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If so, please provide link.\r\n#119 \r\n\r\nChecklist for PR Reviewer\r\n- [ ] Make sure all updates from master branch are pulled to branch issuing pull request\r\n- [ ] Confirm package dependencies are installed by running `renv::install()`\r\n- [ ] For bug corrections, check that unit test was added\r\n- [ ] `usethis::use_spell_check()` runs with no spelling errors in documentation\r\n- [ ] R CMD Check runs without errors, warnings, and notes\r\n- [ ] Document changes from this pull request in `NEWS.md` file\r\n- [ ] Run `pkgdown::build_site()`. Check the R console for errors, and review the rendered website. If there are errors returned, try running `pkgdown::build_site(new_process = FALSE)` for better error messaging.\r\n- [ ] Code coverage is suitable for any new functions/features. Review coverage with `covr::report()`. Before you run, begin in a fresh R session without any packages loaded and set `Sys.setenv(NOT_CRAN=\"true\")`.\r\n- [ ] Increment the version number using `usethis::use_version(which = \"dev\")`\r\n- [ ] Approve and merge pull request\r\n","reactions":{"url":"https://api.github.com/repos/GENIE-BPC/genieBPC/issues/122/reactions","total_count":0,"+1":0,"-1":0,"laugh":0,"hooray":0,"confused":0,"heart":0,"rocket":0,"eyes":0},"timeline_url":"https://api.github.com/repos/GENIE-BPC/genieBPC/issues/122/timeline","performed_via_github_app":null,"state_reason":null},"comment":{"url":"https://api.github.com/repos/GENIE-BPC/genieBPC/issues/comments/2020955691","html_url":"https://github.com/GENIE-BPC/genieBPC/pull/122#issuecomment-2020955691","issue_url":"https://api.github.com/repos/GENIE-BPC/genieBPC/issues/122","id":2020955691,"node_id":"IC_kwDOEsDnY854dVYr","user":{"login":"karissawhiting","id":10888683,"node_id":"MDQ6VXNlcjEwODg4Njgz","avatar_url":"https://avatars.githubusercontent.com/u/10888683?v=4","gravatar_id":"","url":"https://api.github.com/users/karissawhiting","html_url":"https://github.com/karissawhiting","followers_url":"https://api.github.com/users/karissawhiting/followers","following_url":"https://api.github.com/users/karissawhiting/following{/other_user}","gists_url":"https://api.github.com/users/karissawhiting/gists{/gist_id}","starred_url":"https://api.github.com/users/karissawhiting/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/karissawhiting/subscriptions","organizations_url":"https://api.github.com/users/karissawhiting/orgs","repos_url":"https://api.github.com/users/karissawhiting/repos","events_url":"https://api.github.com/users/karissawhiting/events{/privacy}","received_events_url":"https://api.github.com/users/karissawhiting/received_events","type":"User","site_admin":false},"created_at":"2024-03-26T16:43:21Z","updated_at":"2024-03-26T16:43:21Z","author_association":"COLLABORATOR","body":"Tests accessing data using username and password are not working, and I commented one out. This needs to be 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#' \\itemize{\n #' \\item \\href{https://www.synapse.org/#!Synapse:syn23002641}{NSCLC v1.1-Consortium Analytic Data Guide}\n #' \\item \\href{https://www.synapse.org/#!Synapse:syn26008058}{NSCLC v2.1-Consortium Analytic Data Guide}\n+#' \\item \\href{https://www.synapse.org/#!Synapse:syn53463493}{NSCLC v2.2-Consortium Analytic Data Guide}","path":"R/pull_data_synapse.R","commit_id":"1f6d94e4981029971d2a404ad1b0757a9eacabde","original_commit_id":"9de8df78aa98632792847d877ec6c5d0ea987980","user":{"login":"karissawhiting","id":10888683,"node_id":"MDQ6VXNlcjEwODg4Njgz","avatar_url":"https://avatars.githubusercontent.com/u/10888683?v=4","gravatar_id":"","url":"https://api.github.com/users/karissawhiting","html_url":"https://github.com/karissawhiting","followers_url":"https://api.github.com/users/karissawhiting/followers","following_url":"https://api.github.com/users/karissawhiting/following{/other_user}","gists_url":"https://api.github.com/users/karissawhiting/gists{/gist_id}","starred_url":"https://api.github.com/users/karissawhiting/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/karissawhiting/subscriptions","organizations_url":"https://api.github.com/users/karissawhiting/orgs","repos_url":"https://api.github.com/users/karissawhiting/repos","events_url":"https://api.github.com/users/karissawhiting/events{/privacy}","received_events_url":"https://api.github.com/users/karissawhiting/received_events","type":"User","site_admin":false},"body":"Should NSCLC 1.2, 2.1 and CRC 1.1 and 1.2 be removed from this list?","created_at":"2024-02-16T20:59:00Z","updated_at":"2024-03-21T20:25:32Z","html_url":"https://github.com/GENIE-BPC/genieBPC/pull/129#discussion_r1492980747","pull_request_url":"https://api.github.com/repos/GENIE-BPC/genieBPC/pulls/129","author_association":"COLLABORATOR","_links":{"self":{"href":"https://api.github.com/repos/GENIE-BPC/genieBPC/pulls/comments/1492980747"},"html":{"href":"https://github.com/GENIE-BPC/genieBPC/pull/129#discussion_r1492980747"},"pull_request":{"href":"https://api.github.com/repos/GENIE-BPC/genieBPC/pulls/129"}},"reactions":{"url":"https://api.github.com/repos/GENIE-BPC/genieBPC/pulls/comments/1492980747/reactions","total_count":0,"+1":0,"-1":0,"laugh":0,"hooray":0,"confused":0,"heart":0,"rocket":0,"eyes":0},"start_line":null,"original_start_line":null,"start_side":null,"line":56,"original_line":56,"side":"RIGHT","original_position":23,"position":25,"subject_type":"line"},"pull_request":{"url":"https://api.github.com/repos/GENIE-BPC/genieBPC/pulls/129","id":1717607448,"node_id":"PR_kwDOEsDnY85mYJwY","html_url":"https://github.com/GENIE-BPC/genieBPC/pull/129","diff_url":"https://github.com/GENIE-BPC/genieBPC/pull/129.diff","patch_url":"https://github.com/GENIE-BPC/genieBPC/pull/129.patch","issue_url":"https://api.github.com/repos/GENIE-BPC/genieBPC/issues/129","number":129,"state":"open","locked":false,"title":"Update NSCLC and CRC consortium releases","user":{"login":"jalavery","id":46568753,"node_id":"MDQ6VXNlcjQ2NTY4NzUz","avatar_url":"https://avatars.githubusercontent.com/u/46568753?v=4","gravatar_id":"","url":"https://api.github.com/users/jalavery","html_url":"https://github.com/jalavery","followers_url":"https://api.github.com/users/jalavery/followers","following_url":"https://api.github.com/users/jalavery/following{/other_user}","gists_url":"https://api.github.com/users/jalavery/gists{/gist_id}","starred_url":"https://api.github.com/users/jalavery/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jalavery/subscriptions","organizations_url":"https://api.github.com/users/jalavery/orgs","repos_url":"https://api.github.com/users/jalavery/repos","events_url":"https://api.github.com/users/jalavery/events{/privacy}","received_events_url":"https://api.github.com/users/jalavery/received_events","type":"User","site_admin":false},"body":"What changes are involved in this pull request? \r\nNSCLC v1.2-consortium and v2.1-consortium and CRC v1.1-consortium and v1.2-consortium had an incidental PHI release (ages >89). Those releases have been removed and replaced with NSCLC v2.2-consortium and CRC v1.3-consortium releases. \r\n\r\nThis PR is to update the synapse tables df to reflect those removals and additions, add error messaging related to this change, and update tests accordingly. \r\n\r\nAlso includes a miscellaneous change to remove the R Universe badge from the README since we no longer push updated versions of the package there.\r\n\r\nIs there a GitHub issue corresponding to this pull request? 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in `.check_for_study_id()`:\r\n! You must provide a `study_id`. See `get_studies()` to view available studies on your database\r\ncbioportalR::get_studies()\r\nError: 'get_studies' is not an exported object from 'namespace:cbioportalR'\r\ncbioportalR::available_studies()\r\n# A tibble: 399 × 13\r\n studyId name description publicStudy pmid citation groups status importDate allSampleCount\r\n \r\n 1 acbc_mskcc_2015 Aden… Whole exom… TRUE 2609… Martelo… ACYC;… 0 2023-12-0… 12\r\n 2 acyc_mskcc_2013 Aden… Whole-exom… TRUE 2368… Ho et a… ACYC;… 0 2023-12-0… 60\r\n 3 acyc_fmi_2014 Aden… Targeted S… TRUE 2441… Ross et… ACYC;… 0 2023-12-0… 28\r\n 4 acyc_jhu_2016 Aden… Whole-geno… TRUE 2686… Rettig … ACYC;… 0 2023-12-0… 25\r\n 5 acyc_mda_2015 Aden… WGS of 21 … TRUE 2663… Mitani … ACYC;… 0 2023-12-0… 102\r\n 6 acyc_mgh_2016 Aden… Whole-geno… TRUE 2682… Drier e… ACYC 0 2023-12-0… 10\r\n 7 acyc_sanger_20… Aden… Whole exom… TRUE 2377… Stephen… ACYC;… 0 2023-12-0… 24\r\n 8 acc_2019 Aden… Multi-Inst… TRUE 3148… Allen e… ACYC;… 0 2023-12-0… 1049\r\n 9 bcc_unige_2016 Basa… Whole-exom… TRUE 2695… Bonilla… PUBLIC 0 2023-12-0… 293\r\n10 all_stjude_2015 Acut… Comprehens… TRUE 2573… Anderss… PUBLIC 0 2023-12-0… 93\r\n```\r\n\r\nI think the \"get_studies()\" should be replaced with \"available_studies()\".","reactions":{"url":"https://api.github.com/repos/karissawhiting/cbioportalR/issues/73/reactions","total_count":0,"+1":0,"-1":0,"laugh":0,"hooray":0,"confused":0,"heart":0,"rocket":0,"eyes":0},"timeline_url":"https://api.github.com/repos/karissawhiting/cbioportalR/issues/73/timeline","performed_via_github_app":null,"state_reason":"completed"},"comment":{"url":"https://api.github.com/repos/karissawhiting/cbioportalR/issues/comments/1979488574","html_url":"https://github.com/karissawhiting/cbioportalR/issues/73#issuecomment-1979488574","issue_url":"https://api.github.com/repos/karissawhiting/cbioportalR/issues/73","id":1979488574,"node_id":"IC_kwDOFHTVlc51_Jk-","user":{"login":"karissawhiting","id":10888683,"node_id":"MDQ6VXNlcjEwODg4Njgz","avatar_url":"https://avatars.githubusercontent.com/u/10888683?v=4","gravatar_id":"","url":"https://api.github.com/users/karissawhiting","html_url":"https://github.com/karissawhiting","followers_url":"https://api.github.com/users/karissawhiting/followers","following_url":"https://api.github.com/users/karissawhiting/following{/other_user}","gists_url":"https://api.github.com/users/karissawhiting/gists{/gist_id}","starred_url":"https://api.github.com/users/karissawhiting/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/karissawhiting/subscriptions","organizations_url":"https://api.github.com/users/karissawhiting/orgs","repos_url":"https://api.github.com/users/karissawhiting/repos","events_url":"https://api.github.com/users/karissawhiting/events{/privacy}","received_events_url":"https://api.github.com/users/karissawhiting/received_events","type":"User","site_admin":false},"created_at":"2024-03-05T19:29:39Z","updated_at":"2024-03-05T19:29:39Z","author_association":"OWNER","body":"Hi @clarrity,\r\n\r\nI named the functions in this way to distinguish the primary ways users may interact with the database: \r\n\r\n1. browsing/seeing what's available (`available_*()`) and \r\n2. pulling data for specific items in the database (`get_*()`). \r\n\r\nIn the above case, a user can see what studies are available in the database for data extraction using `cbioportalR::available_studies()`. Then, once they've selected a study they are interested in, they can use `get_study_info()` which will return the metadata for that particular study. From there, they may want to browse what clinical data (`available_clinical_attributes()`) or molecular data is available (`available_profiles()`) for that select study, etc. \r\n\r\nHere's some additional info on guiding principles used in development of {cbioportalR} if you're interested: https://www.karissawhiting.com/cbioportalR/articles/internal-structure.html \r\n\r\nThanks for using {cbioportalR}!\r\n","reactions":{"url":"https://api.github.com/repos/karissawhiting/cbioportalR/issues/comments/1979488574/reactions","total_count":0,"+1":0,"-1":0,"laugh":0,"hooray":0,"confused":0,"heart":0,"rocket":0,"eyes":0},"performed_via_github_app":null}},"public":true,"created_at":"2024-03-05T19:29:41Z"},{"id":"36273516542","type":"IssuesEvent","actor":{"id":10888683,"login":"karissawhiting","display_login":"karissawhiting","gravatar_id":"","url":"https://api.github.com/users/karissawhiting","avatar_url":"https://avatars.githubusercontent.com/u/10888683?"},"repo":{"id":343201173,"name":"karissawhiting/cbioportalR","url":"https://api.github.com/repos/karissawhiting/cbioportalR"},"payload":{"action":"closed","issue":{"url":"https://api.github.com/repos/karissawhiting/cbioportalR/issues/73","repository_url":"https://api.github.com/repos/karissawhiting/cbioportalR","labels_url":"https://api.github.com/repos/karissawhiting/cbioportalR/issues/73/labels{/name}","comments_url":"https://api.github.com/repos/karissawhiting/cbioportalR/issues/73/comments","events_url":"https://api.github.com/repos/karissawhiting/cbioportalR/issues/73/events","html_url":"https://github.com/karissawhiting/cbioportalR/issues/73","id":2110318906,"node_id":"I_kwDOFHTVlc59yOk6","number":73,"title":"get_study_info() refers to incorrect function","user":{"login":"clarrity","id":8891092,"node_id":"MDQ6VXNlcjg4OTEwOTI=","avatar_url":"https://avatars.githubusercontent.com/u/8891092?v=4","gravatar_id":"","url":"https://api.github.com/users/clarrity","html_url":"https://github.com/clarrity","followers_url":"https://api.github.com/users/clarrity/followers","following_url":"https://api.github.com/users/clarrity/following{/other_user}","gists_url":"https://api.github.com/users/clarrity/gists{/gist_id}","starred_url":"https://api.github.com/users/clarrity/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/clarrity/subscriptions","organizations_url":"https://api.github.com/users/clarrity/orgs","repos_url":"https://api.github.com/users/clarrity/repos","events_url":"https://api.github.com/users/clarrity/events{/privacy}","received_events_url":"https://api.github.com/users/clarrity/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2024-01-31T15:09:52Z","updated_at":"2024-03-05T19:29:39Z","closed_at":"2024-03-05T19:29:39Z","author_association":"NONE","active_lock_reason":null,"body":"```\r\ncbioportalR::get_study_info()\r\nError in `.check_for_study_id()`:\r\n! You must provide a `study_id`. See `get_studies()` to view available studies on your database\r\ncbioportalR::get_studies()\r\nError: 'get_studies' is not an exported object from 'namespace:cbioportalR'\r\ncbioportalR::available_studies()\r\n# A tibble: 399 × 13\r\n studyId name description publicStudy pmid citation groups status importDate allSampleCount\r\n \r\n 1 acbc_mskcc_2015 Aden… Whole exom… TRUE 2609… Martelo… ACYC;… 0 2023-12-0… 12\r\n 2 acyc_mskcc_2013 Aden… Whole-exom… TRUE 2368… Ho et a… ACYC;… 0 2023-12-0… 60\r\n 3 acyc_fmi_2014 Aden… Targeted S… TRUE 2441… Ross et… ACYC;… 0 2023-12-0… 28\r\n 4 acyc_jhu_2016 Aden… Whole-geno… TRUE 2686… Rettig … ACYC;… 0 2023-12-0… 25\r\n 5 acyc_mda_2015 Aden… WGS of 21 … TRUE 2663… Mitani … ACYC;… 0 2023-12-0… 102\r\n 6 acyc_mgh_2016 Aden… Whole-geno… TRUE 2682… Drier e… ACYC 0 2023-12-0… 10\r\n 7 acyc_sanger_20… Aden… Whole exom… TRUE 2377… Stephen… ACYC;… 0 2023-12-0… 24\r\n 8 acc_2019 Aden… Multi-Inst… TRUE 3148… Allen e… ACYC;… 0 2023-12-0… 1049\r\n 9 bcc_unige_2016 Basa… Whole-exom… TRUE 2695… Bonilla… PUBLIC 0 2023-12-0… 293\r\n10 all_stjude_2015 Acut… Comprehens… TRUE 2573… Anderss… PUBLIC 0 2023-12-0… 93\r\n```\r\n\r\nI think the \"get_studies()\" should be replaced with \"available_studies()\".","reactions":{"url":"https://api.github.com/repos/karissawhiting/cbioportalR/issues/73/reactions","total_count":0,"+1":0,"-1":0,"laugh":0,"hooray":0,"confused":0,"heart":0,"rocket":0,"eyes":0},"timeline_url":"https://api.github.com/repos/karissawhiting/cbioportalR/issues/73/timeline","performed_via_github_app":null,"state_reason":"completed"}},"public":true,"created_at":"2024-03-05T19:29:40Z"},{"id":"36273187121","type":"IssuesEvent","actor":{"id":10888683,"login":"karissawhiting","display_login":"karissawhiting","gravatar_id":"","url":"https://api.github.com/users/karissawhiting","avatar_url":"https://avatars.githubusercontent.com/u/10888683?"