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  1. Bug Repository
  2. BUG-281

IOException when loading EST files from BioViz (Das2) server

          Details

          • Type: Bug
          • Status: Closed (View Workflow)
          • Priority: Minor
          • Resolution: Fixed
          • Labels:
            None

            Description

            Steps to reproduce:
            1. Load IGB 6.7
            2. Choose Bioviz Das2 server
            3. Check EST (Multimap) and EST single map files
            4. Click Load Data Button

            java.io.IOException: Could not parse bar-file header.
            at com.affymetrix.genometryImpl.parsers.graph.BarParser.parseBarHeader(BarParser.java:654)
            at com.affymetrix.genometryImpl.parsers.graph.BarParser.parse(BarParser.java:391)
            at com.affymetrix.genometryImpl.parsers.graph.BarParser.parse(BarParser.java:925)
            at com.affymetrix.genometryImpl.symloader.SymLoader.parse(SymLoader.java:383)
            at com.affymetrix.igb.featureloader.Das2.LoadFeaturesFromQuery(Das2.java:276)
            at com.affymetrix.igb.featureloader.Das2.loadSpan(Das2.java:77)
            at com.affymetrix.igb.featureloader.Das2.loadFeatures(Das2.java:57)
            at com.affymetrix.igb.view.load.GeneralLoadUtils.loadFeaturesForSym(GeneralLoadUtils.java:893)
            at com.affymetrix.igb.view.load.GeneralLoadUtils.access$200(GeneralLoadUtils.java:88)
            at com.affymetrix.igb.view.load.GeneralLoadUtils$2.runInBackground(GeneralLoadUtils.java:839)
            at com.affymetrix.igb.view.load.GeneralLoadUtils$2.runInBackground(GeneralLoadUtils.java:834)
            at com.affymetrix.genometryImpl.thread.CThreadWorker.doInBackground(CThreadWorker.java:38)
            at javax.swing.SwingWorker$1.call(SwingWorker.java:277)
            at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
            at java.util.concurrent.FutureTask.run(FutureTask.java:138)
            at javax.swing.SwingWorker.run(SwingWorker.java:316)
            at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
            at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
            at java.lang.Thread.run(Thread.java:680)
            Caused by: java.io.EOFException
            at java.io.DataInputStream.readFully(DataInputStream.java:180)
            at java.io.DataInputStream.readFully(DataInputStream.java:152)
            at com.affymetrix.genometryImpl.parsers.graph.BarParser.parseBarHeader(BarParser.java:629)
            ... 18 more

              Attachments

                Issue Links

                relates to

                Task - A task that needs to be done. BUG-622 File format issues

                • Blocker - Blocks development and/or testing work, production could not run.
                • Closed

                  Activity

                  Ascending order - Click to sort in descending order
                  david David Norris (Inactive) created issue -
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                  hiralv Hiral Vora (Inactive) added a comment -

                  Fixed.

                  Show
                  hiralv Hiral Vora (Inactive) added a comment - Fixed.
                  hiralv Hiral Vora (Inactive) made changes -
                  Field Original Value New Value
                  Assignee Hiral Vora [ hiralv ] Alyssa Gulledge [ alyssa ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Open [ 1 ] Resolved [ 5 ]
                  Assignee Alyssa Gulledge [ alyssa ]
                  Resolution Fixed [ 1 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Resolved [ 5 ] Closed [ 6 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Project IGB 6.7 [ 10040 ] Bug Repository [ 10030 ]
                  Key IGBB-313 BUG-281
                  fwang4 Fuquan Wang (Inactive) made changes -
                  Resolution Fixed [ 1 ]
                  Status Closed [ 6 ] Reopened [ 4 ]
                  Assignee Fuquan Wang [ fwang4 ]
                  Hide
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                  fwang4 Fuquan Wang (Inactive) added a comment - - edited

                  Failed for 7.0.0 (11884) Mac:

                  Getting IGB long running(no response) or below error:

                  Exception in thread "AWT-EventQueue-0" java.lang.OutOfMemoryError: Java heap space
                  at java.util.HashMap.resize(HashMap.java:462)
                  at java.util.HashMap.addEntry(HashMap.java:755)
                  at java.util.HashMap.put(HashMap.java:385)
                  at com.affymetrix.genoviz.widget.NeoAbstractWidget.setDataModel(NeoAbstractWidget.java:314)
                  at com.affymetrix.igb.tiers.AffyTieredMap.setDataModelFromOriginalSym(AffyTieredMap.java:509)
                  at com.affymetrix.igb.view.SeqMapView.setDataModelFromOriginalSym(SeqMapView.java:1359)
                  at com.affymetrix.igb.viewmode.AnnotationGlyphFactory.addChildren(AnnotationGlyphFactory.java:296)
                  at com.affymetrix.igb.viewmode.AnnotationGlyphFactory.determinePGlyph(AnnotationGlyphFactory.java:180)
                  at com.affymetrix.igb.viewmode.AnnotationGlyphFactory.addToTier(AnnotationGlyphFactory.java:159)
                  at com.affymetrix.igb.viewmode.AnnotationGlyphFactory.addLeafsToTier(AnnotationGlyphFactory.java:122)
                  at com.affymetrix.igb.viewmode.AnnotationGlyphFactory.addLeafsToTier(AnnotationGlyphFactory.java:119)
                  at com.affymetrix.igb.viewmode.AnnotationGlyphFactory.getViewModeGlyph(AnnotationGlyphFactory.java:570)
                  at com.affymetrix.igb.shared.TierGlyph.setViewModeGlyph(TierGlyph.java:103)
                  at com.affymetrix.igb.shared.TierGlyph.setInfo(TierGlyph.java:474)
                  at com.affymetrix.igb.view.TrackView.addAnnotationGlyphs(TrackView.java:232)
                  at com.affymetrix.igb.view.TrackView.addTracks(TrackView.java:153)
                  at com.affymetrix.igb.view.SeqMapView.addAnnotationTracks(SeqMapView.java:1197)
                  at com.affymetrix.igb.view.SeqMapView.addGlyphs(SeqMapView.java:961)
                  at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:778)
                  at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:700)
                  at com.affymetrix.igb.view.load.GeneralLoadUtils$3.finished(GeneralLoadUtils.java:769)
                  at com.affymetrix.genometryImpl.thread.CThreadWorker.done(CThreadWorker.java:41)
                  at javax.swing.SwingWorker$5.run(SwingWorker.java:717)
                  at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.run(SwingWorker.java:814)
                  at sun.swing.AccumulativeRunnable.run(AccumulativeRunnable.java:95)
                  at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.actionPerformed(SwingWorker.java:824)
                  at javax.swing.Timer.fireActionPerformed(Timer.java:291)
                  at javax.swing.Timer$DoPostEvent.run(Timer.java:221)
                  at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
                  at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:682)
                  at java.awt.EventQueue.access$000(EventQueue.java:85)
                  at java.awt.EventQueue$1.run(EventQueue.java:643)
                  Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
                  at com.affymetrix.genoviz.bioviews.Scene.removeGlyph(Scene.java:391)
                  at com.affymetrix.genoviz.widget.NeoMap.removeItem(NeoMap.java:1021)
                  at com.affymetrix.igb.tiers.AffyTieredMap.removeItem(AffyTieredMap.java:277)
                  at com.affymetrix.igb.tiers.AffyTieredMap.removeTier(AffyTieredMap.java:296)
                  at com.affymetrix.igb.tiers.AffyLabelledTierMap.removeTier(AffyLabelledTierMap.java:251)
                  at com.affymetrix.igb.view.SeqMapView.copyMapTierGlyphs(SeqMapView.java:946)
                  at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:752)
                  at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:700)
                  at com.affymetrix.igb.view.load.GeneralLoadUtils$3.finished(GeneralLoadUtils.java:769)
                  at com.affymetrix.genometryImpl.thread.CThreadWorker.done(CThreadWorker.java:41)
                  at javax.swing.SwingWorker$5.run(SwingWorker.java:717)
                  at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.run(SwingWorker.java:814)
                  at sun.swing.AccumulativeRunnable.run(AccumulativeRunnable.java:95)
                  at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.actionPerformed(SwingWorker.java:824)
                  at javax.swing.Timer.fireActionPerformed(Timer.java:291)
                  at javax.swing.Timer$DoPostEvent.run(Timer.java:221)
                  at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
                  at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:682)
                  at java.awt.EventQueue.access$000(EventQueue.java:85)
                  at java.awt.EventQueue$1.run(EventQueue.java:643)
                  at java.awt.EventQueue$1.run(EventQueue.java:641)
                  at java.security.AccessController.doPrivileged(Native Method)
                  at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
                  at java.awt.EventQueue.dispatchEvent(EventQueue.java:652)
                  at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
                  at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
                  at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
                  at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
                  at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
                  at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)

                  Show
                  fwang4 Fuquan Wang (Inactive) added a comment - - edited Failed for 7.0.0 (11884) Mac: Getting IGB long running(no response) or below error: Exception in thread "AWT-EventQueue-0" java.lang.OutOfMemoryError: Java heap space at java.util.HashMap.resize(HashMap.java:462) at java.util.HashMap.addEntry(HashMap.java:755) at java.util.HashMap.put(HashMap.java:385) at com.affymetrix.genoviz.widget.NeoAbstractWidget.setDataModel(NeoAbstractWidget.java:314) at com.affymetrix.igb.tiers.AffyTieredMap.setDataModelFromOriginalSym(AffyTieredMap.java:509) at com.affymetrix.igb.view.SeqMapView.setDataModelFromOriginalSym(SeqMapView.java:1359) at com.affymetrix.igb.viewmode.AnnotationGlyphFactory.addChildren(AnnotationGlyphFactory.java:296) at com.affymetrix.igb.viewmode.AnnotationGlyphFactory.determinePGlyph(AnnotationGlyphFactory.java:180) at com.affymetrix.igb.viewmode.AnnotationGlyphFactory.addToTier(AnnotationGlyphFactory.java:159) at com.affymetrix.igb.viewmode.AnnotationGlyphFactory.addLeafsToTier(AnnotationGlyphFactory.java:122) at com.affymetrix.igb.viewmode.AnnotationGlyphFactory.addLeafsToTier(AnnotationGlyphFactory.java:119) at com.affymetrix.igb.viewmode.AnnotationGlyphFactory.getViewModeGlyph(AnnotationGlyphFactory.java:570) at com.affymetrix.igb.shared.TierGlyph.setViewModeGlyph(TierGlyph.java:103) at com.affymetrix.igb.shared.TierGlyph.setInfo(TierGlyph.java:474) at com.affymetrix.igb.view.TrackView.addAnnotationGlyphs(TrackView.java:232) at com.affymetrix.igb.view.TrackView.addTracks(TrackView.java:153) at com.affymetrix.igb.view.SeqMapView.addAnnotationTracks(SeqMapView.java:1197) at com.affymetrix.igb.view.SeqMapView.addGlyphs(SeqMapView.java:961) at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:778) at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:700) at com.affymetrix.igb.view.load.GeneralLoadUtils$3.finished(GeneralLoadUtils.java:769) at com.affymetrix.genometryImpl.thread.CThreadWorker.done(CThreadWorker.java:41) at javax.swing.SwingWorker$5.run(SwingWorker.java:717) at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.run(SwingWorker.java:814) at sun.swing.AccumulativeRunnable.run(AccumulativeRunnable.java:95) at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.actionPerformed(SwingWorker.java:824) at javax.swing.Timer.fireActionPerformed(Timer.java:291) at javax.swing.Timer$DoPostEvent.run(Timer.java:221) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:682) at java.awt.EventQueue.access$000(EventQueue.java:85) at java.awt.EventQueue$1.run(EventQueue.java:643) Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at com.affymetrix.genoviz.bioviews.Scene.removeGlyph(Scene.java:391) at com.affymetrix.genoviz.widget.NeoMap.removeItem(NeoMap.java:1021) at com.affymetrix.igb.tiers.AffyTieredMap.removeItem(AffyTieredMap.java:277) at com.affymetrix.igb.tiers.AffyTieredMap.removeTier(AffyTieredMap.java:296) at com.affymetrix.igb.tiers.AffyLabelledTierMap.removeTier(AffyLabelledTierMap.java:251) at com.affymetrix.igb.view.SeqMapView.copyMapTierGlyphs(SeqMapView.java:946) at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:752) at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:700) at com.affymetrix.igb.view.load.GeneralLoadUtils$3.finished(GeneralLoadUtils.java:769) at com.affymetrix.genometryImpl.thread.CThreadWorker.done(CThreadWorker.java:41) at javax.swing.SwingWorker$5.run(SwingWorker.java:717) at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.run(SwingWorker.java:814) at sun.swing.AccumulativeRunnable.run(AccumulativeRunnable.java:95) at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.actionPerformed(SwingWorker.java:824) at javax.swing.Timer.fireActionPerformed(Timer.java:291) at javax.swing.Timer$DoPostEvent.run(Timer.java:221) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:682) at java.awt.EventQueue.access$000(EventQueue.java:85) at java.awt.EventQueue$1.run(EventQueue.java:643) at java.awt.EventQueue$1.run(EventQueue.java:641) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87) at java.awt.EventQueue.dispatchEvent(EventQueue.java:652) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188) at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
                  fwang4 Fuquan Wang (Inactive) made changes -
                  Assignee Fuquan Wang [ fwang4 ] Alyssa Gulledge [ alyssa ]
                  Hide
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                  alyssa Alyssa Gulledge (Inactive) added a comment -

                  Is this an issue in Windows?

                  Show
                  alyssa Alyssa Gulledge (Inactive) added a comment - Is this an issue in Windows?
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Assignee Alyssa Gulledge [ alyssa ] Katharine Kubiak [ kkubiak ]
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                  kkubiak Katharine Kubiak (Inactive) added a comment -

                  No issue Windows v11948

                  Show
                  kkubiak Katharine Kubiak (Inactive) added a comment - No issue Windows v11948
                  kkubiak Katharine Kubiak (Inactive) made changes -
                  Assignee Katharine Kubiak [ kkubiak ] Alyssa Gulledge [ alyssa ]
                  Hide
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                  fwang4 Fuquan Wang (Inactive) added a comment -

                  Passed on 7.0.0 (11959) Mac.

                  Show
                  fwang4 Fuquan Wang (Inactive) added a comment - Passed on 7.0.0 (11959) Mac.
                  fwang4 Fuquan Wang (Inactive) made changes -
                  Status Reopened [ 4 ] Resolved [ 5 ]
                  Assignee Alyssa Gulledge [ alyssa ]
                  Resolution Fixed [ 1 ]
                  richard Richard Linchangco (Inactive) made changes -
                  Resolution Fixed [ 1 ]
                  Status Resolved [ 5 ] Reopened [ 4 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Link This issue relates to BUG-622 [ BUG-622 ]
                  Hide
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                  richard Richard Linchangco (Inactive) added a comment -

                  Passed V.13526, Mac, Java 1.06.0_37

                  Show
                  richard Richard Linchangco (Inactive) added a comment - Passed V.13526, Mac, Java 1.06.0_37
                  richard Richard Linchangco (Inactive) made changes -
                  Status Reopened [ 4 ] Resolved [ 5 ]
                  Assignee Alyssa Gulledge [ alyssa ]
                  Resolution Fixed [ 1 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Link This issue is blocked by BUG-647 [ BUG-647 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Link This issue is blocked by BUG-647 [ BUG-647 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Resolution Fixed [ 1 ]
                  Status Resolved [ 5 ] Reopened [ 4 ]
                  Assignee Alyssa Gulledge [ alyssa ]
                  Hide
                  Permalink
                  richard Richard Linchangco (Inactive) added a comment -

                  Passed V.13655, Mac, Java 1.06.0_37

                  Steps revised for clarity:

                  • Open IGB
                  • Choose ANY genome
                  • In 'Available Data' JTree panel of 'Data Access' Tab open the 'IGB Quickload'
                    • Under 'IGB Quickload' check the EST box and then click 'Load Data' in the main viewer

                  If data loads then PASS

                  Show
                  richard Richard Linchangco (Inactive) added a comment - Passed V.13655, Mac, Java 1.06.0_37 Steps revised for clarity: Open IGB Choose ANY genome In 'Available Data' JTree panel of 'Data Access' Tab open the 'IGB Quickload' Under 'IGB Quickload' check the EST box and then click 'Load Data' in the main viewer If data loads then PASS
                  richard Richard Linchangco (Inactive) made changes -
                  Status Reopened [ 4 ] Resolved [ 5 ]
                  Assignee Alyssa Gulledge [ alyssa ]
                  Resolution Fixed [ 1 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Resolved [ 5 ] Closed [ 6 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Resolution Fixed [ 1 ]
                  Status Closed [ 6 ] Reopened [ 4 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Reopened [ 4 ] Closed [ 6 ]
                  Assignee Alyssa Gulledge [ alyssa ]
                  Resolution Fixed [ 1 ]

                    People

                    • Assignee:
                      Unassigned
                      Reporter:
                      david David Norris (Inactive)
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                      Dates

                      • Created:
                        Updated:
                        Resolved: