{"action":"created","issue":{"url":"https://api.github.com/repos/geneontology/amigo/issues/241","labels_url":"https://api.github.com/repos/geneontology/amigo/issues/241/labels{/name}","comments_url":"https://api.github.com/repos/geneontology/amigo/issues/241/comments","events_url":"https://api.github.com/repos/geneontology/amigo/issues/241/events","html_url":"https://github.com/geneontology/amigo/issues/241","id":104526983,"number":241,"title":"GOlr can no longer be loaded with annotations or bioentities","user":{"login":"kltm","id":2687900,"avatar_url":"https://avatars.githubusercontent.com/u/2687900?v=3","gravatar_id":"","url":"https://api.github.com/users/kltm","html_url":"https://github.com/kltm","followers_url":"https://api.github.com/users/kltm/followers","following_url":"https://api.github.com/users/kltm/following{/other_user}","gists_url":"https://api.github.com/users/kltm/gists{/gist_id}","starred_url":"https://api.github.com/users/kltm/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kltm/subscriptions","organizations_url":"https://api.github.com/users/kltm/orgs","repos_url":"https://api.github.com/users/kltm/repos","events_url":"https://api.github.com/users/kltm/events{/privacy}","received_events_url":"https://api.github.com/users/kltm/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/geneontology/amigo/labels/bug%20(A:%20showstopper)","name":"bug (A: showstopper)","color":"fc2929"}],"state":"open","locked":false,"assignee":null,"milestone":{"url":"https://api.github.com/repos/geneontology/amigo/milestones/10","html_url":"https://github.com/geneontology/amigo/milestones/hotfix","labels_url":"https://api.github.com/repos/geneontology/amigo/milestones/10/labels","id":1150116,"number":10,"title":"hotfix","description":"This is an issue that needs to be fixed now, and probably ported to all used (master and current production) branches.","creator":{"login":"kltm","id":2687900,"avatar_url":"https://avatars.githubusercontent.com/u/2687900?v=3","gravatar_id":"","url":"https://api.github.com/users/kltm","html_url":"https://github.com/kltm","followers_url":"https://api.github.com/users/kltm/followers","following_url":"https://api.github.com/users/kltm/following{/other_user}","gists_url":"https://api.github.com/users/kltm/gists{/gist_id}","starred_url":"https://api.github.com/users/kltm/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kltm/subscriptions","organizations_url":"https://api.github.com/users/kltm/orgs","repos_url":"https://api.github.com/users/kltm/repos","events_url":"https://api.github.com/users/kltm/events{/privacy}","received_events_url":"https://api.github.com/users/kltm/received_events","type":"User","site_admin":false},"open_issues":2,"closed_issues":6,"state":"open","created_at":"2015-06-04T20:52:53Z","updated_at":"2015-09-08T19:49:16Z","due_on":null,"closed_at":null},"comments":10,"created_at":"2015-09-02T16:55:08Z","updated_at":"2015-09-09T23:21:37Z","closed_at":null,"body":"Ugh, cannot get /anything/ loaded anymore:\r\n```text\r\n    While trying various reloads to track down the issue behind\r\n\r\n    https://github.com/geneontology/amigo/issues/240\r\n\r\n    I found two serious problems, both possibly related to owltools\r\n    (although a schema error is possible for one). The first, and\r\n    least severe, is that the load time has jumped from 4hrs to 14hrs\r\n    for the \"production\" load, which is a huge hit. I believe that the\r\n    memory required has also jumped up.\r\n    \r\n    The second thing, which is rather nasty, is that I am now no\r\n    longer able to commit any GAF information, and the way the error\r\n    is thrown, it effectively means that no annotation or bioentity\r\n    data can get loaded.\r\n    \r\n    Since these have both come on rather suddenly, I wanted to warn 1)\r\n    to avoid updating your tool chain until #240 is fixed (you should\r\n    tag on to that item) and 2) check loads for annotation and\r\n    bioentity information before pushing to production.\r\n    \r\n    I'll try to keep everybody up to date as we look at this.\r\n```\r\nSince I sent this email, I've reverted owltools to about a month ago (7919c6e) and still have the same problem, so I'm no longer going to look in that direction for the issue.\r\n\r\nNext, schema (amigo) and java (???).\r\n\r\nTagging @stuartmiyasato, @cmungall, and @hdietze as this may affect the pipeline elsewhere.\r\n\r\nPossible (temporal) relation to #240."},"comment":{"url":"https://api.github.com/repos/geneontology/amigo/issues/comments/139070545","html_url":"https://github.com/geneontology/amigo/issues/241#issuecomment-139070545","issue_url":"https://api.github.com/repos/geneontology/amigo/issues/241","id":139070545,"user":{"login":"cmungall","id":50745,"avatar_url":"https://avatars.githubusercontent.com/u/50745?v=3","gravatar_id":"","url":"https://api.github.com/users/cmungall","html_url":"https://github.com/cmungall","followers_url":"https://api.github.com/users/cmungall/followers","following_url":"https://api.github.com/users/cmungall/following{/other_user}","gists_url":"https://api.github.com/users/cmungall/gists{/gist_id}","starred_url":"https://api.github.com/users/cmungall/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cmungall/subscriptions","organizations_url":"https://api.github.com/users/cmungall/orgs","repos_url":"https://api.github.com/users/cmungall/repos","events_url":"https://api.github.com/users/cmungall/events{/privacy}","received_events_url":"https://api.github.com/users/cmungall/received_events","type":"User","site_admin":false},"created_at":"2015-09-09T23:21:37Z","updated_at":"2015-09-09T23:21:37Z","body":"Do we have a mini test set? Either whole ontology + GAF subsets\n\nOr if ontology size is an issue, we have some GAF subsets with matching \nontology subset modules, in owltools test/resources folders\n\nOn 9 Sep 2015, at 16:17, kltm wrote:\n\n> Well, not a direct schema mismatch, but still possible something is \n> out of sync. Will try and get a minimal set that I can load fast (and \n> fails) and will start tracking it through owltools.\n>\n> ---\n> Reply to this email directly or view it on GitHub:\n> https://github.com/geneontology/amigo/issues/241#issuecomment-139069967\n"}}