrypoint.sh VOLUME ["/data"] -ENV HOME /data +ENV HOME=/data EXPOSE 9000 COPY --chown=django:django . /app -# RUN chown -R django /app - -# COPY --from=nodebuilder /app/root/.cache /root/.cache USER django WORKDIR /data ENTRYPOINT ["/docker-entrypoint.sh"] CMD ["uwsgi"] - diff --git a/docs/setup/osx.md b/docs/setup/osx.md index 1437610f0..7b8c4022d 100644 --- a/docs/setup/osx.md +++ b/docs/setup/osx.md @@ -7,8 +7,7 @@ A guide to setting up your OSX environment for developing on the Mac Docker -> https://www.docker.com/ (download, create a docker account and login) XCode -> install from app store (make sure you open and agree to licence) Brew -> /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install.sh)" - pyenv -> https://github.com/pyenv/pyenv - pyenv-virtualenv -> https://github.com/pyenv/pyenv-virtualenv + uv -> curl -LsSf https://astral.sh/uv/install.sh | sh ### Dependencies @@ -17,19 +16,9 @@ A guide to setting up your OSX environment for developing on the Mac brew install unixodbc -### Python - - pyenv init - pyenv install 3.9.0 - pyenv global 3.9.0 - pyenv virtualenv 3.9.0 trrf-dev - pyenv shell trrf-dev - pip install --upgrade pip - - - ### Installing modules for local development - pip install -r requirements/requirements.txt - pip install -r requirements/dev-requirements.txt - pip install -r requirements/test-requirements.txt + cd /path/to/trrf + uv sync --all-extras + +This will create a virtual environment in `.venv` and install all dependencies. diff --git a/docs/setup/windows.md b/docs/setup/windows.md index 7dda51ce4..5e41ab57c 100644 --- a/docs/setup/windows.md +++ b/docs/setup/windows.md @@ -42,39 +42,27 @@ Running Launch from the Microsoft Store once it has downloaded will install it. 5. Update packages: `sudo apt update -y` -6. Install pyenv - * Go to https://github.com/pyenv/pyenv#installation - * Under pre-requisites, follow the link to install the Python build dependencies first - * Use the `The automatic installer` instructions for installation of pyenv - * Confirm it's working by running `pyenv`. If this doesn't work you'll need to add `$HOME/.pyenv/bin` to your PATH in your WSL - * Follow the instructions output by `pyenv init` - -7. Install python. Check the current python version in the `Dockerfile`. +6. Install uv (Python package manager) ```shell - pyenv global 3.9 + curl -LsSf https://astral.sh/uv/install.sh | sh ``` - Confirm it's working: `python --version` -8. Configure Git + Restart your shell or run `source ~/.local/bin/env` to add uv to your PATH. + +7. Configure Git * Configure your Git client, as desired, on your WSL distribution * Clone the trrf repo into your WSL to an unmounted directory. N.B Cloning to a mounted windows directory will cause significant performance issues! -9. Configure TRRF virtual python environment. - ```shell - pyenv virtualenv 3.9 trrf - pyenv shell trrf - ``` -10. Install pre-requisite packages +8. Install pre-requisite packages Note: these packages are specific to Ubuntu and may differ if you've installed a different distribution. ```shell sudo apt install postgresql-client libpq-dev unixodbc-dev ``` -11. Install project dependencies +9. Install project dependencies ```shell cd /path/to/trrf - pip install -r requirements/requirements.txt - pip install -r requirements/dev-requirements.txt - pip install -r requirements/test-requirements.txt + uv sync --all-extras ``` + This will create a virtual environment in `.venv` and install all dependencies. ### Run TRRF locally @@ -101,7 +89,7 @@ Running Launch from the Microsoft Store once it has downloaded will install it. ### General development setup 1. Open the `trrf` project, selecting the cloned repo within the wsl directory structure 2. Setup WSL as the Python interpreter: https://www.jetbrains.com/help/pycharm/using-wsl-as-a-remote-interpreter.html#configure-wsl - * Python executable path - select the python executable in the virtual environment you created for trrf. e.g. `/home/totagian/.pyenv/versions/trrf/bin/python`. + * Python executable path - select the python executable in the `.venv` directory. e.g. `/path/to/trrf/.venv/bin/python`. 3. Enable Django support: 1. File > Settings > Languages and Frameworks > Enable Django Support * Django project root: `\\wsl$\Ubuntu-20.04\path\to\trrf\rdrf` @@ -132,25 +120,14 @@ Running Launch from the Microsoft Store once it has downloaded will install it. git submodule init git submodule update ``` -2. Create a virtual environment using WLS and pyenv - ``` - pyenv virtualenv mnd - pyenv shell mnd +2. Install the python dependencies using uv ``` -3. Install the python lib dependencies - ``` - cd path/to/mnd/rdrf/requirements - - pip install -r requirements.txt - pip install -r dev-requirements.txt - pip install -r test-requirements.txt - - cd path/to/mnd/requirements - - pip install -r requirements.txt - pip install -r dev-requirements.txt - pip install -r test-requirements.txt + cd path/to/mnd/rdrf + uv sync --all-extras + + cd path/to/mnd + uv sync --all-extras ``` -4. Configure the python interpreter in IntelliJ using wsl as the interpreter - * Python Interpreter path needs to point to the python exe in the virtual environment you created for this site. - e.g. `/home/totagian/.pyenv/versions/mnd/bin/python` +3. Configure the python interpreter in IntelliJ using wsl as the interpreter + * Python Interpreter path needs to point to the python exe in the `.venv` directory. + e.g. `/path/to/mnd/.venv/bin/python` diff --git a/pyproject.toml b/pyproject.toml index 047f07d38..0c801c8a0 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,3 +1,102 @@ +[build-system] +requires = ["hatchling"] +build-backend = "hatchling.build" + +[project] +name = "trrf" +version = "1.0.0" +description = "Trial Ready Registry Framework" +authors = [ + { name = "Queensland University of Technology - eResearch" }, + { name = "Murdoch University - Centre for Comparative Genomics" }, +] +requires-python = ">=3.13" +dependencies = [ + "ccg-django-utils==0.4.2", + "Django==5.2.1", + "django-anymail==14.0", + "django-countries==7.6.1", + "django-csp==3.8", + "django-extensions==3.2.3", + "django-registration-redux==2.13", + "djangorestframework==3.16.0", + "django-storages==1.14.6", + "django-stronghold==0.4.0", + "jsonschema==4.4.0", + "openpyxl==3.0.9", + "psycopg2-binary==2.9.10", + "pycountry==24.6.1", + "python-dateutil==2.8.2", + "python-magic==0.4.24", + "pyyaml==6.0.3", + "six==1.16.0", + "SQLAlchemy==1.3.24", + "uwsgi==2.0.30", + "django-formtools==2.5.1", + "django-otp==1.6.3", + "django-two-factor-auth==1.18.0", + "phonenumberslite==8.12.39", + "Pillow==11.3.0", + "qrcode==6.1", + "django-reversion==6.1.0", + "ua-parser==0.10.0", + "user-agents==2.2.0", + "django-user-agents==0.4.0", + "django-simple-history==3.11.0", + "lark==1.0.0", + "boto3==1.40.41", + "aws-xray-sdk==2.15.0", + "graphene-django==3.2.3", + "django-filter==25.1", + "flatten_json==0.1.13", + "gql-query-builder @ git+https://github.com/eresearchqut/gql-query-builder@a983448", + "awslambdaric==3.1.1", + "django-cache-memoize==0.1.10", + "openapi-client", + "langcodes==3.3.0", + "language_data==1.3", +] + +[project.optional-dependencies] +dev = [ + "sphinx", + "sphinxcontrib-fulltoc", + "Werkzeug==3.1.5", + "python-Levenshtein", + "ipython", + "django-silk==4.4.0", + "ruff", +] +test = [ + "sure==1.4.11", + "django-nose==1.4.7", + "pytest==7.1.1", + "pytest-django==4.5.2", + "pynose==1.5.5", + "nose-timer==0.7.5", + "aloe==0.2.0", + "aloe_django==0.2.0", + "pyvirtualdisplay==0.2.5", + "selenium>=4.10.0", + "unittest-xml-reporting==3.2.0", + "requests==2.32.4", + "sqlalchemy-utils==0.36.1", + "stellar==0.4.5", + "coverage==5.5", +] + +[tool.uv.sources] +openapi-client = { path = "./clients/xnat/generated" } + +[tool.uv] +exclude-dependencies = ["nose"] + +[tool.hatch.metadata] +allow-direct-references = true + +[tool.hatch.build.targets.wheel] +packages = ["rdrf", "registry", "report", "useraudit"] + [tool.ruff] line-length = 80 exclude = [ @@ -18,4 +117,4 @@ exclude = [ ] [tool.ruff.format] -quote-style = "double" \ No newline at end of file +quote-style = "double" diff --git a/rdrf/rdrf/auth/views.py b/rdrf/rdrf/auth/views.py index bae89cd68..23c25f132 100644 --- a/rdrf/rdrf/auth/views.py +++ b/rdrf/rdrf/auth/views.py @@ -6,6 +6,7 @@ from django.dispatch import receiver from django.shortcuts import redirect from django.urls import reverse +from django.utils.decorators import method_decorator from django.utils.safestring import mark_safe from django.utils.translation import gettext as _ from django.views.decorators.cache import never_cache @@ -25,8 +26,8 @@ logger = logging.getLogger(__name__) -@tfv.utils.class_view_decorator(sensitive_post_parameters()) -@tfv.utils.class_view_decorator(never_cache) +@method_decorator(sensitive_post_parameters(), name="dispatch") +@method_decorator(never_cache, name="dispatch") class LoginView(tfv.LoginView): form_list = ( ("auth", LoginAuthenticationForm), @@ -79,17 +80,17 @@ def user_login_callback(sender, request=None, user=None, **kwargs): # Customised Two Factor views -@tfv.utils.class_view_decorator(never_cache) +@method_decorator(never_cache, name="dispatch") class QRGeneratorView(tfv.core.QRGeneratorView): session_key_name = "two_fact_auth_key" -@tfv.utils.class_view_decorator(never_cache) +@method_decorator(never_cache, name="dispatch") class SetupView(tfv.core.SetupView): session_key_name = "two_fact_auth_key" -@tfv.utils.class_view_decorator(never_cache) +@method_decorator(never_cache, name="dispatch") class DisableView(tfv.profile.DisableView): def form_valid(self, form): user = self.request.user diff --git a/rdrf/rdrf/db/dynamic_data.py b/rdrf/rdrf/db/dynamic_data.py index ddd820c25..f1f130159 100644 --- a/rdrf/rdrf/db/dynamic_data.py +++ b/rdrf/rdrf/db/dynamic_data.py @@ -5,6 +5,7 @@ from aws_xray_sdk.core import xray_recorder from django.core.files.uploadedfile import InMemoryUploadedFile +from django.utils import timezone from rdrf.db.filestorage import create_filestorage from rdrf.forms.file_upload import FileUpload, wrap_fs_data_for_form @@ -246,7 +247,7 @@ def __init__( self.django_model = None def update_timestamps(self, form_model): - t = datetime.datetime.now() + t = timezone.now() form_timestamp = form_model.name + "_timestamp" self.global_timestamp = t self.form_timestamps[form_timestamp] = t @@ -893,7 +894,7 @@ def save_dynamic_data( else: record = self._get_record(registry.code, collection_name).first() - form_data["timestamp"] = datetime.datetime.now() + form_data["timestamp"] = timezone.now() if self.current_form_model: form_timestamp_key = "%s_timestamp" % self.current_form_model.name @@ -940,7 +941,7 @@ def _save_longitudinal_snapshot( self, registry_code, record, form_name=None, form_user=None ): try: - timestamp = str(datetime.datetime.now()) + timestamp = str(timezone.now()) patient_id = record.data["django_id"] snapshot = { "django_id": patient_id, diff --git a/rdrf/rdrf/db/generalised_field_expressions.py b/rdrf/rdrf/db/generalised_field_expressions.py index 63677d802..615aaaea8 100644 --- a/rdrf/rdrf/db/generalised_field_expressions.py +++ b/rdrf/rdrf/db/generalised_field_expressions.py @@ -565,7 +565,7 @@ def evaluate(self, patient_model, mongo_record): ) def set_value(self, patient_model, mongo_record, new_value, **kwargs): - from datetime import datetime + from django.utils import timezone from rdrf.db.contexts_api import RDRFContextManager @@ -587,7 +587,7 @@ def set_value(self, patient_model, mongo_record, new_value, **kwargs): } form_timestamp_key = "%s_timestamp" % self.form_model.name - form_timestamp_value = datetime.now() + form_timestamp_value = timezone.now() form_dict = { "name": self.form_model.name, @@ -638,7 +638,7 @@ def set_value(self, patient_model, mongo_record, new_value, **kwargs): form_dict["sections"].append(section_dict) if not form_exists: form_timestamp_key = "%s_timestamp" - form_timestamp_value = datetime.now() + form_timestamp_value = timezone.now() form_dict = { "name": self.form_model.name, "sections": [ diff --git a/rdrf/rdrf/exporter_utils.py b/rdrf/rdrf/exporter_utils.py index 5970cdd55..1cc038283 100644 --- a/rdrf/rdrf/exporter_utils.py +++ b/rdrf/rdrf/exporter_utils.py @@ -1,10 +1,10 @@ import io import logging import zipfile -from datetime import datetime from functools import reduce from django.http import HttpResponse +from django.utils import timezone from rdrf.services.io.defs.exporter import Exporter, ExportType @@ -19,7 +19,7 @@ def write_export_single_file(yaml_data, registry, export_type): if yaml_data is None: return - export_time = str(datetime.now()) + export_time = str(timezone.now()) yaml_export_filename = f"export_{export_time}_{registry.name}{partial_descriptor_str(export_type)}.yaml" @@ -49,7 +49,7 @@ def write_export_zip(exports, export_type): response = HttpResponse( zip_stream.getvalue(), content_type="application/zip" ) - export_time = str(datetime.now()) + export_time = str(timezone.now()) name = ( "export_" + export_time diff --git a/rdrf/rdrf/forms/progress/form_progress.py b/rdrf/rdrf/forms/progress/form_progress.py index 961810734..31cf48cef 100644 --- a/rdrf/rdrf/forms/progress/form_progress.py +++ b/rdrf/rdrf/forms/progress/form_progress.py @@ -201,10 +201,12 @@ def _calculate_form_progress(self): return result def _calculate_form_currency(self): - from datetime import datetime, timedelta + from datetime import timedelta + + from django.utils import timezone form_timestamp_key = "%s_timestamp" % self.form_model.name - one_year_ago = datetime.now() - timedelta(weeks=52) + one_year_ago = timezone.now() - timedelta(weeks=52) if self.dynamic_data is None: return False diff --git a/rdrf/rdrf/helpers/utils.py b/rdrf/rdrf/helpers/utils.py index f68215151..d235daa21 100644 --- a/rdrf/rdrf/helpers/utils.py +++ b/rdrf/rdrf/helpers/utils.py @@ -406,21 +406,6 @@ def display(form_or_formset, field, error): return results -def timed(func): - logger = logging.getLogger(__name__) - - def wrapper(*args, **kwargs): - a = datetime.datetime.now() - result = func(*args, **kwargs) - b = datetime.datetime.now() - c = b - a - func_name = func.__name__ - logger.debug("%s time = %s secs" % (func_name, c)) - return result - - return wrapper - - def get_cde_value( form_model, section_model, cde_model, patient_record, form_index=None ): diff --git a/rdrf/rdrf/management/commands/check_logins.py b/rdrf/rdrf/management/commands/check_logins.py index 9780ef8e8..1d1c4c97c 100644 --- a/rdrf/rdrf/management/commands/check_logins.py +++ b/rdrf/rdrf/management/commands/check_logins.py @@ -1,7 +1,8 @@ import sys -from datetime import datetime, timedelta +from datetime import timedelta from django.core.management import BaseCommand +from django.utils import timezone from registry.groups.models import CustomUser from rdrf.models.definition.models import Registry @@ -86,7 +87,7 @@ def _get_numdays(self, registry_model): return 365 def _get_threshold(self, num_days): - return datetime.now() - timedelta(days=num_days) + return timezone.now() - timedelta(days=num_days) def handle(self, *args, **options): action = options.get("action") diff --git a/rdrf/rdrf/management/commands/create_longitudinal_followup_entries.py b/rdrf/rdrf/management/commands/create_longitudinal_followup_entries.py index 7df8bd682..5472e8520 100644 --- a/rdrf/rdrf/management/commands/create_longitudinal_followup_entries.py +++ b/rdrf/rdrf/management/commands/create_longitudinal_followup_entries.py @@ -1,6 +1,5 @@ -from datetime import datetime - from django.core.management.base import BaseCommand, CommandError +from django.utils import timezone from registry.patients.models import ( LivingStates, LongitudinalFollowupEntry, @@ -71,7 +70,7 @@ def handle(self, *args, **options): self.style.SUCCESS(f"Found {len(pending_entries)} pending entries") ) - now = datetime.now() + now = timezone.now() patients = Patient.objects.filter(rdrf_registry=registry) def can_add(patient): diff --git a/rdrf/rdrf/management/commands/send_longitudinal_followups.py b/rdrf/rdrf/management/commands/send_longitudinal_followups.py index ee95062e3..07852ef42 100644 --- a/rdrf/rdrf/management/commands/send_longitudinal_followups.py +++ b/rdrf/rdrf/management/commands/send_longitudinal_followups.py @@ -1,6 +1,7 @@ -from datetime import datetime, timedelta +from datetime import timedelta from django.core.management import BaseCommand +from django.utils import timezone from rdrf.services.io.notifications.longitudinal_followups import ( send_longitudinal_followups, @@ -16,5 +17,5 @@ def add_arguments(self, parser): def handle(self, *args, **options): delta_seconds = options["delta_seconds"] - now = datetime.now() + now = timezone.now() send_longitudinal_followups(now + timedelta(seconds=delta_seconds)) diff --git a/rdrf/rdrf/models/workflow_models.py b/rdrf/rdrf/models/workflow_models.py index b52931554..f452bc25d 100644 --- a/rdrf/rdrf/models/workflow_models.py +++ b/rdrf/rdrf/models/workflow_models.py @@ -1,8 +1,8 @@ import logging -from datetime import datetime from django.db import models from django.urls import reverse +from django.utils import timezone from registry.groups.models import CustomUser from rdrf.events.events import EventType @@ -43,7 +43,7 @@ class ClinicianSignupRequest(models.Model): def send_request(self): self._send_email() self.state = "emailed" - self.emailed_date = datetime.now() + self.emailed_date = timezone.now() self.save() def notify_participant_on_verification(self, diagnosis=""): diff --git a/rdrf/rdrf/services/io/content/export_import/main_exporters.py b/rdrf/rdrf/services/io/content/export_import/main_exporters.py index 30429f137..c1c38738a 100644 --- a/rdrf/rdrf/services/io/content/export_import/main_exporters.py +++ b/rdrf/rdrf/services/io/content/export_import/main_exporters.py @@ -4,7 +4,8 @@ import shutil import tempfile from collections import OrderedDict -from datetime import datetime + +from django.utils import timezone from rdrf.models.definition.models import Registry @@ -63,7 +64,7 @@ def export(self, filename=None, verbose=False, indented_logs=True): ) if exporter.export(**self.export_context): self.meta.append(exporter.get_meta_info(top_level=True)) - self.exported_at = datetime.now() + self.exported_at = timezone.now() self.write_out_meta_info() diff --git a/rdrf/rdrf/services/io/defs/exporter.py b/rdrf/rdrf/services/io/defs/exporter.py index cd09d99c1..e81fb6b48 100644 --- a/rdrf/rdrf/services/io/defs/exporter.py +++ b/rdrf/rdrf/services/io/defs/exporter.py @@ -1,4 +1,3 @@ -import datetime import json import logging from decimal import Decimal @@ -8,6 +7,7 @@ from django.contrib.auth.models import Group from django.core.exceptions import ValidationError from django.forms.models import model_to_dict +from django.utils import timezone from registry.patients.models import ( NextOfKinRelationship, PatientStage, @@ -332,7 +332,7 @@ def _skeleton_export(self, export_type): data["RDRF_VERSION"] = VERSION data["EXPORT_TYPE"] = export_type - data["EXPORT_TIME"] = str(datetime.datetime.now()) + data["EXPORT_TIME"] = str(timezone.now()) data["REGISTRY_VERSION"] = self._get_registry_version() if self.registry: diff --git a/rdrf/rdrf/services/io/notifications/longitudinal_followups.py b/rdrf/rdrf/services/io/notifications/longitudinal_followups.py index f601ef1f8..e1d741957 100644 --- a/rdrf/rdrf/services/io/notifications/longitudinal_followups.py +++ b/rdrf/rdrf/services/io/notifications/longitudinal_followups.py @@ -13,6 +13,7 @@ ) from django.db.models.functions import Coalesce from django.urls import reverse +from django.utils import timezone from registry.patients.models import ( ConsentValue, LongitudinalFollowupEntry, @@ -40,7 +41,7 @@ def handle_longitudinal_followups(user, patient, registry, context_form_group): if context_form_group is None: return - now = datetime.datetime.now() + now = timezone.now() new_entries = [ LongitudinalFollowupEntry( longitudinal_followup=longitudinal_followup, @@ -147,7 +148,7 @@ def _serialize_entries(patient_entries): def with_now(func): def wrapper(now=None): - return func(now=now or datetime.datetime.now()) + return func(now=now or timezone.now()) return wrapper @@ -237,7 +238,7 @@ def send_longitudinal_followups(now): if not any(entry.send_at <= now for entry in patient_entries): continue - sent_at = datetime.datetime.now() + sent_at = timezone.now() longitudinal_followups = _serialize_entries(patient_entries) diff --git a/rdrf/rdrf/services/io/notifications/reminders.py b/rdrf/rdrf/services/io/notifications/reminders.py index 47bcc2a43..0a68d3eb8 100644 --- a/rdrf/rdrf/services/io/notifications/reminders.py +++ b/rdrf/rdrf/services/io/notifications/reminders.py @@ -1,6 +1,7 @@ import json import logging -from datetime import datetime + +from django.utils import timezone from rdrf.services.io.notifications.email_notification import ( EmailNotificationHistory, @@ -21,7 +22,7 @@ def __init__(self, user, registry_model, process_func=process_notification): def _can_send(self): # These are the rules for MTM - should we push into config? - now = datetime.now() + now = timezone.now() existing_reminders = self._get_reminders() num_sent = len(existing_reminders) if num_sent >= 2: diff --git a/rdrf/rdrf/settings.py b/rdrf/rdrf/settings.py index 7183eee6c..40fde3c3f 100644 --- a/rdrf/rdrf/settings.py +++ b/rdrf/rdrf/settings.py @@ -312,9 +312,23 @@ # Use S3 by default to avoid writing sensitive data to FS in production if env.get("FILE_STORAGE", "S3") == "FS": - DEFAULT_FILE_STORAGE = "django.core.files.storage.FileSystemStorage" + STORAGES = { + "default": { + "BACKEND": "django.core.files.storage.FileSystemStorage", + }, + "staticfiles": { + "BACKEND": "django.contrib.staticfiles.storage.StaticFilesStorage", + }, + } else: - DEFAULT_FILE_STORAGE = "rdrf.db.filestorage.CustomS3Storage" + STORAGES = { + "default": { + "BACKEND": "rdrf.db.filestorage.CustomS3Storage", + }, + "staticfiles": { + "BACKEND": "django.contrib.staticfiles.storage.StaticFilesStorage", + }, + } # Configure different aspects of file uploads to S3 diff --git a/rdrf/rdrf/settings_test.py b/rdrf/rdrf/settings_test.py index 31ea192db..67d5ffae1 100644 --- a/rdrf/rdrf/settings_test.py +++ b/rdrf/rdrf/settings_test.py @@ -1,5 +1,5 @@ from .settings import * # noqa -from .settings import INSTALLED_APPS +from .settings import INSTALLED_APPS, LOGGING INSTALLED_APPS += [ "aloe_django", @@ -16,3 +16,6 @@ "rdrf.testing.behaviour.features.runner.GherkinNoDjangoTestDBTestRunner" ) GHERKIN_TEST_CLASS = "aloe.testclass.TestCase" + +# Remove verbose error handler from root logger during tests +LOGGING["loggers"][""]["handlers"] = ["console"] diff --git a/rdrf/rdrf/static/js/session_timeout_manager.js b/rdrf/rdrf/static/js/session_timeout_manager.js index 1c07e646b..961c847ed 100644 --- a/rdrf/rdrf/static/js/session_timeout_manager.js +++ b/rdrf/rdrf/static/js/session_timeout_manager.js @@ -169,9 +169,30 @@ function SessionManager(sessionNotifier, options) { } function logout() { - window.location.href = settings.urls.logout; + const csrfToken = document.querySelector('[name=csrfmiddlewaretoken]'); + + if (!csrfToken) { + console.error("CSRF Token not found"); + return; + } + + fetch(settings.urls.logout, { + method: 'POST', + headers: { + 'X-CSRFToken': csrfToken.value + }, + }) + .then(response => { + if (response.ok) { + window.location.href = response.url; + } else { + console.error('Logout failed'); + } + }) + .catch(error => console.error('Error:', error)); } + function goToLoginPage() { window.location.href = settings.urls.login; } diff --git a/rdrf/rdrf/templates/rdrf_cdes/cde.html b/rdrf/rdrf/templates/rdrf_cdes/cde.html index c9c6facbb..0edd1f02a 100644 --- a/rdrf/rdrf/templates/rdrf_cdes/cde.html +++ b/rdrf/rdrf/templates/rdrf_cdes/cde.html @@ -28,7 +28,10 @@

Duchenne Muscular Dystrophy Registry (1.7.0)

Change password / - Log out +
+ {% csrf_token %} + +
diff --git a/rdrf/rdrf/templates/rdrf_cdes/navbar_links.html b/rdrf/rdrf/templates/rdrf_cdes/navbar_links.html index dc6b0d663..890bda77c 100644 --- a/rdrf/rdrf/templates/rdrf_cdes/navbar_links.html +++ b/rdrf/rdrf/templates/rdrf_cdes/navbar_links.html @@ -149,9 +149,12 @@ {% endif %} {% block patient_menu %} {% endblock %} -
  • - {% trans 'Logout' %}
    • +
  • +
    + {% csrf_token %} + +
    +
    • diff --git a/rdrf/rdrf/testing/behaviour/features/auth/page.py b/rdrf/rdrf/testing/behaviour/features/auth/page.py index 806f57975..21574fb5e 100644 --- a/rdrf/rdrf/testing/behaviour/features/auth/page.py +++ b/rdrf/rdrf/testing/behaviour/features/auth/page.py @@ -103,7 +103,7 @@ def set_token(self, token): return self def submit(self): - self._get_element(self.SUBMIT_BUTTON).submit() + self._get_element(self.SUBMIT_BUTTON).click() class TwoFactorTokenGeneratorPage(TwoFactorLoginTokenPage): diff --git a/rdrf/rdrf/testing/behaviour/features/auth/steps.py b/rdrf/rdrf/testing/behaviour/features/auth/steps.py index 863443568..0312e06eb 100644 --- a/rdrf/rdrf/testing/behaviour/features/auth/steps.py +++ b/rdrf/rdrf/testing/behaviour/features/auth/steps.py @@ -81,12 +81,12 @@ def patient_self_registration(_step, client_name, email_address, password): # Populate plain text fields for key, value in params.items(): - world.browser.find_element_by_id(key).send_keys(value + Keys.TAB) + world.browser.find_element(By.ID, key).send_keys(value + Keys.TAB) # Select the gender radio button # 1 - Male, 2 - Female, 3 - Indeterminate - world.browser.find_element_by_css_selector( - "input[name='gender'][value='1']" + world.browser.find_element( + By.CSS_SELECTOR, "input[name='gender'][value='1']" ).click() captcha_iframe_element = world.browser.find_element( @@ -96,7 +96,7 @@ def patient_self_registration(_step, client_name, email_address, password): world.browser.switch_to.frame(captcha_iframe_element) scroll_to_y(500) - world.browser.find_element_by_id("recaptcha-anchor").send_keys(Keys.SPACE) + world.browser.find_element(By.ID, "recaptcha-anchor").send_keys(Keys.SPACE) world.browser.switch_to.default_content() @@ -118,7 +118,14 @@ def login(_step, username, password): @step("logout") def logout(_step): - open_option_from_menu(_step, "Logout", "user") + BasePage(world.browser).open_menu("user") + button = world.browser.find_element(by=By.ID, value="logout-button") + button.click() + WebDriverWait(world.browser, TEST_WAIT).until( + expected_conditions.presence_of_element_located( + LoginPage.USERNAME_ELEMENT + ) + ) @step('reauthenticate with username "([^"]+)" and password "([^"]+)"') @@ -129,6 +136,11 @@ def reauthenticate(_step, username, password): @step("am logged in successfully") def assert_is_logged_in(self): + WebDriverWait(world.browser, TEST_WAIT).until( + expected_conditions.presence_of_element_located( + BasePage.SITE_MENU.get("user") + ) + ) assert_equal( BasePage(world.browser).get_user_menu_text(), f"{world.user_first_name} {world.user_last_name}", @@ -191,8 +203,8 @@ def open_option_from_menu(_step, option, menu): @step('"([^"]+)" image is displayed') def assert_is_image_displayed(_step, image_alt): - image = world.browser.find_element_by_css_selector( - f'img[alt="{image_alt}"]' + image = world.browser.find_element( + By.CSS_SELECTOR, f'img[alt="{image_alt}"]' ) assert_true(image.is_displayed()) @@ -213,7 +225,13 @@ def setup_initial_otp_token(_step): @step("enter my generated OTP token") def enter_otp_token(_step): + current_url = world.browser.current_url utils.set_otp_token(TwoFactorLoginTokenPage(world.browser), world.key) + # Wait for the URL to change away from the 2FA login page + # Use longer timeout to handle CI environment delays + WebDriverWait(world.browser, TEST_WAIT * 2).until( + expected_conditions.url_changes(current_url) + ) @step("confirm to disable two-factor auth") diff --git a/rdrf/rdrf/testing/behaviour/features/exported_data/ang.zip b/rdrf/rdrf/testing/behaviour/features/exported_data/ang.zip index 155c04502..8385ace05 100644 Binary files a/rdrf/rdrf/testing/behaviour/features/exported_data/ang.zip and b/rdrf/rdrf/testing/behaviour/features/exported_data/ang.zip differ diff --git a/rdrf/rdrf/testing/behaviour/features/exported_data/dd.zip b/rdrf/rdrf/testing/behaviour/features/exported_data/dd.zip index 71fad2db5..720385d9a 100644 Binary files a/rdrf/rdrf/testing/behaviour/features/exported_data/dd.zip and b/rdrf/rdrf/testing/behaviour/features/exported_data/dd.zip differ diff --git a/rdrf/rdrf/testing/behaviour/features/exported_data/fh.zip b/rdrf/rdrf/testing/behaviour/features/exported_data/fh.zip index 6b46c47b9..bb9f998c0 100644 Binary files a/rdrf/rdrf/testing/behaviour/features/exported_data/fh.zip and b/rdrf/rdrf/testing/behaviour/features/exported_data/fh.zip differ diff --git a/rdrf/rdrf/testing/behaviour/features/longitudinal_followups/steps.py b/rdrf/rdrf/testing/behaviour/features/longitudinal_followups/steps.py index f97856a77..3b3e4bcb1 100644 --- a/rdrf/rdrf/testing/behaviour/features/longitudinal_followups/steps.py +++ b/rdrf/rdrf/testing/behaviour/features/longitudinal_followups/steps.py @@ -1,6 +1,7 @@ -from datetime import datetime, timedelta +from datetime import timedelta from aloe import step, world +from django.utils import timezone from nose.tools import assert_equal from selenium.webdriver.common.by import By from selenium.webdriver.support import expected_conditions as ec @@ -35,7 +36,7 @@ def fill_out_form(step, form_name, patient_name, again=None): @step(r"(\d+) hour(?:s)? pass(?:es)?") def pass_time(_step, hours): - now = (datetime.now() + timedelta(hours=int(hours))).timestamp() + now = (timezone.now() + timedelta(hours=int(hours))).timestamp() go_to_url(f"mail/send_longitudinal_followups?now={int(now)}") @@ -71,7 +72,7 @@ def empty_mail(_step): def check_mail(_step, count): go_to_url("mail/outbox") sent_emails = len( - world.browser.find_elements_by_css_selector(EMAIL_SELECTOR) + world.browser.find_elements(By.CSS_SELECTOR, EMAIL_SELECTOR) ) assert_equal(sent_emails, int(count)) diff --git a/rdrf/rdrf/testing/behaviour/features/longitudinal_followups/utils.py b/rdrf/rdrf/testing/behaviour/features/longitudinal_followups/utils.py index 9ba7ca622..0644b45b0 100644 --- a/rdrf/rdrf/testing/behaviour/features/longitudinal_followups/utils.py +++ b/rdrf/rdrf/testing/behaviour/features/longitudinal_followups/utils.py @@ -1,4 +1,5 @@ from aloe import world +from selenium.webdriver.common.by import By from rdrf.testing.behaviour.features.utils import wait_for_first_section @@ -6,8 +7,8 @@ def get_email(n): - return world.browser.find_elements_by_css_selector( - f"{EMAIL_SELECTOR}:nth-child({n}) > td a" + return world.browser.find_elements( + By.CSS_SELECTOR, f"{EMAIL_SELECTOR}:nth-child({n}) > td a" ) diff --git a/rdrf/rdrf/testing/behaviour/features/steps.py b/rdrf/rdrf/testing/behaviour/features/steps.py index e3ac36b6a..690d1008e 100644 --- a/rdrf/rdrf/testing/behaviour/features/steps.py +++ b/rdrf/rdrf/testing/behaviour/features/steps.py @@ -3,7 +3,6 @@ from aloe import step, world from aloe.registry import STEP_REGISTRY -from aloe_webdriver.webdriver