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  1. IGB
  2. IGBF-2537

Enable Quickload to specify the 2bit file for a genome

    Details

    • Story Points:
      3
    • Sprint:
      Fall 1: 14 Sep - 25 Sep, Fall 2: 28 Sep - 9 Oct, Fall 3: Oct 12 - Oct 23, Fall 6 Nov 30 - Dec 11

      Description

      Currently, IGB assumes that the genome sequence for a genome version resides physically on the same server as the Quickload metadata files and that the genome version file is named for the genome.

      (For details see, the wiki documentation on IGB Quickload.)

      Modify this so that a user can specific the genome file using the "file" tag.

      e.g.,

      <file name="foo.2bit" reference="true"/>
      

      and

      <file name="https://example.com/foo.2bit" reference="True"/>
      

      and

      <file name="http://example.com/foo.2bit" reference="True"/>
      

      For example 2bit files corresponding to various genomes, see:

      This location contains multiple subdirectories for different genome versions. For example,

      contains a file named mm10.2bit (http://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/mm10.2bit) which contains the same data shown for IGB genome version M_musculus_Dec_2011.

        Attachments

          Activity

          Hide
          nfreese Nowlan Freese added a comment -

          Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
          at com.affymetrix.igb.view.load.FeatureTreeView.addOrFindNode(FeatureTreeView.java:263)
          at com.affymetrix.igb.view.load.FeatureTreeView.lambda$createTree$206(FeatureTreeView.java:244)
          at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184)
          at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
          at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1382)
          at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
          at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
          at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151)
          at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174)
          at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
          at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418)
          at com.affymetrix.igb.view.load.FeatureTreeView.createTree(FeatureTreeView.java:243)
          at com.affymetrix.igb.view.load.FeatureTreeView.initOrRefreshTree(FeatureTreeView.java:162)
          at com.affymetrix.igb.view.load.GeneralLoadView.refreshTree(GeneralLoadView.java:439)
          at com.affymetrix.genometry.util.ThreadUtils.runOnEventQueue(ThreadUtils.java:34)
          at com.affymetrix.igb.view.load.GeneralLoadView.refreshTreeView(GeneralLoadView.java:431)
          at com.affymetrix.igb.view.SeqGroupView.versionNameChanged(SeqGroupView.java:440)
          at com.affymetrix.igb.view.SeqGroupView.groupSelectionChanged(SeqGroupView.java:382)
          at com.affymetrix.genometry.GenometryModel.fireGroupSelectionEvent(GenometryModel.java:161)
          at com.affymetrix.genometry.GenometryModel.setSelectedGenomeVersion(GenometryModel.java:147)
          at com.affymetrix.igb.view.SeqGroupView$InitVersionWorker.finished(SeqGroupView.java:691)
          at com.affymetrix.genometry.thread.CThreadWorker.done(CThreadWorker.java:51)
          at javax.swing.SwingWorker$5.run(SwingWorker.java:737)
          at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.run(SwingWorker.java:832)
          at sun.swing.AccumulativeRunnable.run(AccumulativeRunnable.java:112)
          at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.actionPerformed(SwingWorker.java:842)
          at javax.swing.Timer.fireActionPerformed(Timer.java:313)
          at javax.swing.Timer$DoPostEvent.run(Timer.java:245)
          at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
          at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
          at java.awt.EventQueue.access$500(EventQueue.java:97)
          at java.awt.EventQueue$3.run(EventQueue.java:709)
          at java.awt.EventQueue$3.run(EventQueue.java:703)
          at java.security.AccessController.doPrivileged(Native Method)
          at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
          at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
          at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205)
          at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
          at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
          at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
          at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
          at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

          Show
          nfreese Nowlan Freese added a comment - Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at com.affymetrix.igb.view.load.FeatureTreeView.addOrFindNode(FeatureTreeView.java:263) at com.affymetrix.igb.view.load.FeatureTreeView.lambda$createTree$206(FeatureTreeView.java:244) at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184) at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175) at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1382) at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481) at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471) at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151) at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174) at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234) at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418) at com.affymetrix.igb.view.load.FeatureTreeView.createTree(FeatureTreeView.java:243) at com.affymetrix.igb.view.load.FeatureTreeView.initOrRefreshTree(FeatureTreeView.java:162) at com.affymetrix.igb.view.load.GeneralLoadView.refreshTree(GeneralLoadView.java:439) at com.affymetrix.genometry.util.ThreadUtils.runOnEventQueue(ThreadUtils.java:34) at com.affymetrix.igb.view.load.GeneralLoadView.refreshTreeView(GeneralLoadView.java:431) at com.affymetrix.igb.view.SeqGroupView.versionNameChanged(SeqGroupView.java:440) at com.affymetrix.igb.view.SeqGroupView.groupSelectionChanged(SeqGroupView.java:382) at com.affymetrix.genometry.GenometryModel.fireGroupSelectionEvent(GenometryModel.java:161) at com.affymetrix.genometry.GenometryModel.setSelectedGenomeVersion(GenometryModel.java:147) at com.affymetrix.igb.view.SeqGroupView$InitVersionWorker.finished(SeqGroupView.java:691) at com.affymetrix.genometry.thread.CThreadWorker.done(CThreadWorker.java:51) at javax.swing.SwingWorker$5.run(SwingWorker.java:737) at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.run(SwingWorker.java:832) at sun.swing.AccumulativeRunnable.run(AccumulativeRunnable.java:112) at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.actionPerformed(SwingWorker.java:842) at javax.swing.Timer.fireActionPerformed(Timer.java:313) at javax.swing.Timer$DoPostEvent.run(Timer.java:245) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
          Hide
          nfreese Nowlan Freese added a comment -

          Ann Loraine please advise how you would like to proceed.

          After further investigation the issue stems from a potential bug introduced in 8.4.0 which requires that each file in the quickload annots.xml have a title. Note that the title is currently listed as optional in the igb users guide. The quickload attached to this issue for testing does not include a title in the annots.xml for the 2bit reference. This is what causes the null pointer exception and failure to load any data in IGB 8.4.0 - 9.1.4.

          If a title is added to the reference 2bit file in the annots.xml then no null pointer exception is thrown for IGB 9.1.4. The reference title will appear in the available data and be selectable. If the user selects the reference title and clicks load data the sequence will be loaded in the coordinates track. This allows for 2bit or fa reference sequence files to be remotely specified in IGB 9.1.4. If the 2bit file is available in the quickload then clicking load sequence will load the sequence in the coordinates track.

          In IGB 9.1.6 the title is ignored and the reference does not appear in the available data.

          The easiest resolution to this issue would be to make no further code changes in IGB, but update the users guide to state that the title is required. New quickloads that include a remote reference sequence will appear with a reference data option in the available data for versions of IGB less than 9.1.6.

          It may be possible to edit IGB code to add a new XML root element, but this may require some significant code changes.

          Show
          nfreese Nowlan Freese added a comment - Ann Loraine please advise how you would like to proceed. After further investigation the issue stems from a potential bug introduced in 8.4.0 which requires that each file in the quickload annots.xml have a title. Note that the title is currently listed as optional in the igb users guide. The quickload attached to this issue for testing does not include a title in the annots.xml for the 2bit reference. This is what causes the null pointer exception and failure to load any data in IGB 8.4.0 - 9.1.4. If a title is added to the reference 2bit file in the annots.xml then no null pointer exception is thrown for IGB 9.1.4. The reference title will appear in the available data and be selectable. If the user selects the reference title and clicks load data the sequence will be loaded in the coordinates track. This allows for 2bit or fa reference sequence files to be remotely specified in IGB 9.1.4. If the 2bit file is available in the quickload then clicking load sequence will load the sequence in the coordinates track. In IGB 9.1.6 the title is ignored and the reference does not appear in the available data. The easiest resolution to this issue would be to make no further code changes in IGB, but update the users guide to state that the title is required. New quickloads that include a remote reference sequence will appear with a reference data option in the available data for versions of IGB less than 9.1.6. It may be possible to edit IGB code to add a new XML root element, but this may require some significant code changes.
          Hide
          aloraine Ann Loraine added a comment - - edited

          A clarification question:

          • If a 2bit file is provided in the quickload and the 2bit file is listed using the "file" tag with proper "name" and "title" attributes, what happens when the user clicks "Load Data"? Does the sequence get loaded along with all the other tracks with "Load Mode" set to "Region in View"?

          (If yes, this almost counts as a feature, not a bug!)

          Regardless of the answer to the question, I would be OK with the described behavior, since we can easily avoid breaking 9.1.4 by including the "title" attribute in our annots.xml files.

          Show
          aloraine Ann Loraine added a comment - - edited A clarification question: If a 2bit file is provided in the quickload and the 2bit file is listed using the "file" tag with proper "name" and "title" attributes, what happens when the user clicks "Load Data"? Does the sequence get loaded along with all the other tracks with "Load Mode" set to "Region in View"? (If yes, this almost counts as a feature, not a bug!) Regardless of the answer to the question, I would be OK with the described behavior, since we can easily avoid breaking 9.1.4 by including the "title" attribute in our annots.xml files.
          Hide
          nfreese Nowlan Freese added a comment - - edited

          In 9.1.4
          If a 2bit file is provided in the quickload and the 2bit file is listed:
          If the user selects the 2bit file in the available data then no track appears for the 2bit file, but if the user clicks load data then the sequence is loaded for the region in view in the coordinates track along with whatever data/annotations are present.

          Show
          nfreese Nowlan Freese added a comment - - edited In 9.1.4 If a 2bit file is provided in the quickload and the 2bit file is listed: If the user selects the 2bit file in the available data then no track appears for the 2bit file, but if the user clicks load data then the sequence is loaded for the region in view in the coordinates track along with whatever data/annotations are present.
          Hide
          nfreese Nowlan Freese added a comment -

          After discussion with Dr. Loraine the current decision is to make no further changes to the IGB code. I have updated the IGB users guide so that the title attribute is now listed as being required.

          Closing issue.

          Show
          nfreese Nowlan Freese added a comment - After discussion with Dr. Loraine the current decision is to make no further changes to the IGB code. I have updated the IGB users guide so that the title attribute is now listed as being required. Closing issue.

            People

            • Assignee:
              noor91zahara Noor Zahara
              Reporter:
              aloraine Ann Loraine
            • Votes:
              0 Vote for this issue
              Watchers:
              5 Start watching this issue

              Dates

              • Created:
                Updated:
                Resolved: