diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml new file mode 100644 index 0000000..5351aba --- /dev/null +++ b/.github/workflows/build.yml @@ -0,0 +1,49 @@ +name: build +on: + push: + branches: + - devel +jobs: + rworkflows: + permissions: write-all + runs-on: ${{ matrix.config.os }} + name: ${{ matrix.config.os }} (${{ matrix.config.r }}) + container: ${{ matrix.config.cont }} + strategy: + fail-fast: ${{ false }} + matrix: + config: + - os: ubuntu-latest + bioc: devel + r: auto + cont: ghcr.io/bioconductor/bioconductor_docker:devel + rspm: ~ + - os: macOS-latest + bioc: devel + r: auto + cont: ~ + rspm: ~ + - os: windows-latest + bioc: devel + r: auto + cont: ~ + rspm: ~ + steps: + - uses: neurogenomics/rworkflows@master + with: + run_bioccheck: ${{ false }} + run_rcmdcheck: ${{ false }} + as_cran: ${{ true }} + run_vignettes: ${{ true }} + has_testthat: ${{ true }} + run_covr: ${{ true }} + run_pkgdown: ${{ true }} + has_runit: ${{ false }} + has_latex: ${{ false }} + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + run_docker: ${{ false }} + DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }} + CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} + runner_os: ${{ runner.os }} + cache_version: cache-v1 + docker_registry: ghcr.io diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml new file mode 100644 index 0000000..339e919 --- /dev/null +++ b/.github/workflows/test.yml @@ -0,0 +1,52 @@ +name: test +on: + pull-request: + branches: + - devel +jobs: + rworkflows: + permissions: write-all + runs-on: ${{ matrix.config.os }} + name: ${{ matrix.config.os }} (${{ matrix.config.r }}) + container: ${{ matrix.config.cont }} + strategy: + fail-fast: ${{ false }} + matrix: + config: + - os: ubuntu-latest + bioc: devel + r: auto + cont: ghcr.io/bioconductor/bioconductor_docker:devel + rspm: ~ + - os: macOS-latest + bioc: devel + r: auto + cont: ~ + rspm: ~ + - os: windows-latest + bioc: devel + r: auto + cont: ~ + rspm: ~ + env: + EP_USERNAME: ${{ secrets.EP_USERNAME }} + EP_PASSWORD: ${{ secrets.EP_PASSWORD }} + steps: + - uses: neurogenomics/rworkflows@master + with: + run_bioccheck: ${{ true }} + run_rcmdcheck: ${{ true }} + as_cran: ${{ true }} + run_vignettes: ${{ false }} + has_testthat: ${{ true }} + run_covr: ${{ false }} + run_pkgdown: ${{ false }} + has_runit: ${{ false }} + has_latex: ${{ false }} + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} + run_docker: ${{ false }} + DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }} + CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} + runner_os: ${{ runner.os }} + cache_version: cache-v1 + docker_registry: ghcr.io diff --git a/.gitignore b/.gitignore index 508df78..9c63895 100644 --- a/.gitignore +++ b/.gitignore @@ -1,2 +1,7 @@ .Rproj.user .Rhistory +.Renviron +inst/doc +vignettes/*.html +vignettes/*.R +docs/ diff --git a/DESCRIPTION b/DESCRIPTION index fa88828..9e9ebe8 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,17 +1,22 @@ Package: enviPathR Title: R client for enviPath API -Version: 0.0.0.9000 -Authors@R: - person("Giulio", "Benedetti", , "giulio.benedetti@utu.fi", role = c("aut", "cre")) +Version: 0.99.0 +Authors@R: + c(person(given = "Giulio", family = "Benedetti", role = c("aut", "cre"), + email = "giulio.benedetti@utu.fi", + comment = c(ORCID = "0000-0002-8732-7692"))) Description: The environmental pathway database (enviPath) is a key resource for the functional annotation and pathway prediction of microbial communities, providing knowledge on biotransformation pathways along with the chemical reactions and produced compounds. This package enables the programmatic access to enviPath by porting the database API from R. +biocViews: + Software, DataImport, Cheminformatics, Microbiome, Annotation, Pathways, + Visualization, Network, GraphAndNetwork Imports: + BiocParallel, httr2, - jsonlite, stats, stringr, tools @@ -19,3 +24,12 @@ License: Artistic-2.0 Encoding: UTF-8 Roxygen: list(markdown = TRUE) RoxygenNote: 8.0.0 +Suggests: + BiocStyle, + httptest2, + igraph, + knitr, + rmarkdown, + testthat (>= 3.0.0) +Config/testthat/edition: 3 +VignetteBuilder: knitr diff --git a/NAMESPACE b/NAMESPACE index f9d10e0..b8860c8 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -4,6 +4,7 @@ export(epGet) export(epLink) export(epList) export(epLogin) +export(epModel) importFrom(BiocParallel,bplapply) importFrom(BiocParallel,bpmapply) importFrom(httr2,req_body_form) diff --git a/R/constants.R b/R/constants.R index a57aa77..7ca2fc9 100644 --- a/R/constants.R +++ b/R/constants.R @@ -28,7 +28,7 @@ cache <- R_user_dir("enviPathR", "cache") if( !dir.exists(cache) ) dir.create(cache) # Preserve cookies between requests - eP_env$cookies <- tempfile("cookies", tmpdir = cache, fileext = ".txt") + eP_env$cookies <- file.path(cache, "cookies.txt") # Add links eP_env$links <- .make_ep_links() return(eP_env) diff --git a/R/get.R b/R/get.R index 4811005..3e16bc6 100644 --- a/R/get.R +++ b/R/get.R @@ -17,9 +17,21 @@ #' A list of objects #' #' @examples +#' \dontshow{ +#' username <- Sys.getenv("EP_USERNAME") +#' password <- Sys.getenv("EP_PASSWORD") +#' +#' epLogin(username, password) +#' +#' library(httptest2) +#' start_vignette("httptest/get") +#' } #' rxn_id <- "2b6bbcc5-77f4-4bed-92a9-731cdc978f6a" #' #' epGet("reaction", rxn_id) +#' \dontshow{ +#' end_vignette() +#' } NULL #' @export diff --git a/R/link.R b/R/link.R index db05029..fb7ae81 100644 --- a/R/link.R +++ b/R/link.R @@ -17,9 +17,21 @@ #' A data frame with links between from and to. #' #' @examples +#' \dontshow{ +#' username <- Sys.getenv("EP_USERNAME") +#' password <- Sys.getenv("EP_PASSWORD") +#' +#' epLogin(username, password) +#' +#' library(httptest2) +#' start_vignette("httptest/link") +#' } #' rxn_id <- "2b6bbcc5-77f4-4bed-92a9-731cdc978f6a" #' -#' epGet("reaction", rxn_id) +#' epLink("reaction", "compound", rxn_id) +#' \dontshow{ +#' end_vignette() +#' } NULL #' @export diff --git a/R/list.R b/R/list.R index 205ee9b..4a4a0ce 100644 --- a/R/list.R +++ b/R/list.R @@ -13,9 +13,21 @@ #' A data frame. #' #' @examples +#' \dontshow{ +#' username <- Sys.getenv("EP_USERNAME") +#' password <- Sys.getenv("EP_PASSWORD") +#' +#' epLogin(username, password) +#' +#' library(httptest2) +#' start_vignette("httptest/list") +#' } #' epList("package") #' #' epList("pathway", pkg = "32de3cf4-e3e6-4168-956e-32fa5ddb0ce1") +#' \dontshow{ +#' end_vignette() +#' } NULL #' @export @@ -45,7 +57,9 @@ epList <- function(type, pkg = NULL){ # Remove id prefix df$id <- str_remove(df$id, ".*/") - to_keep <- c("name", "id", "reviewStatus") + to_keep <- c("name", "id") + # Include review status except for type setting + if( type != "setting" ) to_keep <- c(to_keep, "reviewStatus") if( type == "package" ){ diff --git a/R/login.R b/R/login.R index e88e3c9..6404026 100644 --- a/R/login.R +++ b/R/login.R @@ -14,8 +14,11 @@ #' A message upon successful login. #' #' @examples -#' # epLogin("FirstLast", "abc123") -#' #> Welcome to enviPath! +#' \dontshow{ +#' username <- Sys.getenv("EP_USERNAME") +#' password <- Sys.getenv("EP_PASSWORD") +#' } +#' epLogin(username, password) NULL #' @importFrom httr2 request req_method req_body_form req_cookie_preserve req_perform diff --git a/R/model.R b/R/model.R new file mode 100644 index 0000000..c8d7b2d --- /dev/null +++ b/R/model.R @@ -0,0 +1,81 @@ +#' Predict biotransformation pathways for compounds +#' +#' @name epModel +#' +#' @description +#' epGet returns a raw object from enviPath. +#' +#' @param smiles \code{Character vector}. +#' +#' @param setting \code{Character scalar}. +#' +#' @returns +#' A list with two data frames with information on nodes and edges, +#' respectively. +#' +#' @examples +#' \dontshow{ +#' username <- Sys.getenv("EP_USERNAME") +#' password <- Sys.getenv("EP_PASSWORD") +#' +#' epLogin(username, password) +#' } +#' library(igraph) +#' +#' # Define smiles of interest +#' smiles <- "ClC(Cl)=C(Cl)Cl" +#' +#' # Perform