import contains_content from nose.tools import assert_equal, assert_true from selenium.webdriver.common.alert import Alert from selenium.webdriver.common.by import By @@ -32,7 +31,7 @@ def login_as_angelman_user(step, user_name): @step('I should be at the welcome page and see a message which says "([^"]+)"') def angelman_user_logged_in(step, welcome_message): - login_message = world.browser.find_element_by_tag_name("h4").text + login_message = world.browser.find_element(By.TAG_NAME, "h4").text # Ensure that the user sees the expected page after successfully logging in assert world.expected_login_message in login_message @@ -43,7 +42,7 @@ def try_to_manually_activate_new_user(step): world.browser.get( world.site_url + "admin/registration/registrationprofile/" ) - world.browser.find_element_by_id("action-toggle").send_keys(Keys.SPACE) + world.browser.find_element(By.ID, "action-toggle").send_keys(Keys.SPACE) world.browser.find_element( by=By.XPATH, @@ -58,13 +57,15 @@ def try_to_manually_activate_new_user(step): def check_user_activated(step): # Ensure that the user has been successfully activated by checking for the green tick icon assert not ( - world.browser.find_elements_by_css_selector( - 'img[src$="/static/admin/img/icon-yes.svg"].ng-hide' + world.browser.find_elements( + By.CSS_SELECTOR, + 'img[src$="/static/admin/img/icon-yes.svg"].ng-hide', ) ) # Log out as the admin user - world.browser.get(world.site_url + "logout?next=/router/") + world.browser.find_element(By.ID, "authMenuDropdown").click() + world.browser.find_element(By.ID, "logout-button").click() @step("I try to surf the site...") @@ -89,7 +90,7 @@ def load_export(step, export_name): @step('should see "([^"]+)"$') def should_see(step, text): - assert_true(contains_content(world.browser, text)) + assert_true(utils.contains_content(text)) @step('click "(.*)"') @@ -132,7 +133,7 @@ def click_patient_listing(step, patient_name): @step('I click on "(.*)" in "(.*)" group in sidebar') def click_sidebar_group_item(step, item_name, group_name): # E.g. And I click "Clinical Data" in "Main" group in sidebar - sidebar = world.browser.find_element_by_id("sidebar") + sidebar = world.browser.find_element(By.ID, "sidebar") form_group_panel = sidebar.find_element( by=By.XPATH, value='//div[@class="card-header"][contains(., "%s")]' % group_name, @@ -145,7 +146,7 @@ def click_sidebar_group_item(step, item_name, group_name): @step('I press "(.*)" button in "(.*)" group in sidebar') def click_button_sidebar_group(step, button_name, group_name): - sidebar = world.browser.find_element_by_id("sidebar") + sidebar = world.browser.find_element(By.ID, "sidebar") form_group_panel = sidebar.find_element( by=By.XPATH, value='//div[@class="card-header"][contains(., "%s")]' % group_name, @@ -163,7 +164,7 @@ def enter_cde_on_form(step, cde_value, form, section, cde): utils.wait_for_first_section() - form_block = world.browser.find_element_by_id("main-form") + form_block = world.browser.find_element(By.ID, "main-form") section_div_heading = form_block.find_element( by=By.XPATH, value=".//div[@class='card-header'][contains(., '%s')]" % section, @@ -207,7 +208,7 @@ def correct_item(input_element): utils.wait_for_first_section() - form_block = world.browser.find_element_by_id("main-form") + form_block = world.browser.find_element(By.ID, "main-form") section_div_heading = form_block.find_element( by=By.XPATH, value=".//div[@class='card-header'][contains(., '%s')]" % section, @@ -231,9 +232,6 @@ def correct_item(input_element): if not correct_item(input_element): continue input_element.send_keys(cde_value) - input_id = input_element.get_attribute("id") - print("input id %s sent keys '%s'" % (input_id, cde_value)) - return except BaseException: pass @@ -265,7 +263,7 @@ def error_message_is(step, error_message): @step('location is "(.*)"') def location_is(step, location_name): - sidebar = world.browser.find_element_by_id("sidebar") + sidebar = world.browser.find_element(By.ID, "sidebar") location_parts = location_name.split("/") if len(location_parts) == 1: sidebar.find_element( @@ -295,7 +293,7 @@ def click_module_dropdown_in_patient_listing(step, module_name, patient_name): else: button_caption, form_name = "Modules", module_name - patients_table = world.browser.find_element_by_id("patients_table") + patients_table = world.browser.find_element(By.ID, "patients_table") patient_row = patients_table.find_element( by=By.XPATH, @@ -315,13 +313,13 @@ def click_module_dropdown_in_patient_listing(step, module_name, patient_name): @step("press the navigate back button") def press_back_button(step): - button = world.browser.find_element_by_css_selector("a.previous-form") + button = world.browser.find_element(By.CSS_SELECTOR, "a.previous-form") utils.click(button) @step("press the navigate forward button") def press_forward_button(step): - button = world.browser.find_element_by_css_selector("a.next-form") + button = world.browser.find_element(By.CSS_SELECTOR, "a.next-form") utils.click(button) @@ -398,7 +396,7 @@ def value_is(step, textfield_label, expected_value): def value_is2(step, section, cde, expected_value): utils.wait_for_first_section() - form_block = world.browser.find_element_by_id("main-form") + form_block = world.browser.find_element(By.ID, "main-form") section_div_heading = form_block.find_element( by=By.XPATH, value=".//div[@class='card-header'][contains(., '%s')]" % section, @@ -431,7 +429,7 @@ def check_checkbox(step, checkbox_label): @step("Sign consent") def sign_consent(step): - signature_div = world.browser.find_element_by_id("signature") + signature_div = world.browser.find_element(By.ID, "signature") utils.click(signature_div) @@ -474,7 +472,7 @@ def goto_patient(step): @step('the page header should be "(.*)"') def the_page_header_should_be(step, header): - sidebar = world.browser.find_element_by_id("sidebar") + sidebar = world.browser.find_element(By.ID, "sidebar") panel_body = sidebar.find_element( by=By.XPATH, value='//div[@class="card-body"]' ) @@ -495,7 +493,7 @@ def login_as_role(step, role): @step('log in as "(.*)" with "(.*)" password') def login_as_user(step, username, password): - utils.click(world.browser.find_element_by_link_text("Log in")) + utils.click(world.browser.find_element(By.LINK_TEXT, "Log in")) username_field = world.browser.find_element( by=By.XPATH, value='.//input[@name="auth-username"]' ) @@ -513,7 +511,7 @@ def should_be_logged_in(step): by=By.PARTIAL_LINK_TEXT, value=world.user ) utils.click(user_link) - world.browser.find_element_by_link_text("Logout") + world.browser.find_element(By.ID, "logout-button") @step("should be on the login page") @@ -537,8 +535,8 @@ def click_user_menu(step): @step('the progress indicator should be "(.*)"') def the_progress_indicator_should_be(step, percentage): - progress_bar = world.browser.find_element_by_css_selector( - ".progress .progress-bar" + progress_bar = world.browser.find_element( + By.CSS_SELECTOR, ".progress .progress-bar" ) logger.info(progress_bar.text.strip()) @@ -556,7 +554,7 @@ def go_home(step): def go_to_registry(step, name): world.browser.get(world.site_url) utils.click( - world.browser.find_element_by_link_text("Registries on this site") + world.browser.find_element(By.LINK_TEXT, "Registries on this site") ) utils.click(world.browser.find_element(by=By.PARTIAL_LINK_TEXT, value=name)) @@ -583,7 +581,7 @@ def accept_alert(step): @step('When I click "(.*)" in sidebar') def sidebar_click(step, sidebar_link_text): - utils.click(world.browser.find_element_by_link_text(sidebar_link_text)) + utils.click(world.browser.find_element(By.LINK_TEXT, sidebar_link_text)) @step("I click Cancel") @@ -661,8 +659,8 @@ def should_be_able_to_download(step, download_name): import re link_pattern = re.compile(r".*\/uploads\/\d+$") - download_link_element = world.browser.find_element_by_link_text( - download_name + download_link_element = world.browser.find_element( + By.LINK_TEXT, download_name ) if not download_link_element: raise Exception("Could not locate download link %s" % download_name) @@ -698,7 +696,7 @@ def check_history_popup(step, form, section, cde, history_values_csv): from selenium.webdriver.support.ui import WebDriverWait history_values = history_values_csv.split(",") - form_block = world.browser.find_element_by_id("main-form") + form_block = world.browser.find_element(By.ID, "main-form") section_div_heading = form_block.find_element( by=By.XPATH, value=".//div[@class='card-header'][contains(., '%s')]" % section, @@ -742,12 +740,11 @@ def find_cell(historical_value): @step('check the clear checkbox for multisection "(.*)" cde "(.*)" file "(.*)"') def clear_file_upload(step, section, cde, download_name): - from selenium.webdriver.common.by import By from selenium.webdriver.support import expected_conditions as ec from selenium.webdriver.support.ui import WebDriverWait - download_link_element = world.browser.find_element_by_link_text( - download_name + download_link_element = world.browser.find_element( + By.LINK_TEXT, download_name ) clear_checkbox_path = ".//following-sibling::input[@type='checkbox']" WebDriverWait(world.browser, TEST_WAIT).until( @@ -765,7 +762,6 @@ def scroll_to_section(step, section): from selenium.webdriver.common.action_chains import ActionChains mover = ActionChains(world.browser) - print("scrolling to section %s" % section) section_xpath = ( ".//div[@class='panel panel-default' and contains(.,'%s') and not(contains(., '__prefix__')) and not(contains(.,'View previous values'))]" % section @@ -775,9 +771,7 @@ def scroll_to_section(step, section): ) if not section_element: raise Exception("could not find section %s" % section) - y = utils.scroll_to(section_element) mover.move_to_element(section_element) - print("scrolled to section %s y = %s" % (section, y)) @step('I click the add button for multisection "(.