{"action":"created","comment":{"url":"https://api.github.com/repos/cBioPortal/cbioportal/pulls/comments/216966464","pull_request_review_id":154568357,"id":216966464,"node_id":"MDI0OlB1bGxSZXF1ZXN0UmV2aWV3Q29tbWVudDIxNjk2NjQ2NA==","diff_hunk":"@@ -2585,29 +2615,6 @@ def __init__(self, chrom_size_url, line):\n         return chrom_size_dict\n \n \n-class ContinuousValuesValidator(GenewiseFileValidator):\n-    \"\"\"Validator for matrix files mapping floats to gene/sample combinations.\n-\n-    Allowing missing values indicated by GenewiseFileValidator.NULL_VALUES.\n-    \"\"\"\n-\n-    def checkValue(self, value, col_index):\n-        \"\"\"Check a value in a sample column.\"\"\"\n-        stripped_value = value.strip()\n-        if stripped_value not in self.NULL_VALUES and not self.checkFloat(stripped_value):\n-            self.logger.error(\"Value is neither a real number nor \" + ', '.join(self.NULL_VALUES),\n-                              extra={'line_number': self.line_number,\n-                                     'column_number': col_index + 1,\n-                                     'cause': value})\n-\n-\n-class CNAContinuousValuesValidator(ContinuousValuesValidator):\n-\n-    \"\"\"Sub-class CNA validator.\"\"\"\n-\n-    OPTIONAL_HEADERS = ['Cytoband'] + GenewiseFileValidator.OPTIONAL_HEADERS","path":"core/src/main/scripts/importer/validateData.py","position":99,"original_position":97,"commit_id":"234c8a9d19daf2a6f46ba7306a48458a9ba105c0","original_commit_id":"be225dd9ecae0a7099433ff507f17a5c878f12b3","user":{"login":"fedde-s","id":4929431,"node_id":"MDQ6VXNlcjQ5Mjk0MzE=","avatar_url":"https://avatars3.githubusercontent.com/u/4929431?v=4","gravatar_id":"","url":"https://api.github.com/users/fedde-s","html_url":"https://github.com/fedde-s","followers_url":"https://api.github.com/users/fedde-s/followers","following_url":"https://api.github.com/users/fedde-s/following{/other_user}","gists_url":"https://api.github.com/users/fedde-s/gists{/gist_id}","starred_url":"https://api.github.com/users/fedde-s/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/fedde-s/subscriptions","organizations_url":"https://api.github.com/users/fedde-s/orgs","repos_url":"https://api.github.com/users/fedde-s/repos","events_url":"https://api.github.com/users/fedde-s/events{/privacy}","received_events_url":"https://api.github.com/users/fedde-s/received_events","type":"User","site_admin":false},"body":"Superclass! 🦸   (I hope this pull request gets integrated before [that emoji](https://emojipedia.org/superhero/) is supported by default on all major operating systems)","created_at":"2018-09-12T09:50:56Z","updated_at":"2018-09-12T09:50:56Z","html_url":"https://github.com/cBioPortal/cbioportal/pull/4666#discussion_r216966464","pull_request_url":"https://api.github.com/repos/cBioPortal/cbioportal/pulls/4666","author_association":"MEMBER","_links":{"self":{"href":"https://api.github.com/repos/cBioPortal/cbioportal/pulls/comments/216966464"},"html":{"href":"https://github.com/cBioPortal/cbioportal/pull/4666#discussion_r216966464"},"pull_request":{"href":"https://api.github.com/repos/cBioPortal/cbioportal/pulls/4666"}},"in_reply_to_id":216661677},"pull_request":{"url":"https://api.github.com/repos/cBioPortal/cbioportal/pulls/4666","id":209552378,"node_id":"MDExOlB1bGxSZXF1ZXN0MjA5NTUyMzc4","html_url":"https://github.com/cBioPortal/cbioportal/pull/4666","diff_url":"https://github.com/cBioPortal/cbioportal/pull/4666.diff","patch_url":"https://github.com/cBioPortal/cbioportal/pull/4666.patch","issue_url":"https://api.github.com/repos/cBioPortal/cbioportal/issues/4666","number":4666,"state":"open","locked":false,"title":"Add validation rule: mutation and CNA data require case lists","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":"# What? Why?\r\nFix #3577.\r\n\r\nChanges proposed in this pull request:\r\n- Add validation rule that mutation and CNA data require case lists (_sequenced and _cna). Report an error when these case lists are missing.\r\n- Add warning when _cnaseq is missing.\r\n- Update old test data to have these case lists.\r\n- Add new tests with study that does not have these case lists.\r\n- Update documentation\r\n- **Remove `cna` as allowed stable ID for discrete CNA genetic profile**. `gistic` is the used stable ID for discrete CNA genetic profile, while `cna` is the stable ID for CNA case list. This format was followed for many studies on DataHub, for example: \r\nhttps://github.com/cBioPortal/datahub/blob/master/public/acc_tcga/meta_CNA.txt\r\nhttps://github.com/cBioPortal/datahub/blob/master/public/acc_tcga/case_lists/cases_cna.txt\r\n- Fix validator crash when no symbol in CNA data to solve https://github.com/cBioPortal/datahub/issues/318","created_at":"2018-08-20T15:07:27Z","updated_at":"2018-09-12T09:50:56Z","closed_at":null,"merged_at":null,"merge_commit_sha":"ce41ac6bd6b03f7cd4e8884ba7a37f4523262e48","assignee":null,"assignees":[],"requested_reviewers":[{"login":"n1zea144","id":366003,"node_id":"MDQ6VXNlcjM2NjAwMw==","avatar_url":"https://avatars1.githubusercontent.com/u/366003?v=4","gravatar_id":"","url":"https://api.github.com/users/n1zea144","html_url":"https://github.com/n1zea144","followers_url":"https://api.github.com/users/n1zea144/followers","following_url":"https://api.github.com/users/n1zea144/following{/other_user}","gists_url":"https://api.github.com/users/n1zea144/gists{/gist_id}","starred_url":"https://api.github.com/users/n1zea144/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/n1zea144/subscriptions","organizations_url":"https://api.github.com/users/n1zea144/orgs","repos_url":"https://api.github.com/users/n1zea144/repos","events_url":"https://api.github.com/users/n1zea144/events{/privacy}","received_events_url":"https://api.github.com/users/n1zea144/received_events","type":"User","site_admin":false},{"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":"angelicaochoa","id":15623749,"node_id":"MDQ6VXNlcjE1NjIzNzQ5","avatar_url":"https://avatars2.githubusercontent.com/u/15623749?v=4","gravatar_id":"","url":"https://api.github.com/users/angelicaochoa","html_url":"https://github.com/angelicaochoa","followers_url":"https://api.github.com/users/angelicaochoa/followers","following_url":"https://api.github.com/users/angelicaochoa/following{/other_user}","gists_url":"https://api.github.com/users/angelicaochoa/gists{/gist_id}","starred_url":"https://api.github.com/users/angelicaochoa/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/angelicaochoa/subscriptions","organizations_url":"https://api.github.com/users/angelicaochoa/orgs","repos_url":"https://api.github.com/users/angelicaochoa/repos","events_url":"https://api.github.com/users/angelicaochoa/events{/privacy}","received_events_url":"https://api.github.com/users/angelicaochoa/received_events","type":"User","site_admin":false}],"requested_teams":[],"labels":[{"id":216414571,"node_id":"MDU6TGFiZWwyMTY0MTQ1NzE=","url":"https://api.github.com/repos/cBioPortal/cbioportal/labels/documentation","name":"documentation","color":"0052cc","default":false},{"id":288494812,"node_id":"MDU6TGFiZWwyODg0OTQ4MTI=","url":"https://api.github.com/repos/cBioPortal/cbioportal/labels/ready%20to%20review","name":"ready 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