{"action":"created","issue":{"url":"https://api.github.com/repos/cBioPortal/cbioportal/issues/1858","repository_url":"https://api.github.com/repos/cBioPortal/cbioportal","labels_url":"https://api.github.com/repos/cBioPortal/cbioportal/issues/1858/labels{/name}","comments_url":"https://api.github.com/repos/cBioPortal/cbioportal/issues/1858/comments","events_url":"https://api.github.com/repos/cBioPortal/cbioportal/issues/1858/events","html_url":"https://github.com/cBioPortal/cbioportal/issues/1858","id":186545827,"number":1858,"title":"Data loading fails for mutation data when using InnoDB","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},"labels":[{"id":270567389,"url":"https://api.github.com/repos/cBioPortal/cbioportal/labels/critical","name":"critical","color":"e11d21","default":false},{"id":284820316,"url":"https://api.github.com/repos/cBioPortal/cbioportal/labels/hotfix","name":"hotfix","color":"eb6420","default":false}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2016-11-01T14:21:53Z","updated_at":"2016-12-06T14:58:29Z","closed_at":null,"body":"Data loading will fail with a message like : \r\n\r\n```\r\nReading data from:  /datasets/tests/acc/tcga/data_mutations_extended.txt\r\nRecaching...\r\nFinished recaching...\r\n--> profile id:  8\r\n--> profile name:  Mutations\r\n--> genetic alteration type:  MUTATION_EXTENDED\r\n--> OMA Scores Column Number:  32\r\n--> records inserted into `mutation` table: 0\r\n\r\nWarnings / Errors:\r\n-------------------\r\n...\r\n\r\nABORTED! java.lang.RuntimeException: org.mskcc.cbio.portal.dao.DaoException: DB Error: only 0 of the 13431 records were inserted in `mutation`. More error/warning details: Row 1 doesn't contain data for all columns\r\nTraceback (most recent call last):\r\n  File \"./cbioportalImporter.py\", line 344, in <module>\r\n```\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/cBioPortal/cbioportal/issues/comments/265170906","html_url":"https://github.com/cBioPortal/cbioportal/issues/1858#issuecomment-265170906","issue_url":"https://api.github.com/repos/cBioPortal/cbioportal/issues/1858","id":265170906,"user":{"login":"ericblanc20","id":18400780,"avatar_url":"https://avatars.githubusercontent.com/u/18400780?v=3","gravatar_id":"","url":"https://api.github.com/users/ericblanc20","html_url":"https://github.com/ericblanc20","followers_url":"https://api.github.com/users/ericblanc20/followers","following_url":"https://api.github.com/users/ericblanc20/following{/other_user}","gists_url":"https://api.github.com/users/ericblanc20/gists{/gist_id}","starred_url":"https://api.github.com/users/ericblanc20/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ericblanc20/subscriptions","organizations_url":"https://api.github.com/users/ericblanc20/orgs","repos_url":"https://api.github.com/users/ericblanc20/repos","events_url":"https://api.github.com/users/ericblanc20/events{/privacy}","received_events_url":"https://api.github.com/users/ericblanc20/received_events","type":"User","site_admin":false},"created_at":"2016-12-06T14:58:29Z","updated_at":"2016-12-06T14:58:29Z","body":"Same problem using thehyve's hotfix branch on `study_es_0`, following the doc. (The branch uses `LinkedHashMap` in `MySQLbulkLoader` & doesn't use bulk loader in `DaoGene.addGene()` ):\r\n\r\n```\r\nReading data from:  ../../../test/scripts/test_data/study_es_0/data_fusions.txt\r\nRecaching...\r\nFinished recaching...\r\n--> profile id:  3\r\n--> profile name:  Fusions\r\n--> genetic alteration type:  FUSION\r\n--> records inserted into `mutation` table: 0\r\n\r\nWarnings / Errors:\r\n-------------------\r\n...\r\nABORTED! java.lang.RuntimeException: org.mskcc.cbio.portal.dao.DaoException: DB Error: only 0 of the 3 records were inserted in `mutation`. More error/warning details: Row 1 doesn't contain data for all columns\r\n```\r\n\r\nmysql version 5.7.13, all tables use InnoDB.\r\nmacosx 10.10.5, Darwin Kernel Version 14.5.0\r\n\r\nIs there a workaround, should I use other versions, and if yes, which one?\r\n\r\nThanks!"}}
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