From 490d182219e11cb73f5c03045f2bff6f74b3c383 Mon Sep 17 00:00:00 2001 From: RiboRings Date: Wed, 2 Sep 2026 19:59:03 +1200 Subject: [PATCH 01/11] Initialise tests --- .github/workflows/build.yml | 49 ++++++++++++++++++++++++++++++++++ .github/workflows/test.yml | 52 +++++++++++++++++++++++++++++++++++++ DESCRIPTION | 3 +++ tests/testthat.R | 12 +++++++++ tests/testthat/setup.R | 3 +++ tests/testthat/test-get.R | 6 +++++ tests/testthat/test-link.R | 8 ++++++ tests/testthat/test-list.R | 12 +++++++++ tests/testthat/test-login.R | 22 ++++++++++++++++ 9 files changed, 167 insertions(+) create mode 100644 .github/workflows/build.yml create mode 100644 .github/workflows/test.yml create mode 100644 tests/testthat.R create mode 100644 tests/testthat/setup.R create mode 100644 tests/testthat/test-get.R create mode 100644 tests/testthat/test-link.R create mode 100644 tests/testthat/test-list.R create mode 100644 tests/testthat/test-login.R 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..c589079 --- /dev/null +++ b/.github/workflows/test.yml @@ -0,0 +1,52 @@ +name: test +on: + pull_request: + branches: + - testing +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/DESCRIPTION b/DESCRIPTION index fa88828..41b1a66 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -19,3 +19,6 @@ License: Artistic-2.0 Encoding: UTF-8 Roxygen: list(markdown = TRUE) RoxygenNote: 8.0.0 +Suggests: + testthat (>= 3.0.0) +Config/testthat/edition: 3 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/setup.R b/tests/testthat/setup.R new file mode 100644 index 0000000..0d87a81 --- /dev/null +++ b/tests/testthat/setup.R @@ -0,0 +1,3 @@ + +username <- Sys.getenv("EP_USERNAME") +password <- Sys.getenv("EP_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..860feeb --- /dev/null +++ b/tests/testthat/test-get.R @@ -0,0 +1,6 @@ + +test_that("get", { + + + +}) \ 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..21a4298 --- /dev/null +++ b/tests/testthat/test-link.R @@ -0,0 +1,8 @@ + +test_that("link", { + + epLogin(username, password) + + + +}) \ 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..f5bba84 --- /dev/null +++ b/tests/testthat/test-list.R @@ -0,0 +1,12 @@ + +test_that("list", { + + epLogin(username, password) + + pkg_df <- epList("package") + + expect_23_class(pkg_df, "data.frame") + + expect_length(pkg_df, 10L) + +}) \ No newline at end of file diff --git a/tests/testthat/test-login.R b/tests/testthat/test-login.R new file mode 100644 index 0000000..638d392 --- /dev/null +++ b/tests/testthat/test-login.R @@ -0,0 +1,22 @@ + +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 RiboRings, welcome to enviPath!", + fixed = TRUE + ) + +}) \ No newline at end of file From 2c141706b028d738904e4270a56c9c4501e8765a Mon Sep 17 00:00:00 2001 From: RiboRings Date: Wed, 2 Sep 2026 20:00:39 +1200 Subject: [PATCH 02/11] test --- .github/workflows/test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index c589079..8c69e44 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -1,6 +1,6 @@ name: test on: - pull_request: + push: branches: - testing jobs: From 44cc5d27dcd0fabd16fed553da4888243f047095 Mon Sep 17 00:00:00 2001 From: RiboRings Date: Wed, 2 Sep 2026 20:04:02 +1200 Subject: [PATCH 03/11] Add BiocParallel to Imports --- DESCRIPTION | 1 + 1 file changed, 1 insertion(+) diff --git a/DESCRIPTION b/DESCRIPTION index 41b1a66..c67adde 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -10,6 +10,7 @@ Description: reactions and produced compounds. This package enables the programmatic access to enviPath by porting the database API from R. Imports: + BiocParallel, httr2, jsonlite, stats, From 736c00b75c44a49ff5329507dd9b1879207614a1 Mon Sep 17 00:00:00 2001 From: RiboRings Date: Wed, 2 Sep 2026 20:21:24 +1200 Subject: [PATCH 04/11] Try to fix tests and vignettes login --- DESCRIPTION | 1 - R/get.R | 6 ++++++ R/link.R | 8 +++++++- R/list.R | 6 ++++++ man/epGet.Rd | 6 ++++++ man/epLink.Rd | 8 +++++++- man/epList.Rd | 6 ++++++ tests/testthat/test-link.R | 4 ++++ 8 files changed, 42 insertions(+), 3 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index c67adde..5f7b9c4 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -12,7 +12,6 @@ Description: Imports: BiocParallel, httr2, - jsonlite, stats, stringr, tools diff --git a/R/get.R b/R/get.R index 4811005..4fac98f 100644 --- a/R/get.R +++ b/R/get.R @@ -17,6 +17,12 @@ #' A list of objects #' #' @examples +#' \dontshow{ +#' username <- Sys.getenv("EP_USERNAME") +#' password <- Sys.getenv("EP_PASSWORD") +#' } +#' epLogin(username, password) +#' #' rxn_id <- "2b6bbcc5-77f4-4bed-92a9-731cdc978f6a" #' #' epGet("reaction", rxn_id) diff --git a/R/link.R b/R/link.R index db05029..96bbf40 100644 --- a/R/link.R +++ b/R/link.R @@ -17,9 +17,15 @@ #' A data frame with links between from and to. #' #' @examples +#' #' \dontshow{ +#' username <- Sys.getenv("EP_USERNAME") +#' password <- Sys.getenv("EP_PASSWORD") +#' } +#' epLogin(username, password) +#' #' rxn_id <- "2b6bbcc5-77f4-4bed-92a9-731cdc978f6a" #' -#' epGet("reaction", rxn_id) +#' epLink("reaction", "compound", rxn_id) NULL #' @export diff --git a/R/list.R b/R/list.R index 205ee9b..f58229b 100644 --- a/R/list.R +++ b/R/list.R @@ -13,6 +13,12 @@ #' A data frame. #' #' @examples +#' #' \dontshow{ +#' username <- Sys.getenv("EP_USERNAME") +#' password <- Sys.getenv("EP_PASSWORD") +#' } +#' epLogin(username, password) +#' #' epList("package") #' #' epList("pathway", pkg = "32de3cf4-e3e6-4168-956e-32fa5ddb0ce1") diff --git a/man/epGet.Rd b/man/epGet.Rd index bbb64a5..710ad91 100644 --- a/man/epGet.Rd +++ b/man/epGet.Rd @@ -22,6 +22,12 @@ 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) + rxn_id <- "2b6bbcc5-77f4-4bed-92a9-731cdc978f6a" epGet("reaction", rxn_id) diff --git a/man/epLink.Rd b/man/epLink.Rd index 72a703d..a1f8f9b 100644 --- a/man/epLink.Rd +++ b/man/epLink.Rd @@ -22,7 +22,13 @@ 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) + rxn_id <- "2b6bbcc5-77f4-4bed-92a9-731cdc978f6a" -epGet("reaction", rxn_id) +epLink("reaction", "compound", rxn_id) } diff --git a/man/epList.Rd b/man/epList.Rd index 6a984ef..138f4ef 100644 --- a/man/epList.Rd +++ b/man/epList.Rd @@ -18,6 +18,12 @@ 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) + epList("package") epList("pathway", pkg = "32de3cf4-e3e6-4168-956e-32fa5ddb0ce1") diff --git a/tests/testthat/test-link.R b/tests/testthat/test-link.R index 21a4298..b2cfa47 100644 --- a/tests/testthat/test-link.R +++ b/tests/testthat/test-link.R @@ -3,6 +3,10 @@ test_that("link", { epLogin(username, password) + 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 From ed05501382f456bed786c3a17a7e2e0ca4b6a821 Mon Sep 17 00:00:00 2001 From: RiboRings Date: Wed, 2 Sep 2026 20:28:08 +1200 Subject: [PATCH 05/11] Fix vignettes login --- R/link.R | 2 +- R/list.R | 2 +- R/login.R | 7 +++++-- man/epLink.Rd | 2 +- man/epList.Rd | 2 +- man/epLogin.Rd | 7 +++++-- 6 files changed, 14 insertions(+), 8 deletions(-) diff --git a/R/link.R b/R/link.R index 96bbf40..3aa3b89 100644 --- a/R/link.R +++ b/R/link.R @@ -17,7 +17,7 @@ #' A data frame with links between from and to. #' #' @examples -#' #' \dontshow{ +#' \dontshow{ #' username <- Sys.getenv("EP_USERNAME") #' password <- Sys.getenv("EP_PASSWORD") #' } diff --git a/R/list.R b/R/list.R index f58229b..2a9b5a4 100644 --- a/R/list.R +++ b/R/list.R @@ -13,7 +13,7 @@ #' A data frame. #' #' @examples -#' #' \dontshow{ +#' \dontshow{ #' username <- Sys.getenv("EP_USERNAME") #' password <- Sys.getenv("EP_PASSWORD") #' } 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/man/epLink.Rd b/man/epLink.Rd index a1f8f9b..3045827 100644 --- a/man/epLink.Rd +++ b/man/epLink.Rd @@ -22,7 +22,7 @@ A data frame with links between from and to. epLink returns mappings between enviPath object types. } \examples{ -#' \dontshow{ +\dontshow{ username <- Sys.getenv("EP_USERNAME") password <- Sys.getenv("EP_PASSWORD") } diff --git a/man/epList.Rd b/man/epList.Rd index 138f4ef..6c30486 100644 --- a/man/epList.Rd +++ b/man/epList.Rd @@ -18,7 +18,7 @@ A data frame. epList returns a list with info on objects available in enviPath. } \examples{ -#' \dontshow{ +\dontshow{ username <- Sys.getenv("EP_USERNAME") password <- Sys.getenv("EP_PASSWORD") } 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) } From 33efc32a7b7cc7453dee944047db3ddd3192301a Mon Sep 17 00:00:00 2001 From: RiboRings Date: Wed, 2 Sep 2026 20:46:52 +1200 Subject: [PATCH 06/11] Overwrite cookie path with github workspace --- R/get.R | 1 + R/link.R | 1 + R/list.R | 1 + R/login.R | 1 + man/epGet.Rd | 1 + man/epLink.Rd | 1 + man/epList.Rd | 1 + man/epLogin.Rd | 1 + 8 files changed, 8 insertions(+) diff --git a/R/get.R b/R/get.R index 4fac98f..37775f6 100644 --- a/R/get.R +++ b/R/get.R @@ -20,6 +20,7 @@ #' \dontshow{ #' username <- Sys.getenv("EP_USERNAME") #' password <- Sys.getenv("EP_PASSWORD") +#' eP_env$cookies <- file.path(Sys.getenv("GITHUB_WORKSPACE"), "eP_cookies") #' } #' epLogin(username, password) #' diff --git a/R/link.R b/R/link.R index 3aa3b89..62799fb 100644 --- a/R/link.R +++ b/R/link.R @@ -20,6 +20,7 @@ #' \dontshow{ #' username <- Sys.getenv("EP_USERNAME") #' password <- Sys.getenv("EP_PASSWORD") +#' eP_env$cookies <- file.path(Sys.getenv("GITHUB_WORKSPACE"), "eP_cookies") #' } #' epLogin(username, password) #' diff --git a/R/list.R b/R/list.R index 2a9b5a4..c559d3c 100644 --- a/R/list.R +++ b/R/list.R @@ -16,6 +16,7 @@ #' \dontshow{ #' username <- Sys.getenv("EP_USERNAME") #' password <- Sys.getenv("EP_PASSWORD") +#' eP_env$cookies <- file.path(Sys.getenv("GITHUB_WORKSPACE"), "eP_cookies") #' } #' epLogin(username, password) #' diff --git a/R/login.R b/R/login.R index 6404026..2023bf0 100644 --- a/R/login.R +++ b/R/login.R @@ -17,6 +17,7 @@ #' \dontshow{ #' username <- Sys.getenv("EP_USERNAME") #' password <- Sys.getenv("EP_PASSWORD") +#' eP_env$cookies <- file.path(Sys.getenv("GITHUB_WORKSPACE"), "eP_cookies") #' } #' epLogin(username, password) NULL diff --git a/man/epGet.Rd b/man/epGet.Rd index 710ad91..ded89e7 100644 --- a/man/epGet.Rd +++ b/man/epGet.Rd @@ -25,6 +25,7 @@ epGet returns a raw object from enviPath. \dontshow{ username <- Sys.getenv("EP_USERNAME") password <- Sys.getenv("EP_PASSWORD") + eP_env$cookies <- file.path(Sys.getenv("GITHUB_WORKSPACE"), "eP_cookies") } epLogin(username, password) diff --git a/man/epLink.Rd b/man/epLink.Rd index 3045827..50ffa9e 100644 --- a/man/epLink.Rd +++ b/man/epLink.Rd @@ -25,6 +25,7 @@ epLink returns mappings between enviPath object types. \dontshow{ username <- Sys.getenv("EP_USERNAME") password <- Sys.getenv("EP_PASSWORD") + eP_env$cookies <- file.path(Sys.getenv("GITHUB_WORKSPACE"), "eP_cookies") } epLogin(username, password) diff --git a/man/epList.Rd b/man/epList.Rd index 6c30486..7e5a23a 100644 --- a/man/epList.Rd +++ b/man/epList.Rd @@ -21,6 +21,7 @@ epList returns a list with info on objects available in enviPath. \dontshow{ username <- Sys.getenv("EP_USERNAME") password <- Sys.getenv("EP_PASSWORD") + eP_env$cookies <- file.path(Sys.getenv("GITHUB_WORKSPACE"), "eP_cookies") } epLogin(username, password) diff --git a/man/epLogin.Rd b/man/epLogin.Rd index 830e2d1..6923195 100644 --- a/man/epLogin.Rd +++ b/man/epLogin.Rd @@ -19,6 +19,7 @@ enviPath API. (add db link to refs) \dontshow{ username <- Sys.getenv("EP_USERNAME") password <- Sys.getenv("EP_PASSWORD") + eP_env$cookies <- file.path(Sys.getenv("GITHUB_WORKSPACE"), "eP_cookies") } epLogin(username, password) } From d5adcfeac1f41706806e2592e3cb77cfe414406b Mon Sep 17 00:00:00 2001 From: RiboRings Date: Wed, 2 Sep 2026 21:04:10 +1200 Subject: [PATCH 07/11] Make cookie file permanent instead of temporary --- R/constants.R | 2 +- R/get.R | 1 - R/link.R | 1 - R/list.R | 1 - R/login.R | 1 - man/epGet.Rd | 1 - man/epLink.Rd | 1 - man/epList.Rd | 1 - man/epLogin.Rd | 1 - 9 files changed, 1 insertion(+), 9 deletions(-) diff --git a/R/constants.R b/R/constants.R index a57aa77..7ca2fc9 100644 --- a/R/constants.R +++ b/R/constants.R @@ -28,7 +28,7 @@ cache <- R_user_dir("enviPathR", "cache") if( !dir.exists(cache) ) dir.create(cache) # Preserve cookies between requests - eP_env$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 37775f6..4fac98f 100644 --- a/R/get.R +++ b/R/get.R @@ -20,7 +20,6 @@ #' \dontshow{ #' username <- Sys.getenv("EP_USERNAME") #' password <- Sys.getenv("EP_PASSWORD") -#' eP_env$cookies <- file.path(Sys.getenv("GITHUB_WORKSPACE"), "eP_cookies") #' } #' epLogin(username, password) #' diff --git a/R/link.R b/R/link.R index 62799fb..3aa3b89 100644 --- a/R/link.R +++ b/R/link.R @@ -20,7 +20,6 @@ #' \dontshow{ #' username <- Sys.getenv("EP_USERNAME") #' password <- Sys.getenv("EP_PASSWORD") -#' eP_env$cookies <- file.path(Sys.getenv("GITHUB_WORKSPACE"), "eP_cookies") #' } #' epLogin(username, password) #' diff --git a/R/list.R b/R/list.R index c559d3c..2a9b5a4 100644 --- a/R/list.R +++ b/R/list.R @@ -16,7 +16,6 @@ #' \dontshow{ #' username <- Sys.getenv("EP_USERNAME") #' password <- Sys.getenv("EP_PASSWORD") -#' eP_env$cookies <- file.path(Sys.getenv("GITHUB_WORKSPACE"), "eP_cookies") #' } #' epLogin(username, password) #' diff --git a/R/login.R b/R/login.R index 2023bf0..6404026 100644 --- a/R/login.R +++ b/R/login.R @@ -17,7 +17,6 @@ #' \dontshow{ #' username <- Sys.getenv("EP_USERNAME") #' password <- Sys.getenv("EP_PASSWORD") -#' eP_env$cookies <- file.path(Sys.getenv("GITHUB_WORKSPACE"), "eP_cookies") #' } #' epLogin(username, password) NULL diff --git a/man/epGet.Rd b/man/epGet.Rd index ded89e7..710ad91 100644 --- a/man/epGet.Rd +++ b/man/epGet.Rd @@ -25,7 +25,6 @@ epGet returns a raw object from enviPath. \dontshow{ username <- Sys.getenv("EP_USERNAME") password <- Sys.getenv("EP_PASSWORD") - eP_env$cookies <- file.path(Sys.getenv("GITHUB_WORKSPACE"), "eP_cookies") } epLogin(username, password) diff --git a/man/epLink.Rd b/man/epLink.Rd index 50ffa9e..3045827 100644 --- a/man/epLink.Rd +++ b/man/epLink.Rd @@ -25,7 +25,6 @@ epLink returns mappings between enviPath object types. \dontshow{ username <- Sys.getenv("EP_USERNAME") password <- Sys.getenv("EP_PASSWORD") - eP_env$cookies <- file.path(Sys.getenv("GITHUB_WORKSPACE"), "eP_cookies") } epLogin(username, password) diff --git a/man/epList.Rd b/man/epList.Rd index 7e5a23a..6c30486 100644 --- a/man/epList.Rd +++ b/man/epList.Rd @@ -21,7 +21,6 @@ epList returns a list with info on objects available in enviPath. \dontshow{ username <- Sys.getenv("EP_USERNAME") password <- Sys.getenv("EP_PASSWORD") - eP_env$cookies <- file.path(Sys.getenv("GITHUB_WORKSPACE"), "eP_cookies") } epLogin(username, password) diff --git a/man/epLogin.Rd b/man/epLogin.Rd index 6923195..830e2d1 100644 --- a/man/epLogin.Rd +++ b/man/epLogin.Rd @@ -19,7 +19,6 @@ enviPath API. (add db link to refs) \dontshow{ username <- Sys.getenv("EP_USERNAME") password <- Sys.getenv("EP_PASSWORD") - eP_env$cookies <- file.path(Sys.getenv("GITHUB_WORKSPACE"), "eP_cookies") } epLogin(username, password) } From 3dcce5fd1d59588dbb45fa0c9990957bc65efa9c Mon Sep 17 00:00:00 2001 From: RiboRings Date: Thu, 3 Sep 2026 15:50:40 +1200 Subject: [PATCH 08/11] Set up httptest2 --- .gitignore | 1 + DESCRIPTION | 5 +- R/get.R | 8 +- R/link.R | 8 +- R/list.R | 8 +- R/login.R | 6 +- man/epGet.Rd | 8 +- man/epLink.Rd | 8 +- man/epList.Rd | 8 +- man/epLogin.Rd | 6 +- .../2b6bbcc5-77f4-4bed-92a9-731cdc978f6a.json | 51 + .../ec87b463-6a3c-4dfa-8b88-4637fc158896.json | 128 +++ .../list/envipath.org/api/legacy/package.json | 974 ++++++++++++++++++ tests/testthat/setup.R | 6 +- tests/testthat/test-get.R | 15 +- tests/testthat/test-link.R | 21 +- tests/testthat/test-list.R | 22 +- tests/testthat/test-login.R | 7 +- 18 files changed, 1218 insertions(+), 72 deletions(-) create mode 100644 tests/testthat/httptest/get/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/2b6bbcc5-77f4-4bed-92a9-731cdc978f6a.json create mode 100644 tests/testthat/httptest/link/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/ec87b463-6a3c-4dfa-8b88-4637fc158896.json create mode 100644 tests/testthat/httptest/list/envipath.org/api/legacy/package.json diff --git a/.gitignore b/.gitignore index 508df78..b617daf 100644 --- a/.gitignore +++ b/.gitignore @@ -1,2 +1,3 @@ .Rproj.user .Rhistory +.Renviron diff --git a/DESCRIPTION b/DESCRIPTION index 5f7b9c4..f8963e8 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -3,13 +3,13 @@ Title: R client for enviPath API Version: 0.0.0.9000 Authors@R: person("Giulio", "Benedetti", , "giulio.benedetti@utu.fi", role = c("aut", "cre")) -Description: +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. -Imports: +Imports: BiocParallel, httr2, stats, @@ -20,5 +20,6 @@ Encoding: UTF-8 Roxygen: list(markdown = TRUE) RoxygenNote: 8.0.0 Suggests: + httptest2, testthat (>= 3.0.0) Config/testthat/edition: 3 diff --git a/R/get.R b/R/get.R index 4fac98f..2645b78 100644 --- a/R/get.R +++ b/R/get.R @@ -17,15 +17,13 @@ #' A list of objects #' #' @examples -#' \dontshow{ -#' username <- Sys.getenv("EP_USERNAME") -#' password <- Sys.getenv("EP_PASSWORD") -#' } -#' epLogin(username, password) +#' \donttest{ +#' epLogin("username", "password") #' #' rxn_id <- "2b6bbcc5-77f4-4bed-92a9-731cdc978f6a" #' #' epGet("reaction", rxn_id) +#' } NULL #' @export diff --git a/R/link.R b/R/link.R index 3aa3b89..6f67278 100644 --- a/R/link.R +++ b/R/link.R @@ -17,15 +17,13 @@ #' A data frame with links between from and to. #' #' @examples -#' \dontshow{ -#' username <- Sys.getenv("EP_USERNAME") -#' password <- Sys.getenv("EP_PASSWORD") -#' } -#' epLogin(username, password) +#' \donttest{ +#' epLogin("username", "password") #' #' rxn_id <- "2b6bbcc5-77f4-4bed-92a9-731cdc978f6a" #' #' epLink("reaction", "compound", rxn_id) +#' } NULL #' @export diff --git a/R/list.R b/R/list.R index 2a9b5a4..342bb0e 100644 --- a/R/list.R +++ b/R/list.R @@ -13,15 +13,13 @@ #' A data frame. #' #' @examples -#' \dontshow{ -#' username <- Sys.getenv("EP_USERNAME") -#' password <- Sys.getenv("EP_PASSWORD") -#' } -#' epLogin(username, password) +#' \donttest{ +#' epLogin("username", "password") #' #' epList("package") #' #' epList("pathway", pkg = "32de3cf4-e3e6-4168-956e-32fa5ddb0ce1") +#' } NULL #' @export diff --git a/R/login.R b/R/login.R index 6404026..707fda7 100644 --- a/R/login.R +++ b/R/login.R @@ -14,11 +14,9 @@ #' A message upon successful login. #' #' @examples -#' \dontshow{ -#' username <- Sys.getenv("EP_USERNAME") -#' password <- Sys.getenv("EP_PASSWORD") +#' \donttest{ +#' epLogin("username", "password") #' } -#' epLogin(username, password) NULL #' @importFrom httr2 request req_method req_body_form req_cookie_preserve req_perform diff --git a/man/epGet.Rd b/man/epGet.Rd index 710ad91..c958a09 100644 --- a/man/epGet.Rd +++ b/man/epGet.Rd @@ -22,13 +22,11 @@ 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) +\donttest{ +epLogin("username", "password") rxn_id <- "2b6bbcc5-77f4-4bed-92a9-731cdc978f6a" epGet("reaction", rxn_id) } +} diff --git a/man/epLink.Rd b/man/epLink.Rd index 3045827..911ee1a 100644 --- a/man/epLink.Rd +++ b/man/epLink.Rd @@ -22,13 +22,11 @@ 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) +\donttest{ +epLogin("username", "password") rxn_id <- "2b6bbcc5-77f4-4bed-92a9-731cdc978f6a" epLink("reaction", "compound", rxn_id) } +} diff --git a/man/epList.Rd b/man/epList.Rd index 6c30486..f68c5e1 100644 --- a/man/epList.Rd +++ b/man/epList.Rd @@ -18,13 +18,11 @@ 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) +\donttest{ +epLogin("username", "password") epList("package") epList("pathway", pkg = "32de3cf4-e3e6-4168-956e-32fa5ddb0ce1") } +} diff --git a/man/epLogin.Rd b/man/epLogin.Rd index 830e2d1..4ea9178 100644 --- a/man/epLogin.Rd +++ b/man/epLogin.Rd @@ -16,9 +16,7 @@ epLogin lets you perform login to enviPath. An account is required to use the enviPath API. (add db link to refs) } \examples{ -\dontshow{ - username <- Sys.getenv("EP_USERNAME") - password <- Sys.getenv("EP_PASSWORD") +\donttest{ +epLogin("username", "password") } -epLogin(username, password) } 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)", + "externalReferences": { + + }, + "formula": "C2H4Cl2", + "halflifes": [ + + ], + "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/ec87b463-6a3c-4dfa-8b88-4637fc158896/structure/69d4e95c-30b9-43a3-b385-0f9ad853a79a", + "identifier": "structure", + "imageSize": 600, + "inchikey": "WSLDOOZREJYCGB-UHFFFAOYSA-N", + "isDefaultStructure": false, + "mass": 98.96000000000001, + "name": "Normalized structure of 1,2-Dichloroethane", + "pathways": [ + + ], + "pubchemCompoundReferences": [ + + ], + "reactions": [ + + ], + "reviewStatus": "reviewed", + "scenarios": [ + + ], + "smiles": "ClCCCl" + } + ] +} diff --git a/tests/testthat/httptest/list/envipath.org/api/legacy/package.json b/tests/testthat/httptest/list/envipath.org/api/legacy/package.json new file mode 100644 index 0000000..ed99e7c 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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 index 0d87a81..e060323 100644 --- a/tests/testthat/setup.R +++ b/tests/testthat/setup.R @@ -1,3 +1,7 @@ +library(httptest2) + username <- Sys.getenv("EP_USERNAME") -password <- Sys.getenv("EP_PASSWORD") \ No newline at end of file +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 index 860feeb..c77cb23 100644 --- a/tests/testthat/test-get.R +++ b/tests/testthat/test-get.R @@ -1,6 +1,13 @@ -test_that("get", { - - - +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 index b2cfa47..8c7b1af 100644 --- a/tests/testthat/test-link.R +++ b/tests/testthat/test-link.R @@ -1,12 +1,13 @@ -test_that("link", { - - epLogin(username, password) - - types <- c("compound", "inchikey") - cpd_id <- "ec87b463-6a3c-4dfa-8b88-4637fc158896" - - cpd2inchikey <- epLink(types[1], types[2], cpd_id) - - expect_named(cpd2inchikey, types) +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 index f5bba84..85b94bc 100644 --- a/tests/testthat/test-list.R +++ b/tests/testthat/test-list.R @@ -1,12 +1,12 @@ -test_that("list", { - - epLogin(username, password) - - pkg_df <- epList("package") - - expect_23_class(pkg_df, "data.frame") - - expect_length(pkg_df, 10L) - -}) \ No newline at end of file +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 index 638d392..280f0ea 100644 --- a/tests/testthat/test-login.R +++ b/tests/testthat/test-login.R @@ -13,10 +13,5 @@ test_that("login", { fixed = TRUE ) - expect_message( - epLogin(username, password), - "Hi RiboRings, welcome to enviPath!", - fixed = TRUE - ) - + expect_message(epLogin(username, password), "Hi .+, welcome to enviPath!") }) \ No newline at end of file From ab1ce9cf9d4a68db0279739beac2ea008742c11a Mon Sep 17 00:00:00 2001 From: RiboRings Date: Sat, 5 Sep 2026 17:36:01 +1200 Subject: [PATCH 09/11] Add preliminary vignettes --- .github/workflows/build.yml | 2 +- .gitignore | 4 + DESCRIPTION | 7 +- NAMESPACE | 1 + R/get.R | 2 +- R/link.R | 2 +- R/list.R | 6 +- R/login.R | 2 +- R/model.R | 83 ++ README.md | 4 +- man/epGet.Rd | 2 +- man/epLink.Rd | 2 +- man/epList.Rd | 2 +- man/epLogin.Rd | 2 +- man/epModel.Rd | 52 + vignettes/enviPathR.Rmd | 172 +++ .../0/envipath.org/api/legacy/package.json | 974 ++++++++++++ .../pathway.json | 1318 +++++++++++++++++ .../2b6bbcc5-77f4-4bed-92a9-731cdc978f6a.json | 51 + .../0/envipath.org/api/legacy/setting.json | 24 + 20 files changed, 2699 insertions(+), 13 deletions(-) create mode 100644 R/model.R create mode 100644 man/epModel.Rd create mode 100644 vignettes/enviPathR.Rmd create mode 100644 vignettes/httptest/0/envipath.org/api/legacy/package.json create mode 100644 vignettes/httptest/0/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway.json create mode 100644 vignettes/httptest/0/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/2b6bbcc5-77f4-4bed-92a9-731cdc978f6a.json create mode 100644 vignettes/httptest/0/envipath.org/api/legacy/setting.json diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 5351aba..0859a04 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -2,7 +2,7 @@ name: build on: push: branches: - - devel + - testing jobs: rworkflows: permissions: write-all diff --git a/.gitignore b/.gitignore index b617daf..9c63895 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,7 @@ .Rproj.user .Rhistory .Renviron +inst/doc +vignettes/*.html +vignettes/*.R +docs/ diff --git a/DESCRIPTION b/DESCRIPTION index f8963e8..0a88dc1 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -19,7 +19,12 @@ License: Artistic-2.0 Encoding: UTF-8 Roxygen: list(markdown = TRUE) RoxygenNote: 8.0.0 -Suggests: +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/get.R b/R/get.R index 2645b78..ac473fe 100644 --- a/R/get.R +++ b/R/get.R @@ -17,7 +17,7 @@ #' A list of objects #' #' @examples -#' \donttest{ +#' \dontrun{ #' epLogin("username", "password") #' #' rxn_id <- "2b6bbcc5-77f4-4bed-92a9-731cdc978f6a" diff --git a/R/link.R b/R/link.R index 6f67278..dd3d8ec 100644 --- a/R/link.R +++ b/R/link.R @@ -17,7 +17,7 @@ #' A data frame with links between from and to. #' #' @examples -#' \donttest{ +#' \dontrun{ #' epLogin("username", "password") #' #' rxn_id <- "2b6bbcc5-77f4-4bed-92a9-731cdc978f6a" diff --git a/R/list.R b/R/list.R index 342bb0e..006aa5d 100644 --- a/R/list.R +++ b/R/list.R @@ -13,7 +13,7 @@ #' A data frame. #' #' @examples -#' \donttest{ +#' \dontrun{ #' epLogin("username", "password") #' #' epList("package") @@ -49,7 +49,9 @@ 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 707fda7..71e52ba 100644 --- a/R/login.R +++ b/R/login.R @@ -14,7 +14,7 @@ #' A message upon successful login. #' #' @examples -#' \donttest{ +#' \dontrun{ #' epLogin("username", "password") #' } NULL diff --git a/R/model.R b/R/model.R new file mode 100644 index 0000000..375d212 --- /dev/null +++ b/R/model.R @@ -0,0 +1,83 @@ +#' 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 +#' \dontrun{ +#' library(igraph) +#' +#' # Perform login +#' epLogin("username", "password") +#' +#' # List available model settings +#' epList("setting") +#' +#' # 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 +#' setting_id <- "3cda8e56-f4ff-47a8-b68c-4cfcfc4e8c2a" +#' +#' # Perform pathway prediction with PEPPER +#' pepper_out <- epModel(smiles, setting_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 c958a09..a5e40a0 100644 --- a/man/epGet.Rd +++ b/man/epGet.Rd @@ -22,7 +22,7 @@ A list of objects epGet returns a raw object from enviPath. } \examples{ -\donttest{ +\dontrun{ epLogin("username", "password") rxn_id <- "2b6bbcc5-77f4-4bed-92a9-731cdc978f6a" diff --git a/man/epLink.Rd b/man/epLink.Rd index 911ee1a..57e4213 100644 --- a/man/epLink.Rd +++ b/man/epLink.Rd @@ -22,7 +22,7 @@ A data frame with links between from and to. epLink returns mappings between enviPath object types. } \examples{ -\donttest{ +\dontrun{ epLogin("username", "password") rxn_id <- "2b6bbcc5-77f4-4bed-92a9-731cdc978f6a" diff --git a/man/epList.Rd b/man/epList.Rd index f68c5e1..c420a4d 100644 --- a/man/epList.Rd +++ b/man/epList.Rd @@ -18,7 +18,7 @@ A data frame. epList returns a list with info on objects available in enviPath. } \examples{ -\donttest{ +\dontrun{ epLogin("username", "password") epList("package") diff --git a/man/epLogin.Rd b/man/epLogin.Rd index 4ea9178..03ddd14 100644 --- a/man/epLogin.Rd +++ b/man/epLogin.Rd @@ -16,7 +16,7 @@ epLogin lets you perform login to enviPath. An account is required to use the enviPath API. (add db link to refs) } \examples{ -\donttest{ +\dontrun{ epLogin("username", "password") } } diff --git a/man/epModel.Rd b/man/epModel.Rd new file mode 100644 index 0000000..5d179ed --- /dev/null +++ b/man/epModel.Rd @@ -0,0 +1,52 @@ +% 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{ +\dontrun{ +library(igraph) + +# Perform login +epLogin("username", "password") + +# List available model settings +epList("setting") + +# 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 +setting_id <- "3cda8e56-f4ff-47a8-b68c-4cfcfc4e8c2a" + +# Perform pathway prediction with PEPPER +pepper_out <- epModel(smiles, setting_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/vignettes/enviPathR.Rmd b/vignettes/enviPathR.Rmd new file mode 100644 index 0000000..e22da46 --- /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$set( + collapse = TRUE, + comment = "#>" +) + +username <- Sys.getenv("EP_USERNAME") +password <- Sys.getenv("EP_PASSWORD") +``` + +## Tutorial + +### Installation + +Bioconductor release version: + +``` +if (!requireNamespace("BiocManager", quietly = TRUE)) + install.packages("BiocManager") + +BiocManager::install("enviPathR") +``` + +Beta version: + +``` +remotes::install_github("Minotau-R/enviPathR") +``` + +Then, we can import enviPathR and another couple of optional packages used in +this tutorial. + +```{r setup} +library(enviPathR) +library(igraph) +library(knitr) +``` + +### Login + +```{r login} +# Log into your enviPath account +epLogin(username, password) +``` + +```{r httpstart, include = FALSE} +library(httptest2) + +start_vignette("httptest") +``` + +### List + +```{r list-pkg} +pkg_df <- epList("package") + +to_keep <- pkg_df$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/0/envipath.org/api/legacy/package.json b/vignettes/httptest/0/envipath.org/api/legacy/package.json new file mode 100644 index 0000000..ed99e7c --- /dev/null +++ b/vignettes/httptest/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": [ + 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"https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/b41738ce-c67e-414f-b048-00bd331d3bfb", + "name": "Dibenzofuran", + "reviewStatus": "reviewed", + "identifier": "pathway" + }, + { + "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/94f145b0-9581-4e73-9c55-9ad4baf89198", + "name": "Benzoate", + "reviewStatus": "reviewed", + "identifier": "pathway" + }, + { + "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/53b41a8f-305f-417c-b321-85154d9b8a6d", + "name": "Pyrene", + "reviewStatus": "reviewed", + "identifier": "pathway" + }, + { + "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/b93bb1c3-5cc8-4232-bfb7-2b7896c8df6d", + "name": "Hypophosphite", + "reviewStatus": "reviewed", + "identifier": "pathway" + }, + { + "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/9986b407-f77b-4466-9c07-38c11d5da726", + "name": "2,4-Dichlorobenzoate", + "reviewStatus": "reviewed", + "identifier": "pathway" + }, + { + "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/e144d01a-114e-4414-86b8-e7d60e7ce87c", + "name": "2,4-Dichlorotoluene", + "reviewStatus": "reviewed", + "identifier": "pathway" + }, + { + "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/deaf53bb-fc6e-4e85-bdc4-5434e65b06cd", + "name": "Tetrachloroethene (anaerobic)", + "reviewStatus": "reviewed", + "identifier": "pathway" + }, + { + "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/16bf59ca-a54b-41f4-85ea-68dfa04b89a6", + "name": "3-Fluorobenzoate", + "reviewStatus": "reviewed", + "identifier": "pathway" + }, + { + "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/4a8a7825-5cea-4ac5-a717-e7bcd7bbf821", + "name": "N-Cyclopropylmelamine", + "reviewStatus": "reviewed", + "identifier": "pathway" + }, + { + "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/673c1604-4a14-45b9-bf2f-15f130d1d41e", + "name": "4-Carboxy-4`-Sulfoazobenzene", + "reviewStatus": "reviewed", + "identifier": "pathway" + }, + { + "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/9daec55c-eb02-4a7d-b4bb-4f0848a8a997", + "name": "N,N-Diethyl-m-toluamide", + "reviewStatus": "reviewed", + "identifier": "pathway" + } + ] +} diff --git a/vignettes/httptest/0/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/2b6bbcc5-77f4-4bed-92a9-731cdc978f6a.json b/vignettes/httptest/0/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/vignettes/httptest/0/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/vignettes/httptest/0/envipath.org/api/legacy/setting.json