pathway prediction with enviFormer +#' former_out <- epModel(smiles) +#' +#' # Set id for PEPPER model setting +#' set_id <- "3cda8e56-f4ff-47a8-b68c-4cfcfc4e8c2a" +#' +#' # Perform pathway prediction with PEPPER +#' pepper_out <- epModel(smiles, set_id) +#' +#' # Convert model output to igraph object +#' path_graph <- graph_from_data_frame( +#' pepper_out$edges, +#' vertices = pepper_out$nodes +#' ) +#' +#' # Visualise predicted pathway +#' plot(path_graph) +NULL + +#' @export +#' @rdname epModel +#' @importFrom httr2 request req_method req_url_path_append req_body_form req_cookie_preserve req_perform resp_body_json +epModel <- function(smiles, setting = NULL){ + + if( smiles == "" ){ + stop("'smiles' must be a valid SMILES string.", call. = FALSE) + } + + if( is.null(setting) ) setting <- "1d915a48-286a-4394-9693-bfaa187326a5" + + setting <- paste0("https://envipath.org/setting/", setting) + + req <- request(eP_env$url) |> + req_method("POST") |> + req_url_path_append("util") |> + req_body_form(smiles = smiles, settingUri = setting) |> + req_cookie_preserve(path = eP_env$cookies) + + resp <- req_perform(req) + + out <- resp_body_json(resp, simplifyVector = TRUE) + + if( is.data.frame(out$edges$rule) ){ + out$edges$ruleId <- out$edges$rule$uuid + out$edges$ruleName <- out$edges$rule$name + out$edges$rule <- NULL + } + + out$nodes$name <- out$nodes$smiles + out$nodes$smiles <- NULL + + out$nodes <- out$nodes[c("id", "name", "depth")] + return(out) +} \ No newline at end of file diff --git a/README.md b/README.md index a5e1dfa..60bf22f 100644 --- a/README.md +++ b/README.md @@ -13,13 +13,13 @@ Bioconductor release version: if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") -BiocManager::install("mia") +BiocManager::install("enviPathR") ``` Beta version: ``` -remotes::install_github("Minotau-R/ariadne") +remotes::install_github("Minotau-R/enviPathR") ``` ## References diff --git a/man/epGet.Rd b/man/epGet.Rd index bbb64a5..24044c8 100644 --- a/man/epGet.Rd +++ b/man/epGet.Rd @@ -22,7 +22,19 @@ A list of objects epGet returns a raw object from enviPath. } \examples{ +\dontshow{ + username <- Sys.getenv("EP_USERNAME") + password <- Sys.getenv("EP_PASSWORD") + + epLogin(username, password) + + library(httptest2) + start_vignette("httptest/get") +} rxn_id <- "2b6bbcc5-77f4-4bed-92a9-731cdc978f6a" epGet("reaction", rxn_id) +\dontshow{ + end_vignette() +} } diff --git a/man/epLink.Rd b/man/epLink.Rd index 72a703d..4bff3ab 100644 --- a/man/epLink.Rd +++ b/man/epLink.Rd @@ -22,7 +22,19 @@ A data frame with links between from and to. epLink returns mappings between enviPath object types. } \examples{ +\dontshow{ + username <- Sys.getenv("EP_USERNAME") + password <- Sys.getenv("EP_PASSWORD") + + epLogin(username, password) + + library(httptest2) + start_vignette("httptest/link") +} rxn_id <- "2b6bbcc5-77f4-4bed-92a9-731cdc978f6a" -epGet("reaction", rxn_id) +epLink("reaction", "compound", rxn_id) +\dontshow{ + end_vignette() +} } diff --git a/man/epList.Rd b/man/epList.Rd index 6a984ef..e641b66 100644 --- a/man/epList.Rd +++ b/man/epList.Rd @@ -18,7 +18,19 @@ A data frame. epList returns a list with info on objects available in enviPath. } \examples{ +\dontshow{ + username <- Sys.getenv("EP_USERNAME") + password <- Sys.getenv("EP_PASSWORD") + + epLogin(username, password) + + library(httptest2) + start_vignette("httptest/list") +} epList("package") epList("pathway", pkg = "32de3cf4-e3e6-4168-956e-32fa5ddb0ce1") +\dontshow{ + end_vignette() +} } diff --git a/man/epLogin.Rd b/man/epLogin.Rd index 0654e14..830e2d1 100644 --- a/man/epLogin.Rd +++ b/man/epLogin.Rd @@ -16,6 +16,9 @@ epLogin lets you perform login to enviPath. An account is required to use the enviPath API. (add db link to refs) } \examples{ -# epLogin("FirstLast", "abc123") -#> Welcome to enviPath! +\dontshow{ + username <- Sys.getenv("EP_USERNAME") + password <- Sys.getenv("EP_PASSWORD") +} +epLogin(username, password) } diff --git a/man/epModel.Rd b/man/epModel.Rd new file mode 100644 index 0000000..9f73842 --- /dev/null +++ b/man/epModel.Rd @@ -0,0 +1,50 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/model.R +\name{epModel} +\alias{epModel} +\title{Predict biotransformation pathways for compounds} +\usage{ +epModel(smiles, setting = NULL) +} +\arguments{ +\item{smiles}{\code{Character vector}.