{"action":"created","comment":{"url":"https://api.github.com/repos/cBioPortal/cbioportal/pulls/comments/217646667","pull_request_review_id":155402975,"id":217646667,"node_id":"MDI0OlB1bGxSZXF1ZXN0UmV2aWV3Q29tbWVudDIxNzY0NjY2Nw==","diff_hunk":"@@ -1984,6 +1985,12 @@ class ClinicalValidator(Validator):\n             'datatype': 'STRING'\n         },\n     }\n+\n+    # For some attributes, only a warning should be reported when they are in the wrong data file.\n+    # This was added to successfully validate old study data.\n+    WARNING_ATTRIBUTES = ['PRIMARY_SITE', 'METASTATIC_SITE', 'TUMOR_TISSUE_SITE']","path":"core/src/main/scripts/importer/validateData.py","position":17,"original_position":17,"commit_id":"d82c5fc7b40dd1f4a5fcffa67976e150dad4f382","original_commit_id":"d82c5fc7b40dd1f4a5fcffa67976e150dad4f382","user":{"login":"pieterlukasse","id":2900303,"node_id":"MDQ6VXNlcjI5MDAzMDM=","avatar_url":"https://avatars1.githubusercontent.com/u/2900303?v=4","gravatar_id":"","url":"https://api.github.com/users/pieterlukasse","html_url":"https://github.com/pieterlukasse","followers_url":"https://api.github.com/users/pieterlukasse/followers","following_url":"https://api.github.com/users/pieterlukasse/following{/other_user}","gists_url":"https://api.github.com/users/pieterlukasse/gists{/gist_id}","starred_url":"https://api.github.com/users/pieterlukasse/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pieterlukasse/subscriptions","organizations_url":"https://api.github.com/users/pieterlukasse/orgs","repos_url":"https://api.github.com/users/pieterlukasse/repos","events_url":"https://api.github.com/users/pieterlukasse/events{/privacy}","received_events_url":"https://api.github.com/users/pieterlukasse/received_events","type":"User","site_admin":false},"body":"please add a few words on how it was tested/verified that having these attributes (only) in the wrong file does not affect functionality. And does this mean these were previously set to `logger.error` without a good reason? Or is the original problem solved (e.g. in the frontend)?","created_at":"2018-09-14T09:03:00Z","updated_at":"2018-09-14T09:03:30Z","html_url":"https://github.com/cBioPortal/cbioportal/pull/4781#discussion_r217646667","pull_request_url":"https://api.github.com/repos/cBioPortal/cbioportal/pulls/4781","author_association":"MEMBER","_links":{"self":{"href":"https://api.github.com/repos/cBioPortal/cbioportal/pulls/comments/217646667"},"html":{"href":"https://github.com/cBioPortal/cbioportal/pull/4781#discussion_r217646667"},"pull_request":{"href":"https://api.github.com/repos/cBioPortal/cbioportal/pulls/4781"}}},"pull_request":{"url":"https://api.github.com/repos/cBioPortal/cbioportal/pulls/4781","id":214893966,"node_id":"MDExOlB1bGxSZXF1ZXN0MjE0ODkzOTY2","html_url":"https://github.com/cBioPortal/cbioportal/pull/4781","diff_url":"https://github.com/cBioPortal/cbioportal/pull/4781.diff","patch_url":"https://github.com/cBioPortal/cbioportal/pull/4781.patch","issue_url":"https://api.github.com/repos/cBioPortal/cbioportal/issues/4781","number":4781,"state":"open","locked":false,"title":"Warning instead of error for some incorrectly placed clinical attributes","user":{"login":"sandertan","id":9624990,"node_id":"MDQ6VXNlcjk2MjQ5OTA=","avatar_url":"https://avatars2.githubusercontent.com/u/9624990?v=4","gravatar_id":"","url":"https://api.github.com/users/sandertan","html_url":"https://github.com/sandertan","followers_url":"https://api.github.com/users/sandertan/followers","following_url":"https://api.github.com/users/sandertan/following{/other_user}","gists_url":"https://api.github.com/users/sandertan/gists{/gist_id}","starred_url":"https://api.github.com/users/sandertan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sandertan/subscriptions","organizations_url":"https://api.github.com/users/sandertan/orgs","repos_url":"https://api.github.com/users/sandertan/repos","events_url":"https://api.github.com/users/sandertan/events{/privacy}","received_events_url":"https://api.github.com/users/sandertan/received_events","type":"User","site_admin":false},"body":"Recently we changed the validation of whether clinical attributes should be in the sample or