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  1. IGB
  2. IGBF-675

Reopening a file that was just deleted from a custom genome generates a null pointer exception

    Details

      Description

      While testing IGBF-621 I noticed that a null pointer exception was being generated when reopening a file that was just deleted. This is seen in files that were loaded into a custom genome or an "incorrect" genome after they are deleted.

      To reproduce:

      1) Drag a file into IGB to open the file in a custom genome; alternatively, you could open a file into an "incorrect" genome (such as opening a human genome file into the arabadopsis genome).
      2) Delete the file that was just loaded.
      3) Attempt to reopen the file by dragging and dropping into IGB.

      *Observe: A null pointer exception is generated (see below)

      14:37:38.956 ERROR c.a.genometry.thread.CThreadWorker - null
      java.lang.NullPointerException: null
      at com.affymetrix.genometry.util.SeqUtils.addInvertChildren(SeqUtils.java:262) ~[na:na]
      at com.affymetrix.genometry.util.SeqUtils.inverse(SeqUtils.java:241) ~[na:na]
      at com.affymetrix.igb.view.factories.AbstractTierGlyph.addMiddleGlyphs(AbstractTierGlyph.java:161) ~[na:na]
      at com.affymetrix.igb.view.factories.AbstractTierGlyph.initUnloaded(AbstractTierGlyph.java:145) ~[na:na]
      at com.affymetrix.igb.view.TrackView.addTierFor(TrackView.java:256) ~[na:na]
      at com.affymetrix.igb.view.TrackView.addEmptyTierFor(TrackView.java:231) ~[na:na]
      at com.affymetrix.igb.view.load.GeneralLoadView$3.runInBackground(GeneralLoadView.java:538) ~[na:na]
      at com.affymetrix.genometry.thread.CThreadWorker.doInBackground(CThreadWorker.java:73) ~[na:na]
      at javax.swing.SwingWorker$1.call(Unknown Source) [na:1.8.0_40]
      at java.util.concurrent.FutureTask.run(Unknown Source) [na:1.8.0_40]
      at javax.swing.SwingWorker.run(Unknown Source) [na:1.8.0_40]
      at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) [na:1.8.0_40]
      at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) [na:1.8.0_40]
      at java.lang.Thread.run(Unknown Source) [na:1.8.0_40]

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            mason Mason Meyer (Inactive) created issue -
            mason Mason Meyer (Inactive) made changes -
            Field Original Value New Value
            Epic Link IGBF-497 [ 15559 ]
            mason Mason Meyer (Inactive) made changes -
            Link This issue relates to IGBF-621 [ IGBF-621 ]
            ann.loraine Ann Loraine made changes -
            Story Points 0.5
            Hide
            mason Mason Meyer (Inactive) added a comment -

            I re-tested this issue on IGB 9.0.0 and could no longer reproduce the issue. Since this issue is resolved, I am now closing this issue.

            Show
            mason Mason Meyer (Inactive) added a comment - I re-tested this issue on IGB 9.0.0 and could no longer reproduce the issue. Since this issue is resolved, I am now closing this issue.
            mason Mason Meyer (Inactive) made changes -
            Resolution Done [ 10000 ]
            Status Open [ 1 ] Closed [ 6 ]
            ieclabau Ivory Blakley (Inactive) made changes -
            Fix Version/s 9.0.1 Minor Release [ 10500 ]
            ann.loraine Ann Loraine made changes -
            Workflow Loraine Lab Workflow [ 15968 ] Fall 2019 Workflow Update [ 19501 ]
            ann.loraine Ann Loraine made changes -
            Workflow Fall 2019 Workflow Update [ 19501 ] Revised Fall 2019 Workflow Update [ 21618 ]

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              • Assignee:
                Unassigned
                Reporter:
                mason Mason Meyer (Inactive)
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                • Created:
                  Updated:
                  Resolved: