[BUG-523] Loading tbi indexed file from the web throws npe - JIRA UNCC

Details

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

Description

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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relates to

BUG-622 File format issues

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Hiral Vora (Inactive) created issue - 19/Jun/12 7:14 AM

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Lance Frohman (Inactive) added a comment - 25/Jun/12 6:48 AM

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

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Lance Frohman (Inactive) added a comment - 25/Jun/12 6:48 AM can't reprodice can you give me exact steps to reproduce?

Lance Frohman (Inactive) made changes - 25/Jun/12 6:48 AM

Field	Original Value	New Value
Assignee	Lance Frohman [ lfrohman ]	Hiral Vora [ hiralv ]

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Hiral Vora (Inactive) added a comment - 25/Jun/12 10:05 AM

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

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Hiral Vora (Inactive) added a comment - 25/Jun/12 10:05 AM Drag IGIS Gene Models.gff.gz from http://bioviz.org/filerepo and it would throw NPE.

Hiral Vora (Inactive) made changes - 25/Jun/12 10:05 AM

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Hiral Vora [ hiralv ]

Lance Frohman [ lfrohman ]

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Lance Frohman (Inactive) added a comment - 25/Jun/12 10:40 AM

fixed
rev 12147

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Lance Frohman (Inactive) added a comment - 25/Jun/12 10:40 AM fixed rev 12147

Lance Frohman (Inactive) made changes - 25/Jun/12 10:40 AM

Assignee

Lance Frohman [ lfrohman ]

Hiral Vora [ hiralv ]

Hiral Vora (Inactive) made changes - 25/Jun/12 11:20 AM

Status	Open [ 1 ]	Resolved [ 5 ]
Assignee	Hiral Vora [ hiralv ]
Resolution		Fixed [ 1 ]

Hiral Vora (Inactive) made changes - 25/Jun/12 11:20 AM

Status

Resolved [ 5 ]

Closed [ 6 ]

Alyssa Gulledge (Inactive) made changes - 05/Jul/12 7:28 AM

Project	IGB 7.0 [ 10140 ]	Bug Repository [ 10030 ]
Key	~~IGBC-336~~	~~BUG-523~~

Alyssa Gulledge (Inactive) made changes - 13/Nov/12 9:49 AM

Resolution	Fixed [ 1 ]
Status	Closed [ 6 ]	Reopened [ 4 ]

Alyssa Gulledge (Inactive) made changes - 13/Nov/12 10:07 AM

Priority

Blocker [ 1 ]

Major [ 3 ]

Alyssa Gulledge (Inactive) made changes - 15/Nov/12 10:16 AM

Link

This issue relates to ~~BUG-622~~ [ ~~BUG-622~~ ]

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Richard Linchangco (Inactive) added a comment - 27/Nov/12 11:44 AM - 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)

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Richard Linchangco (Inactive) added a comment - 27/Nov/12 11:44 AM - 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)

Richard Linchangco (Inactive) made changes - 27/Nov/12 11:44 AM

Status	Reopened [ 4 ]	Resolved [ 5 ]
Assignee		Alyssa Gulledge [ alyssa ]
Resolution		Fixed [ 1 ]

Richard Linchangco (Inactive) made changes - 27/Nov/12 11:49 AM

Resolution	Fixed [ 1 ]
Status	Resolved [ 5 ]	Reopened [ 4 ]

Richard Linchangco (Inactive) made changes - 28/Nov/12 9:15 AM

Status	Reopened [ 4 ]	Resolved [ 5 ]
Resolution		Fixed [ 1 ]

Richard Linchangco (Inactive) made changes - 28/Nov/12 10:33 AM

Resolution	Fixed [ 1 ]
Status	Resolved [ 5 ]	Reopened [ 4 ]

Alyssa Gulledge (Inactive) made changes - 28/Nov/12 10:53 AM

Assignee

Alyssa Gulledge [ alyssa ]

Hiral Vora [ hiralv ]

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Hiral Vora (Inactive) added a comment - 29/Nov/12 10:17 AM

Worked fine for me on r13640.

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Hiral Vora (Inactive) added a comment - 29/Nov/12 10:17 AM Worked fine for me on r13640.

Hiral Vora (Inactive) made changes - 29/Nov/12 10:17 AM

Assignee

Hiral Vora [ hiralv ]

Alyssa Gulledge [ alyssa ]

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Richard Linchangco (Inactive) added a comment - 04/Dec/12 9:25 AM

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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Richard Linchangco (Inactive) added a comment - 04/Dec/12 9:25 AM 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 Gulledge (Inactive) added a comment - 05/Dec/12 4:41 AM

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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Alyssa Gulledge (Inactive) added a comment - 05/Dec/12 4:41 AM 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.

Alyssa Gulledge (Inactive) made changes - 05/Dec/12 4:41 AM

Status	Reopened [ 4 ]	Resolved [ 5 ]
Assignee	Alyssa Gulledge [ alyssa ]
Resolution		Fixed [ 1 ]

Alyssa Gulledge (Inactive) made changes - 06/Dec/12 7:43 AM

Status

Resolved [ 5 ]

Closed [ 6 ]

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Assignee:

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Reporter:

Hiral Vora (Inactive)

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Dates

Created:

19/Jun/12 7:14 AM

Updated:

06/Dec/12 7:43 AM

Resolved:

05/Dec/12 4:41 AM