From bb2ad7576acee75589fb7f488b524ad606029cf1 Mon Sep 17 00:00:00 2001 From: RiboRings Date: Thu, 1 Oct 2026 10:10:40 +0800 Subject: [PATCH 1/3] Implement CRAN feedback --- .Rbuildignore | 2 + CRAN-SUBMISSION | 3 + DESCRIPTION | 4 +- cran-comments.md | 2 +- .../2b6bbcc5-77f4-4bed-92a9-731cdc978f6a.json | 8 +- .../get/package_reaction}/wrong.R | 12 +- .../ec87b463-6a3c-4dfa-8b88-4637fc158896.json | 18 +- .../link/package_compound}/wrong.R | 12 +- .../api/legacy => httptest/list}/package.json | 162 +++---- .../list}/package/wrong/reaction.R | 12 +- .../login/NA-26b34d-POST.json} | 0 .../login/NA-2f7c1a-POST.R} | 14 +- .../model}/util-078746-POST.json | 0 .../model}/util-e1f28b-POST.R | 10 +- tests/testthat/setup.R | 16 +- tests/testthat/test-get.R | 2 +- tests/testthat/test-link.R | 2 +- tests/testthat/test-list.R | 2 +- tests/testthat/test-login.R | 2 +- tests/testthat/test-model.R | 2 +- vignettes/enviPathR.Rmd | 21 +- ...y-26b34d-POST.json => NA-26b34d-POST.json} | 0 .../node.json | 22 - .../node.json | 22 - .../api/legacy => }/package.json | 162 +++---- .../pathway.json => package_pathway.json} | 438 +++++++++--------- .../1e7066c2-ff45-44f4-9086-e37db18400df.json | 34 +- .../259b990e-d653-4201-9282-04f2c6b05ca0.json | 38 +- .../httptest/1/package_pathway_node.json | 22 + .../2b6bbcc5-77f4-4bed-92a9-731cdc978f6a.json | 8 +- .../api/legacy => }/setting.json | 0 .../api/legacy => 1}/util-078746-POST.json | 0 .../api/legacy => 1}/util-672736-POST.json | 82 ++-- 33 files changed, 566 insertions(+), 568 deletions(-) create mode 100644 CRAN-SUBMISSION rename tests/{testthat/httptest/get/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction => httptest/get/package_reaction}/2b6bbcc5-77f4-4bed-92a9-731cdc978f6a.json (57%) rename tests/{testthat/httptest/get/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction => httptest/get/package_reaction}/wrong.R (98%) rename tests/{testthat/httptest/link/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound => httptest/link/package_compound}/ec87b463-6a3c-4dfa-8b88-4637fc158896.json (72%) rename tests/{testthat/httptest/link/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound => httptest/link/package_compound}/wrong.R (98%) rename tests/{testthat/httptest/list/envipath.org/api/legacy => httptest/list}/package.json (67%) rename tests/{testthat/httptest/list/envipath.org/api/legacy => httptest/list}/package/wrong/reaction.R (98%) rename tests/{testthat/httptest/login/envipath.org/api/legacy-26b34d-POST.json => httptest/login/NA-26b34d-POST.json} (100%) rename tests/{testthat/httptest/login/envipath.org/api/legacy-2f7c1a-POST.R => httptest/login/NA-2f7c1a-POST.R} (98%) rename tests/{testthat/httptest/model/envipath.org/api/legacy => httptest/model}/util-078746-POST.json (100%) rename tests/{testthat/httptest/model/envipath.org/api/legacy => httptest/model}/util-e1f28b-POST.R (61%) rename vignettes/httptest/1/{envipath.org/api/legacy-26b34d-POST.json => NA-26b34d-POST.json} (100%) delete mode 100644 vignettes/httptest/1/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/1e7066c2-ff45-44f4-9086-e37db18400df/node.json delete mode 100644 vignettes/httptest/1/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/259b990e-d653-4201-9282-04f2c6b05ca0/node.json rename vignettes/httptest/1/{envipath.org/api/legacy => }/package.json (67%) rename vignettes/httptest/1/{envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway.json => package_pathway.json} (51%) rename vignettes/httptest/1/{envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway => package_pathway}/1e7066c2-ff45-44f4-9086-e37db18400df.json (54%) rename vignettes/httptest/1/{envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway => package_pathway}/259b990e-d653-4201-9282-04f2c6b05ca0.json (57%) create mode 100644 vignettes/httptest/1/package_pathway_node.json rename vignettes/httptest/1/{envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction => package_reaction}/2b6bbcc5-77f4-4bed-92a9-731cdc978f6a.json (57%) rename vignettes/httptest/1/{envipath.org/api/legacy => }/setting.json (100%) rename vignettes/httptest/{2/envipath.org/api/legacy => 1}/util-078746-POST.json (100%) rename vignettes/httptest/{3/envipath.org/api/legacy => 1}/util-672736-POST.json (75%) diff --git a/.Rbuildignore b/.Rbuildignore index 0e9cbb3..9cbd157 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,5 +1,7 @@ +^docs$ ^\.github$ ^pkgdown$ ^_pkgdown\.yml$ ^\.Rproj\.user$ ^cran-comments\.md$ +^CRAN-SUBMISSION$ diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION new file mode 100644 index 0000000..f3428b7 --- /dev/null +++ b/CRAN-SUBMISSION @@ -0,0 +1,3 @@ +Version: 1.0.0 +Date: 2026-09-29 12:46:34 UTC +SHA: a50a5a817c2e8abba916110bc0b4292c91db1d4d diff --git a/DESCRIPTION b/DESCRIPTION index d6712de..a0e17cf 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: enviPathR -Title: The R client for the enviPath RESTful API +Title: Client for the 'enviPath' RESTful API Version: 1.0.0 Authors@R: c(person(given = "Giulio", family = "Benedetti", @@ -7,7 +7,7 @@ Authors@R: email = "giulio.benedetti@utu.fi", comment = c(ORCID = "0000-0002-8732-7692"))) Description: - The environmental pathway database (enviPath) is a key resource for the + 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 diff --git a/cran-comments.md b/cran-comments.md index 9b5ce7c..a39bee1 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,5 +1,5 @@ ## R CMD check results -0 errors ✔ | 0 warnings ✔ | 2 notes ✖ +0 errors ✔ | 0 warnings ✔ | 0 notes ✔ * This is a new release. 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/httptest/get/package_reaction/2b6bbcc5-77f4-4bed-92a9-731cdc978f6a.json similarity index 57% rename from tests/testthat/httptest/get/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/2b6bbcc5-77f4-4bed-92a9-731cdc978f6a.json rename to tests/httptest/get/package_reaction/2b6bbcc5-77f4-4bed-92a9-731cdc978f6a.json index eb997bd..64b08a4 100644 --- a/tests/testthat/httptest/get/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/2b6bbcc5-77f4-4bed-92a9-731cdc978f6a.json +++ b/tests/httptest/get/package_reaction/2b6bbcc5-77f4-4bed-92a9-731cdc978f6a.json @@ -9,11 +9,11 @@ "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", + "id": "https://envipath.org/package_compound_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", + "id": "https://envipath.org/package_reaction/2b6bbcc5-77f4-4bed-92a9-731cdc978f6a", "identifier": "reaction", "medlineRefs": [ @@ -22,7 +22,7 @@ "name": "Eawag BBD reaction r0014", "pathways": [ { - "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/c3d1b8d5-9ffb-49b8-a1bf-bf3d7dfd1ac3", + "id": "https://envipath.org/package_pathway/c3d1b8d5-9ffb-49b8-a1bf-bf3d7dfd1ac3", "name": "Tetrahydrofuran", "reviewStatus": "reviewed", "identifier": "pathway" @@ -31,7 +31,7 @@ "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", + "id": "https://envipath.org/package_compound_structure/befe8eeb-e8f8-4b4a-90b1-d0584a75f8cb", "smiles": "C(CC(=O)[O-])CO" } ], diff --git a/tests/testthat/httptest/get/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/wrong.R b/tests/httptest/get/package_reaction/wrong.R similarity index 98% rename from tests/testthat/httptest/get/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/wrong.R rename to tests/httptest/get/package_reaction/wrong.R index 9e640ea..8b7b7ce 100644 --- a/tests/testthat/httptest/get/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/wrong.R +++ b/tests/httptest/get/package_reaction/wrong.R @@ -1,12 +1,12 @@ -structure(list(method = "GET", url = "https://envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/wrong", +structure(list(method = "GET", url = "https://package_reaction/wrong", status_code = 404L, headers = structure(list(Server = "nginx/1.24.0 (Ubuntu)", - Date = "Tue, 29 Sep 2026 12:28:09 GMT", `Content-Type` = "text/html; charset=utf-8", + Date = "Thu, 01 Oct 2026 02:05:28 GMT", `Content-Type` = "text/html; charset=utf-8", `Transfer-Encoding` = "chunked", Connection = "keep-alive", Vary = "Authorization, Cookie", `X-Frame-Options` = "DENY", `X-Content-Type-Options` = "nosniff", `Referrer-Policy` = "same-origin", - `Cross-Origin-Opener-Policy` = "same-origin", `Set-Cookie` = "REDACTED", + `Cross-Origin-Opener-Policy` = "same-origin", `Set-Cookie` = "csrftoken=jbKz8jrQ5jD9akE1MIVnlSQL3pyhdL4S; expires=Thu, 30 Sep 2027 02:05:28 GMT; Max-Age=31449600; Path=/; SameSite=Lax", `Content-Encoding` = "gzip"), class = "httr2_headers"), - body = charToRaw("\n\n \n \n enviPath\n \n \n \n\n \n \n\n \n \n\n \n \n \n\n \n \n \n \n \n \n \n \n\n \n \n\n \n \n\n \n\n \n \n\n \n \n \n \n \n \n \n \n\n
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  • \n Settings\n
  • \n
  • \n \n \n \n \n Logout\n
  • \n \n
    \n \n
    \n
    \n
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    \n \n
      \n \n
    • \n
      \n Menu\n \n \n \n \n \n
      \n
    • \n \n
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    \n\n\n\n\n\n \n
    \n \n \n \n\n \n \n \n \n\n \n \n
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    Page Not Found

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    The page you're looking for doesn't exist.

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    404 Error

    \n

    \n The page or resource you requested could not be found. It may have\n been moved, deleted, or the URL might be incorrect.\n

    \n
    \n \n \n \n \n Go Home\n \n \n Learn More\n \n \n \n \n
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  • Text
  • \n
  • \n \n Text\n \n
  • \n
  • SMILES
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  • \n \n Default\n \n
  • \n
  • \n \n Canonical\n \n
  • \n
  • \n \n Exact\n \n
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  • InChI
  • \n
  • \n \n InChIKey\n \n
  • \n \n
    \n\n \n \n \n \n \n \n \n \n
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    \n\n \n
    \n \n \n \n \n\n \n \n \n \n \n \n Add Package\n \n
    \n\n \n \n \n
  • Reviewed Packages
  • \n \n
  • \n \n EAWAG-BBD\n \n \n \n \n
  • \n \n
  • \n \n EAWAG-SEDIMENT\n \n \n \n \n
  • \n \n
  • \n \n EAWAG-SLUDGE\n \n \n \n \n
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  • \n \n EAWAG-SOIL\n \n \n \n \n
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  • \n \n Public Prediction Models\n \n \n \n \n
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  • \n \n enviPath-PFAS\n \n \n \n \n
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  • Unreviewed Packages
  • \n \n
  • \n \n Autogenerated Package for Batch Prediction 2026-09-01 00:04:40.517620\n \n \n \n \n
  • \n \n
  • \n \n RiboRings’ Package\n \n \n \n \n
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  • \n \n Autogenerated Package for Batch Prediction 2026-09-01 00:06:57.531194\n \n \n \n \n
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  • \n \n 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1\n \n \n \n \n
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  • \n \n Autogenerated Package for Batch Prediction 2026-09-01 00:04:22.775931\n \n \n \n \n
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  • \n \n Autogenerated Package for Batch Prediction 2026-09-01 00:08:26.613909\n \n \n \n \n
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  • \n \n 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1\n \n \n \n \n
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    \n\n\n \n\n \n \n\n"), - timing = c(redirect = 0, namelookup = 7.8e-05, connect = 0, - pretransfer = 0.000368, starttransfer = 0.29781, total = 0.298693 + body = charToRaw("\n\n \n \n enviPath\n \n \n \n\n \n \n\n \n \n\n \n \n \n\n \n \n \n \n \n \n \n \n\n \n \n\n \n \n\n \n\n \n \n\n \n \n \n \n \n \n \n \n\n
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    \n \n
  • \n Settings\n
  • \n
  • \n \n \n \n \n Logout\n
  • \n \n
    \n \n
    \n
    \n
    \n \n
    \n \n
      \n \n
    • \n
      \n Menu\n \n \n \n \n \n
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    • \n \n
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    \n\n\n\n\n\n \n
    \n \n \n \n\n \n \n \n \n\n \n \n
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    Page Not Found

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    The page you're looking for doesn't exist.

