Uploaded image for project: 'Deep Backlog'
  1. Deep Backlog
  2. DB-15

Examine bugs caused from running a script

          Details

          • Type: Bug
          • Status: Open (View Workflow)
          • Priority: Major
          • Resolution: Unresolved
          • Labels:
            None

            Description

            I noticed several new problems when I try to run a script that had previouslt worked before today.

            To reproduce:

            1) Drag the "loadData.igb" script (attached) to start running the script.

            Observe:
            a null pointer exception is generated (see screenshot), the "Load Data" button is now disabled, a URL is still seen in the track label for one of the files, loading another file under available data will generate another null pointer exception (see screenshot).

            We should examine this and fix this before the release of 8.4.0

              Attachments

                Issue Links

                relates to

                Bug - A problem which impairs or prevents the functions of the product. IGBF-705 deleting a data set disables Load Data button, only for local files

                • Major - Major loss of function.
                • Closed

                  Activity

                  Ascending order - Click to sort in descending order
                  Hide
                  Permalink
                  mason Mason Meyer (Inactive) added a comment -

                  It seems all the issues mentioned above are fixed through the fix for IGBF-705 except for the URL seen in the track label for one of the files.

                  Reassigning to David to take a look at.

                  Show
                  mason Mason Meyer (Inactive) added a comment - It seems all the issues mentioned above are fixed through the fix for IGBF-705 except for the URL seen in the track label for one of the files. Reassigning to David to take a look at.
                  Hide
                  Permalink
                  mason Mason Meyer (Inactive) added a comment -

                  I also noticed an exception when testing at one point:

                  16:56:33.705 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: unload http://www.igbquickload.org/cyto/A_thaliana_Jun_2009/TH2.0.5processed/Control1_2.sm.bam
                  Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
                  at com.affymetrix.igb.view.SeqMapView.getViewSeqSpan(SeqMapView.java:1995)
                  at com.affymetrix.igb.view.factories.AnnotationGlyphFactory.updateSymSpan(AnnotationGlyphFactory.java:595)
                  at com.affymetrix.igb.view.factories.AnnotationGlyphFactory.addTopChild(AnnotationGlyphFactory.java:147)
                  at com.affymetrix.igb.view.factories.AnnotationGlyphFactory.addLeafsToTier(AnnotationGlyphFactory.java:137)
                  at com.affymetrix.igb.view.factories.AnnotationGlyphFactory.addLeafsToTier(AnnotationGlyphFactory.java:134)
                  at com.affymetrix.igb.view.factories.AnnotationGlyphFactory.createGlyphs(AnnotationGlyphFactory.java:530)
                  at com.affymetrix.igb.view.TrackView.addAnnotationGlyphs(TrackView.java:165)
                  at com.affymetrix.igb.view.TrackView.addTracks(TrackView.java:149)
                  at com.affymetrix.igb.view.SeqMapView.addAnnotationTracks(SeqMapView.java:1002)
                  at com.affymetrix.igb.view.SeqMapView.addGlyphs(SeqMapView.java:954)
                  at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:788)
                  at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:732)
                  at com.affymetrix.igb.view.load.GeneralLoadUtils$2.finished(GeneralLoadUtils.java:747)
                  at com.affymetrix.genometry.thread.CThreadWorker.done(CThreadWorker.java:51)
                  at javax.swing.SwingWorker$5.run(Unknown Source)
                  at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.run(Unknown Source)
                  at sun.swing.AccumulativeRunnable.run(Unknown Source)
                  at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.actionPerformed(Unknown Source)
                  at javax.swing.Timer.fireActionPerformed(Unknown Source)
                  at javax.swing.Timer$DoPostEvent.run(Unknown Source)
                  at java.awt.event.InvocationEvent.dispatch(Unknown Source)
                  at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
                  at java.awt.EventQueue.access$500(Unknown Source)
                  at java.awt.EventQueue$3.run(Unknown Source)
                  at java.awt.EventQueue$3.run(Unknown Source)
                  at java.security.AccessController.doPrivileged(Native Method)
                  at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
                  at java.awt.EventQueue.dispatchEvent(Unknown Source)
                  at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
                  at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
                  at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
                  at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
                  at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
                  at java.awt.EventDispatchThread.run(Unknown Source)

                  Show
                  mason Mason Meyer (Inactive) added a comment - I also noticed an exception when testing at one point: 16:56:33.705 INFO com.gene.igbscript.IGBScriptEngine - doSingleAction line: unload http://www.igbquickload.org/cyto/A_thaliana_Jun_2009/TH2.0.5processed/Control1_2.sm.bam Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at com.affymetrix.igb.view.SeqMapView.getViewSeqSpan(SeqMapView.java:1995) at com.affymetrix.igb.view.factories.AnnotationGlyphFactory.updateSymSpan(AnnotationGlyphFactory.java:595) at com.affymetrix.igb.view.factories.AnnotationGlyphFactory.addTopChild(AnnotationGlyphFactory.java:147) at com.affymetrix.igb.view.factories.AnnotationGlyphFactory.addLeafsToTier(AnnotationGlyphFactory.java:137) at com.affymetrix.igb.view.factories.AnnotationGlyphFactory.addLeafsToTier(AnnotationGlyphFactory.java:134) at com.affymetrix.igb.view.factories.AnnotationGlyphFactory.createGlyphs(AnnotationGlyphFactory.java:530) at com.affymetrix.igb.view.TrackView.addAnnotationGlyphs(TrackView.java:165) at com.affymetrix.igb.view.TrackView.addTracks(TrackView.java:149) at com.affymetrix.igb.view.SeqMapView.addAnnotationTracks(SeqMapView.java:1002) at com.affymetrix.igb.view.SeqMapView.addGlyphs(SeqMapView.java:954) at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:788) at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:732) at com.affymetrix.igb.view.load.GeneralLoadUtils$2.finished(GeneralLoadUtils.java:747) at com.affymetrix.genometry.thread.CThreadWorker.done(CThreadWorker.java:51) at javax.swing.SwingWorker$5.run(Unknown Source) at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.run(Unknown Source) at sun.swing.AccumulativeRunnable.run(Unknown Source) at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.actionPerformed(Unknown Source) at javax.swing.Timer.fireActionPerformed(Unknown Source) at javax.swing.Timer$DoPostEvent.run(Unknown Source) at java.awt.event.InvocationEvent.dispatch(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$500(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source)
                  Hide
                  Permalink
                  dcnorris David Norris (Inactive) added a comment - - edited

                  Unfortunately, I can't reproduce any of this on linux on IGB 8.4.0.

                  Show
                  dcnorris David Norris (Inactive) added a comment - - edited Unfortunately, I can't reproduce any of this on linux on IGB 8.4.0.
                  Hide
                  Permalink
                  dcnorris David Norris (Inactive) added a comment -

                  I was able to reproduce this on IGB 8.3.4, but its not an issue during each run and appears to be the result of some race condition more likely on the live version than IGB 8.4.0

                  Show
                  dcnorris David Norris (Inactive) added a comment - I was able to reproduce this on IGB 8.3.4, but its not an issue during each run and appears to be the result of some race condition more likely on the live version than IGB 8.4.0
                  Hide
                  Permalink
                  dcnorris David Norris (Inactive) added a comment -

                  I think this is going to be a will not fix for IGB 8.4.0 since it is not a regression and appears to be a race condition. We cannot easily fix race conditions at the moment since we do not have asynchronous call backs on the completion of scripting commands at the moment. Slowing the script down with the sleep command should fix the bug on all versions, so please confirm this is the case.

                  Show
                  dcnorris David Norris (Inactive) added a comment - I think this is going to be a will not fix for IGB 8.4.0 since it is not a regression and appears to be a race condition. We cannot easily fix race conditions at the moment since we do not have asynchronous call backs on the completion of scripting commands at the moment. Slowing the script down with the sleep command should fix the bug on all versions, so please confirm this is the case.
                  Hide
                  Permalink
                  mason Mason Meyer (Inactive) added a comment -

                  I retested this issue and can confirm the I am experiencing multiple issues using 8.4.0 on both Mac and Windows when trying to run the attached script, even when I put in a sleep command of 30 seconds.

                  I am seeing URLs displayed in the track label when they shouldn't be (consistently on Windows and seldomly on Mac) and am also seeing null pointer exceptions (consistently on Windows and seldomly on Mac).

                  Let me know if you would like me to show you these issues on my machine.

                  Show
                  mason Mason Meyer (Inactive) added a comment - I retested this issue and can confirm the I am experiencing multiple issues using 8.4.0 on both Mac and Windows when trying to run the attached script, even when I put in a sleep command of 30 seconds. I am seeing URLs displayed in the track label when they shouldn't be (consistently on Windows and seldomly on Mac) and am also seeing null pointer exceptions (consistently on Windows and seldomly on Mac). Let me know if you would like me to show you these issues on my machine.
                  Hide
                  Permalink
                  mason Mason Meyer (Inactive) added a comment -

                  There are known issues with scripting that will not be fixed for the moment so I am moving this story to the bottom of the backlog.

                  Show
                  mason Mason Meyer (Inactive) added a comment - There are known issues with scripting that will not be fixed for the moment so I am moving this story to the bottom of the backlog.

                    People

                    • Assignee:
                      Unassigned
                      Reporter:
                      mason Mason Meyer (Inactive)
                    • Votes:
                      0 Vote for this issue
                      Watchers:
                      2 Start watching this issue

                      Dates

                      • Created:
                        Updated: