{"action":"created","issue":{"url":"https://api.github.com/repos/GMOD/Apollo/issues/850","repository_url":"https://api.github.com/repos/GMOD/Apollo","labels_url":"https://api.github.com/repos/GMOD/Apollo/issues/850/labels{/name}","comments_url":"https://api.github.com/repos/GMOD/Apollo/issues/850/comments","events_url":"https://api.github.com/repos/GMOD/Apollo/issues/850/events","html_url":"https://github.com/GMOD/Apollo/issues/850","id":131100912,"number":850,"title":"merging fails in some cases:","user":{"login":"nathandunn","id":751274,"avatar_url":"https://avatars.githubusercontent.com/u/751274?v=3","gravatar_id":"","url":"https://api.github.com/users/nathandunn","html_url":"https://github.com/nathandunn","followers_url":"https://api.github.com/users/nathandunn/followers","following_url":"https://api.github.com/users/nathandunn/following{/other_user}","gists_url":"https://api.github.com/users/nathandunn/gists{/gist_id}","starred_url":"https://api.github.com/users/nathandunn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nathandunn/subscriptions","organizations_url":"https://api.github.com/users/nathandunn/orgs","repos_url":"https://api.github.com/users/nathandunn/repos","events_url":"https://api.github.com/users/nathandunn/events{/privacy}","received_events_url":"https://api.github.com/users/nathandunn/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/GMOD/Apollo/labels/bug","name":"bug","color":"fc2929"},{"url":"https://api.github.com/repos/GMOD/Apollo/labels/Important","name":"Important","color":"eb6420"},{"url":"https://api.github.com/repos/GMOD/Apollo/labels/Ready","name":"Ready","color":"fbca04"}],"state":"closed","locked":false,"assignee":{"login":"monicacecilia","id":1714621,"avatar_url":"https://avatars.githubusercontent.com/u/1714621?v=3","gravatar_id":"","url":"https://api.github.com/users/monicacecilia","html_url":"https://github.com/monicacecilia","followers_url":"https://api.github.com/users/monicacecilia/followers","following_url":"https://api.github.com/users/monicacecilia/following{/other_user}","gists_url":"https://api.github.com/users/monicacecilia/gists{/gist_id}","starred_url":"https://api.github.com/users/monicacecilia/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/monicacecilia/subscriptions","organizations_url":"https://api.github.com/users/monicacecilia/orgs","repos_url":"https://api.github.com/users/monicacecilia/repos","events_url":"https://api.github.com/users/monicacecilia/events{/privacy}","received_events_url":"https://api.github.com/users/monicacecilia/received_events","type":"User","site_admin":false},"milestone":{"url":"https://api.github.com/repos/GMOD/Apollo/milestones/18","html_url":"https://github.com/GMOD/Apollo/milestones/2.0.2","labels_url":"https://api.github.com/repos/GMOD/Apollo/milestones/18/labels","id":1245678,"number":18,"title":"2.0.2","description":"","creator":{"login":"nathandunn","id":751274,"avatar_url":"https://avatars.githubusercontent.com/u/751274?v=3","gravatar_id":"","url":"https://api.github.com/users/nathandunn","html_url":"https://github.com/nathandunn","followers_url":"https://api.github.com/users/nathandunn/followers","following_url":"https://api.github.com/users/nathandunn/following{/other_user}","gists_url":"https://api.github.com/users/nathandunn/gists{/gist_id}","starred_url":"https://api.github.com/users/nathandunn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nathandunn/subscriptions","organizations_url":"https://api.github.com/users/nathandunn/orgs","repos_url":"https://api.github.com/users/nathandunn/repos","events_url":"https://api.github.com/users/nathandunn/events{/privacy}","received_events_url":"https://api.github.com/users/nathandunn/received_events","type":"User","site_admin":false},"open_issues":6,"closed_issues":88,"state":"open","created_at":"2015-08-07T15:36:37Z","updated_at":"2016-03-04T03:22:47Z","due_on":"2016-02-05T08:00:00Z","closed_at":null},"comments":5,"created_at":"2016-02-03T17:46:01Z","updated_at":"2016-03-04T03:22:47Z","closed_at":"2016-03-04T03:22:47Z","body":"Found in #842, but I was able to reproduce this with 2.0.1, but only was able to do it for the exact gene pairing in Group1.33 (as opposed to 1.10). \r\n\r\nBug 3: add A1 B1, modify B1 (delete exon A1 B2), modify A1 (Set readthrough stop codon = A2 B2), merge (expected AB, but fails) \r\n\r\nBug 3 described here:\r\n[issues_on_pull_request_842.pdf](https://github.com/GMOD/Apollo/files/116081/issues_on_pull_request_842.pdf)\r\n\r\nStacktrace of failure in 2.0.1:\r\n```\r\n2016-02-03 09:35:42,104 [clientInboundChannel-4] ERROR springwebsocket.GrailsSimpAnnotationMethodMessageHandler  - Unhandled exception\r\njava.lang.reflect.InvocationTargetException\r\n\tat org.bbop.apollo.AnnotationEditorController$__do_annotationEditor_closure3_closure4_closure5.doCall(AnnotationEditorController.groovy:1075)\r\n\tat org.bbop.apollo.AnnotationEditorController$__do_annotationEditor_closure3_closure4.doCall(AnnotationEditorController.groovy:1074)\r\n\tat org.bbop.apollo.AnnotationEditorController$__do_annotationEditor_closure3.doCall(AnnotationEditorController.groovy:1070)\r\n\tat groovyx.gpars.group.PGroup$3.call(PGroup.java:289)\r\n\tat groovyx.gpars.group.PGroup$4.run(PGroup.java:313)\r\n\tat java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)\r\n\tat java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)\r\n\tat java.lang.Thread.run(Thread.java:745)\r\nCaused by: org.springframework.dao.InvalidDataAccessApiUsageException: deleted object would be re-saved by cascade (remove deleted object from associations): [org.bbop.apollo.FeatureRelationship#205086]; nested exception is org.hibernate.ObjectDeletedException: deleted object would be re-saved by cascade (remove deleted object from associations): [org.bbop.apollo.FeatureRelationship#205086]\r\n\tat org.grails.datastore.gorm.GormStaticApi$_methodMissing_closure2.doCall(GormStaticApi.groovy:102)\r\n\tat org.bbop.apollo.FeatureRelationshipService.$tt__removeFeatureRelationship(FeatureRelationshipService.groovy:168)\r\n\tat org.bbop.apollo.TranscriptService.$tt__deleteTranscript(TranscriptService.groovy:110)\r\n\tat org.bbop.apollo.TranscriptService.$tt__mergeTranscripts(TranscriptService.groovy:461)\r\n\tat org.bbop.apollo.RequestHandlingService.$tt__mergeTranscripts(RequestHandlingService.groovy:2120)\r\n\t... 8 more\r\nCaused by: org.hibernate.ObjectDeletedException: deleted object would be re-saved by cascade (remove deleted object from associations): [org.bbop.apollo.FeatureRelationship#205086]\r\n\t... 13 more\r\n```\r\n\r\nFailure in 2.0.2-SNAPSHOT:\r\n\r\n<img width=\"842\" alt=\"screen shot 2016-02-03 at 9 47 29 am\" src=\"https://cloud.githubusercontent.com/assets/751274/12791276/3c5e30b4-ca5b-11e5-8f0e-44237bbd20df.png\">\r\n"},"comment":{"url":"https://api.github.com/repos/GMOD/Apollo/issues/comments/192080010","html_url":"https://github.com/GMOD/Apollo/issues/850#issuecomment-192080010","issue_url":"https://api.github.com/repos/GMOD/Apollo/issues/850","id":192080010,"user":{"login":"monicacecilia","id":1714621,"avatar_url":"https://avatars.githubusercontent.com/u/1714621?v=3","gravatar_id":"","url":"https://api.github.com/users/monicacecilia","html_url":"https://github.com/monicacecilia","followers_url":"https://api.github.com/users/monicacecilia/followers","following_url":"https://api.github.com/users/monicacecilia/following{/other_user}","gists_url":"https://api.github.com/users/monicacecilia/gists{/gist_id}","starred_url":"https://api.github.com/users/monicacecilia/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/monicacecilia/subscriptions","organizations_url":"https://api.github.com/users/monicacecilia/orgs","repos_url":"https://api.github.com/users/monicacecilia/repos","events_url":"https://api.github.com/users/monicacecilia/events{/privacy}","received_events_url":"https://api.github.com/users/monicacecilia/received_events","type":"User","site_admin":false},"created_at":"2016-03-04T03:22:47Z","updated_at":"2016-03-04T03:22:47Z","body":"Closing, but does not get a dancer.  -- bug still open in #792.  :person_with_pouting_face: "}}