{"action":"created","issue":{"url":"https://api.github.com/repos/GMOD/Apollo/issues/539","labels_url":"https://api.github.com/repos/GMOD/Apollo/issues/539/labels{/name}","comments_url":"https://api.github.com/repos/GMOD/Apollo/issues/539/comments","events_url":"https://api.github.com/repos/GMOD/Apollo/issues/539/events","html_url":"https://github.com/GMOD/Apollo/issues/539","id":100835376,"number":539,"title":"(4h) provide a mechanism for deleting organisms with attached annotation data","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":[{"url":"https://api.github.com/repos/GMOD/Apollo/labels/bug","name":"bug","color":"fc2929"},{"url":"https://api.github.com/repos/GMOD/Apollo/labels/enhancement","name":"enhancement","color":"84b6eb"},{"url":"https://api.github.com/repos/GMOD/Apollo/labels/NAL","name":"NAL","color":"fad8c7"}],"state":"open","locked":false,"assignee":{"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},"milestone":{"url":"https://api.github.com/repos/GMOD/Apollo/milestones/13","html_url":"https://github.com/GMOD/Apollo/milestones/2.0.1","labels_url":"https://api.github.com/repos/GMOD/Apollo/milestones/13/labels","id":1059255,"number":13,"title":"2.0.1","description":"Important issues minimally include:\r\n- proper isoform overlap handling when making changes to genomic feature structure\r\n- track permissions change\r\n- proper session logout (including a possible change of framework libraries)\r\n- some optimizations\r\n","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":12,"closed_issues":23,"state":"open","created_at":"2015-04-08T21:05:39Z","updated_at":"2015-10-01T20:31:54Z","due_on":"2015-09-26T07:00:00Z","closed_at":null},"comments":10,"created_at":"2015-08-13T18:22:53Z","updated_at":"2015-10-02T18:58:37Z","closed_at":null,"body":"I actually noted this problem yesterday and was hoping it was a fluke, but I noticed that deleting an organism has problems via the \"Delete organism\" button on OrganismPanel\r\n\r\nLog:\r\n\r\n\r\n    | Error 2015-08-13 13:10:18,729 [http-bio-8080-exec-4] ERROR errors.GrailsExceptionResolver  - ObjectDeletedException occurred when processing request: [POST] /apollo/organism/deleteOrganism - parameters:\r\n    data: {\"id\":\"72274\", \"commonName\":\"Amel4\", \"directory\":\"/opt/apollo/honeybee/data\", \"genus\":\"Apis\", \"species\":\"mellifera\", \"sequences\":543, \"annotationCount\":543}\r\n    deleted object would be re-saved by cascade (remove deleted object from associations): [org.bbop.apollo.FeatureLocation#82921]. Stacktrace follows:\r\n    Message: deleted object would be re-saved by cascade (remove deleted object from associations): [org.bbop.apollo.FeatureLocation#82921]\r\n        Line | Method\r\n    ->>  101 | doCall                in org.grails.datastore.gorm.GormStaticApi$_methodMissing_closure2\r\n    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\r\n    |     35 | isAdmin               in org.bbop.apollo.PermissionService\r\n    |    192 | $tt__findAllOrganisms in org.bbop.apollo.OrganismController\r\n    |     49 | $tt__deleteOrganism   in     ''\r\n    |    198 | doFilter . . . . . .  in grails.plugin.cache.web.filter.PageFragmentCachingFilter\r\n    |     63 | doFilter              in grails.plugin.cache.web.filter.AbstractFilter\r\n    |    449 | executeChain . . . .  in org.apache.shiro.web.servlet.AbstractShiroFilter\r\n    |    365 | call                  in org.apache.shiro.web.servlet.AbstractShiroFilter$1\r\n    |     90 | doCall . . . . . . .  in org.apache.shiro.subject.support.SubjectCallable\r\n    |     83 | call                  in     ''\r\n    |    383 | execute . . . . . . . in org.apache.shiro.subject.support.DelegatingSubject\r\n    |    362 | doFilterInternal      in org.apache.shiro.web.servlet.AbstractShiroFilter\r\n    |    125 | doFilter . . . . . .  in org.apache.shiro.web.servlet.OncePerRequestFilter\r\n    |   1145 | runWorker             in java.util.concurrent.ThreadPoolExecutor\r\n    |    615 | run . . . . . . . . . in java.util.concurrent.ThreadPoolExecutor$Worker\r\n    ^    744 | run                   in java.lang.Thread\r\n\r\n\r\n\r\n\r\nThis only appears to happen if there are annotations added for the organism.\r\n\r\nI also tested this on icebox and it appears to cause problems there too. It just says \"Processing ...\" and this overlay does not disappear after several minutes. I don't know the logs on icebox though"},"comment":{"url":"https://api.github.com/repos/GMOD/Apollo/issues/comments/145126191","html_url":"https://github.com/GMOD/Apollo/issues/539#issuecomment-145126191","issue_url":"https://api.github.com/repos/GMOD/Apollo/issues/539","id":145126191,"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},"created_at":"2015-10-02T18:58:36Z","updated_at":"2015-10-02T18:58:36Z","body":"\nI think having flags that this makes sense it terms of OGS and 2.2.  The concept of a deleted status flag and how it gets interpreted throughout the interface is pretty involved. \n\nWe are already going to have a web service to handle annotation deletion of organisms.   In the interim (WRT to this update) . . I think that the most appropriate thing to do (before going nuclear) is:\n\n1 - warn that there are N annotations associated with this organism that need to be deleted before the organism can be deleted. \n2 - suggest that they use the web service to delete all of them . . \n\nNathan\n\n> On Oct 2, 2015, at 11:49 AM, Colin Diesh <notifications@github.com> wrote:\n> \n> I think we might want to reconsider that act of \"deletion\". Instead of just wiping it out, gone for good, which can introduce data inconsistencies, we can just flag it as deleted and then not show it\n> \n> We could have a \"big hammer\" to actually delete things, but I think flagging things at deleted can solve more headaches in the short term, and it actually provides a better record\n> \n> This can go for deleted organisms, deleted users, deleted annotations etc. Just flag as deleted instead of actually deleting.\n> \n> —\n> Reply to this email directly or view it on GitHub <https://github.com/GMOD/Apollo/issues/539#issuecomment-145123303>.\n> \n\n"}}