} + +\item{setting}{\code{Character scalar}.} +} +\value{ +A list with two data frames with information on nodes and edges, +respectively. +} +\description{ +epGet returns a raw object from enviPath. +} +\examples{ +\dontshow{ + username <- Sys.getenv("EP_USERNAME") + password <- Sys.getenv("EP_PASSWORD") + + epLogin(username, password) +} +library(igraph) + +# Define smiles of interest +smiles <- "ClC(Cl)=C(Cl)Cl" + +# Perform pathway prediction with enviFormer +former_out <- epModel(smiles) + +# Set id for PEPPER model setting +set_id <- "3cda8e56-f4ff-47a8-b68c-4cfcfc4e8c2a" + +# Perform pathway prediction with PEPPER +pepper_out <- epModel(smiles, set_id) + +# Convert model output to igraph object +path_graph <- graph_from_data_frame( + pepper_out$edges, + vertices = pepper_out$nodes +) + +# Visualise predicted pathway +plot(path_graph) +} diff --git a/tests/testthat.R b/tests/testthat.R new file mode 100644 index 0000000..0bc4596 --- /dev/null +++ b/tests/testthat.R @@ -0,0 +1,12 @@ +# This file is part of the standard setup for testthat. +# It is recommended that you do not modify it. +# +# Where should you do additional test configuration? +# Learn more about the roles of various files in: +# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview +# * https://testthat.r-lib.org/articles/special-files.html + +library(testthat) +library(enviPathR) + +test_check("enviPathR") diff --git a/tests/testthat/httptest/get/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/2b6bbcc5-77f4-4bed-92a9-731cdc978f6a.json b/tests/testthat/httptest/get/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/2b6bbcc5-77f4-4bed-92a9-731cdc978f6a.json new file mode 100644 index 0000000..eb997bd --- /dev/null +++ b/tests/testthat/httptest/get/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/2b6bbcc5-77f4-4bed-92a9-731cdc978f6a.json @@ -0,0 +1,51 @@ +{ + "aliases": [ + + ], + "description": "no description", + "ecNumbers": [ + + ], + "educts": [ + { + "compoundName": "4-Hydroxybutyraldehyde", + "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/d2c48ebe-5a5a-4f5b-b42e-8ff23c873f6c/structure/7281d994-9f4a-4f7f-9e50-90b131c11da3", + "smiles": "C(CCO)C=O" + } + ], + "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/2b6bbcc5-77f4-4bed-92a9-731cdc978f6a", + "identifier": "reaction", + "medlineRefs": [ + + ], + "multistep": false, + "name": "Eawag BBD reaction r0014", + "pathways": [ + { + "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/c3d1b8d5-9ffb-49b8-a1bf-bf3d7dfd1ac3", + "name": "Tetrahydrofuran", + "reviewStatus": "reviewed", + "identifier": "pathway" + } + ], + "products": [ + { + "compoundName": "4-Hydroxybutanoate", + "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/a41e6b76-b462-49d4-ae42-391ef00bf98c/structure/befe8eeb-e8f8-4b4a-90b1-d0584a75f8cb", + "smiles": "C(CC(=O)[O-])CO" + } + ], + "references": { + "rheaReferences": [ + + ], + "uniprotCount": [ + + ] + }, + "reviewStatus": "reviewed", + "scenarios": [ + + ], + "smirks": "C(CCO)C=O>>C(CC(=O)[O-])CO" +} diff --git a/tests/testthat/httptest/link/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/ec87b463-6a3c-4dfa-8b88-4637fc158896.json b/tests/testthat/httptest/link/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/ec87b463-6a3c-4dfa-8b88-4637fc158896.json new file mode 100644 index 0000000..7765060 --- /dev/null +++ b/tests/testthat/httptest/link/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/ec87b463-6a3c-4dfa-8b88-4637fc158896.json @@ -0,0 +1,128 @@ +{ + "aliases": [ + + ], + "description": "Eawag BBD compound