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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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Unable to delete more than one exon at a time. #299

Closed monicacecilia closed 9 years ago

monicacecilia commented 9 years ago
  1. I selected three exons (holding down Shift key) and attempted to delete them. First, Apollo only deleted the left-most exon.
  2. I selected the remaining two exons for deletion. Right-click + delete, then Apollo gave the error "Cannot read property 'className' of undefined"
  3. After this happened, I was unable to add any other annotations to Uc-A. I had to refresh the page (which landed me on a different group), and navigated back to the scaffold of interest. The gene model I modified only had one more exon missing.
  4. I tried deleting multiple exons again, and Apollo only deleted the left-most one. I am unable to "Undo" functions, so I cannot check further.
  5. I again tried selecting two and the same error appeared (see big red box in the image).
  6. My conclusion is that Apollo is no longer able to delete more than one exon at a time.

screen shot 2015-04-19 at 12 15 31 pm

From the console: TypeError: Cannot read property 'className' of undefined at declare.renderExonSegments (http://icebox.lbl.gov/WebApollo2/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:167:39) at declare.handleSubFeatures (http://icebox.lbl.gov/WebApollo2/jbrowse/plugins/WebApollo/js/View/Track/DraggableHTMLFeatures.js:568:39) at declare.renderFeature (http://icebox.lbl.gov/WebApollo2/jbrowse/src/JBrowse/View/Track/HTMLFeatures.js:1111:18) at inherited (http://icebox.lbl.gov/WebApollo2/jbrowse/src/dojo/_base/declare.js:189:42) at declare.renderFeature (http://icebox.lbl.gov/WebApollo2/jbrowse/plugins/WebApollo/js/View/Track/DraggableHTMLFeatures.js:316:28) at declare.renderFeature (http://icebox.lbl.gov/WebApollo2/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:485:81) at declare.addFeatureToBlock (http://icebox.lbl.gov/WebApollo2/jbrowse/src/JBrowse/View/Track/HTMLFeatures.js:669:28) at null. (http://icebox.lbl.gov/WebApollo2/jbrowse/src/JBrowse/View/Track/HTMLFeatures.js:619:26) at http://icebox.lbl.gov/WebApollo2/jbrowse/src/dojo/_base/lang.js:375:55 at declare.getFeatures (http://icebox.lbl.gov/WebApollo2/jbrowse/plugins/WebApollo/js/Store/SeqFeature/ScratchPad.js:91:17) TypeError: Cannot read property 'className' of undefineddeclare._handleError @ /WebApollo2/jbrowse/src/JBrowse/View/Track/BlockBased.js:448 /WebApollo2/jbrowse/plugins/WebApollo/js/View/Track/AnnotTrack.js:401 unknown command: undefined

monicacecilia commented 9 years ago

p.s: it works like a charm on 1.0.4

nathandunn commented 9 years ago

The "className" is because its not updating correctly (some of the time). This is the update code failing (which is also a failure). A refresh will make it appear correctly.

It also complains that features are already deleted when multiple.

Will need to write an integration test for this.

Note: I did not ALWAYS get the className error.

monicacecilia commented 9 years ago

working as expected. thanks! this deserves a celebration! :dancer: