{"action":"created","issue":{"url":"https://api.github.com/repos/GMOD/Apollo/issues/555","labels_url":"https://api.github.com/repos/GMOD/Apollo/issues/555/labels{/name}","comments_url":"https://api.github.com/repos/GMOD/Apollo/issues/555/comments","events_url":"https://api.github.com/repos/GMOD/Apollo/issues/555/events","html_url":"https://github.com/GMOD/Apollo/issues/555","id":103614654,"number":555,"title":"Set exon boundary very slow","user":{"login":"cmdcolin","id":6511937,"avatar_url":"https://avatars.githubusercontent.com/u/6511937?v=3","gravatar_id":"","url":"https://api.github.com/users/cmdcolin","html_url":"https://github.com/cmdcolin","followers_url":"https://api.github.com/users/cmdcolin/followers","following_url":"https://api.github.com/users/cmdcolin/following{/other_user}","gists_url":"https://api.github.com/users/cmdcolin/gists{/gist_id}","starred_url":"https://api.github.com/users/cmdcolin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cmdcolin/subscriptions","organizations_url":"https://api.github.com/users/cmdcolin/orgs","repos_url":"https://api.github.com/users/cmdcolin/repos","events_url":"https://api.github.com/users/cmdcolin/events{/privacy}","received_events_url":"https://api.github.com/users/cmdcolin/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-08-27T23:22:09Z","updated_at":"2015-08-27T23:28:23Z","closed_at":null,"body":"Setting exon boundaries can take a very long time on icebox and on genomes (our server).\r\n\r\nIt takes consistently about 25 seconds for me on icebox for the honeybee genomes, but it is unclear why it was taking so long\r\n\r\nI wanted to look into what was taking so much time so I went ahead and added a lot of debugging statements to the setExonBoundaries method (timing in ms)\r\n\r\nResults:\r\n\r\n    2015-08-27 18:12:03,785 [Actor Thread 1] WARN  apollo.RequestHandlingService  - start permissions setExonBoundary\r\n    2015-08-27 18:12:04,236 [Actor Thread 1] WARN  apollo.RequestHandlingService  - getting permissions setExonBoundary 451\r\n    2015-08-27 18:12:04,284 [Actor Thread 1] WARN  apollo.RequestHandlingService  - exon.findByUniqueName 23\r\n    2015-08-27 18:12:04,341 [Actor Thread 1] WARN  apollo.RequestHandlingService  - exonService.getTranscript 57\r\n    2015-08-27 18:12:04,616 [Actor Thread 1] WARN  apollo.RequestHandlingService  - featureService.convertFeatureToJSON 274\r\n    2015-08-27 18:12:04,628 [Actor Thread 1] WARN  apollo.RequestHandlingService  - FeatureLocation.findByFeature 11\r\n    2015-08-27 18:12:04,944 [Actor Thread 1] WARN  apollo.RequestHandlingService  - featureService.removeExonOverlapsAndAdjacencies 316\r\n    2015-08-27 18:12:05,001 [Actor Thread 1] WARN  apollo.RequestHandlingService  - transcriptService.updateGeneBoundaries 57\r\n    2015-08-27 18:12:05,013 [Actor Thread 1] WARN  apollo.RequestHandlingService  - exon.save 12\r\n    2015-08-27 18:12:06,004 [Actor Thread 1] WARN  apollo.RequestHandlingService  - calculateCDS 991\r\n    2015-08-27 18:12:07,520 [Actor Thread 1] WARN  apollo.RequestHandlingService  - nonCanonicalSplitSiteService.findNonCanonicalAcceptorDonorSpliceSites 1515\r\n    2015-08-27 18:12:07,531 [Actor Thread 1] WARN  apollo.RequestHandlingService  - transcript.save 11\r\n    2015-08-27 18:12:45,947 [Actor Thread 1] WARN  apollo.RequestHandlingService  - featureEventService.addNewFeatureEvent 38416\r\n    2015-08-27 18:12:46,010 [Actor Thread 1] WARN  apollo.RequestHandlingService  - fireAnnotationEvent 61\r\n\r\n\r\nSo you can see the main culprit is the addNewFeatureEvent at 38 seconds\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/GMOD/Apollo/issues/comments/135583355","html_url":"https://github.com/GMOD/Apollo/issues/555#issuecomment-135583355","issue_url":"https://api.github.com/repos/GMOD/Apollo/issues/555","id":135583355,"user":{"login":"cmdcolin","id":6511937,"avatar_url":"https://avatars.githubusercontent.com/u/6511937?v=3","gravatar_id":"","url":"https://api.github.com/users/cmdcolin","html_url":"https://github.com/cmdcolin","followers_url":"https://api.github.com/users/cmdcolin/followers","following_url":"https://api.github.com/users/cmdcolin/following{/other_user}","gists_url":"https://api.github.com/users/cmdcolin/gists{/gist_id}","starred_url":"https://api.github.com/users/cmdcolin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cmdcolin/subscriptions","organizations_url":"https://api.github.com/users/cmdcolin/orgs","repos_url":"https://api.github.com/users/cmdcolin/repos","events_url":"https://api.github.com/users/cmdcolin/events{/privacy}","received_events_url":"https://api.github.com/users/cmdcolin/received_events","type":"User","site_admin":false},"created_at":"2015-08-27T23:28:23Z","updated_at":"2015-08-27T23:28:23Z","body":"It looks like maybe this is happening after a feature has built up a \"history\" of changes, and not just for \"First time\" sequence alterations\r\n\r\nThe one that I was editing on icebox had about 5 changes GB42150-RA-00001\r\n\r\n\r\nThe one on genomes had about 10 or so\r\n\r\n"}}