c0001", + "externalReferences": { + + }, + "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/ec87b463-6a3c-4dfa-8b88-4637fc158896", + "halflifes": [ + + ], + "identifier": "compound", + "imageSize": 600, + "name": "1,2-Dichloroethane", + "pathwayScenarios": [ + + ], + "pathways": [ + { + "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/7b3f3e72-4f35-42c8-893d-e29c6b474232", + "name": "1,2-Dichloroethane", + "reviewStatus": "reviewed", + "identifier": "pathway" + } + ], + "pubchemCompoundReferences": [ + + ], + "reactions": [ + { + "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/6e2372bc-b165-4c19-b01c-6b64dff4d40a", + "name": "Eawag BBD reaction r0001", + "reviewStatus": "reviewed", + "identifier": "reaction" + } + ], + "reviewStatus": "reviewed", + "scenarios": [ + + ], + "structures": [ + { + "InChI": "InChI=1S/C2H4Cl2/c3-1-2-4/h1-2H2", + "aliases": [ + + ], + "canonicalSmiles": "ClCCCl", + "charge": 0, + "description": "Eawag BBD compound c0001", + "externalReferences": { + + }, + "formula": "C2H4Cl2", + "halflifes": [ + + ], + "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/ec87b463-6a3c-4dfa-8b88-4637fc158896/structure/7fa796ed-4816-4bc1-8c46-afdfd86ac8a3", + "identifier": "structure", + "imageSize": 600, + "inchikey": "WSLDOOZREJYCGB-UHFFFAOYSA-N", + "isDefaultStructure": true, + "mass": 98.96000000000001, + "name": "1,2-Dichloroethane", + "pathways": [ + { + "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/7b3f3e72-4f35-42c8-893d-e29c6b474232", + "name": "1,2-Dichloroethane", + "reviewStatus": "reviewed", + "identifier": "pathway" + } + ], + "pubchemCompoundReferences": [ + + ], + "reactions": [ + { + "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/6e2372bc-b165-4c19-b01c-6b64dff4d40a", + "name": "Eawag BBD reaction r0001", + "reviewStatus": "reviewed", + "identifier": "reaction" + } + ], + "reviewStatus": "reviewed", + "scenarios": [ + + ], + "smiles": "C(CCl)Cl" + }, + { + "InChI": "InChI=1S/C2H4Cl2/c3-1-2-4/h1-2H2", + "aliases": [ + + ], + "canonicalSmiles": "ClCCCl", + "charge": 0, + "description": "Eawag BBD compound c0001 (in its normalized form)", + 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More details regarding enviPath conventions can be found in our wiki<\/a>.", + "id": "https://envipath.org/package/521c547a-fd2a-491c-ad5b-7eaa1577fb65", + "links": [ + { + "Pathways": [ + "https://envipath.org/package/521c547a-fd2a-491c-ad5b-7eaa1577fb65/pathway", + 183 + ] + }, + { + "Rules": [ + "https://envipath.org/package/521c547a-fd2a-491c-ad5b-7eaa1577fb65/rule", + 0 + ] + }, + { + "Compounds": [ + "https://envipath.org/package/521c547a-fd2a-491c-ad5b-7eaa1577fb65/compound", + 1067 + ] + }, + { + "Reactions": [ + "https://envipath.org/package/521c547a-fd2a-491c-ad5b-7eaa1577fb65/reaction", + 494 + ] + }, + { + "Relative Reasoning": [ + "https://envipath.org/package/521c547a-fd2a-491c-ad5b-7eaa1577fb65/relative-reasoning", + 0 + ] + }, + { + "Scenarios": [ + "https://envipath.org/package/521c547a-fd2a-491c-ad5b-7eaa1577fb65/scenario", + 85 + ] + } + ], + "name": "EAWAG-SLUDGE", + "primaryGroup": null, + "readers": [ + { + "id": "https://envipath.org/user/fce36893-bdb1-4a6f-87bd-5fd893feca89", + "identifier": "user", + "name": "admin" + }, + { + "id": "https://envipath.org/group/bcdd3c74-9abb-4e55-8ffd-04c2f2ab5df0", + "identifier": "group", + "name": "enviPath Users" + } + ], + "reviewComment": "", + "reviewStatus": "reviewed", + "writers": [ + { + "id": "https://envipath.org/user/fce36893-bdb1-4a6f-87bd-5fd893feca89", + "identifier": "user", + "name": "admin" + } + ] + }, + { + "description": "string", + "id": "https://envipath.org/package/7245f711-51d0-4b1e-b49d-99a9d9744c96", + "links": [ + { + "Pathways": [ + "https://envipath.org/package/7245f711-51d0-4b1e-b49d-99a9d9744c96/pathway", + 0 + ] + }, + { + "Rules": [ + "https://envipath.org/package/7245f711-51d0-4b1e-b49d-99a9d9744c96/rule", + 0 + ] + }, + { + "Compounds": [ + "https://envipath.org/package/7245f711-51d0-4b1e-b49d-99a9d9744c96/compound", + 0 + ] + }, + { + "Reactions": [ + "https://envipath.org/package/7245f711-51d0-4b1e-b49d-99a9d9744c96/reaction", + 0 + ] + }, + { + "Relative Reasoning": [ + "https://envipath.org/package/7245f711-51d0-4b1e-b49d-99a9d9744c96/relative-reasoning", + 0 + ] + }, + { + "Scenarios": [ + "https://envipath.org/package/7245f711-51d0-4b1e-b49d-99a9d9744c96/scenario", + 0 + ] + } + ], + "name": "32de3cf4-e3e6-4168-956e-32fa5ddb0ce1", + "primaryGroup": null, + "readers": [ + { + "id": "https://envipath.org/user/f3ce2e6a-b8c4-46d2-a6ed-6be4d8ae23fa", + "identifier": "user", + "name": "RiboRings" + } + ], + "reviewComment": "", + "reviewStatus": "unreviewed", + "writers": [ + { + "id": "https://envipath.org/user/f3ce2e6a-b8c4-46d2-a6ed-6be4d8ae23fa", + "identifier": "user", + "name": "RiboRings" + } + ] + }, + { + "description": "This is a package designed for non-peer-reviewed pathways. Once the pathways are peer-reviewed, this package will be merged into the enviPath-PFAS package.", + "id": "https://envipath.org/package/eb601621-3b32-4b64-b84a-97fdaeb366fb", + "links": [ + { + "Pathways": [ + "https://envipath.org/package/eb601621-3b32-4b64-b84a-97fdaeb366fb/pathway", + 3 + ] + }, + { + "Rules": [ + "https://envipath.org/package/eb601621-3b32-4b64-b84a-97fdaeb366fb/rule", + 0 + ] + }, + { + "Compounds": [ + "https://envipath.org/package/eb601621-3b32-4b64-b84a-97fdaeb366fb/compound", + 13 + ] + }, + { + "Reactions": [ + "https://envipath.org/package/eb601621-3b32-4b64-b84a-97fdaeb366fb/reaction", + 11 + ] + }, + { + "Relative Reasoning": [ + "https://envipath.org/package/eb601621-3b32-4b64-b84a-97fdaeb366fb/relative-reasoning", + 0 + ] + }, + { + "Scenarios": [ + "https://envipath.org/package/eb601621-3b32-4b64-b84a-97fdaeb366fb/scenario", + 3 + ] + } + ], + "name": "enviPath-PFAS_temporary", + "primaryGroup": null, + "readers": [ + { + "id": "https://envipath.org/user/6971e514-9d36-4598-bf11-ee72562b7779", + "identifier": "user", + "name": "flurin_jenny" + }, + { + "id": "https://envipath.org/group/bcdd3c74-9abb-4e55-8ffd-04c2f2ab5df0", + "identifier": "group", + "name": "enviPath Users" + } + ], + "reviewComment": "", + "reviewStatus": "unreviewed", + "writers": [ + { + "id": "https://envipath.org/user/6971e514-9d36-4598-bf11-ee72562b7779", + "identifier": "user", + "name": "flurin_jenny" + } + ] + }, + { + "description": "Migration package for pathways, reactions and compounds from the EAWAG-BBD database", + "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1", + "links": [ + { + "Pathways": [ + "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway", + 219 + ] + }, + { + "Rules": [ + "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/rule", + 499 + ] + }, + { + "Compounds": [ + "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound", + 1399 + ] + }, + { + "Reactions": [ + "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction", + 1480 + ] + }, + { + "Relative Reasoning": [ + "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/relative-reasoning", + 0 + ] + }, + { + "Scenarios": [ + "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/scenario", + 1915 + ] + } + ], + "name": "EAWAG-BBD", + "primaryGroup": null, + "readers": [ + { + "id": "https://envipath.org/user/fce36893-bdb1-4a6f-87bd-5fd893feca89", + "identifier": "user", + "name": "admin" + }, + { + "id": "https://envipath.org/group/bcdd3c74-9abb-4e55-8ffd-04c2f2ab5df0", + "identifier": "group", + "name": "enviPath Users" + } + ], + "reviewComment": "", + "reviewStatus": "reviewed", + "writers": [ + { + "id": "https://envipath.org/user/fce36893-bdb1-4a6f-87bd-5fd893feca89", + "identifier": "user", + "name": "admin" + } + ] + }, + { + "description": "A collection of literature-reported biotransformation pathways for per- and polyfluorinated alkyl substances (PFASs). This version has been replaced by a new