},"repo":{"id":343201173,"name":"karissawhiting/cbioportalR","url":"https://api.github.com/repos/karissawhiting/cbioportalR"},"payload":{"action":"closed","issue":{"url":"https://api.github.com/repos/karissawhiting/cbioportalR/issues/74","repository_url":"https://api.github.com/repos/karissawhiting/cbioportalR","labels_url":"https://api.github.com/repos/karissawhiting/cbioportalR/issues/74/labels{/name}","comments_url":"https://api.github.com/repos/karissawhiting/cbioportalR/issues/74/comments","events_url":"https://api.github.com/repos/karissawhiting/cbioportalR/issues/74/events","html_url":"https://github.com/karissawhiting/cbioportalR/issues/74","id":2140950819,"node_id":"I_kwDOFHTVlc5_nFEj","number":74,"title":"Could not connect to Genie db","user":{"login":"Almogkm","id":160398265,"node_id":"U_kgDOCY97uQ","avatar_url":"https://avatars.githubusercontent.com/u/160398265?v=4","gravatar_id":"","url":"https://api.github.com/users/Almogkm","html_url":"https://github.com/Almogkm","followers_url":"https://api.github.com/users/Almogkm/followers","following_url":"https://api.github.com/users/Almogkm/following{/other_user}","gists_url":"https://api.github.com/users/Almogkm/gists{/gist_id}","starred_url":"https://api.github.com/users/Almogkm/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Almogkm/subscriptions","organizations_url":"https://api.github.com/users/Almogkm/orgs","repos_url":"https://api.github.com/users/Almogkm/repos","events_url":"https://api.github.com/users/Almogkm/events{/privacy}","received_events_url":"https://api.github.com/users/Almogkm/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2024-02-18T11:47:06Z","updated_at":"2024-03-05T19:16:57Z","closed_at":"2024-03-05T19:16:57Z","author_association":"NONE","active_lock_reason":null,"body":"I keep getting this error: \r\n\r\n> > set_cbioportal_db()\r\n> Error in `value[[3L]]()`:\r\n> ! Not able to connect to \"genie.cbioportal.org/api\"\r\n> Backtrace:\r\n> 1. cbioportalR::set_cbioportal_db()\r\n> 2. cbioportalR::test_cbioportal_db()\r\n> 3. base::tryCatch(...)\r\n> 4. base (local) tryCatchList(expr, classes, parentenv, handlers)\r\n> 5. base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])\r\n> 6. value[[3L]](cond)\r\n\r\nI've tried a new token, I've tried reinstalling the package.","reactions":{"url":"https://api.github.com/repos/karissawhiting/cbioportalR/issues/74/reactions","total_count":0,"+1":0,"-1":0,"laugh":0,"hooray":0,"confused":0,"heart":0,"rocket":0,"eyes":0},"timeline_url":"https://api.github.com/repos/karissawhiting/cbioportalR/issues/74/timeline","performed_via_github_app":null,"state_reason":"completed"}},"public":true,"created_at":"2024-03-05T19:16:58Z"},{"id":"36273187621","type":"IssueCommentEvent","actor":{"id":10888683,"login":"karissawhiting","display_login":"karissawhiting","gravatar_id":"","url":"https://api.github.com/users/karissawhiting","avatar_url":"https://avatars.githubusercontent.com/u/10888683?"},"repo":{"id":343201173,"name":"karissawhiting/cbioportalR","url":"https://api.github.com/repos/karissawhiting/cbioportalR"},"payload":{"action":"created","issue":{"url":"https://api.github.com/repos/karissawhiting/cbioportalR/issues/74","repository_url":"https://api.github.com/repos/karissawhiting/cbioportalR","labels_url":"https://api.github.com/repos/karissawhiting/cbioportalR/issues/74/labels{/name}","comments_url":"https://api.github.com/repos/karissawhiting/cbioportalR/issues/74/comments","events_url":"https://api.github.com/repos/karissawhiting/cbioportalR/issues/74/events","html_url":"https://github.com/karissawhiting/cbioportalR/issues/74","id":2140950819,"node_id":"I_kwDOFHTVlc5_nFEj","number":74,"title":"Could not connect to Genie db","user":{"login":"Almogkm","id":160398265,"node_id":"U_kgDOCY97uQ","avatar_url":"https://avatars.githubusercontent.com/u/160398265?v=4","gravatar_id":"","url":"https://api.github.com/users/Almogkm","html_url":"https://github.com/Almogkm","followers_url":"https://api.github.com/users/Almogkm/followers","following_url":"https://api.github.com/users/Almogkm/following{/other_user}","gists_url":"https://api.github.com/users/Almogkm/gists{/gist_id}","starred_url":"https://api.github.com/users/Almogkm/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Almogkm/subscriptions","organizations_url":"https://api.github.com/users/Almogkm/orgs","repos_url":"https://api.github.com/users/Almogkm/repos","events_url":"https://api.github.com/users/Almogkm/events{/privacy}","received_events_url":"https://api.github.com/users/Almogkm/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2024-02-18T11:47:06Z","updated_at":"2024-03-05T19:16:57Z","closed_at":"2024-03-05T19:16:57Z","author_association":"NONE","active_lock_reason":null,"body":"I keep getting this error: \r\n\r\n> > set_cbioportal_db()\r\n> Error in `value[[3L]]()`:\r\n> ! Not able to connect to \"genie.cbioportal.org/api\"\r\n> Backtrace:\r\n> 1. cbioportalR::set_cbioportal_db()\r\n> 2. cbioportalR::test_cbioportal_db()\r\n> 3. base::tryCatch(...)