*)"') diff --git a/rdrf/rdrf/testing/behaviour/features/terrain.py b/rdrf/rdrf/testing/behaviour/features/terrain.py index ca97a90a0..09388249a 100644 --- a/rdrf/rdrf/testing/behaviour/features/terrain.py +++ b/rdrf/rdrf/testing/behaviour/features/terrain.py @@ -4,7 +4,9 @@ from aloe import after, around, before, world from django.conf import settings -from selenium import webdriver +from selenium.webdriver import Remote +from selenium.webdriver.chrome.options import Options as ChromeOptions +from selenium.webdriver.firefox.options import Options as FirefoxOptions from . import utils @@ -23,21 +25,23 @@ ) -def get_desired_capabilities(browser): - return { - "firefox": webdriver.DesiredCapabilities.FIREFOX, - "chrome": webdriver.DesiredCapabilities.CHROME, - }.get(browser, webdriver.DesiredCapabilities.FIREFOX) +def get_browser_options(browser): + options_map = { + "firefox": FirefoxOptions, + "chrome": ChromeOptions, + } + options_class = options_map.get(browser, FirefoxOptions) + return options_class() @around.all @contextmanager def with_browser(): - desired_capabilities = get_desired_capabilities(TEST_BROWSER) + options = get_browser_options(TEST_BROWSER) - world.browser = webdriver.Remote( - desired_capabilities=desired_capabilities, + world.browser = Remote( command_executor=TEST_SELENIUM_HUB, + options=options, ) world.browser.implicitly_wait(TEST_WAIT) diff --git a/rdrf/rdrf/testing/behaviour/features/utils.py b/rdrf/rdrf/testing/behaviour/features/utils.py index 7b96e5006..ff6babf30 100644 --- a/rdrf/rdrf/testing/behaviour/features/utils.py +++ b/rdrf/rdrf/testing/behaviour/features/utils.py @@ -3,6 +3,7 @@ import subprocess from aloe import world +from selenium.common.exceptions import StaleElementReferenceException from selenium.webdriver.common.by import By TEST_WAIT = int(os.environ.get("TEST_WAIT") or "10") @@ -250,13 +251,7 @@ def scroll_to(element): def scroll_to_multisection_cde(section, cde, item=1): - # item 1 means the 1st block of cdes in the multisection - print( - "Attempting to scroll to section %s cde %s item %s" - % (section, cde, item) - ) formset_string = "-%s-" % (int(item) - 1) - print("formset_string = %s" % formset_string) xpath = "//div[@class='card-header' and contains(., '%s')]" % section panel_heading = world.browser.find_element( by=By.XPATH, value=xpath @@ -273,7 +268,6 @@ def scroll_to_multisection_cde(section, cde, item=1): for label_element in default_panel.find_elements( by=By.XPATH, value=label_expression ): - print("found a label element for cde %s" % cde) input_div = label_element.find_element( by=By.XPATH, value=".//following-sibling::div" ) @@ -285,10 +279,6 @@ def scroll_to_multisection_cde(section, cde, item=1): % formset_string, ) scroll_to(input_element) - print( - "found input element: id = %s" - % input_element.get_attribute("id") - ) return input_element except BaseException: continue @@ -344,7 +334,7 @@ def scroll_to_cde(section, cde, item=None): if "__prefix__" in input_id: # hack to avoid this error input_id = input_id.replace("__prefix__", "0") - input_element = world.browser.find_element_by_id(input_id) + input_element = world.browser.find_element(By.ID, input_id) if not input_element: raise Exception("could not locate input with id %s" % input_id) @@ -374,3 +364,35 @@ def wait_for_first_section(): (By.CSS_SELECTOR, ".section-available") ) ) + + +# From aloe_webdriver: https://github.com/aloetesting/aloe_webdriver + + +def string_literal(content): + if '"' in content and "'" in content: + raise ValueError("Cannot represent this string in XPath") + + if '"' in content: + content = "'%s'" % content + else: + content = '"%s"' % content + + return content + + +def contains_content(content): + for elem in world.browser.find_elements( + By.XPATH, + "//*[contains(normalize-space(.), {content}) " + "and not(./*[contains(normalize-space(.), {content})])]".format( + content=string_literal(content) + ), + ): + try: + if elem.is_displayed(): + return True + except StaleElementReferenceException: + pass + + return False diff --git a/rdrf/rdrf/testing/unit/longitudinal_followup_tests.py b/rdrf/rdrf/testing/unit/longitudinal_followup_tests.py index bbae75b21..dae8b352a 100644 --- a/rdrf/rdrf/testing/unit/longitudinal_followup_tests.py +++ b/rdrf/rdrf/testing/unit/longitudinal_followup_tests.py @@ -1,9 +1,10 @@ import json import logging -from datetime import datetime, timedelta +from datetime import date, timedelta from django.core import mail from django.test import TestCase +from django.utils import timezone from registry.patients.models import ( ConsentValue, LongitudinalFollowupEntry, @@ -35,7 +36,7 @@ class LongitudinalFollowupSetupMixin: def create_models(self): - self.now = datetime.now() + self.now = timezone.now() self.registry = Registry.objects.create( code="reg", metadata_json=json.dumps({"features": ["longitudinal_followups"]}), @@ -99,7 +100,7 @@ def test_single_patient_single_lf(self): debounce=timedelta(weeks=26), ) patient = Patient.objects.create( - consent=True, date_of_birth=datetime(1970, 1, 1), sex="3" + consent=True, date_of_birth=date(1970, 1, 1), sex="3" ) patient.rdrf_registry.add(self.registry) @@ -161,7 +162,7 @@ def test_single_patient_multiple_lf(self): debounce=timedelta(weeks=52), ) patient = Patient.objects.create( - consent=True, date_of_birth=datetime(1970, 1, 1), sex="3" + consent=True, date_of_birth=date(1970, 1, 1), sex="3" ) patient.rdrf_registry.add(self.registry) @@ -249,12 +250,12 @@ def test_multiple_patient_single_lf(self): debounce=timedelta(weeks=26), ) patient1 = Patient.objects.create( - consent=True, date_of_birth=datetime(1970, 1, 1), sex="3" + consent=True, date_of_birth=date(1970, 1, 1), sex="3" ) patient1.rdrf_registry.add(self.registry) patient2 = Patient.objects.create( - consent=True, date_of_birth=datetime(1970, 1, 1), sex="3" + consent=True, date_of_birth=date(1970, 1, 1), sex="3" ) patient2.rdrf_registry.add(self.registry) @@ -352,12 +353,12 @@ def test_multiple_patient_multiple_lf(self): ) patient1 = Patient.objects.create( - consent=True, date_of_birth=datetime(1970, 1, 1), sex="3" + consent=True, date_of_birth=date(1970, 1, 1), sex="3" ) patient1.rdrf_registry.add(self.registry) patient2 = Patient.objects.create( - consent=True, date_of_birth=datetime(1970, 1, 1), sex="3" + consent=True, date_of_birth=date(1970, 1, 1), sex="3" ) patient2.rdrf_registry.add(self.registry) @@ -527,7 +528,7 @@ def create_entry(self, condition): ) patient = Patient.objects.create( - consent=True, date_of_birth=datetime(1970, 1, 1), sex="3" + consent=True, date_of_birth=date(1970, 1, 1), sex="3" ) patient.rdrf_registry.add(self.registry) patient.save() @@ -586,7 +587,7 @@ def create_patient_and_followup(self, frequency_weeks, debounce_weeks): debounce=timedelta(weeks=debounce_weeks), ) patient = Patient.objects.create( - consent=True, date_of_birth=datetime(1970, 1, 1), sex="3" + consent=True, date_of_birth=date(1970, 1, 1), sex="3" ) patient.rdrf_registry.add(self.registry) patient.save() diff --git a/rdrf/rdrf/testing/unit/patient_model_tests.py b/rdrf/rdrf/testing/unit/patient_model_tests.py index a9824d488..60495af65 100644 --- a/rdrf/rdrf/testing/unit/patient_model_tests.py +++ b/rdrf/rdrf/testing/unit/patient_model_tests.py @@ -1,10 +1,8 @@ import logging -from datetime import date, datetime +from datetime import date from unittest import mock -from unittest.mock import Mock import pytest -from registry.patients import models from registry.patients.models import Patient from rdrf.models.definition.models import Registry @@ -29,9 +27,9 @@ def _get_calculated_age(self, patient, date_of_birth, date_of_death=None): patient.date_of_death = date_of_death return patient.age - @mock.patch(f"{models.__name__}.datetime", wraps=datetime) - def test_living_patient_age(self, *args, **kwargs): - models.datetime.date.today = Mock(return_value=date(2022, 12, 1)) + @mock.patch("registry.patients.models.timezone") + def test_living_patient_age(self, mock_timezone): + mock_timezone.localdate.return_value = date(2022, 12, 1) self.assertEqual( self._get_calculated_age(self.patient, date(2000, 1, 1)), 22 @@ -51,9 +49,9 @@ def test_living_patient_age(self, *args, **kwargs): self._get_calculated_age(self.patient, date(2017, 2, 29)), 5 ) # Invalid leap year - @mock.patch(f"{models.__name__}.datetime", wraps=datetime) - def test_deceased_patient_age(self, *args, **kwargs): - models.datetime.date.today = Mock(return_value=date(2021, 6, 15)) + @mock.patch("registry.patients.models.timezone") + def test_deceased_patient_age(self, mock_timezone): + mock_timezone.localdate.return_value = date(2021, 6, 15) self.assertEqual( self._get_calculated_age( diff --git a/rdrf/rdrf/testing/unit/tests.py b/rdrf/rdrf/testing/unit/tests.py index 282e8f4d7..0b2d1ba85 100644 --- a/rdrf/rdrf/testing/unit/tests.py +++ b/rdrf/rdrf/testing/unit/tests.py @@ -3,7 +3,7 @@ import logging import os from copy import deepcopy -from datetime import datetime, timedelta +from datetime import date, timedelta import yaml from django.conf import settings @@ -14,6 +14,7 @@ from django.core.management import call_command from django.forms.models import model_to_dict from django.test import RequestFactory, TestCase +from django.utils import timezone from registry.groups import GROUPS as RDRF_GROUPS from registry.groups.models import CustomUser, WorkingGroup from registry.patients.models import AddressType, Patient, PatientAddress, State @@ -631,7 +632,7 @@ def create_patient(self): p = Patient() p.consent = True p.name = "Harry" - p.date_of_birth = datetime(1978, 6, 15) + p.date_of_birth = date(1978, 6, 15) p.working_group = self.working_group p.save() p.rdrf_registry.set([self.registry]) @@ -1660,7 +1661,7 @@ def _clear_notifications(self): EmailTemplate.objects.all().delete() def test_check_logins_command(self): - now = datetime.now() + now = timezone.now() class Time: RECENTLY = now - timedelta(days=1) @@ -1797,7 +1798,7 @@ def create_clinicaldata(self, patient_id, registry_code): def create_new_patient(self): p = Patient() p.name = "Kathy" - p.date_of_birth = datetime(1980, 4, 11) + p.date_of_birth = date(1980, 4, 11) p.consent = True p.save() diff --git a/rdrf/rdrf/users/views.py b/rdrf/rdrf/users/views.py index 5423167ac..ce94b7c91 100644 --- a/rdrf/rdrf/users/views.py +++ b/rdrf/rdrf/users/views.py @@ -1,4 +1,3 @@ -import datetime import logging from django.contrib import auth, messages @@ -12,6 +11,7 @@ from django.http import HttpResponse from django.shortcuts import get_object_or_404, redirect, render from django.urls import reverse +from django.utils import timezone from django.utils.translation import gettext_lazy as _ from django.views import View from registry.groups.models import ( @@ -44,13 +44,15 @@ def _redirect_response(self): def _render_template(self, request, user, form): # An existing email