search

GMOD / Apollo

Genome annotation editor with a Java Server backend and a Javascript client that runs in a web browser as a JBrowse plugin.
http://genomearchitect.readthedocs.io/
Other
126 stars 85 forks source link

re-fix chunked projection HTMLFeatures #712

Closed nathandunn closed 8 years ago

nathandunn commented 8 years ago

this was working fine, but now I'm getting an error

nathandunn commented 8 years ago 
putative sequence path name /opt/apollo/honeybee/data/names/meta.json -> names 
| Error 2015-11-25 11:22:40,592 [http-bio-8080-exec-13] ERROR apollo.AnnotatorController  - null
| Error java.lang.NullPointerException
| Error     at org.codehaus.groovy.runtime.callsite.AbstractCallSite.createGroovyObjectGetPropertySite(AbstractCallSite.java:254)
| Error     at org.codehaus.groovy.runtime.callsite.PogoMetaClassGetPropertySite.acceptGroovyObjectGetProperty(PogoMetaClassGetPropertySite.java:41)
| Error     at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callGroovyObjectGetProperty(AbstractCallSite.java:231)
| Error     at org.bbop.apollo.BookmarkService.$tt__convertBookmarkToJson(BookmarkService.groovy:69)
| Error     at org.bbop.apollo.BookmarkService$_convertBookmarkToJson_closure4.doCall(BookmarkService.groovy)
| Error     at sun.reflect.GeneratedMethodAccessor753.invoke(Unknown Source)
| Error     at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
| Error     at java.lang.reflect.Method.invoke(Method.java:606)
| Error     at org.springsource.loaded.ri.ReflectiveInterceptor.jlrMethodInvoke(ReflectiveInterceptor.java:1270)
| Error     at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:90)
| Error     at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:324)
| Error     at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1206)
| Error     at groovy.lang.ExpandoMetaClass.invokeMethod(ExpandoMetaClass.java:1120)
| Error     at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1015)
| Error     at groovy.lang.Closure.call(Closure.java:423)
| Error     at org.bbop.apollo.BookmarkService$_convertBookmarkToJson_closure4.call(BookmarkService.groovy)
| Error     at groovy.lang.Closure.call(Closure.java:439)
| Error     at org.bbop.apollo.BookmarkService$_convertBookmarkToJson_closure4.call(BookmarkService.groovy)
...
| Error     at org.bbop.apollo.BookmarkService.convertBookmarkToJson(BookmarkService.groovy)
| Error     at org.bbop.apollo.BookmarkService$convertBookmarkToJson.call(Unknown Source)
| Error     at org.bbop.apollo.AnnotatorController.findAnnotationsForSequence(AnnotatorController.groovy:225)
| Error     at org.bbop.apollo.AnnotatorController.findAnnotationsForSequence(AnnotatorController.groovy)
| Error     at sun.reflect.GeneratedMethodAccessor807.invoke(Unknown Source)
gettting projeciton [projection:None, referenceTrack:Official Gene Set v3.2, label:Group1.10, sequenceList:[[name:Group1.10]], padding:0, organism:Honeybee]
does NOT contains the key! org.bbop.apollo.projection.ProjectionDescription@f2755719
| Error 2015-11-25 11:22:22,610 [http-bio-8080-exec-14] ERROR errors.GrailsExceptionResolver  - NullPointerException occurred when processing request: [GET] /apollo/jbrowse/data/tracks/Official%20Gene%20Set%20v3.2/%7B%22padding%22:0,%20%22projection%22:%22None%22,%20%22referenceTrack%22:%22Official%20Gene%20Set%20v3.2%22,%20%22sequenceList%22:[%7B%22name%22:%22Group1.10%22%7D],%20%22label%22:%22Group1.10%22%7D:-1..-1/lf-1.json
Stacktrace follows:
Message: null
    Line | Method
->>  645 | $tt__projectTrackChunk in org.bbop.apollo.TrackService
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
|    188 | data                   in org.bbop.apollo.JbrowseController
|    198 | doFilter . . . . . . . in grails.plugin.cache.web.filter.PageFragmentCachingFilter
|     63 | doFilter               in grails.plugin.cache.web.filter.AbstractFilter
|    449 | executeChain . . . . . in org.apache.shiro.web.servlet.AbstractShiroFilter
|    365 | call                   in org.apache.shiro.web.servlet.AbstractShiroFilter$1
|     90 | doCall . . . . . . . . in org.apache.shiro.subject.support.SubjectCallable
|     83 | call                   in     ''
|    383 | execute . . . . . . .  in org.apache.shiro.subject.support.DelegatingSubject
|    362 | doFilterInternal       in org.apache.shiro.web.servlet.AbstractShiroFilter
|    125 | doFilter . . . . . . . in org.apache.shiro.web.servlet.OncePerRequestFilter