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    404 Error

    \n

    \n The page or resource you requested could not be found. It may have\n been moved, deleted, or the URL might be incorrect.\n

    \n
    \n \n \n \n \n Go Home\n \n \n Learn More\n \n \n \n \n
    \n
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  • Text
  • \n
  • \n \n Text\n \n
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  • SMILES
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  • \n \n Default\n \n
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  • \n \n Canonical\n \n
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  • \n \n Exact\n \n
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  • InChI
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  • \n \n InChIKey\n \n
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    \n\n \n \n \n \n \n \n \n \n
    \n
    \n\n \n
    \n \n \n \n \n\n \n \n \n \n \n \n Add Package\n \n
    \n\n \n \n \n
  • Reviewed Packages
  • \n \n
  • \n \n EAWAG-BBD\n \n \n \n \n
  • \n \n
  • \n \n EAWAG-SEDIMENT\n \n \n \n \n
  • \n \n
  • \n \n EAWAG-SLUDGE\n \n \n \n \n
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  • \n \n EAWAG-SOIL\n \n \n \n \n
  • \n \n
  • \n \n Public Prediction Models\n \n \n \n \n
  • \n \n
  • \n \n enviPath-PFAS\n \n \n \n \n
  • \n \n
  • Unreviewed Packages
  • \n \n
  • \n \n Autogenerated Package for Batch Prediction 2026-09-01 00:04:40.517620\n \n \n \n \n
  • \n \n
  • \n \n RiboRings’ Package\n \n \n \n \n
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  • \n \n Autogenerated Package for Batch Prediction 2026-09-01 00:06:57.531194\n \n \n \n \n
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  • \n \n 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1\n \n \n \n \n
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  • \n \n Autogenerated Package for Batch Prediction 2026-09-01 00:04:22.775931\n \n \n \n \n
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  • \n \n Autogenerated Package for Batch Prediction 2026-09-01 00:08:26.613909\n \n \n \n \n
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  • \n \n 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1\n \n \n \n \n
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    \n \n \n\n \n \n\n \n \n\n \n \n \n \n \n \n\n
    \n \n
    \n\n\n \n\n \n \n\n"), + timing = c(redirect = 0, namelookup = 9.1e-05, connect = 0, + pretransfer = 0.000481, starttransfer = 0.287334, total = 0.288082 ), cache = new.env(parent = emptyenv())), class = "httr2_response") 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/httptest/link/package_compound/ec87b463-6a3c-4dfa-8b88-4637fc158896.json similarity index 72% rename from tests/testthat/httptest/link/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/ec87b463-6a3c-4dfa-8b88-4637fc158896.json rename to tests/httptest/link/package_compound/ec87b463-6a3c-4dfa-8b88-4637fc158896.json index 7c68c96..08c2345 100644 --- a/tests/testthat/httptest/link/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/ec87b463-6a3c-4dfa-8b88-4637fc158896.json +++ b/tests/httptest/link/package_compound/ec87b463-6a3c-4dfa-8b88-4637fc158896.json @@ -11,7 +11,7 @@ "06752" ] }, - "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/ec87b463-6a3c-4dfa-8b88-4637fc158896", + "id": "https://envipath.org/package_compound/ec87b463-6a3c-4dfa-8b88-4637fc158896", "halflifes": [ ], @@ -23,7 +23,7 @@ ], "pathways": [ { - "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/7b3f3e72-4f35-42c8-893d-e29c6b474232", + "id": "https://envipath.org/package_pathway/7b3f3e72-4f35-42c8-893d-e29c6b474232", "name": "1,2-Dichloroethane", "reviewStatus": "reviewed", "identifier": "pathway" @@ -34,7 +34,7 @@ ], "reactions": [ { - "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/6e2372bc-b165-4c19-b01c-6b64dff4d40a", + "id": "https://envipath.org/package_reaction/6e2372bc-b165-4c19-b01c-6b64dff4d40a", "name": "Eawag BBD reaction r0001", "reviewStatus": "reviewed", "identifier": "reaction" @@ -46,7 +46,7 @@ ], "structures": [ { - "InChI": "InChI=1S/C2H4Cl2/c3-1-2-4/h1-2H2", + "InChI": "InChI=1S/C2H4Cl2_h1-2H2", "aliases": [ ], @@ -65,7 +65,7 @@ "halflifes": [ ], - "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/ec87b463-6a3c-4dfa-8b88-4637fc158896/structure/7fa796ed-4816-4bc1-8c46-afdfd86ac8a3", + "id": "https://envipath.org/package_compound_structure/7fa796ed-4816-4bc1-8c46-afdfd86ac8a3", "identifier": "structure", "imageSize": 600, "inchikey": "WSLDOOZREJYCGB-UHFFFAOYSA-N", @@ -74,7 +74,7 @@ "name": "1,2-Dichloroethane", "pathways": [ { - "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/7b3f3e72-4f35-42c8-893d-e29c6b474232", + "id": "https://envipath.org/package_pathway/7b3f3e72-4f35-42c8-893d-e29c6b474232", "name": "1,2-Dichloroethane", "reviewStatus": "reviewed", "identifier": "pathway" @@ -85,7 +85,7 @@ ], "reactions": [ { - "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/6e2372bc-b165-4c19-b01c-6b64dff4d40a", + "id": "https://envipath.org/package_reaction/6e2372bc-b165-4c19-b01c-6b64dff4d40a", "name": "Eawag BBD reaction r0001", "reviewStatus": "reviewed", "identifier": "reaction" @@ -98,7 +98,7 @@ "smiles": "C(CCl)Cl" }, { - "InChI": "InChI=1S/C2H4Cl2/c3-1-2-4/h1-2H2", + "InChI": "InChI=1S/C2H4Cl2_h1-2H2", "aliases": [ ], @@ -112,7 +112,7 @@ "halflifes": [ ], - "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/ec87b463-6a3c-4dfa-8b88-4637fc158896/structure/69d4e95c-30b9-43a3-b385-0f9ad853a79a", + "id": "https://envipath.org/package_compound_structure/69d4e95c-30b9-43a3-b385-0f9ad853a79a", "identifier": "structure", "imageSize": 600, "inchikey": "WSLDOOZREJYCGB-UHFFFAOYSA-N", diff --git a/tests/testthat/httptest/link/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/wrong.R b/tests/httptest/link/package_compound/wrong.R similarity index 98% rename from tests/testthat/httptest/link/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/wrong.R rename to tests/httptest/link/package_compound/wrong.R index b9478ae..2bf0890 100644 --- a/tests/testthat/httptest/link/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/wrong.R +++ b/tests/httptest/link/package_compound/wrong.R @@ -1,12 +1,12 @@ -structure(list(method = "GET", url = "https://envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/wrong", +structure(list(method = "GET", url = "https://package_compound/wrong", status_code = 404L, headers = structure(list(Server = "nginx/1.24.0 (Ubuntu)", - Date = "Tue, 29 Sep 2026 12:28:13 GMT", `Content-Type` = "text/html; charset=utf-8", + Date = "Thu, 01 Oct 2026 02:05:30 GMT", `Content-Type` = "text/html; charset=utf-8", `Transfer-Encoding` = "chunked", Connection = "keep-alive", Vary = "Authorization, Cookie", `X-Frame-Options` = "DENY", `X-Content-Type-Options` = "nosniff", `Referrer-Policy` = "same-origin", - `Cross-Origin-Opener-Policy` = "same-origin", `Set-Cookie` = "REDACTED", + `Cross-Origin-Opener-Policy` = "same-origin", `Set-Cookie` = "csrftoken=jbKz8jrQ5jD9akE1MIVnlSQL3pyhdL4S; expires=Thu, 30 Sep 2027 02:05:30 GMT; Max-Age=31449600; Path=/; SameSite=Lax", `Content-Encoding` = "gzip"), class = "httr2_headers"), - body = charToRaw("\n\n \n \n enviPath\n \n \n \n\n \n \n\n \n \n\n \n \n \n\n \n \n \n \n \n \n \n \n\n \n \n\n \n \n\n \n\n \n \n\n \n \n \n \n \n \n \n \n\n
    \n \n
    \n \n
    \n
    \n \n \n \n \n \n \n \n
    \n\n \n\n
    \n \n \n
    \n \n \n \n \n \n \n
    \n \n
  • \n Settings\n
  • \n
  • \n \n \n \n \n Logout\n
  • \n \n
    \n \n
    \n
    \n
    \n \n
    \n \n
      \n \n
    • \n
      \n Menu\n \n \n \n \n \n
      \n
    • \n \n
    \n
    \n\n\n\n\n\n \n
    \n \n \n \n\n \n \n \n \n\n \n \n
    \n
    \n
    \n \n \n \n
    \n

    Page Not Found

    \n

    The page you're looking for doesn't exist.

    \n
    \n
    \n\n
    \n
    \n

    404 Error

    \n

    \n The page or resource you requested could not be found. It may have\n been moved, deleted, or the URL might be incorrect.\n

    \n
    \n \n \n \n \n Go Home\n \n \n Learn More\n \n \n \n \n
    \n
    \n
    \n
    \n
    \n\n\n \n \n \n \n
    \n\n \n
    \n \n \n
    \n\n\n \n \n\n \n \n
    \n \n
    \n
    \n \n\n \n
    \n \n \n \n \n \n \n \n
  • Text
  • \n
  • \n \n Text\n \n
  • \n
  • SMILES
  • \n
  • \n \n Default\n \n
  • \n
  • \n \n Canonical\n \n
  • \n
  • \n \n Exact\n \n
  • \n
  • InChI
  • \n
  • \n \n InChIKey\n \n
  • \n \n
    \n\n \n \n \n \n \n \n \n \n
    \n
    \n\n \n
    \n \n \n \n \n\n \n \n \n \n \n \n Add Package\n \n
    \n\n \n \n \n
  • Reviewed Packages
  • \n \n
  • \n \n EAWAG-BBD\n \n \n \n \n
  • \n \n
  • \n \n EAWAG-SEDIMENT\n \n \n \n \n
  • \n \n
  • \n \n EAWAG-SLUDGE\n \n \n \n \n
  • \n \n
  • \n \n EAWAG-SOIL\n \n \n \n \n
  • \n \n
  • \n \n Public Prediction Models\n \n \n \n \n
  • \n \n
  • \n \n enviPath-PFAS\n \n \n \n \n
  • \n \n
  • Unreviewed Packages
  • \n \n
  • \n \n Autogenerated Package for Batch Prediction 2026-09-01 00:04:40.517620\n \n \n \n \n
  • \n \n
  • \n \n RiboRings’ Package\n \n \n \n \n
  • \n \n
  • \n \n Autogenerated Package for Batch Prediction 2026-09-01 00:06:57.531194\n \n \n \n \n
  • \n \n
  • \n \n 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1\n \n \n \n \n
  • \n \n
  • \n \n Autogenerated Package for Batch Prediction 2026-09-01 00:04:22.775931\n \n \n \n \n
  • \n \n
  • \n \n Autogenerated Package for Batch Prediction 2026-09-01 00:08:26.613909\n \n \n \n \n
  • \n \n
  • \n \n 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1\n \n \n \n \n
  • \n \n \n \n
    \n\n \n
    \n \n
    \n\n \n
    \n \n \n\n \n \n\n \n \n\n \n \n
    \n \n \n\n \n \n\n \n \n\n \n \n \n \n \n \n\n
    \n \n
    \n\n\n \n\n \n \n\n"), - timing = c(redirect = 0, namelookup = 0.010444, connect = 0.232056, - pretransfer = 0.458801, starttransfer = 0.727557, total = 0.728269 + body = charToRaw("\n\n \n \n enviPath\n \n \n \n\n \n \n\n \n \n\n \n \n \n\n \n \n \n \n \n \n \n \n\n \n \n\n \n \n\n \n\n \n \n\n \n \n \n \n \n \n \n \n\n
    \n \n
    \n \n
    \n
    \n \n \n \n \n \n \n \n
    \n\n \n\n
    \n \n \n
    \n \n \n \n \n \n \n
    \n \n
  • \n Settings\n
  • \n
  • \n \n \n \n \n Logout\n
  • \n \n
    \n \n
    \n
    \n
    \n \n
    \n \n
      \n \n
    • \n
      \n Menu\n \n \n \n \n \n
      \n
    • \n \n
    \n
    \n\n\n\n\n\n \n
    \n \n \n \n\n \n \n \n \n\n \n \n
    \n
    \n
    \n \n \n \n
    \n

    Page Not Found

    \n

    The page you're looking for doesn't exist.

    \n
    \n
    \n\n
    \n
    \n

    404 Error

    \n

    \n The page or resource you requested could not be found. It may have\n been moved, deleted, or the URL might be incorrect.\n

    \n
    \n \n \n \n \n Go Home\n \n \n Learn More\n \n \n \n \n
    \n
    \n
    \n
    \n
    \n\n\n \n \n \n \n
    \n\n \n
    \n \n \n
    \n\n\n \n \n\n \n \n
    \n \n
    \n
    \n \n\n \n
    \n \n \n \n \n \n \n \n
  • Text
  • \n
  • \n \n Text\n \n
  • \n
  • SMILES
  • \n
  • \n \n Default\n \n
  • \n
  • \n \n Canonical\n \n
  • \n
  • \n \n Exact\n \n
  • \n
  • InChI
  • \n
  • \n \n InChIKey\n \n
  • \n \n
    \n\n \n \n \n \n \n \n \n \n
    \n
    \n\n \n
    \n \n \n \n \n\n \n \n \n \n \n \n Add Package\n \n
    \n\n \n \n \n
  • Reviewed Packages
  • \n \n
  • \n \n EAWAG-BBD\n \n \n \n \n
  • \n \n
  • \n \n EAWAG-SEDIMENT\n \n \n \n \n
  • \n \n
  • \n \n EAWAG-SLUDGE\n \n \n \n \n
  • \n \n
  • \n \n EAWAG-SOIL\n \n \n \n \n
  • \n \n
  • \n \n Public Prediction Models\n \n \n \n \n
  • \n \n
  • \n \n enviPath-PFAS\n \n \n \n \n
  • \n \n
  • Unreviewed Packages
  • \n \n
  • \n \n Autogenerated Package for Batch Prediction 2026-09-01 00:04:40.517620\n \n \n \n \n
  • \n \n
  • \n \n RiboRings’ Package\n \n \n \n \n
  • \n \n
  • \n \n Autogenerated Package for Batch Prediction 2026-09-01 00:06:57.531194\n \n \n \n \n
  • \n \n
  • \n \n 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1\n \n \n \n \n
  • \n \n
  • \n \n Autogenerated Package for Batch Prediction 2026-09-01 00:04:22.775931\n \n \n \n \n
  • \n \n
  • \n \n Autogenerated Package for Batch Prediction 2026-09-01 00:08:26.613909\n \n \n \n \n
  • \n \n
  • \n \n 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1\n \n \n \n \n
  • \n \n \n \n
    \n\n \n
    \n \n
    \n\n \n
    \n \n \n\n \n \n\n \n \n\n \n \n
    \n \n \n\n \n \n\n \n \n\n \n \n \n \n \n \n\n
    \n \n
    \n\n\n \n\n \n \n\n"), + timing = c(redirect = 0, namelookup = 0.020328, connect = 0.232652, + pretransfer = 0.441409, starttransfer = 0.714779, total = 0.715411 ), cache = new.env(parent = emptyenv())), class = "httr2_response") diff --git a/tests/testthat/httptest/list/envipath.org/api/legacy/package.json b/tests/httptest/list/package.json similarity index 67% rename from tests/testthat/httptest/list/envipath.org/api/legacy/package.json rename to tests/httptest/list/package.json index 6ba7dfd..8701ebf 100644 --- a/tests/testthat/httptest/list/envipath.org/api/legacy/package.json +++ b/tests/httptest/list/package.json @@ -6,37 +6,37 @@ "links": [ { "Pathways": [ - "https://envipath.org/package/5b594bf6-56a8-4ce5-9a63-5fd4b525756e/pathway", + "https://envipath.org/package_pathway", 1 ] }, { "Rules": [ - "https://envipath.org/package/5b594bf6-56a8-4ce5-9a63-5fd4b525756e/rule", + "https://envipath.org/package_rule", 0 ] }, { "Compounds": [ - "https://envipath.org/package/5b594bf6-56a8-4ce5-9a63-5fd4b525756e/compound", + "https://envipath.org/package_compound", 24 ] }, { "Reactions": [ - "https://envipath.org/package/5b594bf6-56a8-4ce5-9a63-5fd4b525756e/reaction", + "https://envipath.org/package_reaction", 38 ] }, { "Relative Reasoning": [ - "https://envipath.org/package/5b594bf6-56a8-4ce5-9a63-5fd4b525756e/relative-reasoning", + "https://envipath.org/package_relative-reasoning", 0 ] }, { "Scenarios": [ - "https://envipath.org/package/5b594bf6-56a8-4ce5-9a63-5fd4b525756e/scenario", + "https://envipath.org/package_scenario", 0 ] } @@ -66,37 +66,37 @@ "links": [ { "Pathways": [ - "https://envipath.org/package/995230c9-167a-4108-8002-d8fadd242dff/pathway", + "https://envipath.org/package_pathway", 0 ] }, { "Rules": [ - "https://envipath.org/package/995230c9-167a-4108-8002-d8fadd242dff/rule", + "https://envipath.org/package_rule", 0 ] }, { "Compounds": [ - "https://envipath.org/package/995230c9-167a-4108-8002-d8fadd242dff/compound", + "https://envipath.org/package_compound", 0 ] }, { "Reactions": [ - "https://envipath.org/package/995230c9-167a-4108-8002-d8fadd242dff/reaction", + "https://envipath.org/package_reaction", 0 ] }, { "Relative Reasoning": [ - "https://envipath.org/package/995230c9-167a-4108-8002-d8fadd242dff/relative-reasoning", + "https://envipath.org/package_relative-reasoning", 0 ] }, { "Scenarios": [ - "https://envipath.org/package/995230c9-167a-4108-8002-d8fadd242dff/scenario", + "https://envipath.org/package_scenario", 0 ] } @@ -121,42 +121,42 @@ ] }, { - "description": "\"EAWAG-SOIL\" package contains pathway information from soil degradation studies, stored in a biotransformation reaction scheme in the object pathway<\/a>. This information is extracted from pesticide registration dossiers (draft assessment reports, DAR) made publically available through the European Food Safety Authority (EFSA<\/a>). The package also contains information on different experimental conditions that are stored in the object scenario<\/a>. Compounds<\/a> in the pathway are associated with a given scenario<\/a> if they have been observed under the specific experimental conditions. If available, a biotransformation half-life (DT50) value is additionally associated with a given compound in the pathway and a specific scenario. More details concerning enviPath conventions that were used to store specific data from DAR, and their description can be found in our wiki<\/a>.", + "description": "\"EAWAG-SOIL\" package contains pathway information from soil degradation studies, stored in a biotransformation reaction scheme in the object pathway<\/a>. This information is extracted from pesticide registration dossiers (draft assessment reports, DAR) made publically available through the European Food Safety Authority (EFSA<\/a>). The package also contains information on different experimental conditions that are stored in the object scenario<\/a>. Compounds<\/a> in the pathway are associated with a given scenario<\/a> if they have been observed under the specific experimental conditions. If available, a biotransformation half-life (DT50) value is additionally associated with a given compound in the pathway and a specific scenario. More details concerning enviPath conventions that were used to store specific data from DAR, and their description can be found in our wiki<\/a>.", "id": "https://envipath.org/package/5882df9c-dae1-4d80-a40e-db4724271456", "links": [ { "Pathways": [ - "https://envipath.org/package/5882df9c-dae1-4d80-a40e-db4724271456/pathway", + "https://envipath.org/package_pathway", 317 ] }, { "Rules": [ - "https://envipath.org/package/5882df9c-dae1-4d80-a40e-db4724271456/rule", + "https://envipath.org/package_rule", 0 ] }, { "Compounds": [ - "https://envipath.org/package/5882df9c-dae1-4d80-a40e-db4724271456/compound", + "https://envipath.org/package_compound", 2608 ] }, { "Reactions": [ - "https://envipath.org/package/5882df9c-dae1-4d80-a40e-db4724271456/reaction", + "https://envipath.org/package_reaction", 2445 ] }, { "Relative Reasoning": [ - "https://envipath.org/package/5882df9c-dae1-4d80-a40e-db4724271456/relative-reasoning", + "https://envipath.org/package_relative-reasoning", 0 ] }, { "Scenarios": [ - "https://envipath.org/package/5882df9c-dae1-4d80-a40e-db4724271456/scenario", + "https://envipath.org/package_scenario", 4881 ] } @@ -186,37 +186,37 @@ "links": [ { "Pathways": [ - "https://envipath.org/package/aee2524b-79f3-4640-a519-aac543ac05e3/pathway", + "https://envipath.org/package_pathway", 4 ] }, { "Rules": [ - "https://envipath.org/package/aee2524b-79f3-4640-a519-aac543ac05e3/rule", + "https://envipath.org/package_rule", 0 ] }, { "Compounds": [ - "https://envipath.org/package/aee2524b-79f3-4640-a519-aac543ac05e3/compound", + "https://envipath.org/package_compound", 33 ] }, { "Reactions": [ - "https://envipath.org/package/aee2524b-79f3-4640-a519-aac543ac05e3/reaction", + "https://envipath.org/package_reaction", 66 ] }, { "Relative Reasoning": [ - "https://envipath.org/package/aee2524b-79f3-4640-a519-aac543ac05e3/relative-reasoning", + "https://envipath.org/package_relative-reasoning", 0 ] }, { "Scenarios": [ - "https://envipath.org/package/aee2524b-79f3-4640-a519-aac543ac05e3/scenario", + "https://envipath.org/package_scenario", 0 ] } @@ -246,37 +246,37 @@ "links": [ { "Pathways": [ - "https://envipath.org/package/c3c6699a-8c78-4987-af4d-4a041ffc448d/pathway", + "https://envipath.org/package_pathway", 2 ] }, { "Rules": [ - "https://envipath.org/package/c3c6699a-8c78-4987-af4d-4a041ffc448d/rule", + "https://envipath.org/package_rule", 0 ] }, { "Compounds": [ - "https://envipath.org/package/c3c6699a-8c78-4987-af4d-4a041ffc448d/compound", + "https://envipath.org/package_compound", 21 ] }, { "Reactions": [ - "https://envipath.org/package/c3c6699a-8c78-4987-af4d-4a041ffc448d/reaction", + "https://envipath.org/package_reaction", 23 ] }, { "Relative Reasoning": [ - "https://envipath.org/package/c3c6699a-8c78-4987-af4d-4a041ffc448d/relative-reasoning", + "https://envipath.org/package_relative-reasoning", 0 ] }, { "Scenarios": [ - "https://envipath.org/package/c3c6699a-8c78-4987-af4d-4a041ffc448d/scenario", + "https://envipath.org/package_scenario", 0 ] } @@ -301,42 +301,42 @@ ] }, { - "description": "The EAWAG-SLUDGE<\/a> package contains pathways and kinetic information about microbially mediated transformation processes in biological wastewater treatment. The information was extracted from scientific publications in different journals. The biotransformation reaction schemes are stored as pathways<\/a>. The experimental conditions and additional information (e. g. sludge source) are collected in the scenario<\/a> objects. Any observed transformation products (compounds<\/a>) are linked to their corresponding experimental metadata (scenario<\/a>). Kinetic parameters (rate constants and/or half-lives) including corresponding scenarios are indicated for compounds for which such data is available. More details regarding enviPath conventions can be found in our wiki<\/a>.", + "description": "The EAWAG-SLUDGE<\/a> package contains pathways and kinetic information about microbially mediated transformation processes in biological wastewater treatment. The information was extracted from scientific publications in different journals. The biotransformation reaction schemes are stored as pathways<\/a>. The experimental conditions and additional information (e. g. sludge source) are collected in the scenario<\/a> objects. Any observed transformation products (compounds<\/a>) are linked to their corresponding experimental metadata (scenario<\/a>). Kinetic parameters (rate constants and/or half-lives) including corresponding scenarios are indicated for compounds for which such data is available. 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", + "https://envipath.org/package_pathway", 183 ] }, { "Rules": [ - "https://envipath.org/package/521c547a-fd2a-491c-ad5b-7eaa1577fb65/rule", + "https://envipath.org/package_rule", 0 ] }, { "Compounds": [ - "https://envipath.org/package/521c547a-fd2a-491c-ad5b-7eaa1577fb65/compound", + "https://envipath.org/package_compound", 1067 ] }, { "Reactions": [ - "https://envipath.org/package/521c547a-fd2a-491c-ad5b-7eaa1577fb65/reaction", + "https://envipath.org/package_reaction", 494 ] }, { "Relative Reasoning": [ - "https://envipath.org/package/521c547a-fd2a-491c-ad5b-7eaa1577fb65/relative-reasoning", + "https://envipath.org/package_relative-reasoning", 0 ] }, { "Scenarios": [ - "https://envipath.org/package/521c547a-fd2a-491c-ad5b-7eaa1577fb65/scenario", + "https://envipath.org/package_scenario", 85 ] } @@ -366,37 +366,37 @@ "links": [ { "Pathways": [ - "https://envipath.org/package/134886bb-b52e-4ad6-91d3-a02cecde6d95/pathway", + "https://envipath.org/package_pathway", 0 ] }, { "Rules": [ - "https://envipath.org/package/134886bb-b52e-4ad6-91d3-a02cecde6d95/rule", + "https://envipath.org/package_rule", 0 ] }, { "Compounds": [ - "https://envipath.org/package/134886bb-b52e-4ad6-91d3-a02cecde6d95/compound", + "https://envipath.org/package_compound", 0 ] }, { "Reactions": [ - "https://envipath.org/package/134886bb-b52e-4ad6-91d3-a02cecde6d95/reaction", + "https://envipath.org/package_reaction", 0 ] }, { "Relative Reasoning": [ - "https://envipath.org/package/134886bb-b52e-4ad6-91d3-a02cecde6d95/relative-reasoning", + "https://envipath.org/package_relative-reasoning", 3 ] }, { "Scenarios": [ - "https://envipath.org/package/134886bb-b52e-4ad6-91d3-a02cecde6d95/scenario", + "https://envipath.org/package_scenario", 0 ] } @@ -426,37 +426,37 @@ "links": [ { "Pathways": [ - "https://envipath.org/package/7245f711-51d0-4b1e-b49d-99a9d9744c96/pathway", + "https://envipath.org/package_pathway", 0 ] }, { "Rules": [ - "https://envipath.org/package/7245f711-51d0-4b1e-b49d-99a9d9744c96/rule", + "https://envipath.org/package_rule", 0 ] }, { "Compounds": [ - "https://envipath.org/package/7245f711-51d0-4b1e-b49d-99a9d9744c96/compound", + "https://envipath.org/package_compound", 0 ] }, { "Reactions": [ - "https://envipath.org/package/7245f711-51d0-4b1e-b49d-99a9d9744c96/reaction", + "https://envipath.org/package_reaction", 0 ] }, { "Relative Reasoning": [ - "https://envipath.org/package/7245f711-51d0-4b1e-b49d-99a9d9744c96/relative-reasoning", + "https://envipath.org/package_relative-reasoning", 0 ] }, { "Scenarios": [ - "https://envipath.org/package/7245f711-51d0-4b1e-b49d-99a9d9744c96/scenario", + "https://envipath.org/package_scenario", 0 ] } @@ -486,37 +486,37 @@ "links": [ { "Pathways": [ - "https://envipath.org/package/7a3bddd7-c1a2-4699-a885-8b9044fd4fe2/pathway", + "https://envipath.org/package_pathway", 0 ] }, { "Rules": [ - "https://envipath.org/package/7a3bddd7-c1a2-4699-a885-8b9044fd4fe2/rule", + "https://envipath.org/package_rule", 0 ] }, { "Compounds": [ - "https://envipath.org/package/7a3bddd7-c1a2-4699-a885-8b9044fd4fe2/compound", + "https://envipath.org/package_compound", 0 ] }, { "Reactions": [ - "https://envipath.org/package/7a3bddd7-c1a2-4699-a885-8b9044fd4fe2/reaction", + "https://envipath.org/package_reaction", 0 ] }, { "Relative Reasoning": [ - "https://envipath.org/package/7a3bddd7-c1a2-4699-a885-8b9044fd4fe2/relative-reasoning", + "https://envipath.org/package_relative-reasoning", 0 ] }, { "Scenarios": [ - "https://envipath.org/package/7a3bddd7-c1a2-4699-a885-8b9044fd4fe2/scenario", + "https://envipath.org/package_scenario", 0 ] } @@ -546,37 +546,37 @@ "links": [ { "Pathways": [ - "https://envipath.org/package/d1898032-350b-438a-a702-63906c7ed76a/pathway", + "https://envipath.org/package_pathway", 0 ] }, { "Rules": [ - "https://envipath.org/package/d1898032-350b-438a-a702-63906c7ed76a/rule", + "https://envipath.org/package_rule", 0 ] }, { "Compounds": [ - "https://envipath.org/package/d1898032-350b-438a-a702-63906c7ed76a/compound", + "https://envipath.org/package_compound", 0 ] }, { "Reactions": [ - "https://envipath.org/package/d1898032-350b-438a-a702-63906c7ed76a/reaction", + "https://envipath.org/package_reaction", 0 ] }, { "Relative Reasoning": [ - "https://envipath.org/package/d1898032-350b-438a-a702-63906c7ed76a/relative-reasoning", + "https://envipath.org/package_relative-reasoning", 0 ] }, { "Scenarios": [ - "https://envipath.org/package/d1898032-350b-438a-a702-63906c7ed76a/scenario", + "https://envipath.org/package_scenario", 0 ] } @@ -601,42 +601,42 @@ ] }, { - "description": "The \"EAWAG-SEDIMENT\" package contains pathways and kinetic data from biodegradation studies performed in water-sediment systems. This information is extracted from pesticide registration dossiers (draft assessment reports, DAR) made publically available through the European Food Safety Authority (EFSA<\/a>). The package also contains information on different experimental conditions that are stored in the object scenario<\/a>. Compounds<\/a> in the pathway are associated with a given scenario<\/a> if they have been observed under the specific experimental conditions. If available, a total system biotransformation half-life (DT50) value is associated with a given compound in the pathway and a specific scenario, along with dissipation half-lives from the water and the sediment phases.", + "description": "The \"EAWAG-SEDIMENT\" package contains pathways and kinetic data from biodegradation studies performed in water-sediment systems. This information is extracted from pesticide registration dossiers (draft assessment reports, DAR) made publically available through the European Food Safety Authority (EFSA<\/a>). The package also contains information on different experimental conditions that are stored in the object scenario<\/a>. Compounds<\/a> in the pathway are associated with a given scenario<\/a> if they have been observed under the specific experimental conditions. If available, a total system biotransformation half-life (DT50) value is associated with a given compound in the pathway and a specific scenario, along with dissipation half-lives from the water and the sediment phases.", "id": "https://envipath.org/package/f05e38d8-e9b4-4c3e-b0d8-9ab29966eccf", "links": [ { "Pathways": [ - "https://envipath.org/package/f05e38d8-e9b4-4c3e-b0d8-9ab29966eccf/pathway", + "https://envipath.org/package_pathway", 179 ] }, { "Rules": [ - "https://envipath.org/package/f05e38d8-e9b4-4c3e-b0d8-9ab29966eccf/rule", + "https://envipath.org/package_rule", 0 ] }, { "Compounds": [ - "https://envipath.org/package/f05e38d8-e9b4-4c3e-b0d8-9ab29966eccf/compound", + "https://envipath.org/package_compound", 810 ] }, { "Reactions": [ - "https://envipath.org/package/f05e38d8-e9b4-4c3e-b0d8-9ab29966eccf/reaction", + "https://envipath.org/package_reaction", 961 ] }, { "Relative Reasoning": [ - "https://envipath.org/package/f05e38d8-e9b4-4c3e-b0d8-9ab29966eccf/relative-reasoning", + "https://envipath.org/package_relative-reasoning", 0 ] }, { "Scenarios": [ - "https://envipath.org/package/f05e38d8-e9b4-4c3e-b0d8-9ab29966eccf/scenario", + "https://envipath.org/package_scenario", 1622 ] } @@ -666,37 +666,37 @@ "links": [ { "Pathways": [ - "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway", + "https://envipath.org/package_pathway", 219 ] }, { "Rules": [ - "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/rule", + "https://envipath.org/package_rule", 499 ] }, { "Compounds": [ - "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound", + "https://envipath.org/package_compound", 1399 ] }, { "Reactions": [ - "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction", + "https://envipath.org/package_reaction", 1480 ] }, { "Relative Reasoning": [ - "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/relative-reasoning", + "https://envipath.org/package_relative-reasoning", 0 ] }, { "Scenarios": [ - "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/scenario", + "https://envipath.org/package_scenario", 1915 ] } @@ -726,37 +726,37 @@ "links": [ { "Pathways": [ - "https://envipath.org/package/87a49584-d937-482c-9c33-25928dcb02a8/pathway", + "https://envipath.org/package_pathway", 214 ] }, { "Rules": [ - "https://envipath.org/package/87a49584-d937-482c-9c33-25928dcb02a8/rule", + "https://envipath.org/package_rule", 0 ] }, { "Compounds": [ - "https://envipath.org/package/87a49584-d937-482c-9c33-25928dcb02a8/compound", + "https://envipath.org/package_compound", 590 ] }, { "Reactions": [ - "https://envipath.org/package/87a49584-d937-482c-9c33-25928dcb02a8/reaction", + "https://envipath.org/package_reaction", 915 ] }, { "Relative Reasoning": [ - "https://envipath.org/package/87a49584-d937-482c-9c33-25928dcb02a8/relative-reasoning", + "https://envipath.org/package_relative-reasoning", 0 ] }, { "Scenarios": [ - "https://envipath.org/package/87a49584-d937-482c-9c33-25928dcb02a8/scenario", + "https://envipath.org/package_scenario", 288 ] } diff --git a/tests/testthat/httptest/list/envipath.org/api/legacy/package/wrong/reaction.R b/tests/httptest/list/package/wrong/reaction.R similarity index 98% rename from tests/testthat/httptest/list/envipath.org/api/legacy/package/wrong/reaction.R rename to tests/httptest/list/package/wrong/reaction.R index 14dc2d7..3227bfa 100644 --- a/tests/testthat/httptest/list/envipath.org/api/legacy/package/wrong/reaction.R +++ b/tests/httptest/list/package/wrong/reaction.R @@ -1,12 +1,12 @@ -structure(list(method = "GET", url = "https://envipath.org/api/legacy/package/wrong/reaction", +structure(list(method = "GET", url = "https://package/wrong/reaction", status_code = 404L, headers = structure(list(Server = "nginx/1.24.0 (Ubuntu)", - Date = "Tue, 29 Sep 2026 12:28:16 GMT", `Content-Type` = "text/html; charset=utf-8", + Date = "Thu, 01 Oct 2026 02:05:32 GMT", `Content-Type` = "text/html; charset=utf-8", `Transfer-Encoding` = "chunked", Connection = "keep-alive", Vary = "Authorization, Cookie", `X-Frame-Options` = "DENY", `X-Content-Type-Options` = "nosniff", `Referrer-Policy` = "same-origin", - `Cross-Origin-Opener-Policy` = "same-origin", `Set-Cookie` = "REDACTED", + `Cross-Origin-Opener-Policy` = "same-origin", `Set-Cookie` = "csrftoken=jbKz8jrQ5jD9akE1MIVnlSQL3pyhdL4S; expires=Thu, 30 Sep 2027 02:05:32 GMT; Max-Age=31449600; Path=/; SameSite=Lax", `Content-Encoding` = "gzip"), class = "httr2_headers"), - body = charToRaw("\n\n \n \n enviPath\n \n \n \n\n \n \n\n \n \n\n \n \n \n\n \n \n \n \n \n \n \n \n\n \n \n\n \n \n\n \n\n \n \n\n \n \n \n \n \n \n \n \n\n
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  • Text
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  • Reviewed Packages
  • \n \n
  • \n \n EAWAG-BBD\n \n \n \n \n
  • \n \n
  • \n \n EAWAG-SEDIMENT\n \n \n \n \n
  • \n \n
  • \n \n EAWAG-SLUDGE\n \n \n \n \n
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  • \n \n EAWAG-SOIL\n \n \n \n \n
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  • \n \n Public Prediction Models\n \n \n \n \n
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  • Unreviewed Packages
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  • \n \n Autogenerated Package for Batch Prediction 2026-09-01 00:04:40.517620\n \n \n \n \n
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  • \n \n RiboRings’ Package\n \n \n \n \n
  • \n \n
  • \n \n Autogenerated Package for Batch Prediction 2026-09-01 00:06:57.531194\n \n \n \n \n
  • \n \n
  • \n \n 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1\n \n \n \n \n
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  • \n \n Autogenerated Package for Batch Prediction 2026-09-01 00:04:22.775931\n \n \n \n \n
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  • \n \n Autogenerated Package for Batch Prediction 2026-09-01 00:08:26.613909\n \n \n \n \n
  • \n \n
  • \n \n 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1\n \n \n \n \n
  • \n \n \n \n
    \n\n \n
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    \n \n \n\n \n \n\n \n \n\n \n \n \n \n \n \n\n
    \n \n
    \n\n\n \n\n \n \n\n"), + timing = c(redirect = 0, namelookup = 0.014201, connect = 0.215712, + pretransfer = 0.430346, starttransfer = 0.68023, total = 0.680857 ), cache = new.env(parent = emptyenv())), class = "httr2_response") diff --git a/tests/testthat/httptest/login/envipath.org/api/legacy-26b34d-POST.json b/tests/httptest/login/NA-26b34d-POST.json similarity index 100% rename from tests/testthat/httptest/login/envipath.org/api/legacy-26b34d-POST.json rename to tests/httptest/login/NA-26b34d-POST.json diff --git a/tests/testthat/httptest/login/envipath.org/api/legacy-2f7c1a-POST.R b/tests/httptest/login/NA-2f7c1a-POST.R similarity index 98% rename from tests/testthat/httptest/login/envipath.org/api/legacy-2f7c1a-POST.R rename to tests/httptest/login/NA-2f7c1a-POST.R index c3a5014..7394f79 100644 --- a/tests/testthat/httptest/login/envipath.org/api/legacy-2f7c1a-POST.R +++ b/tests/httptest/login/NA-2f7c1a-POST.R @@ -1,11 +1,11 @@ -structure(list(method = "POST", url = "https://envipath.org/api/legacy/", - status_code = 500L, headers = structure(list(Server = "nginx/1.24.0 (Ubuntu)", - Date = "Tue, 29 Sep 2026 12:28:18 GMT", `Content-Type` = "text/html; charset=utf-8", +structure(list(method = "POST", url = "https://", status_code = 500L, + headers = structure(list(Server = "nginx/1.24.0 (Ubuntu)", + Date = "Thu, 01 Oct 2026 02:05:33 GMT", `Content-Type` = "text/html; charset=utf-8", `Content-Length` = "42985", Connection = "keep-alive", Vary = "Authorization, Cookie", `X-Frame-Options` = "DENY", `X-Content-Type-Options` = "nosniff", `Referrer-Policy` = "same-origin", - `Cross-Origin-Opener-Policy` = "same-origin", `Set-Cookie` = "REDACTED"), class = "httr2_headers"), - body = charToRaw("\n\n \n \n enviPath\n \n \n \n\n \n \n\n \n \n\n \n \n \n\n \n \n \n \n \n \n \n \n\n \n \n\n \n \n\n \n\n \n \n\n \n \n \n \n \n \n \n \n\n
    \n \n
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    \n \n \n \n \n \n \n \n
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  • Text
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  • \n
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  • \n \n
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  • Reviewed Packages
  • \n \n
  • \n \n EAWAG-BBD\n \n \n \n \n
  • \n \n
  • \n \n EAWAG-SEDIMENT\n \n \n \n \n
  • \n \n
  • \n \n EAWAG-SLUDGE\n \n \n \n \n
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  • Unreviewed Packages
  • \n \n
  • \n \n Autogenerated Package for Batch Prediction 2026-09-01 00:04:40.517620\n \n \n \n \n
  • \n \n
  • \n \n RiboRings’ Package\n \n \n \n \n
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  • \n \n Autogenerated Package for Batch Prediction 2026-09-01 00:06:57.531194\n \n \n \n \n
  • \n \n
  • \n \n 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1\n \n \n \n \n
  • \n \n
  • \n \n Autogenerated Package for Batch Prediction 2026-09-01 00:04:22.775931\n \n \n \n \n
  • \n \n
  • \n \n Autogenerated Package for Batch Prediction 2026-09-01 00:08:26.613909\n \n \n \n \n
  • \n \n
  • \n \n 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1\n \n \n \n \n
  • \n \n \n \n
    \n\n \n
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    \n \n
    \n\n\n \n\n \n \n\n"), - timing = c(redirect = 0, namelookup = 3.6e-05, connect = 0, - pretransfer = 0.000183, starttransfer = 1.136047, total = 2.75423 + `Cross-Origin-Opener-Policy` = "same-origin", `Set-Cookie` = "csrftoken=jbKz8jrQ5jD9akE1MIVnlSQL3pyhdL4S; expires=Thu, 30 Sep 2027 02:05:33 GMT; Max-Age=31449600; Path=/; SameSite=Lax"), class = "httr2_headers"), + body = charToRaw("\n\n \n \n enviPath\n \n \n \n\n \n \n\n \n \n\n \n \n \n\n \n \n \n \n \n \n \n \n\n \n \n\n \n \n\n \n\n \n \n\n \n \n \n \n \n \n \n \n\n
    \n \n
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    \n \n \n \n \n \n \n \n
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    • \n \n
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    \n\n\n\n\n\n \n
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    \n \n \n \n
    \n

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  • Text
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  • \n
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  • \n \n
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  • Reviewed Packages
  • \n \n
  • \n \n EAWAG-BBD\n \n \n \n \n
  • \n \n
  • \n \n EAWAG-SEDIMENT\n \n \n \n \n
  • \n \n
  • \n \n EAWAG-SLUDGE\n \n \n \n \n
  • \n \n
  • \n \n EAWAG-SOIL\n \n \n \n \n
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  • \n \n Public Prediction Models\n \n \n \n \n
  • \n \n
  • \n \n enviPath-PFAS\n \n \n \n \n
  • \n \n
  • Unreviewed Packages
  • \n \n
  • \n \n Autogenerated Package for Batch Prediction 2026-09-01 00:04:40.517620\n \n \n \n \n
  • \n \n
  • \n \n RiboRings’ Package\n \n \n \n \n
  • \n \n
  • \n \n Autogenerated Package for Batch Prediction 2026-09-01 00:06:57.531194\n \n \n \n \n
  • \n \n
  • \n \n 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1\n \n \n \n \n
  • \n \n
  • \n \n Autogenerated Package for Batch Prediction 2026-09-01 00:04:22.775931\n \n \n \n \n
  • \n \n
  • \n \n Autogenerated Package for Batch Prediction 2026-09-01 00:08:26.613909\n \n \n \n \n
  • \n \n
  • \n \n 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1\n \n \n \n \n
  • \n \n \n \n
    \n\n \n
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    \n \n \n\n \n \n\n \n \n\n \n \n \n \n \n \n\n
    \n \n
    \n\n\n \n\n \n \n\n"), + timing = c(redirect = 0, namelookup = 3.1e-05, connect = 0, + pretransfer = 0.000197, starttransfer = 0.27129, total = 0.474832 ), cache = new.env(parent = emptyenv())), class = "httr2_response") diff --git a/tests/testthat/httptest/model/envipath.org/api/legacy/util-078746-POST.json b/tests/httptest/model/util-078746-POST.json similarity index 100% rename from tests/testthat/httptest/model/envipath.org/api/legacy/util-078746-POST.json rename to tests/httptest/model/util-078746-POST.json diff --git a/tests/testthat/httptest/model/envipath.org/api/legacy/util-e1f28b-POST.R b/tests/httptest/model/util-e1f28b-POST.R similarity index 61% rename from tests/testthat/httptest/model/envipath.org/api/legacy/util-e1f28b-POST.R rename to tests/httptest/model/util-e1f28b-POST.R index b39b15d..d9c2fb3 100644 --- a/tests/testthat/httptest/model/envipath.org/api/legacy/util-e1f28b-POST.R +++ b/tests/httptest/model/util-e1f28b-POST.R @@ -1,11 +1,11 @@ -structure(list(method = "POST", url = "https://envipath.org/api/legacy/util", - status_code = 403L, headers = structure(list(Server = "nginx/1.24.0 (Ubuntu)", - Date = "Tue, 29 Sep 2026 12:28:22 GMT", `Content-Type` = "application/json; charset=utf-8", +structure(list(method = "POST", url = "https://util", status_code = 403L, + headers = structure(list(Server = "nginx/1.24.0 (Ubuntu)", + Date = "Thu, 01 Oct 2026 02:05:34 GMT", `Content-Type` = "application/json; charset=utf-8", `Content-Length` = "139", Connection = "keep-alive", Vary = "Authorization, Cookie", `X-Frame-Options` = "DENY", `X-Content-Type-Options` = "nosniff", `Referrer-Policy` = "same-origin", `Cross-Origin-Opener-Policy` = "same-origin"), class = "httr2_headers"), body = charToRaw("{\"message\": \"Getting Setting with id https://envipath.org/setting/1d915a48-286a-4394-9693-bfaa187326a5 failed due to insufficient rights!\"}"), - timing = c(redirect = 0, namelookup = 3.4e-05, connect = 0, - pretransfer = 0.000197, starttransfer = 0.236713, total = 0.236748 + timing = c(redirect = 0, namelookup = 3.1e-05, connect = 0, + pretransfer = 0.000165, starttransfer = 0.247818, total = 0.247872 ), cache = new.env(parent = emptyenv())), class = "httr2_response") diff --git a/tests/testthat/setup.R b/tests/testthat/setup.R index 5c2097b..80af6dd 100644 --- a/tests/testthat/setup.R +++ b/tests/testthat/setup.R @@ -1,11 +1,11 @@ library(httptest2) - +# Retrieve login credentials username <- Sys.getenv("EP_USERNAME") password <- Sys.getenv("EP_PASSWORD") - +# Check if login credentials exist is_active <- nzchar(username) && nzchar(password) - +# If login credentials exist if( is_active ){ # Log into enviPath epLogin(username, password) @@ -16,3 +16,13 @@ if( is_active ){ force = TRUE ) } +# Redact httptest output +set_redactor(function (x) { + # Remove address prefix + x <- gsub_response(x, "envipath.org/api/legacy/", "") + # Reduce unique identifiers + x <- gsub_response(x, "/(?:[0-9a-z]+-){2,}[0-9a-z]+/", "_") + return(x) +}) +# Add parent directory to httptest paths +.mockPaths("../") diff --git a/tests/testthat/test-get.R b/tests/testthat/test-get.R index 761b7c7..09863b9 100644 --- a/tests/testthat/test-get.R +++ b/tests/testthat/test-get.R @@ -1,5 +1,5 @@ -with_mock_dir("httptest/get", { +with_mock_dir("../httptest/get", { test_that("get", { diff --git a/tests/testthat/test-link.R b/tests/testthat/test-link.R index 022a5ee..c7de4b9 100644 --- a/tests/testthat/test-link.R +++ b/tests/testthat/test-link.R @@ -1,5 +1,5 @@ -with_mock_dir("httptest/link", { +with_mock_dir("../httptest/link", { test_that("link", { diff --git a/tests/testthat/test-list.R b/tests/testthat/test-list.R index a7ca441..e96f8ca 100644 --- a/tests/testthat/test-list.R +++ b/tests/testthat/test-list.R @@ -1,4 +1,4 @@ -with_mock_dir("httptest/list", { +with_mock_dir("../httptest/list", { test_that("list", { diff --git a/tests/testthat/test-login.R b/tests/testthat/test-login.R index 2d087c5..8a279d1 100644 --- a/tests/testthat/test-login.R +++ b/tests/testthat/test-login.R @@ -1,5 +1,5 @@ -with_mock_dir("httptest/login", { +with_mock_dir("../httptest/login", { test_that("login", { diff --git a/tests/testthat/test-model.R b/tests/testthat/test-model.R index 7a0da89..e36585f 100644 --- a/tests/testthat/test-model.R +++ b/tests/testthat/test-model.R @@ -1,5 +1,5 @@ -with_mock_dir("httptest/model", { +with_mock_dir("../httptest/model", { test_that("model", { diff --git a/vignettes/enviPathR.Rmd b/vignettes/enviPathR.Rmd index 6501971..4ad307f 100644 --- a/vignettes/enviPathR.Rmd +++ b/vignettes/enviPathR.Rmd @@ -28,11 +28,14 @@ knitr::opts_chunk$set( comment = "#>" ) +# Retrieve login credentials username <- Sys.getenv("EP_USERNAME") password <- Sys.getenv("EP_PASSWORD") +# Check if login credentials exist is_active <- nzchar(username) && nzchar(password) +# If login credentials exist if( is_active ){ # Clear httptest cache unlink( @@ -43,6 +46,16 @@ if( is_active ){ } library(httptest2) + +# Redact httptest output +set_redactor(function (x) { + # Remove address prefix + x <- gsub_response(x, "envipath.org/api/legacy/", "") + # Reduce unique identifiers + x <- gsub_response(x, "/(?:[0-9a-z]+-){2,}[0-9a-z]+/", "_") + return(x) +}) + start_vignette("httptest") ``` @@ -281,10 +294,6 @@ Pathway prediction is performed with `epModel`, which uses the enviFormer model by default. The output list contains two data frames representing the nodes (compounds) and edges (reactions) of the predicted pathway, respectively. -```{r, include = FALSE} -change_state() -``` - ```{r model-former} # Define smiles of interest smiles <- "ClC(Cl)=C(Cl)Cl" @@ -303,10 +312,6 @@ Different model settings can be specified with the argument `setting`. For example, the PEPPER model can be used which also returns half-lime estimates for the predicted degradation steps. -```{r, include = FALSE} -change_state() -``` - ```{r model-pepper} # Set id for PEPPER model setting set_name <- "Global Setting - ECC and App Domain - PEPPER" diff --git a/vignettes/httptest/1/envipath.org/api/legacy-26b34d-POST.json b/vignettes/httptest/1/NA-26b34d-POST.json similarity index 100% rename from vignettes/httptest/1/envipath.org/api/legacy-26b34d-POST.json rename to vignettes/httptest/1/NA-26b34d-POST.json diff --git a/vignettes/httptest/1/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/1e7066c2-ff45-44f4-9086-e37db18400df/node.json b/vignettes/httptest/1/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/1e7066c2-ff45-44f4-9086-e37db18400df/node.json deleted file mode 100644 index 00b9ddb..0000000 --- a/vignettes/httptest/1/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/1e7066c2-ff45-44f4-9086-e37db18400df/node.json +++ /dev/null @@ -1,22 +0,0 @@ -{ - "node": [ - { - "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/1e7066c2-ff45-44f4-9086-e37db18400df/node/85cfcbd7-1f89-49b9-a3a6-725a54920a01", - "name": "3-Sulfocatechol", - "reviewStatus": "reviewed", - "identifier": "node" - }, - { - "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/1e7066c2-ff45-44f4-9086-e37db18400df/node/9838a66c-c9c1-4155-a5cc-5c4705dd817c", - "name": "2-Aminobenzenesulfonate", - "reviewStatus": "reviewed", - "identifier": "node" - }, - { - "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/1e7066c2-ff45-44f4-9086-e37db18400df/node/739d1209-f196-4038-99df-d92423c94b06", - "name": "2-Hydroxymuconate", - "reviewStatus": "reviewed", - "identifier": "node" - } - ] -} diff --git a/vignettes/httptest/1/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/259b990e-d653-4201-9282-04f2c6b05ca0/node.json b/vignettes/httptest/1/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/259b990e-d653-4201-9282-04f2c6b05ca0/node.json deleted file mode 100644 index 7bc0018..0000000 --- a/vignettes/httptest/1/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/259b990e-d653-4201-9282-04f2c6b05ca0/node.json +++ /dev/null @@ -1,22 +0,0 @@ -{ - "node": [ - { - "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/259b990e-d653-4201-9282-04f2c6b05ca0/node/dd59cd8c-6e19-4dec-b119-47595607776e", - "name": "Hydrogen uranyl phosphate", - "reviewStatus": "reviewed", - "identifier": "node" - }, - { - "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/259b990e-d653-4201-9282-04f2c6b05ca0/node/f06d31fa-d9fe-470d-b1b8-72237d1f96e1", - "name": "Uraninite", - "reviewStatus": "reviewed", - "identifier": "node" - }, - { - "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/259b990e-d653-4201-9282-04f2c6b05ca0/node/b36d17e7-e73f-47f7-8136-b5f357fa7e26", - "name": "Uranyl ion", - "reviewStatus": "reviewed", - "identifier": "node" - } - ] -} diff --git a/vignettes/httptest/1/envipath.org/api/legacy/package.json b/vignettes/httptest/1/package.json similarity index 67% rename from vignettes/httptest/1/envipath.org/api/legacy/package.json rename to vignettes/httptest/1/package.json index 6ba7dfd..8701ebf 100644 --- a/vignettes/httptest/1/envipath.org/api/legacy/package.json +++ b/vignettes/httptest/1/package.json @@ -6,37 +6,37 @@ "links": [ { "Pathways": [ - "https://envipath.org/package/5b594bf6-56a8-4ce5-9a63-5fd4b525756e/pathway", + "https://envipath.org/package_pathway", 1 ] }, { "Rules": [ - "https://envipath.org/package/5b594bf6-56a8-4ce5-9a63-5fd4b525756e/rule", + "https://envipath.org/package_rule", 0 ] }, { "Compounds": [ - "https://envipath.org/package/5b594bf6-56a8-4ce5-9a63-5fd4b525756e/compound", + "https://envipath.org/package_compound", 24 ] }, { "Reactions": [ - "https://envipath.org/package/5b594bf6-56a8-4ce5-9a63-5fd4b525756e/reaction", + "https://envipath.org/package_reaction", 38 ] }, { "Relative Reasoning": [ - "https://envipath.org/package/5b594bf6-56a8-4ce5-9a63-5fd4b525756e/relative-reasoning", + "https://envipath.org/package_relative-reasoning", 0 ] }, { "Scenarios": [ - "https://envipath.org/package/5b594bf6-56a8-4ce5-9a63-5fd4b525756e/scenario", + "https://envipath.org/package_scenario", 0 ] } @@ -66,37 +66,37 @@ "links": [ { "Pathways": [ - "https://envipath.org/package/995230c9-167a-4108-8002-d8fadd242dff/pathway", + "https://envipath.org/package_pathway", 0 ] }, { "Rules": [ - "https://envipath.org/package/995230c9-167a-4108-8002-d8fadd242dff/rule", + "https://envipath.org/package_rule", 0 ] }, { "Compounds": [ - "https://envipath.org/package/995230c9-167a-4108-8002-d8fadd242dff/compound", + "https://envipath.org/package_compound", 0 ] }, { "Reactions": [ - "https://envipath.org/package/995230c9-167a-4108-8002-d8fadd242dff/reaction", + "https://envipath.org/package_reaction", 0 ] }, { "Relative Reasoning": [ - "https://envipath.org/package/995230c9-167a-4108-8002-d8fadd242dff/relative-reasoning", + "https://envipath.org/package_relative-reasoning", 0 ] }, { "Scenarios": [ - "https://envipath.org/package/995230c9-167a-4108-8002-d8fadd242dff/scenario", + "https://envipath.org/package_scenario", 0 ] } @@ -121,42 +121,42 @@ ] }, { - "description": "\"EAWAG-SOIL\" package contains pathway information from soil degradation studies, stored in a biotransformation reaction scheme in the object pathway<\/a>. This information is extracted from pesticide registration dossiers (draft assessment reports, DAR) made publically available through the European Food Safety Authority (EFSA<\/a>). The package also contains information on different experimental conditions that are stored in the object scenario<\/a>. Compounds<\/a> in the pathway are associated with a given scenario<\/a> if they have been observed under the specific experimental conditions. If available, a biotransformation half-life (DT50) value is additionally associated with a given compound in the pathway and a specific scenario. More details concerning enviPath conventions that were used to store specific data from DAR, and their description can be found in our wiki<\/a>.", + "description": "\"EAWAG-SOIL\" package contains pathway information from soil degradation studies, stored in a biotransformation reaction scheme in the object pathway<\/a>. This information is extracted from pesticide registration dossiers (draft assessment reports, DAR) made publically available through the European Food Safety Authority (EFSA<\/a>). The package also contains information on different experimental conditions that are stored in the object scenario<\/a>. Compounds<\/a> in the pathway are associated with a given scenario<\/a> if they have been observed under the specific experimental conditions. If available, a biotransformation half-life (DT50) value is additionally associated with a given compound in the pathway and a specific scenario. More details concerning enviPath conventions that were used to store specific data from DAR, and their description can be found in our wiki<\/a>.", "id": "https://envipath.org/package/5882df9c-dae1-4d80-a40e-db4724271456", "links": [ { "Pathways": [ - "https://envipath.org/package/5882df9c-dae1-4d80-a40e-db4724271456/pathway", + "https://envipath.org/package_pathway", 317 ] }, { "Rules": [ - "https://envipath.org/package/5882df9c-dae1-4d80-a40e-db4724271456/rule", + "https://envipath.org/package_rule", 0 ] }, { "Compounds": [ - "https://envipath.org/package/5882df9c-dae1-4d80-a40e-db4724271456/compound", + "https://envipath.org/package_compound", 2608 ] }, { "Reactions": [ - "https://envipath.org/package/5882df9c-dae1-4d80-a40e-db4724271456/reaction", + "https://envipath.org/package_reaction", 2445 ] }, { "Relative Reasoning": [ - "https://envipath.org/package/5882df9c-dae1-4d80-a40e-db4724271456/relative-reasoning", + "https://envipath.org/package_relative-reasoning", 0 ] }, { "Scenarios": [ - "https://envipath.org/package/5882df9c-dae1-4d80-a40e-db4724271456/scenario", + "https://envipath.org/package_scenario", 4881 ] } @@ -186,37 +186,37 @@ "links": [ { "Pathways": [ - "https://envipath.org/package/aee2524b-79f3-4640-a519-aac543ac05e3/pathway", + "https://envipath.org/package_pathway", 4 ] }, { "Rules": [ - "https://envipath.org/package/aee2524b-79f3-4640-a519-aac543ac05e3/rule", + "https://envipath.org/package_rule", 0 ] }, { "Compounds": [ - "https://envipath.org/package/aee2524b-79f3-4640-a519-aac543ac05e3/compound", + "https://envipath.org/package_compound", 33 ] }, { "Reactions": [ - "https://envipath.org/package/aee2524b-79f3-4640-a519-aac543ac05e3/reaction", + "https://envipath.org/package_reaction", 66 ] }, { "Relative Reasoning": [ - "https://envipath.org/package/aee2524b-79f3-4640-a519-aac543ac05e3/relative-reasoning", + "https://envipath.org/package_relative-reasoning", 0 ] }, { "Scenarios": [ - "https://envipath.org/package/aee2524b-79f3-4640-a519-aac543ac05e3/scenario", + "https://envipath.org/package_scenario", 0 ] } @@ -246,37 +246,37 @@ "links": [ { "Pathways": [ - "https://envipath.org/package/c3c6699a-8c78-4987-af4d-4a041ffc448d/pathway", + "https://envipath.org/package_pathway", 2 ] }, { "Rules": [ - "https://envipath.org/package/c3c6699a-8c78-4987-af4d-4a041ffc448d/rule", + "https://envipath.org/package_rule", 0 ] }, { "Compounds": [ - "https://envipath.org/package/c3c6699a-8c78-4987-af4d-4a041ffc448d/compound", + "https://envipath.org/package_compound", 21 ] }, { "Reactions": [ - "https://envipath.org/package/c3c6699a-8c78-4987-af4d-4a041ffc448d/reaction", + "https://envipath.org/package_reaction", 23 ] }, { "Relative Reasoning": [ - "https://envipath.org/package/c3c6699a-8c78-4987-af4d-4a041ffc448d/relative-reasoning", + "https://envipath.org/package_relative-reasoning", 0 ] }, { "Scenarios": [ - "https://envipath.org/package/c3c6699a-8c78-4987-af4d-4a041ffc448d/scenario", + "https://envipath.org/package_scenario", 0 ] } @@ -301,42 +301,42 @@ ] }, { - "description": "The EAWAG-SLUDGE<\/a> package contains pathways and kinetic information about microbially mediated transformation processes in biological wastewater treatment. The information was extracted from scientific publications in different journals. The biotransformation reaction schemes are stored as pathways<\/a>. The experimental conditions and additional information (e. g. sludge source) are collected in the scenario<\/a> objects. Any observed transformation products (compounds<\/a>) are linked to their corresponding experimental metadata (scenario<\/a>). Kinetic parameters (rate constants and/or half-lives) including corresponding scenarios are indicated for compounds for which such data is available. More details regarding enviPath conventions can be found in our wiki<\/a>.", + "description": "The EAWAG-SLUDGE<\/a> package contains pathways and kinetic information about microbially mediated transformation processes in biological wastewater treatment. The information was extracted from scientific publications in different journals. The biotransformation reaction schemes are stored as pathways<\/a>. The experimental conditions and additional information (e. g. sludge source) are collected in the scenario<\/a> objects. Any observed transformation products (compounds<\/a>) are linked to their corresponding experimental metadata (scenario<\/a>). Kinetic parameters (rate constants and/or half-lives) including corresponding scenarios are indicated for compounds for which such data is available. 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", + "https://envipath.org/package_pathway", 183 ] }, { "Rules": [ - "https://envipath.org/package/521c547a-fd2a-491c-ad5b-7eaa1577fb65/rule", + "https://envipath.org/package_rule", 0 ] }, { "Compounds": [ - "https://envipath.org/package/521c547a-fd2a-491c-ad5b-7eaa1577fb65/compound", + "https://envipath.org/package_compound", 1067 ] }, { "Reactions": [ - "https://envipath.org/package/521c547a-fd2a-491c-ad5b-7eaa1577fb65/reaction", + "https://envipath.org/package_reaction", 494 ] }, { "Relative Reasoning": [ - "https://envipath.org/package/521c547a-fd2a-491c-ad5b-7eaa1577fb65/relative-reasoning", + "https://envipath.org/package_relative-reasoning", 0 ] }, { "Scenarios": [ - "https://envipath.org/package/521c547a-fd2a-491c-ad5b-7eaa1577fb65/scenario", + "https://envipath.org/package_scenario", 85 ] } @@ -366,37 +366,37 @@ "links": [ { "Pathways": [ - "https://envipath.org/package/134886bb-b52e-4ad6-91d3-a02cecde6d95/pathway", + "https://envipath.org/package_pathway", 0 ] }, { "Rules": [ - "https://envipath.org/package/134886bb-b52e-4ad6-91d3-a02cecde6d95/rule", + "https://envipath.org/package_rule", 0 ] }, { "Compounds": [ - "https://envipath.org/package/134886bb-b52e-4ad6-91d3-a02cecde6d95/compound", + "https://envipath.org/package_compound", 0 ] }, { "Reactions": [ - "https://envipath.org/package/134886bb-b52e-4ad6-91d3-a02cecde6d95/reaction", + "https://envipath.org/package_reaction", 0 ] }, { "Relative Reasoning": [ - "https://envipath.org/package/134886bb-b52e-4ad6-91d3-a02cecde6d95/relative-reasoning", + "https://envipath.org/package_relative-reasoning", 3 ] }, { "Scenarios": [ - "https://envipath.org/package/134886bb-b52e-4ad6-91d3-a02cecde6d95/scenario", + "https://envipath.org/package_scenario", 0 ] } @@ -426,37 +426,37 @@ "links": [ { "Pathways": [ - "https://envipath.org/package/7245f711-51d0-4b1e-b49d-99a9d9744c96/pathway", + "https://envipath.org/package_pathway", 0 ] }, { "Rules": [ - "https://envipath.org/package/7245f711-51d0-4b1e-b49d-99a9d9744c96/rule", + "https://envipath.org/package_rule", 0 ] }, { "Compounds": [ - "https://envipath.org/package/7245f711-51d0-4b1e-b49d-99a9d9744c96/compound", + "https://envipath.org/package_compound", 0 ] }, { "Reactions": [ - "https://envipath.org/package/7245f711-51d0-4b1e-b49d-99a9d9744c96/reaction", + "https://envipath.org/package_reaction", 0 ] }, { "Relative Reasoning": [ - "https://envipath.org/package/7245f711-51d0-4b1e-b49d-99a9d9744c96/relative-reasoning", + "https://envipath.org/package_relative-reasoning", 0 ] }, { "Scenarios": [ - "https://envipath.org/package/7245f711-51d0-4b1e-b49d-99a9d9744c96/scenario", + "https://envipath.org/package_scenario", 0 ] } @@ -486,37 +486,37 @@ "links": [ { "Pathways": [ - "https://envipath.org/package/7a3bddd7-c1a2-4699-a885-8b9044fd4fe2/pathway", + "https://envipath.org/package_pathway", 0 ] }, { "Rules": [ - "https://envipath.org/package/7a3bddd7-c1a2-4699-a885-8b9044fd4fe2/rule", + "https://envipath.org/package_rule", 0 ] }, { "Compounds": [ - "https://envipath.org/package/7a3bddd7-c1a2-4699-a885-8b9044fd4fe2/compound", + "https://envipath.org/package_compound", 0 ] }, { "Reactions": [ - "https://envipath.org/package/7a3bddd7-c1a2-4699-a885-8b9044fd4fe2/reaction", + "https://envipath.org/package_reaction", 0 ] }, { "Relative Reasoning": [ - "https://envipath.org/package/7a3bddd7-c1a2-4699-a885-8b9044fd4fe2/relative-reasoning", + "https://envipath.org/package_relative-reasoning", 0 ] }, { "Scenarios": [ - "https://envipath.org/package/7a3bddd7-c1a2-4699-a885-8b9044fd4fe2/scenario", + "https://envipath.org/package_scenario", 0 ] } @@ -546,37 +546,37 @@ "links": [ { "Pathways": [ - "https://envipath.org/package/d1898032-350b-438a-a702-63906c7ed76a/pathway", + "https://envipath.org/package_pathway", 0 ] }, { "Rules": [ - "https://envipath.org/package/d1898032-350b-438a-a702-63906c7ed76a/rule", + "https://envipath.org/package_rule", 0 ] }, { "Compounds": [ - "https://envipath.org/package/d1898032-350b-438a-a702-63906c7ed76a/compound", + "https://envipath.org/package_compound", 0 ] }, { "Reactions": [ - "https://envipath.org/package/d1898032-350b-438a-a702-63906c7ed76a/reaction", + "https://envipath.org/package_reaction", 0 ] }, { "Relative Reasoning": [ - "https://envipath.org/package/d1898032-350b-438a-a702-63906c7ed76a/relative-reasoning", + "https://envipath.org/package_relative-reasoning", 0 ] }, { "Scenarios": [ - "https://envipath.org/package/d1898032-350b-438a-a702-63906c7ed76a/scenario", + "https://envipath.org/package_scenario", 0 ] } @@ -601,42 +601,42 @@ ] }, { - "description": "The \"EAWAG-SEDIMENT\" package contains pathways and kinetic data from biodegradation studies performed in water-sediment systems. This information is extracted from pesticide registration dossiers (draft assessment reports, DAR) made publically available through the European Food Safety Authority (EFSA<\/a>). The package also contains information on different experimental conditions that are stored in the object scenario<\/a>. Compounds<\/a> in the pathway are associated with a given scenario<\/a> if they have been observed under the specific experimental conditions. If available, a total system biotransformation half-life (DT50) value is associated with a given compound in the pathway and a specific scenario, along with dissipation half-lives from the water and the sediment phases.", + "description": "The \"EAWAG-SEDIMENT\" package contains pathways and kinetic data from biodegradation studies performed in water-sediment systems. This information is extracted from pesticide registration dossiers (draft assessment reports, DAR) made publically available through the European Food Safety Authority (EFSA<\/a>). The package also contains information on different experimental conditions that are stored in the object scenario<\/a>. Compounds<\/a> in the pathway are associated with a given scenario<\/a> if they have been observed under the specific experimental conditions. If available, a total system biotransformation half-life (DT50) value is associated with a given compound in the pathway and a specific scenario, along with dissipation half-lives from the water and the sediment phases.", "id": "https://envipath.org/package/f05e38d8-e9b4-4c3e-b0d8-9ab29966eccf", "links": [ { "Pathways": [ - "https://envipath.org/package/f05e38d8-e9b4-4c3e-b0d8-9ab29966eccf/pathway", + "https://envipath.org/package_pathway", 179 ] }, { "Rules": [ - "https://envipath.org/package/f05e38d8-e9b4-4c3e-b0d8-9ab29966eccf/rule", + "https://envipath.org/package_rule", 0 ] }, { "Compounds": [ - "https://envipath.org/package/f05e38d8-e9b4-4c3e-b0d8-9ab29966eccf/compound", + "https://envipath.org/package_compound", 810 ] }, { "Reactions": [ - "https://envipath.org/package/f05e38d8-e9b4-4c3e-b0d8-9ab29966eccf/reaction", + "https://envipath.org/package_reaction", 961 ] }, { "Relative Reasoning": [ - "https://envipath.org/package/f05e38d8-e9b4-4c3e-b0d8-9ab29966eccf/relative-reasoning", + "https://envipath.org/package_relative-reasoning", 0 ] }, { "Scenarios": [ - "https://envipath.org/package/f05e38d8-e9b4-4c3e-b0d8-9ab29966eccf/scenario", + "https://envipath.org/package_scenario", 1622 ] } @@ -666,37 +666,37 @@ "links": [ { "Pathways": [ - "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway", + "https://envipath.org/package_pathway", 219 ] }, { "Rules": [ - "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/rule", + "https://envipath.org/package_rule", 499 ] }, { "Compounds": [ - "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound", + "https://envipath.org/package_compound", 1399 ] }, { "Reactions": [ - "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction", + "https://envipath.org/package_reaction", 1480 ] }, { "Relative Reasoning": [ - "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/relative-reasoning", + "https://envipath.org/package_relative-reasoning", 0 ] }, { "Scenarios": [ - "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/scenario", + "https://envipath.org/package_scenario", 1915 ] } @@ -726,37 +726,37 @@ "links": [ { "Pathways": [ - 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Hundreds of thousands of kilograms of 2-aminobenzenesulfonic acid are produced for use in the U.S. annually. It is used in organic synthesis and in the manufacture of various dyes and medicines. The initial step in the degradation of 2-aminobenzenesulfonate involves the transport of the compound across the outer membrane of the cell. Alcaligenes sp. O-1 has a selective permeability barrier, allowing three aromatic sulfonates (benzene sulfonate, toluene-4-sulfonate, and 2-aminobenzenesulfonate) to pass through, as described by [http://www.ncbi.nlm.nih.gov/pubmed/8075807|Junker et al. (1994)]. Cell extracts of this species were shown to be capable of degrading at least seven substrates. Deamination of the aromatic ring in strain O-1 has been shown by [http://www.ncbi.nlm.nih.gov/pubmed/8002948|Junker et al. (1994)] to precede desulfurization. Desulfurization of the compound has been shown to precede deamination when degraded by other organisms.", - "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/1e7066c2-ff45-44f4-9086-e37db18400df", + "id": "https://envipath.org/package_pathway/1e7066c2-ff45-44f4-9086-e37db18400df", "isIncremental": false, "isPredicted": false, "lastModified": 1768822786, @@ -13,7 +13,7 @@ "ecNumbers": [ ], - "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/1e7066c2-ff45-44f4-9086-e37db18400df/edge/9244af83-bc43-47a2-b515-c676544f062d", + "id": "https://envipath.org/package_pathway_edge/9244af83-bc43-47a2-b515-c676544f062d", "idreaction": null, "multstep": null, "name": "Eawag BBD reaction r0218", @@ -21,7 +21,7 @@ "rule": null, "scenarios": [ { - "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/scenario/60a06cd9-49d0-497d-a97c-06f44908580b", + "id": "https://envipath.org/package_scenario/60a06cd9-49d0-497d-a97c-06f44908580b", "name": "EAWAG-BBD reaction (r0218)", "reviewStatus": "reviewed", "identifier": "scenario" @@ -34,7 +34,7 @@ "ecNumbers": [ ], - 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"id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/1e7066c2-ff45-44f4-9086-e37db18400df/node/85cfcbd7-1f89-49b9-a3a6-725a54920a01", - "idcomp": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/d753429b-b3af-4944-97d7-8ddd833e92aa/structure/8a806897-4fa6-4c32-a14f-28f81a0f8091", - "idreact": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/d753429b-b3af-4944-97d7-8ddd833e92aa/structure/8a806897-4fa6-4c32-a14f-28f81a0f8091", - "image": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/1e7066c2-ff45-44f4-9086-e37db18400df/node/85cfcbd7-1f89-49b9-a3a6-725a54920a01?image=svg", + "id": "https://envipath.org/package_pathway_node/85cfcbd7-1f89-49b9-a3a6-725a54920a01", + "idcomp": "https://envipath.org/package_compound_structure/8a806897-4fa6-4c32-a14f-28f81a0f8091", + "idreact": "https://envipath.org/package_compound_structure/8a806897-4fa6-4c32-a14f-28f81a0f8091", + "image": "https://envipath.org/package_pathway_node/85cfcbd7-1f89-49b9-a3a6-725a54920a01?image=svg", "imageSize": 400, "name": "3-Sulfocatechol", "proposed": [ diff --git a/vignettes/httptest/1/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/259b990e-d653-4201-9282-04f2c6b05ca0.json b/vignettes/httptest/1/package_pathway/259b990e-d653-4201-9282-04f2c6b05ca0.json similarity index 57% rename from vignettes/httptest/1/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/259b990e-d653-4201-9282-04f2c6b05ca0.json rename to vignettes/httptest/1/package_pathway/259b990e-d653-4201-9282-04f2c6b05ca0.json index 2eb0a76..c645cd0 100644 --- a/vignettes/httptest/1/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/259b990e-d653-4201-9282-04f2c6b05ca0.json +++ b/vignettes/httptest/1/package_pathway/259b990e-d653-4201-9282-04f2c6b05ca0.json @@ -4,7 +4,7 @@ ], "completed": "true", "description": "Uranium (U) is the most common radionuclide contaminant at US Department of Energy facilities (Riley et al., DOE/ER-0547T, 1992). More information on this element can be found at the Web Elements U page. The uranyl ion [U(VI)O2]2+ is a common, soluble form of this element in the environment. Microbes can immobilize uranyl ion in several ways, three of which are shown here. The mineral uraninite, U (IV)O2, is highly insoluble. Microbes can reduce uranyl ion to hydrated uraninite. The reduction can be carried out by a cytochrome-c3 hydrogenase from Desulfovibrio vulgaris ([http://www.ncbi.nlm.nih.gov/pubmed/8285665|Lovley et al., 1993]) and other organisms, as shown in the left-most pathway branch. Reaction A, in the middle branch, can be carried out by Deinococcus radiodurans R1 in the laboratory with concomitant oxidation of the humic acid analog anthranhydroquinone-2,6-disulfonate (AQDSH2) to its quinone form ([http://www.ncbi.nlm.nih.gov/pubmed/10788374|Fredrickson et al., 2000]). Humic acid, a brown-colored mixture of polymers, found in lignite, peat, and soils, is assumed to be the environmental cofactor. Uranyl ion can be precipitated as cell-bound hydrogen uranyl phosphate without change in oxidation state of the uranium, as shown in the right-most pathway branch. This reaction is facilitated by acid phosphatase N from Citrobacter sp. N14 ([http://www.ncbi.nlm.nih.gov/pubmed/9763695|Basnakova et al., 1998]).", - "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/259b990e-d653-4201-9282-04f2c6b05ca0", + "id": "https://envipath.org/package_pathway/259b990e-d653-4201-9282-04f2c6b05ca0", "isIncremental": false, "isPredicted": false, "lastModified": 1768822786, @@ -13,7 +13,7 @@ "ecNumbers": [ ], - "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/259b990e-d653-4201-9282-04f2c6b05ca0/edge/30122d3f-2729-490b-9def-7067cf89adf7", + "id": "https://envipath.org/package_pathway_edge/30122d3f-2729-490b-9def-7067cf89adf7", "idreaction": null, "multstep": null, "name": "Eawag BBD reaction r0793", @@ -21,7 +21,7 @@ "rule": null, "scenarios": [ { - "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/scenario/d0e9a0cc-2248-4056-943c-865bd3dd5e25", + "id": "https://envipath.org/package_scenario/d0e9a0cc-2248-4056-943c-865bd3dd5e25", "name": "EAWAG-BBD reaction (r0793)", "reviewStatus": "reviewed", "identifier": "scenario" @@ -34,7 +34,7 @@ "ecNumbers": [ ], - "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/259b990e-d653-4201-9282-04f2c6b05ca0/edge/e7957b99-ad83-4c17-97e6-e4fa8a3bcfbc", + "id": "https://envipath.org/package_pathway_edge/e7957b99-ad83-4c17-97e6-e4fa8a3bcfbc", "idreaction": null, "multstep": null, "name": "Eawag BBD reaction r0761, Eawag BBD reaction r0794", @@ -42,7 +42,7 @@ "rule": null, "scenarios": [ { - "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/scenario/ff9fb2e5-82aa-4a04-bd38-39b5c212e8a0", + "id": "https://envipath.org/package_scenario/ff9fb2e5-82aa-4a04-bd38-39b5c212e8a0", "name": "EAWAG-BBD reaction (r0761)", "reviewStatus": "reviewed", "identifier": "scenario" @@ -55,7 +55,7 @@ "ecNumbers": [ ], - "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/259b990e-d653-4201-9282-04f2c6b05ca0/edge/355b409c-499e-44c2-9947-69163729615c", + "id": "https://envipath.org/package_pathway_edge/355b409c-499e-44c2-9947-69163729615c", "idreaction": null, "multstep": null, "name": "Eawag BBD reaction r0761, Eawag BBD reaction r0794", @@ -63,7 +63,7 @@ "rule": null, "scenarios": [ { - 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"id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/259b990e-d653-4201-9282-04f2c6b05ca0/node/b36d17e7-e73f-47f7-8136-b5f357fa7e26", - "idcomp": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/e9511feb-acb6-4a51-94c8-d023c8143c3b/structure/db2b3598-11c1-4b0e-8663-9bc4ebbd5215", - "idreact": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/e9511feb-acb6-4a51-94c8-d023c8143c3b/structure/db2b3598-11c1-4b0e-8663-9bc4ebbd5215", - "image": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/259b990e-d653-4201-9282-04f2c6b05ca0/node/b36d17e7-e73f-47f7-8136-b5f357fa7e26?image=svg", + "id": "https://envipath.org/package_pathway_node/b36d17e7-e73f-47f7-8136-b5f357fa7e26", + "idcomp": "https://envipath.org/package_compound_structure/db2b3598-11c1-4b0e-8663-9bc4ebbd5215", + "idreact": "https://envipath.org/package_compound_structure/db2b3598-11c1-4b0e-8663-9bc4ebbd5215", + "image": "https://envipath.org/package_pathway_node/b36d17e7-e73f-47f7-8136-b5f357fa7e26?image=svg", "imageSize": 400, "name": "Uranyl ion", "proposed": [ diff --git a/vignettes/httptest/1/package_pathway_node.json b/vignettes/httptest/1/package_pathway_node.json new file mode 100644 index 0000000..daee866 --- /dev/null +++ b/vignettes/httptest/1/package_pathway_node.json @@ -0,0 +1,22 @@ +{ + "node": [ + { + "id": "https://envipath.org/package_pathway_node/85cfcbd7-1f89-49b9-a3a6-725a54920a01", + "name": "3-Sulfocatechol", + "reviewStatus": "reviewed", + "identifier": "node" + }, + { + "id": "https://envipath.org/package_pathway_node/9838a66c-c9c1-4155-a5cc-5c4705dd817c", + "name": "2-Aminobenzenesulfonate", + "reviewStatus": "reviewed", + "identifier": "node" + }, + { + "id": "https://envipath.org/package_pathway_node/739d1209-f196-4038-99df-d92423c94b06", + "name": "2-Hydroxymuconate", + "reviewStatus": "reviewed", + "identifier": "node" + } + ] +} diff --git a/vignettes/httptest/1/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/2b6bbcc5-77f4-4bed-92a9-731cdc978f6a.json b/vignettes/httptest/1/package_reaction/2b6bbcc5-77f4-4bed-92a9-731cdc978f6a.json similarity index 57% rename from vignettes/httptest/1/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/2b6bbcc5-77f4-4bed-92a9-731cdc978f6a.json rename to vignettes/httptest/1/package_reaction/2b6bbcc5-77f4-4bed-92a9-731cdc978f6a.json index eb997bd..64b08a4 100644 --- a/vignettes/httptest/1/envipath.org/api/legacy/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/2b6bbcc5-77f4-4bed-92a9-731cdc978f6a.json +++ b/vignettes/httptest/1/package_reaction/2b6bbcc5-77f4-4bed-92a9-731cdc978f6a.json @@ -9,11 +9,11 @@ "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", + "id": "https://envipath.org/package_compound_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", + "id": "https://envipath.org/package_reaction/2b6bbcc5-77f4-4bed-92a9-731cdc978f6a", "identifier": "reaction", "medlineRefs": [ @@ -22,7 +22,7 @@ "name": "Eawag BBD reaction r0014", "pathways": [ { - "id": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/c3d1b8d5-9ffb-49b8-a1bf-bf3d7dfd1ac3", + "id": "https://envipath.org/package_pathway/c3d1b8d5-9ffb-49b8-a1bf-bf3d7dfd1ac3", "name": "Tetrahydrofuran", "reviewStatus": "reviewed", "identifier": "pathway" @@ -31,7 +31,7 @@ "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", + "id": "https://envipath.org/package_compound_structure/befe8eeb-e8f8-4b4a-90b1-d0584a75f8cb", "smiles": "C(CC(=O)[O-])CO" } ], diff --git a/vignettes/httptest/1/envipath.org/api/legacy/setting.json b/vignettes/httptest/1/setting.json similarity index 100% rename from vignettes/httptest/1/envipath.org/api/legacy/setting.json rename to vignettes/httptest/1/setting.json diff --git a/vignettes/httptest/2/envipath.org/api/legacy/util-078746-POST.json b/vignettes/httptest/1/util-078746-POST.json similarity index 100% rename from vignettes/httptest/2/envipath.org/api/legacy/util-078746-POST.json rename to vignettes/httptest/1/util-078746-POST.json diff --git a/vignettes/httptest/3/envipath.org/api/legacy/util-672736-POST.json b/vignettes/httptest/1/util-672736-POST.json similarity index 75% rename from vignettes/httptest/3/envipath.org/api/legacy/util-672736-POST.json rename to vignettes/httptest/1/util-672736-POST.json index 92c692b..0f4b528 100644 --- a/vignettes/httptest/3/envipath.org/api/legacy/util-672736-POST.json +++ b/vignettes/httptest/1/util-672736-POST.json @@ -58,7 +58,7 @@ 4 ], "rule": { - "url": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/af13a678-1d06-402c-ae13-cb00f8830af4", + "url": "https://envipath.org/package_parallel-rule/af13a678-1d06-402c-ae13-cb00f8830af4", "uuid": "af13a678-1d06-402c-ae13-cb00f8830af4", "name": "bt0029" }, @@ -66,43 +66,17 @@ "multiGenProbability": 0.03981369974318422 }, { - "from": 1, - "to": [ - 2 - ], - "rule": { - "url": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/af13a678-1d06-402c-ae13-cb00f8830af4", - "uuid": "af13a678-1d06-402c-ae13-cb00f8830af4", - "name": "bt0029" - }, - "probability": 0.3414634146341463, - "multiGenProbability": 0.11659726353361093 - }, - { - "from": 3, + "from": 4, "to": [ - 4 + 6 ], "rule": { - "url": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/af13a678-1d06-402c-ae13-cb00f8830af4", + "url": "https://envipath.org/package_parallel-rule/af13a678-1d06-402c-ae13-cb00f8830af4", "uuid": "af13a678-1d06-402c-ae13-cb00f8830af4", "name": "bt0029" }, "probability": 0.3414634146341463, - "multiGenProbability": 0.03981369974318422 - }, - { - "from": 2, - "to": [ - 5 - ], - "rule": { - "url": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/b7d77873-65b8-4164-9349-b8e7da31dcd6", - "uuid": "b7d77873-65b8-4164-9349-b8e7da31dcd6", - "name": "bt0049" - }, - "probability": 0.25, - "multiGenProbability": 0.02914931588340273 + "multiGenProbability": 0.013594921863526316 }, { "from": 4, @@ -110,7 +84,7 @@ 7 ], "rule": { - "url": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/b7d77873-65b8-4164-9349-b8e7da31dcd6", + "url": "https://envipath.org/package_parallel-rule/b7d77873-65b8-4164-9349-b8e7da31dcd6", "uuid": "b7d77873-65b8-4164-9349-b8e7da31dcd6", "name": "bt0049" }, @@ -123,7 +97,7 @@ 8 ], "rule": { - "url": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/f628ec30-7088-4c16-a37b-bb4c313236a9", + "url": "https://envipath.org/package_parallel-rule/f628ec30-7088-4c16-a37b-bb4c313236a9", "uuid": "f628ec30-7088-4c16-a37b-bb4c313236a9", "name": "bt0050" }, @@ -136,33 +110,59 @@ 1 ], "rule": { - "url": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/af13a678-1d06-402c-ae13-cb00f8830af4", + "url": "https://envipath.org/package_parallel-rule/af13a678-1d06-402c-ae13-cb00f8830af4", "uuid": "af13a678-1d06-402c-ae13-cb00f8830af4", "name": "bt0029" }, "probability": 0.3414634146341463, "multiGenProbability": 0.3414634146341463 }, + { + "from": 3, + "to": [ + 4 + ], + "rule": { + "url": "https://envipath.org/package_parallel-rule/af13a678-1d06-402c-ae13-cb00f8830af4", + "uuid": "af13a678-1d06-402c-ae13-cb00f8830af4", + "name": "bt0029" + }, + "probability": 0.3414634146341463, + "multiGenProbability": 0.03981369974318422 + }, { "from": 1, "to": [ - 3 + 2 ], "rule": { - "url": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/af13a678-1d06-402c-ae13-cb00f8830af4", + "url": "https://envipath.org/package_parallel-rule/af13a678-1d06-402c-ae13-cb00f8830af4", "uuid": "af13a678-1d06-402c-ae13-cb00f8830af4", "name": "bt0029" }, "probability": 0.3414634146341463, "multiGenProbability": 0.11659726353361093 }, + { + "from": 2, + "to": [ + 5 + ], + "rule": { + "url": "https://envipath.org/package_parallel-rule/b7d77873-65b8-4164-9349-b8e7da31dcd6", + "uuid": "b7d77873-65b8-4164-9349-b8e7da31dcd6", + "name": "bt0049" + }, + "probability": 0.25, + "multiGenProbability": 0.02914931588340273 + }, { "from": 6, "to": [ 9 ], "rule": { - "url": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/b7d77873-65b8-4164-9349-b8e7da31dcd6", + "url": "https://envipath.org/package_parallel-rule/b7d77873-65b8-4164-9349-b8e7da31dcd6", "uuid": "b7d77873-65b8-4164-9349-b8e7da31dcd6", "name": "bt0049" }, @@ -170,17 +170,17 @@ "multiGenProbability": 0.003398730465881579 }, { - "from": 4, + "from": 1, "to": [ - 6 + 3 ], "rule": { - "url": "https://envipath.org/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/af13a678-1d06-402c-ae13-cb00f8830af4", + "url": "https://envipath.org/package_parallel-rule/af13a678-1d06-402c-ae13-cb00f8830af4", "uuid": "af13a678-1d06-402c-ae13-cb00f8830af4", "name": "bt0029" }, "probability": 0.3414634146341463, - "multiGenProbability": 0.013594921863526316 + "multiGenProbability": 0.11659726353361093 } ] } From ea8992bcb71e793ab552533358dd36154ee06f31 Mon Sep 17 00:00:00 2001 From: RiboRings Date: Thu, 1 Oct 2026 13:25:26 +0800 Subject: [PATCH 2/3] Import gsub_response --- .gitignore | 1 + tests/testthat/setup.R | 4 ++-- vignettes/enviPathR.Rmd | 4 ++-- 3 files changed, 5 insertions(+), 4 deletions(-) diff --git a/.gitignore b/.gitignore index 9c63895..e996963 100644 --- a/.gitignore +++ b/.gitignore @@ -5,3 +5,4 @@ inst/doc vignettes/*.html vignettes/*.R docs/ +CRAN-SUBMISSION diff --git a/tests/testthat/setup.R b/tests/testthat/setup.R index 80af6dd..3d32aa6 100644 --- a/tests/testthat/setup.R +++ b/tests/testthat/setup.R @@ -19,9 +19,9 @@ if( is_active ){ # Redact httptest output set_redactor(function (x) { # Remove address prefix - x <- gsub_response(x, "envipath.org/api/legacy/", "") + x <- httptest2::gsub_response(x, "envipath.org/api/legacy/", "") # Reduce unique identifiers - x <- gsub_response(x, "/(?:[0-9a-z]+-){2,}[0-9a-z]+/", "_") + x <- httptest2::gsub_response(x, "/(?:[0-9a-z]+-){2,}[0-9a-z]+/", "_") return(x) }) # Add parent directory to httptest paths diff --git a/vignettes/enviPathR.Rmd b/vignettes/enviPathR.Rmd index 4ad307f..26929d0 100644 --- a/vignettes/enviPathR.Rmd +++ b/vignettes/enviPathR.Rmd @@ -50,9 +50,9 @@ library(httptest2) # Redact httptest output set_redactor(function (x) { # Remove address prefix - x <- gsub_response(x, "envipath.org/api/legacy/", "") + x <- httptest2::gsub_response(x, "envipath.org/api/legacy/", "") # Reduce unique identifiers - x <- gsub_response(x, "/(?:[0-9a-z]+-){2,}[0-9a-z]+/", "_") + x <- httptest2::gsub_response(x, "/(?:[0-9a-z]+-){2,}[0-9a-z]+/", "_") return(x) }) From c237eeeb51d42adef083065357ccdf47abe52993 Mon Sep 17 00:00:00 2001 From: Giulio Benedetti Date: Thu, 1 Oct 2026 13:27:53 +0800 Subject: [PATCH 3/3] Delete CRAN-SUBMISSION --- CRAN-SUBMISSION | 3 --- 1 file changed, 3 deletions(-) delete mode 100644 CRAN-SUBMISSION diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION deleted file mode 100644 index f3428b7..0000000 --- a/CRAN-SUBMISSION +++ /dev/null @@ -1,3 +0,0 @@ -Version: 1.0.0 -Date: 2026-09-29 12:46:34 UTC -SHA: a50a5a817c2e8abba916110bc0b4292c91db1d4d