change request is only considered current if it was requested within the last 2 weeks - last_2_weeks = datetime.datetime.now() + datetime.timedelta(weeks=-2) + from datetime import timedelta + + last_2_weeks = timezone.now() + timedelta(weeks=-2) current_request = EmailChangeRequest.objects.filter( user=user, request_date__gte=last_2_weeks ).first() # Has the activation link most likely expired? - activation_expiry_hours = datetime.datetime.now() + datetime.timedelta( + activation_expiry_hours = timezone.now() + timedelta( hours=-EMAIL_CHANGE_REQUEST_EXPIRY_HOURS ) is_expired = ( diff --git a/rdrf/rdrf/views/mailbox_view.py b/rdrf/rdrf/views/mailbox_view.py index dc4a64609..b830d1b2e 100644 --- a/rdrf/rdrf/views/mailbox_view.py +++ b/rdrf/rdrf/views/mailbox_view.py @@ -1,9 +1,11 @@ import logging from datetime import datetime +from datetime import timezone as dt_timezone from django.core import mail from django.shortcuts import redirect, render from django.urls import reverse +from django.utils import timezone from django.views import View from rdrf.services.io.notifications.longitudinal_followups import ( @@ -34,10 +36,12 @@ def get(self, request): class MailboxSendLongitudinalFollowups(View): def get(self, request): if now_param := request.GET.get("now", None): - now = datetime.fromtimestamp(int(now_param)) + # Use Python's datetime.timezone.utc directly for clarity + now = datetime.fromtimestamp(int(now_param), tz=dt_timezone.utc) else: - now = datetime.now() + now = timezone.now() + logger.info(f"Sending longitudinal followups with now={now}") send_longitudinal_followups(now) return redirect(reverse("mailbox")) diff --git a/rdrf/registry/groups/migrations/0026_history_date.py b/rdrf/registry/groups/migrations/0026_history_date.py new file mode 100644 index 000000000..60fa6960d --- /dev/null +++ b/rdrf/registry/groups/migrations/0026_history_date.py @@ -0,0 +1,22 @@ +# Generated by Django 5.2.1 on 2026-01-05 06:32 + +from django.db import migrations, models + + +class Migration(migrations.Migration): + + dependencies = [ + ('groups', '0025_alter_workinggrouptype'), + ] + + operations = [ + migrations.AlterModelOptions( + name='historicalemailchangerequest', + options={'get_latest_by': ('history_date', 'history_id'), 'ordering': ('-history_date', '-history_id'), 'verbose_name': 'historical email change request', 'verbose_name_plural': 'historical email change requests'}, + ), + migrations.AlterField( + model_name='historicalemailchangerequest', + name='history_date', + field=models.DateTimeField(db_index=True), + ), + ] diff --git a/rdrf/registry/patients/admin.py b/rdrf/registry/patients/admin.py index f037c35de..22f0187e3 100644 --- a/rdrf/registry/patients/admin.py +++ b/rdrf/registry/patients/admin.py @@ -1,4 +1,3 @@ -import datetime import json import logging import os @@ -8,6 +7,7 @@ from django.db.models import Q from django.http import HttpResponse from django.urls import re_path, reverse +from django.utils import timezone from django.utils.translation import gettext as _ from rdrf.db.dynamic_data import DynamicDataWrapper from rdrf.helpers.registry_features import RegistryFeatures @@ -439,7 +439,7 @@ def freshness(self, obj): if not hasattr(obj, "patient_diagnosis"): return "" - delta = datetime.datetime.now() - obj.patient_diagnosis.updated + delta = timezone.now() - obj.patient_diagnosis.updated age = delta.days if age > 365: @@ -455,7 +455,7 @@ def freshness(self, obj): def last_updated(self, obj): if not hasattr(obj, "diagnosis"): return "" - delta = datetime.datetime.now() - obj.diagnosis.updated + delta = timezone.now() - obj.diagnosis.updated age = delta.days if age == 0: diff --git a/rdrf/registry/patients/migrations/0067_history_date.py b/rdrf/registry/patients/migrations/0067_history_date.py new file mode 100644 index 000000000..e408fbb23 --- /dev/null +++ b/rdrf/registry/patients/migrations/0067_history_date.py @@ -0,0 +1,130 @@ +# Generated by Django 5.2.1 on 2026-01-05 06:32 + +from django.db import migrations, models + + +class Migration(migrations.Migration): + + dependencies = [ + ('patients', '0066_patient_list_guid'), + ] + + operations = [ + migrations.AlterModelOptions( + name='historicaladdresstype', + options={'get_latest_by': ('history_date', 'history_id'), 'ordering': ('-history_date', '-history_id'), 'verbose_name': 'historical address type', 'verbose_name_plural': 'historical address types'}, + ), + migrations.AlterModelOptions( + name='historicalclinicianother', + options={'get_latest_by': ('history_date', 'history_id'), 'ordering': ('-history_date', '-history_id'), 'verbose_name': 'historical clinician other', 'verbose_name_plural': 'historical clinician others'}, + ), + migrations.AlterModelOptions( + name='historicalconsentvalue', + options={'get_latest_by': ('history_date', 'history_id'), 'ordering': ('-history_date', '-history_id'), 'verbose_name': 'historical consent value', 'verbose_name_plural': 'historical consent values'}, + ), + migrations.AlterModelOptions( + name='historicaldoctor', + options={'get_latest_by': ('history_date', 'history_id'), 'ordering': ('-history_date', '-history_id'), 'verbose_name': 'historical doctor', 'verbose_name_plural': 'historical doctors'}, + ), + migrations.AlterModelOptions( + name='historicalnextofkinrelationship', + options={'get_latest_by': ('history_date', 'history_id'), 'ordering': ('-history_date', '-history_id'), 'verbose_name': 'historical Next of Kin Relationship', 'verbose_name_plural': 'historical Next of Kin Relationships'}, + ), + migrations.AlterModelOptions( + name='historicalparentguardian', + options={'get_latest_by': ('history_date', 'history_id'), 'ordering': ('-history_date', '-history_id'), 'verbose_name': 'historical parent guardian', 'verbose_name_plural': 'historical parent guardians'}, + ), + migrations.AlterModelOptions( + name='historicalpatient', + options={'get_latest_by': ('history_date', 'history_id'), 'ordering': ('-history_date', '-history_id'), 'verbose_name': 'historical patient', 'verbose_name_plural': 'historical Patient List'}, + ), + migrations.AlterModelOptions( + name='historicalpatientaddress', + options={'get_latest_by': ('history_date', 'history_id'), 'ordering': ('-history_date', '-history_id'), 'verbose_name': 'historical patient address', 'verbose_name_plural': 'historical Patient Addresses'}, + ), + migrations.AlterModelOptions( + name='historicalpatientconsent', + options={'get_latest_by': ('history_date', 'history_id'), 'ordering': ('-history_date', '-history_id'), 'verbose_name': 'historical patient consent', 'verbose_name_plural': 'historical patient consents'}, + ), + migrations.AlterModelOptions( + name='historicalpatientdoctor', + options={'get_latest_by': ('history_date', 'history_id'), 'ordering': ('-history_date', '-history_id'), 'verbose_name': 'historical medical professionals for patient', 'verbose_name_plural': 'historical medical professionals for patient'}, + ), + migrations.AlterModelOptions( + name='historicalpatientrelative', + options={'get_latest_by': ('history_date', 'history_id'), 'ordering': ('-history_date', '-history_id'), 'verbose_name': 'historical patient relative', 'verbose_name_plural': 'historical patient relatives'}, + ), + migrations.AlterModelOptions( + name='historicalspeciality', + options={'get_latest_by': ('history_date', 'history_id'), 'ordering': ('-history_date', '-history_id'), 'verbose_name': 'historical speciality', 'verbose_name_plural': 'historical specialitys'}, + ), + migrations.AlterModelOptions( + name='historicalstate', + options={'get_latest_by': ('history_date', 'history_id'), 'ordering': ('-history_date', '-history_id'), 'verbose_name': 'historical state', 'verbose_name_plural': 'historical states'}, + ), + migrations.AlterField( + model_name='historicaladdresstype', + name='history_date', + field=models.DateTimeField(db_index=True), + ), + migrations.AlterField( + model_name='historicalclinicianother', + name='history_date', + field=models.DateTimeField(db_index=True), + ), + migrations.AlterField( + model_name='historicalconsentvalue', + name='history_date', + field=models.DateTimeField(db_index=True), + ), + migrations.AlterField( + model_name='historicaldoctor', + name='history_date', + field=models.DateTimeField(db_index=True), + ), + migrations.AlterField( + model_name='historicalnextofkinrelationship', + name='history_date', + field=models.DateTimeField(db_index=True), + ), + migrations.AlterField( + model_name='historicalparentguardian', + name='history_date', + field=models.DateTimeField(db_index=True), + ), + migrations.AlterField( + model_name='historicalpatient', + name='history_date', + field=models.DateTimeField(db_index=True), + ), + migrations.AlterField( + model_name='historicalpatientaddress', + name='history_date', + field=models.DateTimeField(db_index=True), + ), + migrations.AlterField( + model_name='historicalpatientconsent', + name='history_date', + field=models.DateTimeField(db_index=True), + ), + migrations.AlterField( + model_name='historicalpatientdoctor', + name='history_date', + field=models.DateTimeField(db_index=True), + ), + migrations.AlterField( + model_name='historicalpatientrelative', + name='history_date', + field=models.DateTimeField(db_index=True), + ), + migrations.AlterField( + model_name='historicalspeciality', + name='history_date', + field=models.DateTimeField(db_index=True), + ), + migrations.AlterField( + model_name='historicalstate', + name='history_date', + field=models.DateTimeField(db_index=True), + ), + ] diff --git a/rdrf/registry/patients/migrations/0068_country.py b/rdrf/registry/patients/migrations/0068_country.py new file mode 100644 index 000000000..c050e0db5 --- /dev/null +++ b/rdrf/registry/patients/migrations/0068_country.py @@ -0,0 +1,23 @@ +# Generated by Django 5.2.1 on 2026-01-16 00:37 + +from django.db import migrations, models + + +class Migration(migrations.Migration): + + dependencies = [ + ('patients', '0067_history_date'), + ] + + operations = [ + migrations.AlterField( + model_name='historicalpatientrelative', + name='location', + field=models.CharField(choices=[('AU - WA', 'Australia - WA'), ('AU - SA', 'Australia - SA'), ('AU - NSW', 'Australia - NSW'), ('AU - QLD', 'Australia - QLD'), ('AU - NT', 'Australia - NT'), ('AU - VIC', 'Australia - VIC'), ('AU - TAS', 'Australia - TAS'), ('NZ', 