{"action":"created","issue":{"url":"https://api.github.com/repos/GMOD/Apollo/issues/1193","repository_url":"https://api.github.com/repos/GMOD/Apollo","labels_url":"https://api.github.com/repos/GMOD/Apollo/issues/1193/labels{/name}","comments_url":"https://api.github.com/repos/GMOD/Apollo/issues/1193/comments","events_url":"https://api.github.com/repos/GMOD/Apollo/issues/1193/events","html_url":"https://github.com/GMOD/Apollo/issues/1193","id":168113034,"number":1193,"title":"'JSONObject[\"clientToken\"] not found.' when running add_transcripts_from_gff3_to_annotations.pl","user":{"login":"brkldj","id":20705056,"avatar_url":"https://avatars.githubusercontent.com/u/20705056?v=3","gravatar_id":"","url":"https://api.github.com/users/brkldj","html_url":"https://github.com/brkldj","followers_url":"https://api.github.com/users/brkldj/followers","following_url":"https://api.github.com/users/brkldj/following{/other_user}","gists_url":"https://api.github.com/users/brkldj/gists{/gist_id}","starred_url":"https://api.github.com/users/brkldj/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/brkldj/subscriptions","organizations_url":"https://api.github.com/users/brkldj/orgs","repos_url":"https://api.github.com/users/brkldj/repos","events_url":"https://api.github.com/users/brkldj/events{/privacy}","received_events_url":"https://api.github.com/users/brkldj/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":7,"created_at":"2016-07-28T14:41:45Z","updated_at":"2016-07-28T15:40:27Z","closed_at":null,"body":"Hi,\r\n\r\nI'm trying to add a gff file to the annotation track directly via command line (instead of dragging every gene model), as described [here](http://genomearchitect.readthedocs.io/en/latest/Data_loading.html#gff3). When running add_transcripts_from_gff3_to_annotations.pl, I get errors like this:\r\n```\r\nProcessing evm.TU.scaffold00091.84: http://localhost:8080/apollo/annotationEditor/addFeature \r\nerror: 500 Internal Server Error\r\n```\r\ncatalina.out has entries of this type:\r\n```\r\n2016-07-28 15:57:12,510 [http-bio-8080-exec-49] ERROR errors.GrailsExceptionResolver  - JSONException occurred when processing request: [POST] /apollo/annotationEditor/addFeature\r\nJSONObject[\"clientToken\"] not found.. Stacktrace follows:\r\norg.codehaus.groovy.grails.web.json.JSONException: JSONObject[\"clientToken\"] not found.\r\n        at org.bbop.apollo.PermissionService.$tt__hasPermissions(PermissionService.groovy:412)\r\n        at org.bbop.apollo.AnnotationEditorController.addFeature(AnnotationEditorController.groovy:164)\r\n        at grails.plugin.cache.web.filter.PageFragmentCachingFilter.doFilter(PageFragmentCachingFilter.java:198)\r\n        at grails.plugin.cache.web.filter.AbstractFilter.doFilter(AbstractFilter.java:63)\r\n        at org.apache.shiro.web.servlet.AbstractShiroFilter.executeChain(AbstractShiroFilter.java:449)\r\n        at org.apache.shiro.web.servlet.AbstractShiroFilter$1.call(AbstractShiroFilter.java:365)\r\n        at org.apache.shiro.subject.support.SubjectCallable.doCall(SubjectCallable.java:90)\r\n        at org.apache.shiro.subject.support.SubjectCallable.call(SubjectCallable.java:83)\r\n        at org.apache.shiro.subject.support.DelegatingSubject.execute(DelegatingSubject.java:383)\r\n        at org.apache.shiro.web.servlet.AbstractShiroFilter.doFilterInternal(AbstractShiroFilter.java:362)\r\n        at org.apache.shiro.web.servlet.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:125)\r\n        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)\r\n        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)\r\n        at java.lang.Thread.run(Thread.java:745)\r\n```\r\nI'm assuming this has something to do with authentication. I'm using the admin email address and password - the same as logging in in the browser. Do you have any idea where am I going wrong? It might be something trivial since this is the first time I set up webapollo.\r\n\r\nSemi-related question: is there an easy way to figure out which version am I using? (The Help->Get version link in browser is for some reason not working - but everything else does.)\r\n\r\nThanks!\r\n"},"comment":{"url":"https://api.github.com/repos/GMOD/Apollo/issues/comments/235934512","html_url":"https://github.com/GMOD/Apollo/issues/1193#issuecomment-235934512","issue_url":"https://api.github.com/repos/GMOD/Apollo/issues/1193","id":235934512,"user":{"login":"brkldj","id":20705056,"avatar_url":"https://avatars.githubusercontent.com/u/20705056?v=3","gravatar_id":"","url":"https://api.github.com/users/brkldj","html_url":"https://github.com/brkldj","followers_url":"https://api.github.com/users/brkldj/followers","following_url":"https://api.github.com/users/brkldj/following{/other_user}","gists_url":"https://api.github.com/users/brkldj/gists{/gist_id}","starred_url":"https://api.github.com/users/brkldj/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/brkldj/subscriptions","organizations_url":"https://api.github.com/users/brkldj/orgs","repos_url":"https://api.github.com/users/brkldj/repos","events_url":"https://api.github.com/users/brkldj/events{/privacy}","received_events_url":"https://api.github.com/users/brkldj/received_events","type":"User","site_admin":false},"created_at":"2016-07-28T15:40:27Z","updated_at":"2016-07-28T15:40:27Z","body":"I now have:\r\n```\r\ncommit e387b8beaf43de82eaf2c963066802470e831827\r\nAuthor: Nathan Dunn <nathandunn@users.noreply.github.com>\r\nDate:   Wed Jul 27 12:00:21 2016 -0700\r\n```\r\nThe errors that I now get of the following type:\r\n```\r\nProcessing evm.TU.scaffold00161.4: http://localhost:8080/apollo/annotationEditor/addTranscript \r\nerror: JSONObject[\"clientToken\"] not found.\r\n```\r\n-- the problematic part is now addTranscript (before it was addFeature)."}}
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