b/vignettes/httptest/0/envipath.org/api/legacy/setting.json new file mode 100644 index 0000000..0b5047a --- /dev/null +++ b/vignettes/httptest/0/envipath.org/api/legacy/setting.json @@ -0,0 +1,24 @@ +{ + "setting": [ + { + "id": "https://envipath.org/setting/1d915a48-286a-4394-9693-bfaa187326a5", + "identifier": "setting", + "name": "Global Setting - enviFormer" + }, + { + "id": "https://envipath.org/setting/3c8e789f-cf5f-4db2-9b77-b152d32e52e9", + "identifier": "setting", + "name": "Global Setting - ECC and App Domain" + }, + { + "id": "https://envipath.org/setting/3cda8e56-f4ff-47a8-b68c-4cfcfc4e8c2a", + "identifier": "setting", + "name": "Global Setting - ECC and App Domain - PEPPER" + }, + { + "id": "https://envipath.org/setting/a0fbc3d8-ca45-44f1-9c3c-80d8531ffe25", + "identifier": "setting", + "name": "Global Setting - BBD Rules" + } + ] +} From 82a0af872ae43dd15589af5bd8c82ffc844c8f35 Mon Sep 17 00:00:00 2001 From: RiboRings Date: Sat, 5 Sep 2026 18:19:10 +1200 Subject: [PATCH 10/11] Run function vignettes with httptest2 --- DESCRIPTION | 15 +- R/get.R | 12 +- R/link.R | 12 +- R/list.R | 12 +- R/login.R | 6 +- R/model.R | 18 +- man/epGet.Rd | 12 +- man/epLink.Rd | 12 +- man/epList.Rd | 12 +- man/epLogin.Rd | 6 +- man/epModel.Rd | 18 +- vignettes/enviPathR.Rmd | 2 +- .../0/envipath.org/api/legacy/package.json | 0 .../pathway.json | 0 .../2b6bbcc5-77f4-4bed-92a9-731cdc978f6a.json | 0 .../0/envipath.org/api/legacy/setting.json | 0 .../2b6bbcc5-77f4-4bed-92a9-731cdc978f6a.json | 51 + .../2b6bbcc5-77f4-4bed-92a9-731cdc978f6a.json | 51 + .../0/envipath.org/api/legacy/package.json | 974 ++++++++++++ .../pathway.json | 1318 +++++++++++++++++ 20 files changed, 2489 insertions(+), 42 deletions(-) rename vignettes/httptest/{ => enviPathR}/0/envipath.org/api/legacy/package.json (100%) rename vignettes/httptest/{ => enviPathR}/0/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway.json (100%) rename vignettes/httptest/{ => enviPathR}/0/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/2b6bbcc5-77f4-4bed-92a9-731cdc978f6a.json (100%) rename vignettes/httptest/{ => enviPathR}/0/envipath.org/api/legacy/setting.json (100%) create mode 100644 vignettes/httptest/get/0/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/2b6bbcc5-77f4-4bed-92a9-731cdc978f6a.json create mode 100644 vignettes/httptest/link/0/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/2b6bbcc5-77f4-4bed-92a9-731cdc978f6a.json create mode 100644 vignettes/httptest/list/0/envipath.org/api/legacy/package.json create mode 100644 vignettes/httptest/list/0/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway.json diff --git a/DESCRIPTION b/DESCRIPTION index 0a88dc1..9e9ebe8 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,15 +1,20 @@ 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")) -Description: +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. -Imports: +biocViews: + Software, DataImport, Cheminformatics, Microbiome, Annotation, Pathways, + Visualization, Network, GraphAndNetwork +Imports: BiocParallel, httr2, stats, diff --git a/R/get.R b/R/get.R index ac473fe..3e16bc6 100644 --- a/R/get.R +++ b/R/get.R @@ -17,12 +17,20 @@ #' A list of objects #' #' @examples -#' \dontrun{ -#' epLogin("username", "password") +#' \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 diff --git a/R/link.R b/R/link.R index dd3d8ec..fb7ae81 100644 --- a/R/link.R +++ b/R/link.R @@ -17,12 +17,20 @@ #' A data frame with links between from and to. #' #' @examples -#' \dontrun{ -#' epLogin("username", "password") +#' \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" #' #' epLink("reaction", "compound", rxn_id) +#' \dontshow{ +#' end_vignette() #' } NULL diff --git a/R/list.R b/R/list.R index 006aa5d..4a4a0ce 100644 --- a/R/list.R +++ b/R/list.R @@ -13,12 +13,20 @@ #' A data frame. #' #' @examples -#' \dontrun{ -#' epLogin("username", "password") +#' \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 diff --git a/R/login.R b/R/login.R index 71e52ba..6404026 100644 --- a/R/login.R +++ b/R/login.R @@ -14,9 +14,11 @@ #' A message upon successful login. #' #' @examples -#' \dontrun{ -#' epLogin("username", "password") +#' \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 index 375d212..c8d7b2d 100644 --- a/R/model.R +++ b/R/model.R @@ -14,15 +14,14 @@ #' respectively. #' #' @examples -#' \dontrun{ +#' \dontshow{ +#' username <- Sys.getenv("EP_USERNAME") +#' password <- Sys.getenv("EP_PASSWORD") +#' +#' epLogin(username, password) +#' } #' library(igraph) #' -#' # Perform login -#' epLogin("username", "password") -#' -#' # List available model settings -#' epList("setting") -#' #' # Define smiles of interest #' smiles <- "ClC(Cl)=C(Cl)Cl" #' @@ -30,10 +29,10 @@ #' former_out <- epModel(smiles) #' #' # Set id for PEPPER model setting -#' setting_id <- "3cda8e56-f4ff-47a8-b68c-4cfcfc4e8c2a" +#' set_id <- "3cda8e56-f4ff-47a8-b68c-4cfcfc4e8c2a" #' #' # Perform pathway prediction with PEPPER -#' pepper_out <- epModel(smiles, setting_id) +#' pepper_out <- epModel(smiles, set_id) #' #' # Convert model output to igraph object #' path_graph <- graph_from_data_frame( @@ -43,7 +42,6 @@ #' #' # Visualise predicted pathway #' plot(path_graph) -#' } NULL #' @export diff --git a/man/epGet.Rd b/man/epGet.Rd index a5e40a0..24044c8 100644 --- a/man/epGet.Rd +++ b/man/epGet.Rd @@ -22,11 +22,19 @@ A list of objects epGet returns a raw object from enviPath. } \examples{ -\dontrun{ -epLogin("username", "password") +\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 57e4213..4bff3ab 100644 --- a/man/epLink.Rd +++ b/man/epLink.Rd @@ -22,11 +22,19 @@ A data frame with links between from and to. epLink returns mappings between enviPath object types. } \examples{ -\dontrun{ -epLogin("username", "password") +\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" epLink("reaction", "compound", rxn_id) +\dontshow{ + end_vignette() } } diff --git a/man/epList.Rd b/man/epList.Rd index c420a4d..e641b66 100644 --- a/man/epList.Rd +++ b/man/epList.Rd @@ -18,11 +18,19 @@ A data frame. epList returns a list with info on objects available in enviPath. } \examples{ -\dontrun{ -epLogin("username", "password") +\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 03ddd14..830e2d1 100644 --- a/man/epLogin.Rd +++ b/man/epLogin.Rd @@ -16,7 +16,9 @@ epLogin lets you perform login to enviPath. An account is required to use the enviPath API. (add db link to refs) } \examples{ -\dontrun{ -epLogin("username", "password") +\dontshow{ + username <- Sys.getenv("EP_USERNAME") + password <- Sys.getenv("EP_PASSWORD") } +epLogin(username, password) } diff --git a/man/epModel.Rd b/man/epModel.Rd index 5d179ed..9f73842 100644 --- a/man/epModel.Rd +++ b/man/epModel.Rd @@ -19,15 +19,14 @@ respectively. epGet returns a raw object from enviPath. } \examples{ -\dontrun{ +\dontshow{ + username <- Sys.getenv("EP_USERNAME") + password <- Sys.getenv("EP_PASSWORD") + + epLogin(username, password) +} library(igraph) -# Perform login -epLogin("username", "password") - -# List available model settings -epList("setting") - # Define smiles of interest smiles <- "ClC(Cl)=C(Cl)Cl" @@ -35,10 +34,10 @@ smiles <- "ClC(Cl)=C(Cl)Cl" former_out <- epModel(smiles) # Set id for PEPPER model setting -setting_id <- "3cda8e56-f4ff-47a8-b68c-4cfcfc4e8c2a" +set_id <- "3cda8e56-f4ff-47a8-b68c-4cfcfc4e8c2a" # Perform pathway prediction with PEPPER -pepper_out <- epModel(smiles, setting_id) +pepper_out <- epModel(smiles, set_id) # Convert model output to igraph object path_graph <- graph_from_data_frame( @@ -49,4 +48,3 @@ path_graph <- graph_from_data_frame( # Visualise predicted pathway plot(path_graph) } -} diff --git a/vignettes/enviPathR.Rmd b/vignettes/enviPathR.Rmd index e22da46..edf6193 100644 --- a/vignettes/enviPathR.Rmd +++ b/vignettes/enviPathR.Rmd @@ -70,7 +70,7 @@ epLogin(username, password) ```{r httpstart, include = FALSE} library(httptest2) -start_vignette("httptest") +start_vignette("httptest/enviPathR") ``` ### List diff --git a/vignettes/httptest/0/envipath.org/api/legacy/package.json b/vignettes/httptest/enviPathR/0/envipath.org/api/legacy/package.json similarity index 100% rename from vignettes/httptest/0/envipath.org/api/legacy/package.json rename to vignettes/httptest/enviPathR/0/envipath.org/api/legacy/package.json diff --git a/vignettes/httptest/0/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway.json b/vignettes/httptest/enviPathR/0/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway.json similarity index 100% rename from vignettes/httptest/0/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway.json rename to vignettes/httptest/enviPathR/0/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway.json diff --git a/vignettes/httptest/0/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/2b6bbcc5-77f4-4bed-92a9-731cdc978f6a.json b/vignettes/httptest/enviPathR/0/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/2b6bbcc5-77f4-4bed-92a9-731cdc978f6a.json similarity index 100% rename from vignettes/httptest/0/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/2b6bbcc5-77f4-4bed-92a9-731cdc978f6a.json rename to vignettes/httptest/enviPathR/0/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/2b6bbcc5-77f4-4bed-92a9-731cdc978f6a.json diff --git a/vignettes/httptest/0/envipath.org/api/legacy/setting.json b/vignettes/httptest/enviPathR/0/envipath.org/api/legacy/setting.json similarity index 100% rename from vignettes/httptest/0/envipath.org/api/legacy/setting.json rename to vignettes/httptest/enviPathR/0/envipath.org/api/legacy/setting.json diff --git a/vignettes/httptest/get/0/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/2b6bbcc5-77f4-4bed-92a9-731cdc978f6a.json b/vignettes/httptest/get/0/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/vignettes/httptest/get/0/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/vignettes/httptest/link/0/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/2b6bbcc5-77f4-4bed-92a9-731cdc978f6a.json b/vignettes/httptest/link/0/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/vignettes/httptest/link/0/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": [ + + ], + 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permissions: write-all diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 8c69e44..339e919 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -1,8 +1,8 @@ name: test on: - push: + pull-request: branches: - - testing + - devel jobs: rworkflows: permissions: write-all