'New Zealand'), ('AF', 'Afghanistan'), ('AL', 'Albania'), ('DZ', 'Algeria'), ('AS', 'American Samoa'), ('AD', 'Andorra'), ('AO', 'Angola'), ('AI', 'Anguilla'), ('AQ', 'Antarctica'), ('AG', 'Antigua and Barbuda'), ('AR', 'Argentina'), ('AM', 'Armenia'), ('AW', 'Aruba'), ('AU', 'Australia'), ('AT', 'Austria'), ('AZ', 'Azerbaijan'), ('BS', 'Bahamas'), ('BH', 'Bahrain'), ('BD', 'Bangladesh'), ('BB', 'Barbados'), ('BY', 'Belarus'), ('BE', 'Belgium'), ('BZ', 'Belize'), ('BJ', 'Benin'), ('BM', 'Bermuda'), ('BT', 'Bhutan'), ('BO', 'Bolivia, Plurinational State of'), ('BQ', 'Bonaire, Sint Eustatius and Saba'), ('BA', 'Bosnia and Herzegovina'), ('BW', 'Botswana'), ('BV', 'Bouvet Island'), ('BR', 'Brazil'), ('IO', 'British Indian Ocean Territory'), ('BN', 'Brunei Darussalam'), ('BG', 'Bulgaria'), ('BF', 'Burkina Faso'), ('BI', 'Burundi'), ('CV', 'Cabo Verde'), ('KH', 'Cambodia'), ('CM', 'Cameroon'), ('CA', 'Canada'), ('KY', 'Cayman Islands'), ('CF', 'Central African Republic'), ('TD', 'Chad'), ('CL', 'Chile'), ('CN', 'China'), ('CX', 'Christmas Island'), ('CC', 'Cocos (Keeling) Islands'), ('CO', 'Colombia'), ('KM', 'Comoros'), ('CG', 'Congo'), ('CD', 'Congo, The Democratic Republic of the'), ('CK', 'Cook Islands'), ('CR', 'Costa Rica'), ('HR', 'Croatia'), ('CU', 'Cuba'), ('CW', 'Curaçao'), ('CY', 'Cyprus'), ('CZ', 'Czechia'), ('CI', "Côte d'Ivoire"), ('DK', 'Denmark'), ('DJ', 'Djibouti'), ('DM', 'Dominica'), ('DO', 'Dominican Republic'), ('EC', 'Ecuador'), ('EG', 'Egypt'), ('SV', 'El Salvador'), ('GQ', 'Equatorial Guinea'), ('ER', 'Eritrea'), ('EE', 'Estonia'), ('SZ', 'Eswatini'), ('ET', 'Ethiopia'), ('FK', 'Falkland Islands (Malvinas)'), ('FO', 'Faroe Islands'), ('FJ', 'Fiji'), ('FI', 'Finland'), ('FR', 'France'), ('GF', 'French Guiana'), ('PF', 'French Polynesia'), ('TF', 'French Southern Territories'), ('GA', 'Gabon'), ('GM', 'Gambia'), ('GE', 'Georgia'), ('DE', 'Germany'), ('GH', 'Ghana'), ('GI', 'Gibraltar'), ('GR', 'Greece'), ('GL', 'Greenland'), ('GD', 'Grenada'), ('GP', 'Guadeloupe'), ('GU', 'Guam'), ('GT', 'Guatemala'), ('GG', 'Guernsey'), ('GN', 'Guinea'), ('GW', 'Guinea-Bissau'), ('GY', 'Guyana'), ('HT', 'Haiti'), ('HM', 'Heard Island and McDonald Islands'), ('VA', 'Holy See (Vatican City State)'), ('HN', 'Honduras'), ('HK', 'Hong Kong'), ('HU', 'Hungary'), ('IS', 'Iceland'), ('IN', 'India'), ('ID', 'Indonesia'), ('IR', 'Iran, Islamic Republic of'), ('IQ', 'Iraq'), ('IE', 'Ireland'), ('IM', 'Isle of Man'), ('IL', 'Israel'), ('IT', 'Italy'), ('JM', 'Jamaica'), ('JP', 'Japan'), ('JE', 'Jersey'), ('JO', 'Jordan'), ('KZ', 'Kazakhstan'), ('KE', 'Kenya'), ('KI', 'Kiribati'), ('KP', "Korea, Democratic People's Republic of"), ('KR', 'Korea, Republic of'), ('KW', 'Kuwait'), ('KG', 'Kyrgyzstan'), ('LA', "Lao People's Democratic Republic"), ('LV', 'Latvia'), ('LB', 'Lebanon'), ('LS', 'Lesotho'), ('LR', 'Liberia'), ('LY', 'Libya'), ('LI', 'Liechtenstein'), ('LT', 'Lithuania'), ('LU', 'Luxembourg'), ('MO', 'Macao'), ('MG', 'Madagascar'), ('MW', 'Malawi'), ('MY', 'Malaysia'), ('MV', 'Maldives'), ('ML', 'Mali'), ('MT', 'Malta'), ('MH', 'Marshall Islands'), ('MQ', 'Martinique'), ('MR', 'Mauritania'), ('MU', 'Mauritius'), ('YT', 'Mayotte'), ('MX', 'Mexico'), ('FM', 'Micronesia, Federated States of'), ('MD', 'Moldova, Republic of'), ('MC', 'Monaco'), ('MN', 'Mongolia'), ('ME', 'Montenegro'), ('MS', 'Montserrat'), ('MA', 'Morocco'), ('MZ', 'Mozambique'), ('MM', 'Myanmar'), ('NA', 'Namibia'), ('NR', 'Nauru'), ('NP', 'Nepal'), ('NL', 'Netherlands'), ('NC', 'New Caledonia'), ('NZ', 'New Zealand'), ('NI', 'Nicaragua'), ('NE', 'Niger'), ('NG', 'Nigeria'), ('NU', 'Niue'), ('NF', 'Norfolk Island'), ('MK', 'North Macedonia'), ('MP', 'Northern Mariana Islands'), ('NO', 'Norway'), ('OM', 'Oman'), ('PK', 'Pakistan'), ('PW', 'Palau'), ('PS', 'Palestine, State of'), ('PA', 'Panama'), ('PG', 'Papua New Guinea'), ('PY', 'Paraguay'), ('PE', 'Peru'), ('PH', 'Philippines'), ('PN', 'Pitcairn'), ('PL', 'Poland'), ('PT', 'Portugal'), ('PR', 'Puerto Rico'), ('QA', 'Qatar'), ('RO', 'Romania'), ('RU', 'Russian Federation'), ('RW', 'Rwanda'), ('RE', 'Réunion'), ('BL', 'Saint Barthélemy'), ('SH', 'Saint Helena, Ascension and Tristan da Cunha'), ('KN', 'Saint Kitts and Nevis'), ('LC', 'Saint Lucia'), ('MF', 'Saint Martin (French part)'), ('PM', 'Saint Pierre and Miquelon'), ('VC', 'Saint Vincent and the Grenadines'), ('WS', 'Samoa'), ('SM', 'San Marino'), ('ST', 'Sao Tome and Principe'), ('SA', 'Saudi Arabia'), ('SN', 'Senegal'), ('RS', 'Serbia'), ('SC', 'Seychelles'), ('SL', 'Sierra Leone'), ('SG', 'Singapore'), ('SX', 'Sint Maarten (Dutch part)'), ('SK', 'Slovakia'), ('SI', 'Slovenia'), ('SB', 'Solomon Islands'), ('SO', 'Somalia'), ('ZA', 'South Africa'), ('GS', 'South Georgia and the South Sandwich Islands'), ('SS', 'South Sudan'), ('ES', 'Spain'), ('LK', 'Sri Lanka'), ('SD', 'Sudan'), ('SR', 'Suriname'), ('SJ', 'Svalbard and Jan Mayen'), ('SE', 'Sweden'), ('CH', 'Switzerland'), ('SY', 'Syrian Arab Republic'), ('TW', 'Taiwan, Province of China'), ('TJ', 'Tajikistan'), ('TZ', 'Tanzania, United Republic of'), ('TH', 'Thailand'), ('TL', 'Timor-Leste'), ('TG', 'Togo'), ('TK', 'Tokelau'), ('TO', 'Tonga'), ('TT', 'Trinidad and Tobago'), ('TN', 'Tunisia'), ('TM', 'Turkmenistan'), ('TC', 'Turks and Caicos Islands'), ('TV', 'Tuvalu'), ('TR', 'Türkiye'), ('UG', 'Uganda'), ('UA', 'Ukraine'), ('AE', 'United Arab Emirates'), ('GB', 'United Kingdom'), ('US', 'United States'), ('UM', 'United States Minor Outlying Islands'), ('UY', 'Uruguay'), ('UZ', 'Uzbekistan'), ('VU', 'Vanuatu'), ('VE', 'Venezuela, Bolivarian Republic of'), ('VN', 'Viet Nam'), ('VG', 'Virgin Islands, British'), ('VI', 'Virgin Islands, U.S.'), ('WF', 'Wallis and Futuna'), ('EH', 'Western Sahara'), ('YE', 'Yemen'), ('ZM', 'Zambia'), ('ZW', 'Zimbabwe'), ('AX', 'Ã…land Islands')], max_length=80), + ), + migrations.AlterField( + model_name='patientrelative', + name='location', + field=models.CharField(choices=[('AU - WA', 'Australia - WA'), ('AU - SA', 'Australia - SA'), ('AU - NSW', 'Australia - NSW'), ('AU - QLD', 'Australia - QLD'), ('AU - NT', 'Australia - NT'), ('AU - VIC', 'Australia - VIC'), ('AU - TAS', 'Australia - TAS'), ('NZ', 'New Zealand'), ('AF', 'Afghanistan'), ('AL', 'Albania'), ('DZ', 'Algeria'), ('AS', 'American Samoa'), ('AD', 'Andorra'), ('AO', 'Angola'), ('AI', 'Anguilla'), ('AQ', 'Antarctica'), ('AG', 'Antigua and Barbuda'), ('AR', 'Argentina'), ('AM', 'Armenia'), ('AW', 'Aruba'), ('AU', 'Australia'), ('AT', 'Austria'), ('AZ', 'Azerbaijan'), ('BS', 'Bahamas'), ('BH', 'Bahrain'), ('BD', 'Bangladesh'), ('BB', 'Barbados'), ('BY', 'Belarus'), ('BE', 'Belgium'), ('BZ', 'Belize'), ('BJ', 'Benin'), ('BM', 'Bermuda'), ('BT', 'Bhutan'), ('BO', 'Bolivia, Plurinational State of'), ('BQ', 'Bonaire, Sint Eustatius and Saba'), ('BA', 'Bosnia and Herzegovina'), ('BW', 'Botswana'), ('BV', 'Bouvet Island'), ('BR', 'Brazil'), ('IO', 'British Indian Ocean Territory'), ('BN', 'Brunei Darussalam'), ('BG', 'Bulgaria'), ('BF', 'Burkina Faso'), ('BI', 'Burundi'), ('CV', 'Cabo Verde'), ('KH', 'Cambodia'), ('CM', 'Cameroon'), ('CA', 'Canada'), ('KY', 'Cayman Islands'), ('CF', 'Central African Republic'), ('TD', 'Chad'), ('CL', 'Chile'), ('CN', 'China'), ('CX', 'Christmas Island'), ('CC', 'Cocos (Keeling) Islands'), ('CO', 'Colombia'), ('KM', 'Comoros'), ('CG', 'Congo'), ('CD', 'Congo, The Democratic Republic of the'), ('CK', 'Cook Islands'), ('CR', 'Costa Rica'), ('HR', 'Croatia'), ('CU', 'Cuba'), ('CW', 'Curaçao'), ('CY', 'Cyprus'), ('CZ', 'Czechia'), ('CI', "Côte d'Ivoire"), ('DK', 'Denmark'), ('DJ', 'Djibouti'), ('DM', 'Dominica'), ('DO', 'Dominican Republic'), ('EC', 'Ecuador'), ('EG', 'Egypt'), ('SV', 'El Salvador'), ('GQ', 'Equatorial Guinea'), ('ER', 'Eritrea'), ('EE', 'Estonia'), ('SZ', 'Eswatini'), ('ET', 'Ethiopia'), ('FK', 'Falkland Islands (Malvinas)'), ('FO', 'Faroe Islands'), ('FJ', 'Fiji'), ('FI', 'Finland'), ('FR', 'France'), ('GF', 'French Guiana'), ('PF', 'French Polynesia'), ('TF', 'French Southern Territories'), ('GA', 'Gabon'), ('GM', 'Gambia'), ('GE', 'Georgia'), ('DE', 'Germany'), ('GH', 'Ghana'), ('GI', 'Gibraltar'), ('GR', 'Greece'), ('GL', 'Greenland'), ('GD', 'Grenada'), ('GP', 'Guadeloupe'), ('GU', 'Guam'), ('GT', 'Guatemala'), ('GG', 'Guernsey'), ('GN', 'Guinea'), ('GW', 'Guinea-Bissau'), ('GY', 'Guyana'), ('HT', 'Haiti'), ('HM', 'Heard Island and McDonald Islands'), ('VA', 'Holy See (Vatican City State)'), ('HN', 'Honduras'), ('HK', 'Hong Kong'), ('HU', 'Hungary'), ('IS', 'Iceland'), ('IN', 'India'), ('ID', 'Indonesia'), ('IR', 'Iran, Islamic Republic of'), ('IQ', 'Iraq'), ('IE', 'Ireland'), ('IM', 'Isle of Man'), ('IL', 'Israel'), ('IT', 'Italy'), ('JM', 'Jamaica'), ('JP', 'Japan'), ('JE', 'Jersey'), ('JO', 'Jordan'), ('KZ', 'Kazakhstan'), ('KE', 'Kenya'), ('KI', 'Kiribati'), ('KP', "Korea, Democratic People's Republic of"), ('KR', 'Korea, Republic of'), ('KW', 'Kuwait'), ('KG', 'Kyrgyzstan'), ('LA', "Lao People's Democratic Republic"), ('LV', 'Latvia'), ('LB', 'Lebanon'), ('LS', 'Lesotho'), ('LR', 'Liberia'), ('LY', 'Libya'), ('LI', 'Liechtenstein'), ('LT', 'Lithuania'), ('LU', 'Luxembourg'), ('MO', 'Macao'), ('MG', 'Madagascar'), ('MW', 'Malawi'), ('MY', 'Malaysia'), ('MV', 'Maldives'), ('ML', 'Mali'), ('MT', 'Malta'), ('MH', 'Marshall Islands'), ('MQ', 'Martinique'), ('MR', 'Mauritania'), ('MU', 'Mauritius'), ('YT', 'Mayotte'), ('MX', 'Mexico'), ('FM', 'Micronesia, Federated States of'), ('MD', 'Moldova, Republic of'), ('MC', 'Monaco'), ('MN', 'Mongolia'), ('ME', 'Montenegro'), ('MS', 'Montserrat'), ('MA', 'Morocco'), ('MZ', 'Mozambique'), ('MM', 'Myanmar'), ('NA', 'Namibia'), ('NR', 'Nauru'), ('NP', 'Nepal'), ('NL', 'Netherlands'), ('NC', 'New Caledonia'), ('NZ', 'New Zealand'), ('NI', 'Nicaragua'), ('NE', 'Niger'), ('NG', 'Nigeria'), ('NU', 'Niue'), ('NF', 'Norfolk Island'), ('MK', 'North Macedonia'), ('MP', 'Northern Mariana Islands'), ('NO', 'Norway'), ('OM', 'Oman'), ('PK', 'Pakistan'), ('PW', 'Palau'), ('PS', 'Palestine, State of'), ('PA', 'Panama'), ('PG', 'Papua New Guinea'), ('PY', 'Paraguay'), ('PE', 'Peru'), ('PH', 'Philippines'), ('PN', 'Pitcairn'), ('PL', 'Poland'), ('PT', 'Portugal'), ('PR', 'Puerto Rico'), ('QA', 'Qatar'), ('RO', 'Romania'), ('RU', 'Russian Federation'), ('RW', 'Rwanda'), ('RE', 'Réunion'), ('BL', 'Saint Barthélemy'), ('SH', 'Saint Helena, Ascension and Tristan da