version.", + "id": "https://envipath.org/package/d2cfb5af-4ea0-4375-9a48-f2e776e44636", + "links": [ + { + "Pathways": [ + "https://envipath.org/package/d2cfb5af-4ea0-4375-9a48-f2e776e44636/pathway", + 124 + ] + }, + { + "Rules": [ + "https://envipath.org/package/d2cfb5af-4ea0-4375-9a48-f2e776e44636/rule", + 0 + ] + }, + { + "Compounds": [ + "https://envipath.org/package/d2cfb5af-4ea0-4375-9a48-f2e776e44636/compound", + 468 + ] + }, + { + "Reactions": [ + "https://envipath.org/package/d2cfb5af-4ea0-4375-9a48-f2e776e44636/reaction", + 804 + ] + }, + { + "Relative Reasoning": [ + "https://envipath.org/package/d2cfb5af-4ea0-4375-9a48-f2e776e44636/relative-reasoning", + 0 + ] + }, + { + "Scenarios": [ + "https://envipath.org/package/d2cfb5af-4ea0-4375-9a48-f2e776e44636/scenario", + 156 + ] + } + ], + "name": "enviPath-PFAS-2025", + "primaryGroup": null, + "readers": [ + { + "id": "https://envipath.org/user/159affc8-6988-4cd7-9d09-9dfb56075cd3", + "identifier": "user", + "name": "lorsbach" + }, + { + "id": "https://envipath.org/user/6971e514-9d36-4598-bf11-ee72562b7779", + "identifier": "user", + "name": "flurin_jenny" + }, + { + "id": "https://envipath.org/group/bcdd3c74-9abb-4e55-8ffd-04c2f2ab5df0", + "identifier": "group", + "name": "enviPath Users" + } + ], + "reviewComment": "", + "reviewStatus": "unreviewed", + "writers": [ + { + "id": "https://envipath.org/user/159affc8-6988-4cd7-9d09-9dfb56075cd3", + "identifier": "user", + "name": "lorsbach" + }, + { + "id": "https://envipath.org/user/6971e514-9d36-4598-bf11-ee72562b7779", + "identifier": "user", + "name": "flurin_jenny" + } + ] + } + ] +} diff --git a/tests/testthat/setup.R b/tests/testthat/setup.R new file mode 100644 index 0000000..e060323 --- /dev/null +++ b/tests/testthat/setup.R @@ -0,0 +1,7 @@ + +library(httptest2) + +username <- Sys.getenv("EP_USERNAME") +password <- Sys.getenv("EP_PASSWORD") + +epLogin(username, password) \ No newline at end of file diff --git a/tests/testthat/test-get.R b/tests/testthat/test-get.R new file mode 100644 index 0000000..c77cb23 --- /dev/null +++ b/tests/testthat/test-get.R @@ -0,0 +1,13 @@ + +with_mock_dir("httptest/get", { + + test_that("get", { + + rxn_id <- "2b6bbcc5-77f4-4bed-92a9-731cdc978f6a" + + rxn <- epGet("reaction", rxn_id) + + expect_type(rxn, "list") + expect_length(rxn, 15L) + }) +}) \ No newline at end of file diff --git a/tests/testthat/test-link.R b/tests/testthat/test-link.R new file mode 100644 index 0000000..8c7b1af --- /dev/null +++ b/tests/testthat/test-link.R @@ -0,0 +1,13 @@ + +with_mock_dir("httptest/link", { + + test_that("link", { + + types <- c("compound", "inchikey") + cpd_id <- "ec87b463-6a3c-4dfa-8b88-4637fc158896" + + cpd2inchikey <- epLink(types[1], types[2], cpd_id) + + expect_named(cpd2inchikey, types) + }) +}) \ No newline at end of file diff --git a/tests/testthat/test-list.R b/tests/testthat/test-list.R new file mode 100644 index 0000000..85b94bc --- /dev/null +++ b/tests/testthat/test-list.R @@ -0,0 +1,12 @@ + +with_mock_dir("httptest/list", { + + test_that("list", { + + pkg_df <- epList("package") + + expect_s3_class(pkg_df, "data.frame") + + expect_length(pkg_df, 10L) + }) +}) diff --git a/tests/testthat/test-login.R b/tests/testthat/test-login.R new file mode 100644 index 0000000..280f0ea --- /dev/null +++ b/tests/testthat/test-login.R @@ -0,0 +1,17 @@ + +test_that("login", { + + expect_error( + epLogin("username"), + 'argument "password" is missing, with no default', + fixed = TRUE + ) + + expect_error( + epLogin("wrong_user", "wrong_pass"), + "HTTP 500 Internal Server Error.", + fixed = TRUE + ) + + expect_message(epLogin(username, password), "Hi .