{"action":"created","comment":{"url":"https://api.github.com/repos/cBioPortal/cbioportal/pulls/comments/88884992","pull_request_review_id":9438405,"id":88884992,"diff_hunk":"@@ -104,7 +111,7 @@ public int addGeneticAlterations(int geneticProfileId, long entrezGeneId, String\n        if (MySQLbulkLoader.isBulkLoad() ) {\n           //  write to the temp file maintained by the MySQLbulkLoader\n           MySQLbulkLoader.getMySQLbulkLoader(\"genetic_alteration\").insertRecord(Integer.toString( geneticProfileId ),\n-                  Long.toString( entrezGeneId ), valueBuffer.toString());","path":"core/src/main/java/org/mskcc/cbio/portal/dao/DaoGeneticAlteration.java","position":34,"original_position":34,"commit_id":"0f9b536e0ce780b29f0615120e0a6d311ea80db4","original_commit_id":"0f9b536e0ce780b29f0615120e0a6d311ea80db4","user":{"login":"sheridancbio","id":7747489,"avatar_url":"https://avatars.githubusercontent.com/u/7747489?v=3","gravatar_id":"","url":"https://api.github.com/users/sheridancbio","html_url":"https://github.com/sheridancbio","followers_url":"https://api.github.com/users/sheridancbio/followers","following_url":"https://api.github.com/users/sheridancbio/following{/other_user}","gists_url":"https://api.github.com/users/sheridancbio/gists{/gist_id}","starred_url":"https://api.github.com/users/sheridancbio/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sheridancbio/subscriptions","organizations_url":"https://api.github.com/users/sheridancbio/orgs","repos_url":"https://api.github.com/users/sheridancbio/repos","events_url":"https://api.github.com/users/sheridancbio/events{/privacy}","received_events_url":"https://api.github.com/users/sheridancbio/received_events","type":"User","site_admin":false},"body":"yes .. entrezGeneId should not be Long anyway ... it has been set to an int(11) mysql field everywhere now\r\na 4 space indent would be standard, although fixing style is not necessary for this PR. (another example are the extra spaces around argument in the function call)","created_at":"2016-11-21T12:32:22Z","updated_at":"2016-11-21T12:35:25Z","html_url":"https://github.com/cBioPortal/cbioportal/pull/1902#discussion_r88884992","pull_request_url":"https://api.github.com/repos/cBioPortal/cbioportal/pulls/1902","_links":{"self":{"href":"https://api.github.com/repos/cBioPortal/cbioportal/pulls/comments/88884992"},"html":{"href":"https://github.com/cBioPortal/cbioportal/pull/1902#discussion_r88884992"},"pull_request":{"href":"https://api.github.com/repos/cBioPortal/cbioportal/pulls/1902"}}},"pull_request":{"url":"https://api.github.com/repos/cBioPortal/cbioportal/pulls/1902","id":93983058,"html_url":"https://github.com/cBioPortal/cbioportal/pull/1902","diff_url":"https://github.com/cBioPortal/cbioportal/pull/1902.diff","patch_url":"https://github.com/cBioPortal/cbioportal/pull/1902.patch","issue_url":"https://api.github.com/repos/cBioPortal/cbioportal/issues/1902","number":1902,"state":"open","locked":false,"title":"Introducing Genetic entity","user":{"login":"pieterlukasse","id":2900303,"avatar_url":"https://avatars.githubusercontent.com/u/2900303?v=3","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":"# What? 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This PR makes the necessary changes to support this (no other entities are added here yet).  \r\n\r\n\r\nChanges proposed in this pull request:\r\n- table `genetic_alteration` is linked to `genetic_entity` instead of to `gene` and table `gene` now has a reference to `genetic_entity` (see model in [RFC 28 - Appendix 5](https://docs.google.com/document/d/1g5HPPXrLqJQmfxP1RcWGA6-QdcHCTLr_JAuQklQdfMs/edit#heading=h.h5c0v3jwn3i5))\r\n- respective SQL code added to `migration.sql` and `cgds.sql`\r\n- updated Dao layer accordingly \r\n- updated java unit tests accordingly\r\n- not directly related: update `commons-dbcp` version in 2 pom.xml files\r\n\r\n# Notify reviewers\r\n@jjgao @ersinciftci @n1zea144 @angelicaochoa 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