Cunha'), ('KN', 'Saint Kitts and Nevis'), ('LC', 'Saint Lucia'), ('MF', 'Saint Martin (French part)'), ('PM', 'Saint Pierre and Miquelon'), ('VC', 'Saint Vincent and the Grenadines'), ('WS', 'Samoa'), ('SM', 'San Marino'), ('ST', 'Sao Tome and Principe'), ('SA', 'Saudi Arabia'), ('SN', 'Senegal'), ('RS', 'Serbia'), ('SC', 'Seychelles'), ('SL', 'Sierra Leone'), ('SG', 'Singapore'), ('SX', 'Sint Maarten (Dutch part)'), ('SK', 'Slovakia'), ('SI', 'Slovenia'), ('SB', 'Solomon Islands'), ('SO', 'Somalia'), ('ZA', 'South Africa'), ('GS', 'South Georgia and the South Sandwich Islands'), ('SS', 'South Sudan'), ('ES', 'Spain'), ('LK', 'Sri Lanka'), ('SD', 'Sudan'), ('SR', 'Suriname'), ('SJ', 'Svalbard and Jan Mayen'), ('SE', 'Sweden'), ('CH', 'Switzerland'), ('SY', 'Syrian Arab Republic'), ('TW', 'Taiwan, Province of China'), ('TJ', 'Tajikistan'), ('TZ', 'Tanzania, United Republic of'), ('TH', 'Thailand'), ('TL', 'Timor-Leste'), ('TG', 'Togo'), ('TK', 'Tokelau'), ('TO', 'Tonga'), ('TT', 'Trinidad and Tobago'), ('TN', 'Tunisia'), ('TM', 'Turkmenistan'), ('TC', 'Turks and Caicos Islands'), ('TV', 'Tuvalu'), ('TR', 'Türkiye'), ('UG', 'Uganda'), ('UA', 'Ukraine'), ('AE', 'United Arab Emirates'), ('GB', 'United Kingdom'), ('US', 'United States'), ('UM', 'United States Minor Outlying Islands'), ('UY', 'Uruguay'), ('UZ', 'Uzbekistan'), ('VU', 'Vanuatu'), ('VE', 'Venezuela, Bolivarian Republic of'), ('VN', 'Viet Nam'), ('VG', 'Virgin Islands, British'), ('VI', 'Virgin Islands, U.S.'), ('WF', 'Wallis and Futuna'), ('EH', 'Western Sahara'), ('YE', 'Yemen'), ('ZM', 'Zambia'), ('ZW', 'Zimbabwe'), ('AX', 'Ã…land Islands')], max_length=80), + ), + ] diff --git a/rdrf/registry/patients/models.py b/rdrf/registry/patients/models.py index 7b124a724..6bd71ac62 100644 --- a/rdrf/registry/patients/models.py +++ b/rdrf/registry/patients/models.py @@ -1,8 +1,8 @@ -import datetime import json import logging import random from collections import namedtuple +from datetime import timedelta from functools import reduce from operator import attrgetter @@ -580,7 +580,7 @@ def calculate_age(born): if self.date_of_death: compare_date = self.date_of_death else: - compare_date = datetime.date.today() + compare_date = timezone.localdate() try: birthday = born.replace(year=compare_date.year) @@ -651,9 +651,7 @@ def clinical_data_currency(self, days=365): If some clinical form has been updated in the window then the data for that registry is considered "current" - this mirrors """ - time_window_start = datetime.datetime.now() - datetime.timedelta( - days=days - ) + time_window_start = timezone.now() - timedelta(days=days) currency_map = {} for registry_model in self.rdrf_registry.all(): last_updated_in_window = False @@ -818,7 +816,7 @@ def evaluate_field_expression( mongo_data = { "django_id": self.pk, "django_model": "Patient", - "timestamp": datetime.datetime.now(), + "timestamp": timezone.now(), "context_id": context_model.pk, "forms": [], } @@ -889,7 +887,7 @@ def set_form_value( mongo_data = wrapper.load_dynamic_data(registry_code, "cdes") or {} key = mongo_key(form_name, section_code, data_element_code) timestamp = "%s_timestamp" % form_name - t = datetime.datetime.now() + t = timezone.now() frm = RegistryForm.objects.get( registry__code=registry_code, name=form_name @@ -1033,9 +1031,9 @@ def set_consent(self, consent_model, answer=True, commit=True): answer_changed = cv.answer != answer or created cv.answer = answer if cv.first_save: - cv.last_update = datetime.datetime.now() + cv.last_update = timezone.now() else: - cv.first_save = datetime.datetime.now() + cv.first_save = timezone.now() if commit: cv.save() return cv, answer_changed @@ -1276,7 +1274,7 @@ def form_currency(self, registry_form): if timestamp: if "timestamp" in timestamp: ts = timestamp["timestamp"] - delta = datetime.datetime.now() - ts + delta = timezone.now() - ts return True if delta.days < _6MONTHS_IN_DAYS else False else: return True diff --git a/rdrf/setup.py b/rdrf/setup.py deleted file mode 100644 index baf687390..000000000 --- a/rdrf/setup.py +++ /dev/null @@ -1,104 +0,0 @@ -import os - -from setuptools import find_packages, setup - -package_data = {} -start_dir = os.getcwd() - - -def add_file_for_package(package, subdir, f): - full_path = os.path.join(subdir, f) - # print "%s: %s" % (package, full_path) - return full_path - - -packages = [ - "rdrf", - "rdrf.account_handling", - "rdrf.auth", - "rdrf.context_processors", - "rdrf.db", - "rdrf.events", - "rdrf.forms", - "rdrf.forms.dynamic", - "rdrf.forms.fields", - "rdrf.forms.navigation", - "rdrf.forms.progress", - "rdrf.forms.validation", - "rdrf.forms.widgets", - "rdrf.helpers", - "rdrf.models", - "rdrf.models.definition", - "rdrf.reports", - "rdrf.routing", - "rdrf.security", - "rdrf.services", - "rdrf.services.io", - "rdrf.services.io.content", - "rdrf.services.io.content.export_import", - "rdrf.services.io.defs", - "rdrf.services.io.notifications", - "rdrf.services.rest", - "rdrf.services.rest.urls", - "rdrf.services.rest.views", - "rdrf.services.rpc", - "rdrf.testing", - "rdrf.testing.behaviour", - "rdrf.testing.unit", - "rdrf.views", - "rdrf.views.decorators", - "rdrf.workflows", - "registry", - "registry.common", - "registry.patients", - "registry.groups", - "report", -] - -for package in [ - "rdrf", - "registry.common", - "registry.groups", - "registry.patients", - "registry.humangenome", - "report", -]: - package_data[package] = [] - if "." in package: - base_dir, package_dir = package.split(".") - os.chdir(os.path.join(start_dir, base_dir, package_dir)) - else: - base_dir = package - os.chdir(os.path.join(start_dir, base_dir)) - - for data_dir in ( - "templates", - "static", - "migrations", - "fixtures", - "features", - "schemas", - "templatetags", - "management", - ): - package_data[package].extend( - [ - add_file_for_package(package, subdir, f) - for (subdir, dirs, files) in os.walk(data_dir) - for f in files - ] - ) - - os.chdir(start_dir) - - -setup( - name="trrf", - version="1.0.0", - packages=find_packages(), - description="TRRF", - long_description="Trial Ready Registry Framework", - author="Queensland University of Technology - eResearch", - package_data=package_data, - zip_safe=False, -) diff --git a/rdrf/useraudit/models.py b/rdrf/useraudit/models.py index 695d79d9a..6431e2e34 100644 --- a/rdrf/useraudit/models.py +++ b/rdrf/useraudit/models.py @@ -1,10 +1,10 @@ from __future__ import unicode_literals -import datetime import logging from django.contrib.auth.signals import user_logged_in from django.db import models +from django.utils import timezone from .signals import ( account_has_expired, @@ -25,7 +25,7 @@ class LoginAttempt(models.Model): class LoginAttemptLogger(object): def reset(self, username): - defaults = {"count": 0, "timestamp": datetime.datetime.now()} + defaults = {"count": 0, "timestamp": timezone.now()} LoginAttempt.objects.update_or_create( username=username, defaults=defaults ) @@ -33,7 +33,7 @@ def reset(self, username): def increment(self, username): obj, created = LoginAttempt.objects.get_or_create(username=username) obj.count += 1 - obj.timestamp = datetime.datetime.now() + obj.timestamp = timezone.now() obj.save() diff --git a/rdrf/useraudit/tests/utils.py b/rdrf/useraudit/tests/utils.py index 87e33df2f..9fd68928b 100644 --- a/rdrf/useraudit/tests/utils.py +++ b/rdrf/useraudit/tests/utils.py @@ -1,15 +1,15 @@ -from datetime import datetime, timedelta +from datetime import timedelta from functools import reduce from importlib import import_module from django.conf import settings from django.contrib.auth import authenticate, login - from django.test.client import RequestFactory +from django.utils import timezone def is_recent(time): - return datetime.now() - timedelta(seconds=3) < time + return timezone.now() - timedelta(seconds=3) < time def simulate_login(username, password, headers=None): diff --git a/requirements/clients b/requirements/clients deleted file mode 120000 index 4d613f769..000000000 --- a/requirements/clients +++ /dev/null @@ -1 +0,0 @@ -../clients \ No newline at end of file diff --git a/requirements/dev-requirements.txt b/requirements/dev-requirements.txt deleted file mode 100644 index 07501dc0b..000000000 --- a/requirements/dev-requirements.txt +++ /dev/null @@ -1,7 +0,0 @@ -sphinx -sphinxcontrib-fulltoc -Werkzeug==3.1.4 -python-Levenshtein -ipython -django-silk==4.4.0 -ruff \ No newline at end of file diff --git a/requirements/requirements.txt b/requirements/requirements.txt deleted file mode 100644 index 8794f72d6..000000000 --- a/requirements/requirements.txt +++ /dev/null @@ -1,43 +0,0 @@ -ccg-django-utils==0.4.2 -Django==4.2.27 -django-anymail==8.5 -django-countries==7.2.1 -django-csp==3.7 -django-extensions==3.2.1 -django-registration-redux==2.10 -djangorestframework==3.15.2 -django-storages==1.14.6 -django-stronghold==0.4.0 -jsonschema==4.4.0 -openpyxl==3.0.9 -psycopg2-binary==2.9.10 -pycountry==22.1.10 -python-dateutil==2.8.2 -python-magic==0.4.24 -pyyaml==6.0.3 -six==1.16.0 -SQLAlchemy==1.3.24 -uwsgi==2.0.30 -django-formtools==2.3 -django-otp==1.1.3 -django-two-factor-auth==1.15.5 -phonenumberslite==8.12.39 -Pillow==11.3.0 -qrcode==6.1 -django-reversion==5.0.0 -ua-parser==0.10.0 -user-agents==2.2.0 -django-user-agents==0.4.0 -django-simple-history==3.0.0 -lark==1.0.0 -boto3==1.40.41 -aws-xray-sdk==2.9.0 -graphene-django==3.1.5 -django-filter==21.1 -flatten_json==0.1.13 -gql-query-builder @ git+https://github.com/eresearchqut/gql-query-builder@a983448 -awslambdaric==3.1.1 -django-cache-memoize==0.1.10 -./clients/xnat/generated -langcodes==3.3.0 -language_data==1.3 diff --git a/requirements/test-requirements.txt b/requirements/test-requirements.txt deleted file mode 100644 index a140b4873..000000000 --- a/requirements/test-requirements.txt +++ /dev/null @@ -1,16 +0,0 @@ -sure==1.4.11 -django-nose==1.4.7 -pytest==7.1.1 -pytest-django==4.5.2 -pynose==1.5.5 -nose-timer==0.7.5 -aloe==0.2.0 -aloe_webdriver==0.6.0 -aloe_django==0.2.0 -pyvirtualdisplay==0.2.5 -selenium==4.1.3 -unittest-xml-reporting==3.2.0 -requests==2.32.4 -sqlalchemy-utils==0.36.1 -stellar==0.4.5 -coverage==5.5 diff --git a/scripts/end2end-tests.sh b/scripts/end2end-tests.sh index b03897cdd..6606084f3 100755 --- a/scripts/end2end-tests.sh +++ b/scripts/end2end-tests.sh @@ 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