+, welcome to enviPath!") +}) \ No newline at end of file diff --git a/vignettes/enviPathR.Rmd b/vignettes/enviPathR.Rmd new file mode 100644 index 0000000..edf6193 --- /dev/null +++ b/vignettes/enviPathR.Rmd @@ -0,0 +1,172 @@ +--- +title: "enviPathR" +author: + - name: Giulio Benedetti + affiliation: University of Turku + email: giulio.benedetti@utu.fi +output: + BiocStyle::html_document: + fig_height: 7 + fig_width: 10 + toc: true + toc_float: true + toc_depth: 2 + number_sections: true + self_contained: true + code_folding: show +date: "`r doc_date()`" +package: "`r pkg_ver('enviPathR')`" +vignette: > + %\VignetteIndexEntry{enviPathR: access enviPath and predict pathways from R} + %\VignetteEngine{knitr::rmarkdown} + %\VignetteEncoding{UTF-8} +--- + +```{r, include = FALSE} +knitr::opts_chunk$set( + collapse = TRUE, + comment = "#>" +) + +username <- Sys.getenv("EP_USERNAME") +password <- Sys.getenv("EP_PASSWORD") +``` + +## Tutorial + +### Installation + +Bioconductor release version: + +``` +if (!requireNamespace("BiocManager", quietly = TRUE)) + install.packages("BiocManager") + +BiocManager::install("enviPathR") +``` + +Beta version: + +``` +remotes::install_github("Minotau-R/enviPathR") +``` + +Then, we can import enviPathR and another couple of optional packages used in +this tutorial. + +```{r setup} +library(enviPathR) +library(igraph) +library(knitr) +``` + +### Login + +```{r login} +# Log into your enviPath account +epLogin(username, password) +``` + +```{r httpstart, include = FALSE} +library(httptest2) + +start_vignette("httptest/enviPathR") +``` + +### List + +```{r list-pkg} +pkg_df <- epList("package") + +to_keep <- pkg_df$reviewStatus == "reviewed" +pkg_df <- pkg_df[to_keep, ] + +# View list +kable(pkg_df) +``` + +```{r list-path} +# Select desired package +pkg_name <- "EAWAG-BBD" +pkg_id <- pkg_df$id[pkg_df$name == pkg_name] + +# List pathways from desired package +path_df <- epList("pathway", pkg = pkg_id) + +# View list +kable(path_df) +``` + +Same can be done for all other supported types. + +### Get + +```{r get} +rxn_id <- "2b6bbcc5-77f4-4bed-92a9-731cdc978f6a" + +rxn <- epGet("reaction", rxn_id) + +print(rxn) +``` + +### Link + +```{r link} +rxn2cpd <- epLink("reaction", "compound", rxn_id) + +kable(rxn2cpd) +``` + +### Model + +```{r model-setting} +# List available model settings +set_df <- epList("setting") + +# View list +kable(set_df) +``` + +```{r httpend, include = FALSE} +end_vignette() +``` + +```{r model-former} +# Define smiles of interest +smiles <- "ClC(Cl)=C(Cl)Cl" + +# Perform pathway prediction with enviFormer +former_out <- epModel(smiles) + +former_out +``` + + +```{r model-pepper} +# Set id for PEPPER model setting +set_name <- "Global Setting - ECC and App Domain - PEPPER" +set_id <- set_df$id[set_df$name == set_name] + +# Perform pathway prediction with PEPPER +pepper_out <- epModel(smiles, set_id) + +pepper_out +``` + +```{r model-plot} +# Convert model output to igraph object +path_graph <- graph_from_data_frame( + pepper_out$edges, + vertices = pepper_out$nodes +) + +# Visualise predicted pathway +plot(path_graph) +``` + +## Reproducibility + +```{r} +sessionInfo() +``` + diff --git a/vignettes/httptest/enviPathR/0/envipath.org/api/legacy/package.json b/vignettes/httptest/enviPathR/0/envipath.org/api/legacy/package.json new file mode 100644 index 0000000..ed99e7c --- /dev/null +++ b/vignettes/httptest/enviPathR/0/envipath.org/api/legacy/package.json @@ -0,0 +1,974 @@ +{ + "package": [ + { + "description": "This Package was generated automatically for the batch prediction task.", + "id": "https://envipath.org/package/5b594bf6-56a8-4ce5-9a63-5fd4b525756e", + "links": [ + { + "Pathways": [ + "https://envipath.org/package/5b594bf6-56a8-4ce5-9a63-5fd4b525756e/pathway", + 1 + ] + }, + { + "Rules": [ + "https://envipath.org/package/5b594bf6-56a8-4ce5-9a63-5fd4b525756e/rule", + 0 + ] + }, + { + "Compounds": [ + "https://envipath.org/package/5b594bf6-56a8-4ce5-9a63-5fd4b525756e/compound", + 24 + ] + }, + { + "Reactions": [ + "https://envipath.org/package/5b594bf6-56a8-4ce5-9a63-5fd4b525756e/reaction", + 38 + ] + }, + { + "Relative Reasoning": [ + "https://envipath.org/package/5b594bf6-56a8-4ce5-9a63-5fd4b525756e/relative-reasoning", + 0 + ] 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