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  1. Bug Repository
  2. BUG-523

Loading tbi indexed file from the web throws npe

          Details

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

            Description

            http://bioviz.org/filerepo/

            java.lang.NullPointerException
            at com.affymetrix.genometryImpl.symloader.TbiZoomSymLoader.getRefNo(TbiZoomSymLoader.java:128)
            at com.affymetrix.genometryImpl.symloader.TbiZoomSymLoader.getBinIter(TbiZoomSymLoader.java:149)
            at com.affymetrix.genometryImpl.symloader.TbiZoomSymLoader.getBinIter(TbiZoomSymLoader.java:66)
            at com.affymetrix.genometryImpl.symloader.IndexZoomSymLoader.getRegion(IndexZoomSymLoader.java:64)
            at com.affymetrix.igb.shared.IndexedSemanticZoomGlyphFactory$IndexedSemanticZoomGlyph.getSummaryGlyph(IndexedSemanticZoomGlyphFactory.java:145)
            at com.affymetrix.igb.viewmode.GzIndexedSemanticZoomGlyphFactory$GzIndexedSemanticZoomGlyph.getSummaryGlyph(GzIndexedSemanticZoomGlyphFactory.java:84)
            at com.affymetrix.igb.shared.IndexedSemanticZoomGlyphFactory$IndexedSemanticZoomGlyph.getGlyph(IndexedSemanticZoomGlyphFactory.java:174)
            at com.affymetrix.igb.shared.SemanticZoomGlyphFactory.getViewModeGlyph(SemanticZoomGlyphFactory.java:39)
            at com.affymetrix.igb.shared.IndexedSemanticZoomGlyphFactory.getViewModeGlyph(IndexedSemanticZoomGlyphFactory.java:69)
            at com.affymetrix.igb.view.TrackView.getTrack(TrackView.java:98)
            at com.affymetrix.igb.view.SeqMapView.getTrack(SeqMapView.java:926)
            at com.affymetrix.igb.view.SeqMapView.getTrack(SeqMapView.java:922)
            at com.affymetrix.igb.view.TrackView.addTierFor(TrackView.java:409)
            at com.affymetrix.igb.view.TrackView.addEmptyTierFor(TrackView.java:379)
            at com.affymetrix.igb.view.load.GeneralLoadView$7.runInBackground(GeneralLoadView.java:596)
            at com.affymetrix.genometryImpl.thread.CThreadWorker.doInBackground(CThreadWorker.java:74)
            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)

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                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

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                  lfrohman Lance Frohman (Inactive) added a comment -

                  can't reprodice
                  can you give me exact steps to reproduce?

                  Show
                  lfrohman Lance Frohman (Inactive) added a comment - can't reprodice can you give me exact steps to reproduce?
                  Hide
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                  hiralv Hiral Vora (Inactive) added a comment -

                  Drag IGIS Gene Models.gff.gz from http://bioviz.org/filerepo and it would throw NPE.

                  Show
                  hiralv Hiral Vora (Inactive) added a comment - Drag IGIS Gene Models.gff.gz from http://bioviz.org/filerepo and it would throw NPE.
                  Hide
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                  lfrohman Lance Frohman (Inactive) added a comment -

                  fixed
                  rev 12147

                  Show
                  lfrohman Lance Frohman (Inactive) added a comment - fixed rev 12147
                  Hide
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                  richard Richard Linchangco (Inactive) added a comment - - edited

                  FAILED V.13624, Mac, Java 1.06.0_37

                  Tested with multiple .gz files paired with .gz.tbi files from filerepo:

                  http://bioviz.org/filerepo/LL_ESTs_mm_sorted.psl.gz PASSED
                  http://bioviz.org/filerepo/LL_ESTs_mm_sorted.psl.gz.tbi

                  http://bioviz.org/filerepo/IGIS Gene Models.gff.gz FAILED
                  http://bioviz.org/filerepo/IGIS Gene Models.gff.gz.tbi

                  http://bioviz.org/filerepo/IGIS_Entrez_Canonical.gff3 PASSED
                  http://bioviz.org/filerepo/IGIS_Entrez_Canonical.gff3.gz

                  IGIS Gene Models.gff.gz, when dragged from a browser, will appear as a track but will NOT load in the viewer and throws an error(see end of comment). If the file and its .tbi partner file are downloaded, there is no issue loading it in IGB 7.0.0(13624)

                  IGIS Gene Models.gff.gz browser drag and load error:

                  Nov 28, 2012 3:26:34 PM com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader logException
                  WARNING: null
                  java.lang.NegativeArraySizeException
                  at org.broad.tribble.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:300)
                  at org.broad.tribble.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:288)
                  at org.broad.tribble.util.BlockCompressedInputStream.seek(BlockCompressedInputStream.java:205)
                  at org.broad.tribble.source.tabix.TabixReader$Iterator.next(TabixReader.java:334)
                  at org.broad.tribble.source.tabix.TabixLineReader$TabixIteratorToLineReader.readLine(TabixLineReader.java:111)
                  at com.affymetrix.genometryImpl.symloader.GFF3$1.next(GFF3.java:137)
                  at com.affymetrix.genometryImpl.symloader.GFF3$1.next(GFF3.java:126)
                  at com.affymetrix.genometryImpl.parsers.GFF3Parser.parse(GFF3Parser.java:153)
                  at com.affymetrix.genometryImpl.symloader.GFF3.processLines(GFF3.java:151)
                  at com.affymetrix.genometryImpl.symloader.SymLoaderTabix.getRegion(SymLoaderTabix.java:152)
                  at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.getRegion(QuickLoadSymLoader.java:255)
                  at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.loadAndAddSymmetries(QuickLoadSymLoader.java:133)
                  at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.loadSymmetriesThread(QuickLoadSymLoader.java:107)
                  at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.loadFeatures(QuickLoadSymLoader.java:93)
                  at com.affymetrix.genometryImpl.util.LocalFilesServerType.loadFeatures(LocalFilesServerType.java:99)
                  at com.affymetrix.igb.view.load.GeneralLoadUtils.loadFeaturesForSym(GeneralLoadUtils.java:828)
                  at com.affymetrix.igb.view.load.GeneralLoadUtils$3.runInBackground(GeneralLoadUtils.java:769)
                  at com.affymetrix.igb.view.load.GeneralLoadUtils$3.runInBackground(GeneralLoadUtils.java:764)
                  at com.affymetrix.genometryImpl.thread.CThreadWorker.doInBackground(CThreadWorker.java:74)
                  at javax.swing.SwingWorker$1.call(SwingWorker.java:296)
                  at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
                  at java.util.concurrent.FutureTask.run(FutureTask.java:166)
                  at javax.swing.SwingWorker.run(SwingWorker.java:335)
                  at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
                  at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
                  at java.lang.Thread.run(Thread.java:722)

                  Show
                  richard Richard Linchangco (Inactive) added a comment - - edited FAILED V.13624, Mac, Java 1.06.0_37 Tested with multiple .gz files paired with .gz.tbi files from filerepo: http://bioviz.org/filerepo/LL_ESTs_mm_sorted.psl.gz PASSED http://bioviz.org/filerepo/LL_ESTs_mm_sorted.psl.gz.tbi http://bioviz.org/filerepo/IGIS Gene Models.gff.gz FAILED http://bioviz.org/filerepo/IGIS Gene Models.gff.gz.tbi http://bioviz.org/filerepo/IGIS_Entrez_Canonical.gff3 PASSED http://bioviz.org/filerepo/IGIS_Entrez_Canonical.gff3.gz IGIS Gene Models.gff.gz, when dragged from a browser, will appear as a track but will NOT load in the viewer and throws an error(see end of comment). If the file and its .tbi partner file are downloaded, there is no issue loading it in IGB 7.0.0(13624) IGIS Gene Models.gff.gz browser drag and load error: Nov 28, 2012 3:26:34 PM com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader logException WARNING: null java.lang.NegativeArraySizeException at org.broad.tribble.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:300) at org.broad.tribble.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:288) at org.broad.tribble.util.BlockCompressedInputStream.seek(BlockCompressedInputStream.java:205) at org.broad.tribble.source.tabix.TabixReader$Iterator.next(TabixReader.java:334) at org.broad.tribble.source.tabix.TabixLineReader$TabixIteratorToLineReader.readLine(TabixLineReader.java:111) at com.affymetrix.genometryImpl.symloader.GFF3$1.next(GFF3.java:137) at com.affymetrix.genometryImpl.symloader.GFF3$1.next(GFF3.java:126) at com.affymetrix.genometryImpl.parsers.GFF3Parser.parse(GFF3Parser.java:153) at com.affymetrix.genometryImpl.symloader.GFF3.processLines(GFF3.java:151) at com.affymetrix.genometryImpl.symloader.SymLoaderTabix.getRegion(SymLoaderTabix.java:152) at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.getRegion(QuickLoadSymLoader.java:255) at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.loadAndAddSymmetries(QuickLoadSymLoader.java:133) at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.loadSymmetriesThread(QuickLoadSymLoader.java:107) at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.loadFeatures(QuickLoadSymLoader.java:93) at com.affymetrix.genometryImpl.util.LocalFilesServerType.loadFeatures(LocalFilesServerType.java:99) at com.affymetrix.igb.view.load.GeneralLoadUtils.loadFeaturesForSym(GeneralLoadUtils.java:828) at com.affymetrix.igb.view.load.GeneralLoadUtils$3.runInBackground(GeneralLoadUtils.java:769) at com.affymetrix.igb.view.load.GeneralLoadUtils$3.runInBackground(GeneralLoadUtils.java:764) at com.affymetrix.genometryImpl.thread.CThreadWorker.doInBackground(CThreadWorker.java:74) at javax.swing.SwingWorker$1.call(SwingWorker.java:296) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334) at java.util.concurrent.FutureTask.run(FutureTask.java:166) at javax.swing.SwingWorker.run(SwingWorker.java:335) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603) at java.lang.Thread.run(Thread.java:722)
                  Hide
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                  hiralv Hiral Vora (Inactive) added a comment -

