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.

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)

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

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

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.

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.

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.