{"action":"created","issue":{"url":"https://api.github.com/repos/openmicroscopy/openmicroscopy/issues/3486","labels_url":"https://api.github.com/repos/openmicroscopy/openmicroscopy/issues/3486/labels{/name}","comments_url":"https://api.github.com/repos/openmicroscopy/openmicroscopy/issues/3486/comments","events_url":"https://api.github.com/repos/openmicroscopy/openmicroscopy/issues/3486/events","html_url":"https://github.com/openmicroscopy/openmicroscopy/pull/3486","id":57714350,"number":3486,"title":"Make LightSettings indexing work with Channel and MicrobeamManipulation","user":{"login":"melissalinkert","id":109998,"avatar_url":"https://avatars.githubusercontent.com/u/109998?v=3","gravatar_id":"","url":"https://api.github.com/users/melissalinkert","html_url":"https://github.com/melissalinkert","followers_url":"https://api.github.com/users/melissalinkert/followers","following_url":"https://api.github.com/users/melissalinkert/following{/other_user}","gists_url":"https://api.github.com/users/melissalinkert/gists{/gist_id}","starred_url":"https://api.github.com/users/melissalinkert/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/melissalinkert/subscriptions","organizations_url":"https://api.github.com/users/melissalinkert/orgs","repos_url":"https://api.github.com/users/melissalinkert/repos","events_url":"https://api.github.com/users/melissalinkert/events{/privacy}","received_events_url":"https://api.github.com/users/melissalinkert/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/openmicroscopy/openmicroscopy/labels/develop","name":"develop","color":"02e10c"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-02-15T02:02:14Z","updated_at":"2015-02-16T13:43:12Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/openmicroscopy/openmicroscopy/pulls/3486","html_url":"https://github.com/openmicroscopy/openmicroscopy/pull/3486","diff_url":"https://github.com/openmicroscopy/openmicroscopy/pull/3486.diff","patch_url":"https://github.com/openmicroscopy/openmicroscopy/pull/3486.patch"},"body":"A LightSettings object can be attached to either a Channel (with 2\r\nindexes) or a MicrobeamManipulation (with 3 indexes).  This removes the\r\nhard-coded index counts and updates ReferenceProcessor to fill in the\r\nindex map appropriately for both cases.  This should prevent\r\nOMEXMLModelComparator from incorrectly detecting the LSID equality when\r\nthere are many of both types of LightSettings linkages, which in turn ensures that each LightSettings' reference to a LightSource is properly resolved.\r\n\r\nFixes http://trac.openmicroscopy.org/ome/ticket/12603.\r\n\r\nTo test as in the ticket, run:\r\n\r\n```mkfake test.fake -plates 4 -runs 4 -rows 4 -columns 4 -fields 4```\r\n\r\nand then import ```test.fake```.  Without this PR, an exception should be thrown during metadata processing as in the ticket; with this PR, the import should succeed.\r\n\r\nWhile this does seem to work (at least in my testing), it does worry me that both of the files in question have not been substantially changed in some years.  Especially careful code review would be appreciated in addition to an import test to verify that this is not a bad idea."},"comment":{"url":"https://api.github.com/repos/openmicroscopy/openmicroscopy/issues/comments/74509701","html_url":"https://github.com/openmicroscopy/openmicroscopy/pull/3486#issuecomment-74509701","issue_url":"https://api.github.com/repos/openmicroscopy/openmicroscopy/issues/3486","id":74509701,"user":{"login":"sbesson","id":1355463,"avatar_url":"https://avatars.githubusercontent.com/u/1355463?v=3","gravatar_id":"","url":"https://api.github.com/users/sbesson","html_url":"https://github.com/sbesson","followers_url":"https://api.github.com/users/sbesson/followers","following_url":"https://api.github.com/users/sbesson/following{/other_user}","gists_url":"https://api.github.com/users/sbesson/gists{/gist_id}","starred_url":"https://api.github.com/users/sbesson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sbesson/subscriptions","organizations_url":"https://api.github.com/users/sbesson/orgs","repos_url":"https://api.github.com/users/sbesson/repos","events_url":"https://api.github.com/users/sbesson/events{/privacy}","received_events_url":"https://api.github.com/users/sbesson/received_events","type":"User","site_admin":false},"created_at":"2015-02-16T13:43:12Z","updated_at":"2015-02-16T13:43:12Z","body":"Stack trace received as part of the testing:\r\n\r\n```\r\n2015-02-16 13:33:29,631 ERROR [         ome.io.bioformats.BfPixelBuffer] (.Server-66) Failed to instantiate BfPixelsWrapper with /repositories/OMERO-5.1-merge-deploy/ManagedRepository/user-1_8/2015-02/16/13-13-50.738/Plate000/Run000/WellA000/Field000.fake\r\nERROR: trout-merge Blitz-0:\r\n2015-02-16 13:33:29,632 ERROR [                ome.io.nio.PixelsService] (.Server-66) Error instantiating pixel buffer: /repositories/OMERO-5.1-merge-deploy/ManagedRepository/user-1_8/2015-02/16/13-13-50.738/Plate000/Run000/WellA000/Field000.fake\r\njava.lang.RuntimeException: java.io.FileNotFoundException: /repositories/OMERO-5.1-merge-deploy/ManagedRepository/user-1_8/2015-02/16/13-13-50.738 (Is a directory)\r\n    at ome.io.bioformats.BfPixelBuffer.reader(BfPixelBuffer.java:81) ~[romio.jar:na]\r\n    at ome.io.bioformats.BfPixelBuffer.setSeries(BfPixelBuffer.java:109) ~[romio.jar:na]\r\n    at ome.io.nio.PixelsService.createBfPixelBuffer(PixelsService.java:811) [romio.jar:na]\r\n    at ome.io.nio.PixelsService._getPixelBuffer(PixelsService.java:578) [romio.jar:na]\r\n    at ome.io.nio.PixelsService.getPixelBuffer(PixelsService.java:496) [romio.jar:na]\r\n    at ome.services.ThumbnailBean.retrieveThumbnailSet(ThumbnailBean.java:946) [server.jar:na]\r\n    at ome.services.ThumbnailBean.getThumbnailByLongestSideSet(ThumbnailBean.java:918) [server.jar:na...\r\n```"}}