Details
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Type:
Bug
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Status: Open (View Workflow)
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Priority:
Major
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Resolution: Unresolved
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Labels:None
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Epic Link:
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
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- Closed
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-568 [ 15637 ] |
| Sprint | Sprint 21 [ 26 ] |
| Rank | Ranked higher |
| Attachment | loadData.igb [ 13077 ] |
| 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 to start running the script. Observe: a null pointer exception is generated (see below), 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. We should examine this and fix this before the release of 8.4.0 |
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 below), 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. We should examine this and fix this before the release of 8.4.0 |
| Attachment | NullPointer.PNG [ 13078 ] | |
| Attachment | NumerousScriptProblems.PNG [ 13079 ] |
| 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 below), 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. We should examine this and fix this before the release of 8.4.0 |
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 |
| Status | Open [ 1 ] | Needs Testing [ 10002 ] |
| Assignee | David Norris [ dcnorris ] |
| Status | Needs Testing [ 10002 ] | Open [ 1 ] |
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)
| Status | Open [ 1 ] | In Progress [ 3 ] |
Unfortunately, I can't reproduce any of this on linux on IGB 8.4.0.
| Rank | Ranked lower |
| Rank | Ranked lower |
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
| Attachment | Chromosome 1 (Arabidopsis thaliana TAIR9) - Integrated Genome Browser 8.3.4_033.png [ 13085 ] |
 - Integrated Genome Browser 8.3.4_033.png){kind=link}
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.
| Status | In Progress [ 3 ] | Needs Testing [ 10002 ] |
| Status | Needs Testing [ 10002 ] | Testing In Progress [ 10003 ] |
| Status | Testing In Progress [ 10003 ] | Needs Testing [ 10002 ] |
| Status | Needs Testing [ 10002 ] | Testing In Progress [ 10003 ] |
| Assignee | David Norris [ dcnorris ] | Mason Meyer [ mason ] |
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.
| Assignee | Mason Meyer [ mason ] |
| Status | Testing In Progress [ 10003 ] | Needs Testing [ 10002 ] |
| Sprint | Sprint 21 [ 26 ] | Backlog Grooming Meeting [ 29 ] |
| Rank | Ranked higher |
| Sprint | Backlog Grooming Meeting [ 29 ] | Backlog Grooming Meeting 2 [ 30 ] |
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.
| Sprint | Backlog Grooming Meeting 2 [ 30 ] |
| Rank | Ranked lower |
| Fix Version/s | 8.4.2 Minor Release [ 10004 ] | |
| Fix Version/s | 8.4.0 Major Release [ 10001 ] |
| Fix Version/s | 8.4.3 [ 10100 ] | |
| Fix Version/s | 8.4.2 Minor Release [ 10004 ] |
| Fix Version/s | 8.4.3 Minor Release [ 10100 ] |
It seems all the issues mentioned above are fixed through the fix for
IGBF-705except for the URL seen in the track label for one of the files.Reassigning to David to take a look at.