{"action":"created","issue":{"url":"https://api.github.com/repos/GMOD/Apollo/issues/171","labels_url":"https://api.github.com/repos/GMOD/Apollo/issues/171/labels{/name}","comments_url":"https://api.github.com/repos/GMOD/Apollo/issues/171/comments","events_url":"https://api.github.com/repos/GMOD/Apollo/issues/171/events","html_url":"https://github.com/GMOD/Apollo/issues/171","id":58234573,"number":171,"title":"export CDS fails","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"}],"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/6","labels_url":"https://api.github.com/repos/GMOD/Apollo/milestones/6/labels","id":906037,"number":6,"title":"1.0.4","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":7,"closed_issues":13,"state":"open","created_at":"2014-12-16T19:17:26Z","updated_at":"2015-02-19T16:47:46Z","due_on":"2015-02-11T08:00:00Z","closed_at":null},"comments":1,"created_at":"2015-02-19T16:47:46Z","updated_at":"2015-02-19T16:48:17Z","closed_at":null,"body":"from nicolas.francillonne@versailles.inra.fr:\r\n\r\nI'm working on an instance of WebApollo-2014-04-03 and I wish to export for each annotation CDS fasta sequence.\r\n\r\nOn my \"selectTrack.jsp\" I select all my track then in file ==> export ==> Fasta I download my CDS.\r\nThen I get \"Error writing CDS\"\r\n\r\nI can download all my Gff3, cDNA without issue and when I select some of my reference sequence instead of all of them it works.\r\n\r\nHere the error I get when trying to download all CDS (same error happen when I try to download \"peptide\".\r\n\r\njava.lang.StringIndexOutOfBoundsException: String index out of range: -1\r\n   at java.lang.String.substring(String.java:1904)\r\n   at org.gmod.gbol.bioObject.CDS.getResidues(CDS.java:158)\r\n   at org.bbop.apollo.editor.session.AnnotationSession.getResiduesWithAlterations(AnnotationSession.java:253)\r\n   at org.bbop.apollo.editor.session.AnnotationSession.getResiduesWithAlterationsAndFrameshifts(AnnotationSession.java:226)\r\n   at org.bbop.apollo.web.dataadapter.fasta.FastaIO.getUpdatedSequence(FastaIO.java:112)\r\n   at org.bbop.apollo.web.dataadapter.fasta.FastaIO.writeFeatures(FastaIO.java:53)\r\n   at org.bbop.apollo.web.dataadapter.fasta.FastaJEDatabaseIO.writeFeatures(FastaJEDatabaseIO.java:48)\r\n   at org.bbop.apollo.web.dataadapter.fasta.FastaDataAdapter.write(FastaDataAdapter.java:207)\r\n   at org.bbop.apollo.web.dataadapter.IOService.doPost(IOService.java:191)\r\n\r\nHave you got any ideas  ?"},"comment":{"url":"https://api.github.com/repos/GMOD/Apollo/issues/comments/75088707","html_url":"https://github.com/GMOD/Apollo/issues/171#issuecomment-75088707","issue_url":"https://api.github.com/repos/GMOD/Apollo/issues/171","id":75088707,"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":"2015-02-19T16:48:17Z","updated_at":"2015-02-19T16:48:17Z","body":"Transcript transcript = getTranscript();\r\nString residues = transcript.getResidues();\r\nint begin;\r\nint end;\r\ntranscript.convertSourceCoordinateToLocalCoordinate(getFeatureLocation().getFmax());\r\nif (getFeatureLocation().getStrand() == -1) {\r\n    end = transcript.convertSourceCoordinateToLocalCoordinate(getFeatureLocation().getFmin()) + 1;\r\n    begin = transcript.convertSourceCoordinateToLocalCoordinate(getFeatureLocation().getFmax()) + 1;\r\n}\r\nelse {\r\n    begin = transcript.convertSourceCoordinateToLocalCoordinate(getFeatureLocation().getFmin());\r\n    end = transcript.convertSourceCoordinateToLocalCoordinate(getFeatureLocation().getFmax());\r\n\r\n}\r\nreturn residues.substring(begin, end);\r\n"}}