patient file (https://github.com/cBioPortal/cbioportal/pull/3910). This PR makes this validation less strict for 3 attributes, `PRIMARY_SITE`, `METASTATIC_SITE` and `TUMOR_TISSUE_SITE`. These are currently in the PATIENT file of all TCGA Provisional studies, and it's not possible to move them to the SAMPLE file.","created_at":"2018-09-12T09:29:45Z","updated_at":"2018-09-14T09:03:30Z","closed_at":null,"merged_at":null,"merge_commit_sha":"b5499f573c6acc5873b3f4e8e00e5e3d853910fd","assignee":null,"assignees":[],"requested_reviewers":[{"login":"jjgao","id":840895,"node_id":"MDQ6VXNlcjg0MDg5NQ==","avatar_url":"https://avatars0.githubusercontent.com/u/840895?v=4","gravatar_id":"","url":"https://api.github.com/users/jjgao","html_url":"https://github.com/jjgao","followers_url":"https://api.github.com/users/jjgao/followers","following_url":"https://api.github.com/users/jjgao/following{/other_user}","gists_url":"https://api.github.com/users/jjgao/gists{/gist_id}","starred_url":"https://api.github.com/users/jjgao/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jjgao/subscriptions","organizations_url":"https://api.github.com/users/jjgao/orgs","repos_url":"https://api.github.com/users/jjgao/repos","events_url":"https://api.github.com/users/jjgao/events{/privacy}","received_events_url":"https://api.github.com/users/jjgao/received_events","type":"User","site_admin":false},{"login":"yichaoS","id":5973438,"node_id":"MDQ6VXNlcjU5NzM0Mzg=","avatar_url":"https://avatars1.githubusercontent.com/u/5973438?v=4","gravatar_id":"","url":"https://api.github.com/users/yichaoS","html_url":"https://github.com/yichaoS","followers_url":"https://api.github.com/users/yichaoS/followers","following_url":"https://api.github.com/users/yichaoS/following{/other_user}","gists_url":"https://api.github.com/users/yichaoS/gists{/gist_id}","starred_url":"https://api.github.com/users/yichaoS/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yichaoS/subscriptions","organizations_url":"https://api.github.com/users/yichaoS/orgs","repos_url":"https://api.github.com/users/yichaoS/repos","events_url":"https://api.github.com/users/yichaoS/events{/privacy}","received_events_url":"https://api.github.com/users/yichaoS/received_events","type":"User","site_admin":false},{"login":"ritikakundra","id":12007862,"node_id":"MDQ6VXNlcjEyMDA3ODYy","avatar_url":"https://avatars1.githubusercontent.com/u/12007862?v=4","gravatar_id":"","url":"https://api.github.com/users/ritikakundra","html_url":"https://github.com/ritikakundra","followers_url":"https://api.github.com/users/ritikakundra/followers","following_url":"https://api.github.com/users/ritikakundra/following{/other_user}","gists_url":"https://api.github.com/users/ritikakundra/gists{/gist_id}","starred_url":"https://api.github.com/users/ritikakundra/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ritikakundra/subscriptions","organizations_url":"https://api.github.com/users/ritikakundra/orgs","repos_url":"https://api.github.com/users/ritikakundra/repos","events_url":"https://api.github.com/users/ritikakundra/events{/privacy}","received_events_url":"https://api.github.com/users/ritikakundra/received_events","type":"User","site_admin":false}],"requested_teams":[],"labels":[{"id":288494812,"node_id":"MDU6TGFiZWwyODg0OTQ4MTI=","url":"https://api.github.com/repos/cBioPortal/cbioportal/labels/ready%20to%20review","name":"ready to review","color":"00bb00","default":false},{"id":739697446,"node_id":"MDU6TGFiZWw3Mzk2OTc0NDY=","url":"https://api.github.com/repos/cBioPortal/cbioportal/labels/validator","name":"validator","color":"131b8c","default":false}],"milestone":null,"commits_url":"https://api.github.com/repos/cBioPortal/cbioportal/pulls/4781/commits","review_comments_url":"https://api.github.com/repos/cBioPortal/cbioportal/pulls/4781/comments","review_comment_url":"https://api.github.com/repos/cBioPortal/cbioportal/pulls/comments{/number}","comments_url":"https://api.github.com/repos/cBioPortal/cbioportal/issues/4781/comments","statuses_url":"https://api.github.com/repos/cBioPortal/cbioportal/statuses/d82c5fc7b40dd1f4a5fcffa67976e150dad4f382","head":{"label":"thehyve:validator_warning_attribute","ref":"validator_warning_attribute","sha":"d82c5fc7b40dd1f4a5fcffa67976e150dad4f382","user":{"login":"thehyve","id":1502440,"node_id":"MDEyOk9yZ2FuaXphdGlvbjE1MDI0NDA=","avatar_url":"https://avatars3.githubusercontent.com/u/1502440?v=4","gravatar_id":"","url":"https://api.github.com/users/thehyve","html_url":"https://github.com/thehyve","followers_url":"https://api.github.com/users/thehyve/followers","following_url":"https://api.github.com/users/thehyve/following{/other_user}","gists_url":"https://api.github.com/users/thehyve/gists{/gist_id}","starred_url":"https://api.github.com/users/thehyve/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/thehyve/subscriptions","organizations_url":"https://api.github.com/users/thehyve/orgs","repos_url":"https://api.github.com/users/thehyve/repos","events_url":"https://api.github.com/users/thehyve/events{/privacy}","received_events_url":"https://api.github.com/users/thehyve/received_events","type":"Organization","site_admin":false},"repo":{"id":37332427,"node_id":"MDEwOlJlcG9zaXRvcnkzNzMzMjQyNw==","name":"cbioportal","full_name":"thehyve/cbioportal","owner":{"login":"thehyve","id":1502440,"node_id":"MDEyOk9yZ2FuaXphdGlvbjE1MDI0NDA=","avatar_url":"https://avatars3.githubusercontent.com/u/1502440?v=4","gravatar_id":"","url":"https://api.github.com/users/thehyve","html_url":"https://github.com/thehyve","followers_url":"https://api.github.com/users/thehyve/followers","following_url":"https://api.github.com/users/thehyve/following{/other_user}","gists_url":"https://api.github.com/users/thehyve/gists{/gist_id}","starred_url":"https://api.github.com/users/thehyve/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/thehyve/subscriptions","organizations_url":"https://api.github.com/users/thehyve/orgs","repos_url":"https://api.github.com/users/thehyve/repos","events_url":"https://api.github.com/users/thehyve/events{/privacy}","received_events_url":"https://api.github.com/users/thehyve/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/thehyve/cbioportal","description":"cBioPortal topic branches at The Hyve","fork":true,"url":"https://api.github.com/repos/thehyve/cbioportal","forks_url":"https://api.github.com/repos/thehyve/cbioportal/forks","keys_url":"https://api.github.com/repos/thehyve/cbioportal/keys{/key_id}","collaborators_url":"https://api.github.com/repos/thehyve/cbioportal/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/thehyve/cbioportal/teams","hooks_url":"https://api.github.com/repos/thehyve/cbioportal/hooks","issue_events_url":"https://api.github.com/repos/thehyve/cbioportal/issues/events{/number}","events_url":"https://api.github.com/repos/thehyve/cbioportal/events","assignees_url":"https://api.github.com/repos/thehyve/cbioportal/assignees{/user}","branches_url":"https://api.github.com/repos/thehyve/cbioportal/branches{/branch}","tags_url":"https://api.github.com/repos/thehyve/cbioportal/tags","blobs_url":"https://api.github.com/repos/thehyve/cbioportal/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/thehyve/cbioportal/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/thehyve/cbioportal/git/refs{/sha}","trees_url":"https://api.github.com/repos/thehyve/cbioportal/git/trees{/sha}","statuses_url":"https://api.github.com/repos/thehyve/cbioportal/statuses/{sha}","languages_url":"https://api.github.com/repos/thehyve/cbioportal/languages","stargazers_url":"https://api.github.com/repos/thehyve/cbioportal/stargazers","contributors_url":"https://api.github.com/repos/thehyve/cbioportal/contributors","subscribers_url":"https://api.github.com/repos/thehyve/cbioportal/subscribers","subscription_url":"https://api.github.com/repos/thehyve/cbioportal/subscription","commits_url":"https://api.github.com/repos/thehyve/cbioportal/commits{/sha}","git_commits_url":"https://api.github.com/repos/thehyve/cbioportal/git/commits{/sha}","comments_url":"https://api.github.com/repos/thehyve/cbioportal/comments{/number}","issue_comment_url":"https://api.github.com/repos/thehyve/cbioportal/issues/comments{/number}","contents_url":"https://api.github.com/repos/thehyve/cbioportal/contents/{+path}","compare_url":"https://api.github.com/repos/thehyve/cbioportal/compare/{base}...{head}","merges_url":"https://api.github.com/repos/thehyve/cbioportal/merges","archive_url":"https://api.github.com/repos/thehyve/cbioportal/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/thehyve/cbioportal/downloads","issues_url":"https://api.github.com/repos/thehyve/cbioportal/issues{/number}","pulls_url":"https://api.github.com/repos/thehyve/cbioportal/pulls{/number}","milestones_url":"https://api.github.com/repos/thehyve/cbioportal/milestones{/number}","notifications_url":"https://api.github.com/repos/thehyve/cbioportal/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/thehyve/cbioportal/labels{/name}","releases_url":"https://api.github.com/repos/thehyve/cbioportal/releases{/id}","deployments_url":"https://api.github.com/repos/thehyve/cbioportal/deployments","created_at":"2015-06-12T16:27:05Z","updated_at":"2017-04-05T08:07:39Z","pushed_at":"2018-09-13T10:40:12Z","git_url":"git://github.com/thehyve/cbioportal.git","ssh_url":"git@github.com:thehyve/cbioportal.git","clone_url":"https://github.com/thehyve/cbioportal.git","svn_url":"https://github.com/thehyve/cbioportal","homepage":"","size":224899,"stargazers_count":2,"watchers_count":2,"language":null,"has_issues":false,"has_projects":true,"has_downloads":true,"has_wiki":true,"has_pages":false,"forks_count":2,"mirror_url":null,"archived":false,"open_issues_count":1,"license":null,"forks":2,"open_issues":1,"watchers":2,"default_branch":"default"}},"base":{"label":"cBioPortal:master","ref":"master","sha":"042fe2db25721c158a083fcf5073f05771d131ba","user":{"login":"cBioPortal","id":9876251,"node_id":"MDEyOk9yZ2FuaXphdGlvbjk4NzYyNTE=","avatar_url":"https://avatars2.githubusercontent.com/u/9876251?v=4","gravatar_id":"","url":"https://api.github.com/users/cBioPortal","html_url":"https://github.com/cBioPortal","followers_url":"https://api.github.com/users/cBioPortal/followers","following_url":"https://api.github.com/users/cBioPortal/following{/other_user}","gists_url":"https://api.github.com/users/cBioPortal/gists{/gist_id}","starred_url":"https://api.github.com/users/cBioPortal/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cBioPortal/subscriptions","organizations_url":"https://api.github.com/users/cBioPortal/orgs","repos_url":"https://api.github.com/users/cBioPortal/repos","events_url":"https://api.github.com/users/cBioPortal/events{/privacy}","received_events_url":"https://api.github.com/users/cBioPortal/received_events","type":"Organization","site_admin":false},"repo":{"id":32481543,"node_id":"MDEwOlJlcG9zaXRvcnkzMjQ4MTU0Mw==","name":"cbioportal","full_name":"cBioPortal/cbioportal","owner":{"login":"cBioPortal","id":9876251,"node_id":"MDEyOk9yZ2FuaXphdGlvbjk4NzYyNTE=","avatar_url":"https://avatars2.githubusercontent.com/u/9876251?v=4","gravatar_id":"","url":"https://api.github.com/users/cBioPortal","html_url":"https://github.com/cBioPortal","followers_url":"https://api.github.com/users/cBioPortal/followers","following_url":"https://api.github.com/users/cBioPortal/following{/other_user}","gists_url":"https://api.github.com/users/cBioPortal/gists{/gist_id}","starred_url":"https://api.github.com/users/cBioPortal/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cBioPortal/subscriptions","organizations_url":"https://api.github.com/users/cBioPortal/orgs","repos_url":"https://api.github.com/users/cBioPortal/repos","events_url":"https://api.github.com/users/cBioPortal/events{/privacy}","received_events_url":"https://api.github.com/users/cBioPortal/received_events","type":"Organization","site_admin":false},"private":false,"html_url":"https://github.com/cBioPortal/cbioportal","description":"cBioPortal for Cancer Genomics","fork":false,"url":"https://api.github.com/repos/cBioPortal/cbioportal","forks_url":"https://api.github.com/repos/cBioPortal/cbioportal/forks","keys_url":"https://api.github.com/repos/cBioPortal/cbioportal/keys{/key_id}","collaborators_url":"https://api.github.com/repos/cBioPortal/cbioportal/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/cBioPortal/cbioportal/teams","hooks_url":"https://api.github.com/repos/cBioPortal/cbioportal/hooks","issue_events_url":"https://api.github.com/repos/cBioPortal/cbioportal/issues/events{/number}","events_url":"https://api.github.com/repos/cBioPortal/cbioportal/events","assignees_url":"https://api.github.com/repos/cBioPortal/cbioportal/assignees{/user}","branches_url":"https://api.github.com/repos/cBioPortal/cbioportal/branches{/branch}","tags_url":"https://api.github.com/repos/cBioPortal/cbioportal/tags","blobs_url":"https://api.github.com/repos/cBioPortal/cbioportal/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/cBioPortal/cbioportal/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/cBioPortal/cbioportal/git/refs{/sha}","trees_url":"https://api.github.com/repos/cBioPortal/cbioportal/git/trees{/sha}","statuses_url":"https://api.github.com/repos/cBioPortal/cbioportal/statuses/{sha}","languages_url":"https://api.github.com/repos/cBioPortal/cbioportal/languages","stargazers_url":"https://api.github.com/repos/cBioPortal/cbioportal/stargazers","contributors_url":"https://api.github.com/repos/cBioPortal/cbioportal/contributors","subscribers_url":"https://api.github.com/repos/cBioPortal/cbioportal/subscribers","subscription_url":"https://api.github.com/repos/cBioPortal/cbioportal/subscription","commits_url":"https://api.github.com/repos/cBioPortal/cbioportal/commits{/sha}","git_commits_url":"https://api.github.com/repos/cBioPortal/cbioportal/git/commits{/sha}","comments_url":"https://api.github.com/repos/cBioPortal/cbioportal/comments{/number}","issue_comment_url":"https://api.github.com/repos/cBioPortal/cbioportal/issues/comments{/number}","contents_url":"https://api.github.com/repos/cBioPortal/cbioportal/contents/{+path}","compare_url":"https://api.github.com/repos/cBioPortal/cbioportal/compare/{base}...{head}","merges_url":"https://api.github.com/repos/cBioPortal/cbioportal/merges","archive_url":"https://api.github.com/repos/cBioPortal/cbioportal/{archive_format}{/ref}","downloads_url":"https://api.github.com/repos/cBioPortal/cbioportal/downloads","issues_url":"https://api.github.com/repos/cBioPortal/cbioportal/issues{/number}","pulls_url":"https://api.github.com/repos/cBioPortal/cbioportal/pulls{/number}","milestones_url":"https://api.github.com/repos/cBioPortal/cbioportal/milestones{/number}","notifications_url":"https://api.github.com/repos/cBioPortal/cbioportal/notifications{?since,all,participating}","labels_url":"https://api.github.com/repos/cBioPortal/cbioportal/labels{/name}","releases_url":"https://api.github.com/repos/cBioPortal/cbioportal/releases{/id}","deployments_url":"https://api.github.com/repos/cBioPortal/cbioportal/deployments","created_at":"2015-03-18T20:09:09Z","updated_at":"2018-09-13T08:13:11Z","pushed_at":"2018-09-14T04:00:02Z","git_url":"git://github.com/cBioPortal/cbioportal.git","ssh_url":"git@github.com:cBioPortal/cbioportal.git","clone_url":"https://github.com/cBioPortal/cbioportal.git","svn_url":"https://github.com/cBioPortal/cbioportal","homepage":"http://cbioportal.org","size":218097,"stargazers_count":209,"watchers_count":209,"language":"JavaScript","has_issues":true,"has_projects":true,"has_downloads":true,"has_wiki":true,"has_pages":true,"forks_count":195,"mirror_url":null,"archived":false,"open_issues_count":500,"license":{"key":"agpl-3.0","name":"GNU Affero General Public License v3.0","spdx_id":"AGPL-3.0","url":"https://api.github.com/licenses/agpl-3.0","node_id":"MDc6TGljZW5zZTE="},"forks":195,"open_issues":500,"watchers":209,"default_branch":"master"}},"_links":{"self":{"href":"https://api.github.com/repos/cBioPortal/cbioportal/pulls/4781"},"html":{"href":"https://github.com/cBioPortal/cbioportal/pull/4781"},"issue":{"href":"https://api.github.com/repos/cBioPortal/cbioportal/issues/4781"},"comments":{"href":"https://api.github.com/repos/cBioPortal/cbioportal/issues/4781/comments"},"review_comments":{"href":"https://api.github.com/repos/cBioPortal/cbioportal/pulls/4781/comments"},"review_comment":{"href":"https://api.github.com/repos/cBioPortal/cbioportal/pulls/comments{/number}"},"commits":{"href":"https://api.github.com/repos/cBioPortal/cbioportal/pulls/4781/commits"},"statuses":{"href":"https://api.github.com/repos/cBioPortal/cbioportal/statuses/d82c5fc7b40dd1f4a5fcffa67976e150dad4f382"}},"author_association":"MEMBER"}}
{"actor":{"display_login":"pieterlukasse"}}