\r\n> 4. base (local) tryCatchList(expr, classes, parentenv, handlers)\r\n> 5. base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])\r\n> 6. value[[3L]](cond)\r\n\r\nI've tried a new token, I've tried reinstalling the package.","reactions":{"url":"https://api.github.com/repos/karissawhiting/cbioportalR/issues/74/reactions","total_count":0,"+1":0,"-1":0,"laugh":0,"hooray":0,"confused":0,"heart":0,"rocket":0,"eyes":0},"timeline_url":"https://api.github.com/repos/karissawhiting/cbioportalR/issues/74/timeline","performed_via_github_app":null,"state_reason":"completed"},"comment":{"url":"https://api.github.com/repos/karissawhiting/cbioportalR/issues/comments/1979469988","html_url":"https://github.com/karissawhiting/cbioportalR/issues/74#issuecomment-1979469988","issue_url":"https://api.github.com/repos/karissawhiting/cbioportalR/issues/74","id":1979469988,"node_id":"IC_kwDOFHTVlc51_FCk","user":{"login":"karissawhiting","id":10888683,"node_id":"MDQ6VXNlcjEwODg4Njgz","avatar_url":"https://avatars.githubusercontent.com/u/10888683?v=4","gravatar_id":"","url":"https://api.github.com/users/karissawhiting","html_url":"https://github.com/karissawhiting","followers_url":"https://api.github.com/users/karissawhiting/followers","following_url":"https://api.github.com/users/karissawhiting/following{/other_user}","gists_url":"https://api.github.com/users/karissawhiting/gists{/gist_id}","starred_url":"https://api.github.com/users/karissawhiting/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/karissawhiting/subscriptions","organizations_url":"https://api.github.com/users/karissawhiting/orgs","repos_url":"https://api.github.com/users/karissawhiting/repos","events_url":"https://api.github.com/users/karissawhiting/events{/privacy}","received_events_url":"https://api.github.com/users/karissawhiting/received_events","type":"User","site_admin":false},"created_at":"2024-03-05T19:16:57Z","updated_at":"2024-03-05T19:16:57Z","author_association":"OWNER","body":"Hi @Almogkm\r\n\r\nThis was a temporary issue in the underlying genie cbioportal API that occurred when they updated it, and it should be resolved now. Please let me know if you are still experiencing issues!\r\n\r\nThanks.","reactions":{"url":"https://api.github.com/repos/karissawhiting/cbioportalR/issues/comments/1979469988/reactions","total_count":0,"+1":0,"-1":0,"laugh":0,"hooray":0,"confused":0,"heart":0,"rocket":0,"eyes":0},"performed_via_github_app":null}},"public":true,"created_at":"2024-03-05T19:16:59Z"},{"id":"36273106258","type":"IssueCommentEvent","actor":{"id":10888683,"login":"karissawhiting","display_login":"karissawhiting","gravatar_id":"","url":"https://api.github.com/users/karissawhiting","avatar_url":"https://avatars.githubusercontent.com/u/10888683?"},"repo":{"id":343201173,"name":"karissawhiting/cbioportalR","url":"https://api.github.com/repos/karissawhiting/cbioportalR"},"payload":{"action":"created","issue":{"url":"https://api.github.com/repos/karissawhiting/cbioportalR/issues/72","repository_url":"https://api.github.com/repos/karissawhiting/cbioportalR","labels_url":"https://api.github.com/repos/karissawhiting/cbioportalR/issues/72/labels{/name}","comments_url":"https://api.github.com/repos/karissawhiting/cbioportalR/issues/72/comments","events_url":"https://api.github.com/repos/karissawhiting/cbioportalR/issues/72/events","html_url":"https://github.com/karissawhiting/cbioportalR/issues/72","id":2100912734,"node_id":"I_kwDOFHTVlc59OWJe","number":72,"title":"available_studies()","user":{"login":"kmezhoud","id":4458195,"node_id":"MDQ6VXNlcjQ0NTgxOTU=","avatar_url":"https://avatars.githubusercontent.com/u/4458195?v=4","gravatar_id":"","url":"https://api.github.com/users/kmezhoud","html_url":"https://github.com/kmezhoud","followers_url":"https://api.github.com/users/kmezhoud/followers","following_url":"https://api.github.com/users/kmezhoud/following{/other_user}","gists_url":"https://api.github.com/users/kmezhoud/gists{/gist_id}","starred_url":"https://api.github.com/users/kmezhoud/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kmezhoud/subscriptions","organizations_url":"https://api.github.com/users/kmezhoud/orgs","repos_url":"https://api.github.com/users/kmezhoud/repos","events_url":"https://api.github.com/users/kmezhoud/events{/privacy}","received_events_url":"https://api.github.com/users/kmezhoud/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2024-01-25T18:04:44Z","updated_at":"2024-03-05T19:13:50Z","closed_at":"2024-03-05T19:13:50Z","author_association":"NONE","active_lock_reason":null,"body":"Hi,\r\nPlease, check with me this error.\r\nThanks\r\n```{r}\r\n> library(cbioportalR)\r\n> set_cbioportal_db(\"public\")\r\n✔ You are successfully connected!\r\n✔ base_url for this R session is now set to \"www.cbioportal.org/api\" \r\n> test_cbioportal_db()\r\n✔ You are successfully connected!\r\n> available_studies()\r\nError: API request failed: 404\r\n``` \r\nKarim","reactions":{"url":"https://api.github.com/repos/karissawhiting/cbioportalR/issues/72/reactions","total_count":0,"+1":0,"-1":0,"laugh":0,"hooray":0,"confused":0,"heart":0,"rocket":0,"eyes":0},"timeline_url":"https://api.github.com/repos/karissawhiting/cbioportalR/issues/72/timeline","performed_via_github_app":null,"state_reason":"completed"},"comment":{"url":"https://api.github.com/repos/karissawhiting/cbioportalR/issues/comments/1979465664","html_url":"https://github.com/karissawhiting/cbioportalR/issues/72#issuecomment-1979465664","issue_url":"https://api.github.com/repos/karissawhiting/cbioportalR/issues/72","id":1979465664,"node_id":"IC_kwDOFHTVlc51_D_A","user":{"login":"karissawhiting","id":10888683,"node_id":"MDQ6VXNlcjEwODg4Njgz","avatar_url":"https://avatars.githubusercontent.com/u/10888683?v=4","gravatar_id":"","url":"https://api.github.com/users/karissawhiting","html_url":"https://github.com/karissawhiting","followers_url":"https://api.github.com/users/karissawhiting/followers","following_url":"https://api.github.com/users/karissawhiting/following{/other_user}","gists_url":"https://api.github.com/users/karissawhiting/gists{/gist_id}","starred_url":"https://api.github.com/users/karissawhiting/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/karissawhiting/subscriptions","organizations_url":"https://api.github.com/users/karissawhiting/orgs","repos_url":"https://api.github.com/users/karissawhiting/repos","events_url":"https://api.github.com/users/karissawhiting/events{/privacy}","received_events_url":"https://api.github.com/users/karissawhiting/received_events","type":"User","site_admin":false},"created_at":"2024-03-05T19:13:50Z","updated_at":"2024-03-05T19:13:50Z","author_association":"OWNER","body":"Hi @kmezhoud !\r\n\r\nThis was due to a temporary bug in the underlying cbioportal API that occurred when they updated. It should be fixed now, but let me know if you're still having issues.","reactions":{"url":"https://api.github.com/repos/karissawhiting/cbioportalR/issues/comments/1979465664/reactions","total_count":0,"+1":0,"-1":0,"laugh":0,"hooray":0,"confused":0,"heart":0,"rocket":0,"eyes":0},"performed_via_github_app":null}},"public":true,"created_at":"2024-03-05T19:13:52Z"},{"id":"36273105983","type":"IssuesEvent","actor":{"id":10888683,"login":"karissawhiting","display_login":"karissawhiting","gravatar_id":"","url":"https://api.github.com/users/karissawhiting","avatar_url":"https://avatars.githubusercontent.com/u/10888683?"},"repo":{"id":343201173,"name":"karissawhiting/cbioportalR","url":"https://api.github.com/repos/karissawhiting/cbioportalR"},"payload":{"action":"closed","issue":{"url":"https://api.github.com/repos/karissawhiting/cbioportalR/issues/72","repository_url":"https://api.github.com/repos/karissawhiting/cbioportalR","labels_url":"https://api.github.com/repos/karissawhiting/cbioportalR/issues/72/labels{/name}","comments_url":"https://api.github.com/repos/karissawhiting/cbioportalR/issues/72/comments","events_url":"https://api.github.com/repos/karissawhiting/cbioportalR/issues/72/events","html_url":"https://github.com/karissawhiting/cbioportalR/issues/72","id":2100912734,"node_id":"I_kwDOFHTVlc59OWJe","number":72,"title":"available_studies()","user":{"login":"kmezhoud","id":4458195,"node_id":"MDQ6VXNlcjQ0NTgxOTU=","avatar_url":"https://avatars.githubusercontent.com/u/4458195?v=4","gravatar_id":"","url":"https://api.github.com/users/kmezhoud","html_url":"https://github.com/kmezhoud","followers_url":"https://api.github.com/users/kmezhoud/followers","following_url":"https://api.github.com/users/kmezhoud/following{/other_user}","gists_url":"https://api.github.com/users/kmezhoud/gists{/gist_id}","starred_url":"https://api.github.com/users/kmezhoud/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kmezhoud/subscriptions","organizations_url":"https://api.github.com/users/kmezhoud/orgs","repos_url":"https://api.github.com/users/kmezhoud/repos","events_url":"https://api.github.com/users/kmezhoud/events{/privacy}","received_events_url":"https://api.github.com/users/kmezhoud/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2024-01-25T18:04:44Z","updated_at":"2024-03-05T19:13:50Z","closed_at":"2024-03-05T19:13:50Z","author_association":"NONE","active_lock_reason":null,"body":"Hi,\r\nPlease, check with me this error.\r\nThanks\r\n```{r}\r\n> library(cbioportalR)\r\n> set_cbioportal_db(\"public\")\r\n✔ You are successfully connected!\r\n✔ base_url for this R session is now set to \"www.cbioportal.org/api\" \r\n> test_cbioportal_db()\r\n✔ You are successfully connected!\r\n> available_studies()\r\nError: API request failed: 404\r\n``` \r\nKarim","reactions":{"url":"https://api.github.com/repos/karissawhiting/cbioportalR/issues/72/reactions","total_count":0,"+1":0,"-1":0,"laugh":0,"hooray":0,"confused":0,"heart":0,"rocket":0,"eyes":0},"timeline_url":"https://api.github.com/repos/karissawhiting/cbioportalR/issues/72/timeline","performed_via_github_app":null,"state_reason":"completed"}},"public":true,"created_at":"2024-03-05T19:13:51Z"},{"id":"36273019332","type":"IssuesEvent","actor":{"id":10888683,"login":"karissawhiting","display_login":"karissawhiting","gravatar_id":"","url":"https://api.github.com/users/karissawhiting","avatar_url":"https://avatars.githubusercontent.com/u/10888683?"},"repo":{"id":549761904,"name":"karissawhiting/oncokbR","url":"https://api.github.com/repos/karissawhiting/oncokbR"},"payload":{"action":"opened","issue":{"url":"https://api.github.com/repos/karissawhiting/oncokbR/issues/24","repository_url":"https://api.github.com/repos/karissawhiting/oncokbR","labels_url":"https://api.github.com/repos/karissawhiting/oncokbR/issues/24/labels{/name}","comments_url":"https://api.github.com/repos/karissawhiting/oncokbR/issues/24/comments","events_url":"https://api.github.com/repos/karissawhiting/oncokbR/issues/24/events","html_url":"https://github.com/karissawhiting/oncokbR/issues/24","id":2169969366,"node_id":"I_kwDOIMSzcM6BVxrW","number":24,"title":"Annotator returns NAs when processing data from CDSI","user":{"login":"karissawhiting","id":10888683,"node_id":"MDQ6VXNlcjEwODg4Njgz","avatar_url":"https://avatars.githubusercontent.com/u/10888683?v=4","gravatar_id":"","url":"https://api.github.com/users/karissawhiting","html_url":"https://github.com/karissawhiting","followers_url":"https://api.github.com/users/karissawhiting/followers","following_url":"https://api.github.com/users/karissawhiting/following{/other_user}","gists_url":"https://api.github.com/users/karissawhiting/gists{/gist_id}","starred_url":"https://api.github.com/users/karissawhiting/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/karissawhiting/subscriptions","organizations_url":"https://api.github.com/users/karissawhiting/orgs","repos_url":"https://api.github.com/users/karissawhiting/repos","events_url":"https://api.github.com/users/karissawhiting/events{/privacy}","received_events_url":"https://api.github.com/users/karissawhiting/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2024-03-05T19:10:30Z","updated_at":"2024-03-05T19:10:30Z","closed_at":null,"author_association":"OWNER","active_lock_reason":null,"body":"Differences in file formats between cbioportal API and CDSI github data cause some annotations missing protein start and stop to be skipped when annotating CDSI data. \r\n\r\nBetter messaging and figuring out optimal annotator settings for this format of data are needed. ","reactions":{"url":"https://api.github.com/repos/karissawhiting/oncokbR/issues/24/reactions","total_count":0,"+1":0,"-1":0,"laugh":0,"hooray":0,"confused":0,"heart":0,"rocket":0,"eyes":0},"timeline_url":"https://api.github.com/repos/karissawhiting/oncokbR/issues/24/timeline","performed_via_github_app":null,"state_reason":null}},"public":true,"created_at":"2024-03-05T19:10:31Z"},{"id":"36272974491","type":"GollumEvent","actor":{"id":10888683,"login":"karissawhiting","display_login":"karissawhiting","gravatar_id":"","url":"https://api.github.com/users/karissawhiting","avatar_url":"https://avatars.githubusercontent.com/u/10888683?"},"repo":{"id":343201173,"name":"karissawhiting/cbioportalR","url":"https://api.github.com/repos/karissawhiting/cbioportalR"},"payload":{"pages":[{"page_name":"Home","title":"Home","summary":null,"action":"created","sha":"4ec7a8a6da6024a36486a9c92d54eb91eb5a34e9","html_url":"https://github.com/karissawhiting/cbioportalR/wiki/Home"}]},"public":true,"created_at":"2024-03-05T19:08:52Z"},{"id":"36272974492","type":"GollumEvent","actor":{"id":10888683,"login":"karissawhiting","display_login":"karissawhiting","gravatar_id":"","url":"https://api.github.com/users/karissawhiting","avatar_url":"https://avatars.githubusercontent.com/u/10888683?"},"repo":{"id":343201173,"name":"karissawhiting/cbioportalR","url":"https://api.github.com/repos/karissawhiting/cbioportalR"},"payload":{"pages":[{"page_name":"Variant-Classification-Default-Filtering","title":"Variant 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working"}],"state":"open","locked":false,"assignee":null,"assignees":[{"login":"dippindots","id":15748980,"node_id":"MDQ6VXNlcjE1NzQ4OTgw","avatar_url":"https://avatars.githubusercontent.com/u/15748980?v=4","gravatar_id":"","url":"https://api.github.com/users/dippindots","html_url":"https://github.com/dippindots","followers_url":"https://api.github.com/users/dippindots/followers","following_url":"https://api.github.com/users/dippindots/following{/other_user}","gists_url":"https://api.github.com/users/dippindots/gists{/gist_id}","starred_url":"https://api.github.com/users/dippindots/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dippindots/subscriptions","organizations_url":"https://api.github.com/users/dippindots/orgs","repos_url":"https://api.github.com/users/dippindots/repos","events_url":"https://api.github.com/users/dippindots/events{/privacy}","received_events_url":"https://api.github.com/users/dippindots/received_events","type":"User","site_admin":false},{"login":"sbabyanusha","id":61431648,"node_id":"MDQ6VXNlcjYxNDMxNjQ4","avatar_url":"https://avatars.githubusercontent.com/u/61431648?v=4","gravatar_id":"","url":"https://api.github.com/users/sbabyanusha","html_url":"https://github.com/sbabyanusha","followers_url":"https://api.github.com/users/sbabyanusha/followers","following_url":"https://api.github.com/users/sbabyanusha/following{/other_user}","gists_url":"https://api.github.com/users/sbabyanusha/gists{/gist_id}","starred_url":"https://api.github.com/users/sbabyanusha/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sbabyanusha/subscriptions","organizations_url":"https://api.github.com/users/sbabyanusha/orgs","repos_url":"https://api.github.com/users/sbabyanusha/repos","events_url":"https://api.github.com/users/sbabyanusha/events{/privacy}","received_events_url":"https://api.github.com/users/sbabyanusha/received_events","type":"User","site_admin":false}],"milestone":null,"comments":6,"created_at":"2022-08-28T18:10:07Z","updated_at":"2024-03-01T17:07:38Z","closed_at":null,"author_association":"NONE","active_lock_reason":null,"body":"I noticed some inconsistencies between public cBioPortal and MSK cBioPortal regarding structural variant data. I'm also not able to pull structural variant data anymore via the API endpoint for these studies.\r\n\r\nFor example, for \"blca_nmibc_2017\": \r\n\r\n**Public cBioPortal:**\r\n\r\n\r\n**MSK cBioPortal**: (No SVs shown)\r\n\r\n\r\nAdditionally, for the MSK database, it looks like the molecular profile names are still called `xx-fusions` for many of the studies. With these studies, I can't figure out how to programmatically pull the data anymore. [This is the endpoint](https://www.cbioportal.org/api/swagger-ui/index.html?urls.primaryName=internal#/Structural%20Variants/fetchStructuralVariantsUsingPOST) I was using. It still works for the profiles renamed to `xx-structural-variants` but not ones still called `xx-fusions`.\r\n\r\nFrom the below code, I got 77 studies that had inconsistent SV profiles names between the two MSK/Public data bases.\r\n\r\n``` r\r\n# using {cbioportalR} to get data\r\n# remotes::install_github(\"karissawhiting/cbioportalR\")\r\nlibrary(cbioportalR)\r\nlibrary(dplyr)\r\n\r\n# Public Data -------------------\r\nset_cbioportal_db(\"public\")\r\n#> ✔ You are successfully connected!\r\n#> ✔ base_url for this R session is now set to \"www.cbioportal.org/api\"\r\n\r\n# get all available structural variant profile names in data base\r\npublic_profiles <- available_profiles() %>%\r\n filter(molecularAlterationType == \"STRUCTURAL_VARIANT\") %>%\r\n select(studyId, molecularProfileId)\r\n#> ℹ No `study_id` provided. Returning all available genomic profiles for \r\n\r\n# MSK Data -------------------\r\nset_cbioportal_db(\"msk\")\r\n#> ✔ You are successfully connected!\r\n#> ✔ base_url for this R session is now set to \"cbioportal.mskcc.org/api\"\r\n\r\nmsk_profiles <- available_profiles() %>%\r\n filter(molecularAlterationType == \"STRUCTURAL_VARIANT\") %>%\r\n select(studyId, molecularProfileId)\r\n#> ℹ No `study_id` provided. Returning all available genomic profiles for \r\n\r\n# Compare --------------------\r\nin_both <- msk_profiles %>%\r\n filter(studyId %in% public_profiles$studyId) %>%\r\n left_join(., public_profiles, by = \"studyId\")\r\n\r\n# names do not match in the following:\r\nin_both[which(in_both$molecularProfileId.x != in_both$molecularProfileId.y), ]\r\n#> # A tibble: 77 × 3\r\n#> studyId molecularProfileId.x molecularP…¹\r\n#> \r\n#> 1 all_stjude_2015 all_stjude_2015_fusion all_stjude_…\r\n#> 2 acyc_jhu_2016 acyc_jhu_2016_fusion acyc_jhu_20…\r\n#> 3 blca_plasmacytoid_mskcc_2016 blca_plasmacytoid_mskcc_2016_fusion blca_plasma…\r\n#> 4 blca_nmibc_2017 blca_nmibc_2017_fusion blca_nmibc_…\r\n#> 5 blca_msk_tcga_2020 blca_msk_tcga_2020_fusion blca_msk_tc…\r\n#> 6 ccle_broad_2019 ccle_broad_2019_fusion ccle_broad_…\r\n#> 7 luad_tcga_pub luad_tcga_pub_fusion luad_tcga_p…\r\n#> 8 luad_oncosg_2020 luad_oncosg_2020_fusion luad_oncosg…\r\n#> 9 mpnst_mskcc mpnst_mskcc_fusion mpnst_mskcc…\r\n#> 10 nhl_bcgsc_2011 nhl_bcgsc_2011_fusion nhl_bcgsc_2…\r\n#> # … with 67 more rows, and abbreviated variable name ¹molecularProfileId.y\r\n```\r\n Please let me know if this will be updated or how I can pull data for the older profiles still called \"xx_fusions\".\r\n\r\nThanks for your work on cBioPortal!! \r\n\r\nCreated on 2022-08-28 with [reprex v2.0.2](https://reprex.tidyverse.org)\r\n","reactions":{"url":"https://api.github.com/repos/cBioPortal/icebox/issues/386/reactions","total_count":0,"+1":0,"-1":0,"laugh":0,"hooray":0,"confused":0,"heart":0,"rocket":0,"eyes":0},"timeline_url":"https://api.github.com/repos/cBioPortal/icebox/issues/386/timeline","performed_via_github_app":null,"state_reason":null}},"public":true,"created_at":"2024-03-01T17:07:39Z","org":{"id":9876251,"login":"cBioPortal","gravatar_id":"","url":"https://api.github.com/orgs/cBioPortal","avatar_url":"https://avatars.githubusercontent.com/u/9876251?"}},{"id":"36141810946","type":"PushEvent","actor":{"id":10888683,"login":"karissawhiting","display_login":"karissawhiting","gravatar_id":"","url":"https://api.github.com/users/karissawhiting","avatar_url":"https://avatars.githubusercontent.com/u/10888683?"},"repo":{"id":329814947,"name":"karissawhiting/cureit","url":"https://api.github.com/repos/karissawhiting/cureit"},"payload":{"repository_id":329814947,"push_id":17333914758,"size":1,"distinct_size":1,"ref":"refs/heads/lasso-sims-and-func-edits","head":"dcc6e13bc6e7e2561b18d675f7b4784d31eb1bdf","before":"a1218db4ec1823af94fc954891cc9cbb3a19ce83","commits":[{"sha":"dcc6e13bc6e7e2561b18d675f7b4784d31eb1bdf","author":{"email":"whitingk@mskcc.org","name":"karissawhiting"},"message":"small code changes","distinct":true,"url":"https://api.github.com/repos/karissawhiting/cureit/commits/dcc6e13bc6e7e2561b18d675f7b4784d31eb1bdf"}]},"public":true,"created_at":"2024-02-29T21:41:10Z"},{"id":"36106218214","type":"PushEvent","actor":{"id":10888683,"login":"karissawhiting","display_login":"karissawhiting","gravatar_id":"","url":"https://api.github.com/users/karissawhiting","avatar_url":"https://avatars.githubusercontent.com/u/10888683?"},"repo":{"id":329814947,"name":"karissawhiting/cureit","url":"https://api.github.com/repos/karissawhiting/cureit"},"payload":{"repository_id":329814947,"push_id":17316633864,"size":1,"distinct_size":1,"ref":"refs/heads/lasso-sims-and-func-edits","head":"a1218db4ec1823af94fc954891cc9cbb3a19ce83","before":"ba5773eb43736cd3d26743ee8f253a16ab92d40b","commits":[{"sha":"a1218db4ec1823af94fc954891cc9cbb3a19ce83","author":{"email":"whitingk@mskcc.org","name":"karissawhiting"},"message":"updates","distinct":true,"url":"https://api.github.com/repos/karissawhiting/cureit/commits/a1218db4ec1823af94fc954891cc9cbb3a19ce83"}]},"public":true,"created_at":"2024-02-28T23:01:34Z"}]