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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/
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Error annotating from Canvas tracks #1077

Closed nathandunn closed 8 years ago

nathandunn commented 8 years ago

FYI @monicacecilia Something else we need to remember to test for.

These work fine for HTMLFeatures when doing a right-click.

When annotating a human canvas track (similar results for Volvox):

http://icebox.lbl.gov/Apollo-staging

Some types work and some types do not:

The errors generated (below) are the first for pseudogene /transcript (observed) and the second for repeat region. 

2016-05-28 10:44:07,304 [clientInboundChannel-3] ERROR springwebsocket.GrailsSimpAnnotationMethodMessageHandler  - Unhandled exception
java.lang.reflect.InvocationTargetException
    at org.bbop.apollo.AnnotationEditorController$__do_annotationEditor_closure4$_closure5$_closure6.doCall(AnnotationEditorController.groovy:1096)
    at org.bbop.apollo.AnnotationEditorController$__do_annotationEditor_closure4$_closure5.doCall(AnnotationEditorController.groovy:1095)
    at org.bbop.apollo.AnnotationEditorController$__do_annotationEditor_closure4.doCall(AnnotationEditorController.groovy:1091)
    at groovyx.gpars.group.PGroup$3.call(PGroup.java:289)
    at groovyx.gpars.group.PGroup$4.run(PGroup.java:313)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
Caused by: java.util.NoSuchElementException
    at java.util.ArrayList$Itr.next(ArrayList.java:854)
    at org.bbop.apollo.FeatureService.$tt__addFeature(FeatureService.groovy:2803)
    at org.bbop.apollo.RequestHandlingService.$tt__addFeature(RequestHandlingService.groovy:1691)
    ... 8 more
2016-05-28 10:44:12,858 [clientInboundChannel-2] ERROR 
springwebsocket.GrailsSimpAnnotationMethodMessageHandler  - Unhandled exception
java.lang.reflect.InvocationTargetException
    at org.bbop.apollo.AnnotationEditorController$__do_annotationEditor_closure4$_closure5$_closure6.doCall(AnnotationEditorController.groovy:1096)
    at org.bbop.apollo.AnnotationEditorController$__do_annotationEditor_closure4$_closure5.doCall(AnnotationEditorController.groovy:1095)
    at org.bbop.apollo.AnnotationEditorController$__do_annotationEditor_closure4.doCall(AnnotationEditorController.groovy:1091)
    at groovyx.gpars.group.PGroup$3.call(PGroup.java:289)
    at groovyx.gpars.group.PGroup$4.run(PGroup.java:313)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
Caused by: java.util.NoSuchElementException
    at java.util.ArrayList$Itr.next(ArrayList.java:854)
    at org.bbop.apollo.FeatureService.$tt__addFeature(FeatureService.groovy:2803)
    at org.bbop.apollo.RequestHandlingService.$tt__addFeature(RequestHandlingService.groovy:1691)
    ... 8 more
nathandunn commented 8 years ago

Found when testing: https://github.com/TAMU-CPT/galaxy-apollo/issues/2

deepakunni3 commented 8 years ago

@nathandunn This was because the method call in WebApolloCanvasFeatures.js for pseudogene, repeat region and transposable element are different from DraggableHTMLFeatures.js. This resulted in a wrongly formatted JSON object being sent to the server.

PR #1079 addresses this issue.

nathandunn commented 8 years ago

Awesome thanks.

nathandunn commented 8 years ago

To Test: Annotate a Canvas Track (see Human) for all of the above types and see that they work properly.

monicacecilia commented 8 years ago

💃