                  Worked fine for me on r13640.

                  Show
                  hiralv Hiral Vora (Inactive) added a comment - Worked fine for me on r13640.
                  Hide
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                  richard Richard Linchangco (Inactive) added a comment -

                  Still FAILS when dragging file:
                  *http://bioviz.org/filerepo/IGIS Gene Models.gff.gz
                  into IGB and hitting 'Load Data'.

                  Downloaded version of IGIS Gene Modles.gff.gz and its .tbi file loads into IGB without issue. Only when this specific file is dragged into IGB from the web. All other web based .tbi files work without problem.

                  Java Console Error

                  Happens for ALL chromosomes
                  log4j:WARN No appenders could be found for logger (org.broad.tribble.util.SeekableHTTPStream).
                  log4j:WARN Please initialize the log4j system properly.
                  Dec 04, 2012 2:20:09 PM com.affymetrix.genometryImpl.symloader.SymLoaderTabix init
                  INFO: Sequence not found. Adding chr20 with default length 1,000,000,000

                  THEN
                  Dec 04, 2012 2:20:50 PM com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader logException
                  WARNING: null
                  java.lang.NegativeArraySizeException
                  at org.broad.tribble.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:300)
                  at org.broad.tribble.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:288)
                  at org.broad.tribble.util.BlockCompressedInputStream.seek(BlockCompressedInputStream.java:205)
                  at org.broad.tribble.source.tabix.TabixReader$Iterator.next(TabixReader.java:334)
                  at org.broad.tribble.source.tabix.TabixLineReader$TabixIteratorToLineReader.readLine(TabixLineReader.java:111)
                  at com.affymetrix.genometryImpl.symloader.GFF3$1.next(GFF3.java:137)
                  at com.affymetrix.genometryImpl.symloader.GFF3$1.next(GFF3.java:126)
                  at com.affymetrix.genometryImpl.parsers.GFF3Parser.parse(GFF3Parser.java:153)
                  at com.affymetrix.genometryImpl.symloader.GFF3.processLines(GFF3.java:151)
                  at com.affymetrix.genometryImpl.symloader.SymLoaderTabix.getRegion(SymLoaderTabix.java:152)
                  at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.getRegion(QuickLoadSymLoader.java:255)
                  at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.loadAndAddSymmetries(QuickLoadSymLoader.java:133)
                  at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.loadSymmetriesThread(QuickLoadSymLoader.java:107)
                  at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.loadFeatures(QuickLoadSymLoader.java:93)
                  at com.affymetrix.genometryImpl.util.LocalFilesServerType.loadFeatures(LocalFilesServerType.java:99)
                  at com.affymetrix.igb.view.load.GeneralLoadUtils.loadFeaturesForSym(GeneralLoadUtils.java:852)
                  at com.affymetrix.igb.view.load.GeneralLoadUtils$3.runInBackground(GeneralLoadUtils.java:793)
                  at com.affymetrix.igb.view.load.GeneralLoadUtils$3.runInBackground(GeneralLoadUtils.java:788)
                  at com.affymetrix.genometryImpl.thread.CThreadWorker.doInBackground(CThreadWorker.java:74)
                  at javax.swing.SwingWorker$1.call(SwingWorker.java:296)
                  at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
                  at java.util.concurrent.FutureTask.run(FutureTask.java:166)
                  at javax.swing.SwingWorker.run(SwingWorker.java:335)
                  at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
                  at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
                  at java.lang.Thread.run(Thread.java:722)

                  Show
                  richard Richard Linchangco (Inactive) added a comment - Still FAILS when dragging file: * http://bioviz.org/filerepo/IGIS Gene Models.gff.gz into IGB and hitting 'Load Data'. Downloaded version of IGIS Gene Modles.gff.gz and its .tbi file loads into IGB without issue. Only when this specific file is dragged into IGB from the web. All other web based .tbi files work without problem. Java Console Error Happens for ALL chromosomes log4j:WARN No appenders could be found for logger (org.broad.tribble.util.SeekableHTTPStream). log4j:WARN Please initialize the log4j system properly. Dec 04, 2012 2:20:09 PM com.affymetrix.genometryImpl.symloader.SymLoaderTabix init INFO: Sequence not found. Adding chr20 with default length 1,000,000,000 THEN Dec 04, 2012 2:20:50 PM com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader logException WARNING: null java.lang.NegativeArraySizeException at org.broad.tribble.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:300) at org.broad.tribble.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:288) at org.broad.tribble.util.BlockCompressedInputStream.seek(BlockCompressedInputStream.java:205) at org.broad.tribble.source.tabix.TabixReader$Iterator.next(TabixReader.java:334) at org.broad.tribble.source.tabix.TabixLineReader$TabixIteratorToLineReader.readLine(TabixLineReader.java:111) at com.affymetrix.genometryImpl.symloader.GFF3$1.next(GFF3.java:137) at com.affymetrix.genometryImpl.symloader.GFF3$1.next(GFF3.java:126) at com.affymetrix.genometryImpl.parsers.GFF3Parser.parse(GFF3Parser.java:153) at com.affymetrix.genometryImpl.symloader.GFF3.processLines(GFF3.java:151) at com.affymetrix.genometryImpl.symloader.SymLoaderTabix.getRegion(SymLoaderTabix.java:152) at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.getRegion(QuickLoadSymLoader.java:255) at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.loadAndAddSymmetries(QuickLoadSymLoader.java:133) at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.loadSymmetriesThread(QuickLoadSymLoader.java:107) at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.loadFeatures(QuickLoadSymLoader.java:93) at com.affymetrix.genometryImpl.util.LocalFilesServerType.loadFeatures(LocalFilesServerType.java:99) at com.affymetrix.igb.view.load.GeneralLoadUtils.loadFeaturesForSym(GeneralLoadUtils.java:852) at com.affymetrix.igb.view.load.GeneralLoadUtils$3.runInBackground(GeneralLoadUtils.java:793) at com.affymetrix.igb.view.load.GeneralLoadUtils$3.runInBackground(GeneralLoadUtils.java:788) at com.affymetrix.genometryImpl.thread.CThreadWorker.doInBackground(CThreadWorker.java:74) at javax.swing.SwingWorker$1.call(SwingWorker.java:296) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334) at java.util.concurrent.FutureTask.run(FutureTask.java:166) at javax.swing.SwingWorker.run(SwingWorker.java:335) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603) at java.lang.Thread.run(Thread.java:722)
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                  alyssa Alyssa Gulledge (Inactive) added a comment -

                  I think that specific filepath is somehow damaged - it always loads fine from desktop, but I have seen it fail from the web before. However it seems to be the only file that does that. I am putting this bug to bed.

                  Show
                  alyssa Alyssa Gulledge (Inactive) added a comment - I think that specific filepath is somehow damaged - it always loads fine from desktop, but I have seen it fail from the web before. However it seems to be the only file that does that. I am putting this bug to bed.

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                    • Assignee:
                      Unassigned
                      Reporter:
                      hiralv Hiral Vora (Inactive)
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                      Dates

                      • Created:
                        Updated:
                        Resolved: