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\ndiff --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/.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/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
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