Uploaded image for project: 'Bug Repository'
  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
                  Hide
                  Permalink
                  hiralv Hiral Vora (Inactive) added a comment -

                  Fixed.

                  Show
                  hiralv Hiral Vora (Inactive) added a comment - Fixed.
                  Hide
                  Permalink
                  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)
                  Hide
                  Permalink
                  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?
                  Hide
                  Permalink
                  kkubiak Katharine Kubiak (Inactive) added a comment -

                  No issue Windows v11948

                  Show
                  kkubiak Katharine Kubiak (Inactive) added a comment - No issue Windows v11948
                  Hide
                  Permalink
                  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.
                  Hide
                  Permalink
                  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
                  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

                    People

                    • Assignee:
                      Unassigned
                      Reporter:
                      david David Norris (Inactive)
                    • Votes:
                      0 Vote for this issue
                      Watchers:
                      0 Start watching this issue

                      Dates

                      • Created:
                        Updated:
                        Resolved: