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  1. IGB
  2. IGBF-1471

Fix bigwig parsing code in 9.0.2

        Details

        • Story Points:
          1
        • Sprint:
          Winter 2018 Sprint 1

          Description

          User writes:

          "I have just upgraded IGB to version 9.0.2 (windows 10).
          I cannot upload bigWig files which did load in the previous version.
          The message is "Unable to load data set for this file. Would you like to remve this file...".
          Have tested several bigWig files, all with the same response.
          I was able to load BED file.
          Restarted the PC and restarted the application a couple of times."

          Note: IGB 9.0.2 is using code from this library to open and read bigwig files:
          https://bitbucket.org/lorainelab/bigwig

            Attachments

              Issue Links

              relates to

              Bug - A problem which impairs or prevents the functions of the product. HELP-316 Unable to load bigWig files

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

              Bug - A problem which impairs or prevents the functions of the product. HELP-324 file opening

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

              Bug - A problem which impairs or prevents the functions of the product. HELP-327 Failure to load files with 'Provider "XXX" not found' error

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

              Bug - A problem which impairs or prevents the functions of the product. HELP-328 Cannot load bigWig files IGB 9.1.0

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

              Task - A task that needs to be done. IGBF-2217 Release 9.1.2

              • Major - Major loss of function.
              • Closed

              Bug - A problem which impairs or prevents the functions of the product. IGBF-3670 Fix IGB unable to load files/folders with spaces

              • Major - Major loss of function.
              • Closed

                Activity

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                ann.loraine Ann Loraine created issue -
                ann.loraine Ann Loraine made changes -
                Field Original Value New Value
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                pbole Pawan Bole (Inactive) made changes -
                Assignee Pawan Bole [ pbole ]
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                nfreese Nowlan Freese added a comment -

                The bigWig test file test.bigWig loads correctly in IGB 9.0.2 on macOS 0.13.6.

                Show
                nfreese Nowlan Freese added a comment - The bigWig test file test.bigWig loads correctly in IGB 9.0.2 on macOS 0.13.6.
                nfreese Nowlan Freese made changes -
                Comment [ Exceptions on Windows 8.1 on IGB 9.0.2 startup:

                Exception in thread "AWT-EventQueue-0" htsjdk.samtools.FileTruncatedException: Premature end of file: data stream
                at htsjdk.samtools.util.BlockCompressedInputStream.processNextBlock(BlockCompressedInputStream.java:530)
                at htsjdk.samtools.util.BlockCompressedInputStream.nextBlock(BlockCompressedInputStream.java:468)
                at htsjdk.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:458)
                at htsjdk.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:196)
                at htsjdk.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:331)
                at sun.nio.cs.StreamDecoder.readBytes(Unknown Source)
                at sun.nio.cs.StreamDecoder.implRead(Unknown Source)
                at sun.nio.cs.StreamDecoder.read(Unknown Source)
                at java.io.InputStreamReader.read(Unknown Source)
                at java.io.BufferedReader.fill(Unknown Source)
                at java.io.BufferedReader.read(Unknown Source)
                at org.apache.commons.csv.ExtendedBufferedReader.read(ExtendedBufferedReader.java:60)
                at org.apache.commons.csv.Lexer.nextToken(Lexer.java:89)
                at org.apache.commons.csv.CSVParser.nextRecord(CSVParser.java:498)
                at org.apache.commons.csv.CSVParser$1.getNextRecord(CSVParser.java:439)
                at org.apache.commons.csv.CSVParser$1.hasNext(CSVParser.java:452)
                at java.util.Iterator.forEachRemaining(Unknown Source)
                at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source)
                at java.util.stream.ReferencePipeline$Head.forEach(Unknown Source)
                at org.lorainelab.igb.quickload.util.QuickloadUtils.processContentsTextFile(QuickloadUtils.java:106)
                at org.lorainelab.igb.quickload.util.QuickloadUtils.loadSupportedGenomeVersionInfo(QuickloadUtils.java:96)
                at org.lorainelab.igb.quickload.QuickloadDataProvider.populateSupportedGenomeVersionInfo(QuickloadDataProvider.java:133)
                at org.lorainelab.igb.quickload.QuickloadDataProvider.initialize(QuickloadDataProvider.java:111)
                at com.affymetrix.igb.general.DataProviderManager.initializeDataProvider(DataProviderManager.java:333)
                at com.affymetrix.igb.general.DataProviderManager.lambda$addDataProvider$87(DataProviderManager.java:324)
                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$3.run(Unknown Source)
                at java.security.AccessController.doPrivileged(Native Method)
                at java.security.ProtectionDomain$JavaSecurityAccessImpl.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)
                09:33:21.485 INFO o.l.i.q.QuickloadDataProvider - Initializing Quickload Server http://igbquickload.org/chipseq/
                Exception in thread "AWT-EventQueue-0" htsjdk.samtools.FileTruncatedException: Premature end of file: data stream
                at htsjdk.samtools.util.BlockCompressedInputStream.processNextBlock(BlockCompressedInputStream.java:530)
                at htsjdk.samtools.util.BlockCompressedInputStream.nextBlock(BlockCompressedInputStream.java:468)
                at htsjdk.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:458)
                at htsjdk.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:196)
                at htsjdk.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:331)
                at sun.nio.cs.StreamDecoder.readBytes(Unknown Source)
                at sun.nio.cs.StreamDecoder.implRead(Unknown Source)
                at sun.nio.cs.StreamDecoder.read(Unknown Source)
                at java.io.InputStreamReader.read(Unknown Source)
                at java.io.BufferedReader.fill(Unknown Source)
                at java.io.BufferedReader.read(Unknown Source)
                at org.apache.commons.csv.ExtendedBufferedReader.read(ExtendedBufferedReader.java:60)
                at org.apache.commons.csv.Lexer.nextToken(Lexer.java:89)
                at org.apache.commons.csv.CSVParser.nextRecord(CSVParser.java:498)
                at org.apache.commons.csv.CSVParser$1.getNextRecord(CSVParser.java:439)
                at org.apache.commons.csv.CSVParser$1.hasNext(CSVParser.java:452)
                at java.util.Iterator.forEachRemaining(Unknown Source)
                at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source)
                at java.util.stream.ReferencePipeline$Head.forEach(Unknown Source)
                at org.lorainelab.igb.quickload.util.QuickloadUtils.processContentsTextFile(QuickloadUtils.java:106)
                at org.lorainelab.igb.quickload.util.QuickloadUtils.loadSupportedGenomeVersionInfo(QuickloadUtils.java:96)
                at org.lorainelab.igb.quickload.QuickloadDataProvider.populateSupportedGenomeVersionInfo(QuickloadDataProvider.java:133)
                at org.lorainelab.igb.quickload.QuickloadDataProvider.initialize(QuickloadDataProvider.java:111)
                at com.affymetrix.igb.general.DataProviderManager.initializeDataProvider(DataProviderManager.java:333)
                at com.affymetrix.igb.general.DataProviderManager.lambda$addDataProvider$87(DataProviderManager.java:324)
                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$3.run(Unknown Source)
                at java.security.AccessController.doPrivileged(Native Method)
                at java.security.ProtectionDomain$JavaSecurityAccessImpl.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)
                ]
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                nfreese Nowlan Freese added a comment - - edited

                Windows 8.1
                IGB 9.0.2 release
                Java 1.8.0_191
                Exception when loading test.bigWig:

                Nov 29, 2018 9:47:28 AM com.affymetrix.genometry.quickload.QuickLoadSymLoader logException
                WARNING: Provider "C" not found
                java.nio.file.ProviderNotFoundException: Provider "C" not found
                at java.nio.file.FileSystems.newFileSystem(Unknown Source)
                at htsjdk.samtools.util.IOUtil.getPath(IOUtil.java:1126)
                at htsjdk.samtools.seekablestream.SeekableStreamFactory$DefaultSeekableStreamFactory.getStreamFor(SeekableStreamFactory.java:101)
                at htsjdk.samtools.seekablestream.SeekableStreamFactory$DefaultSeekableStreamFactory.getStreamFor(SeekableStreamFactory.java:77)
                at com.gene.bigwighandler.BigWigSymLoader.initbbReader(BigWigSymLoader.java:89)
                at com.gene.bigwighandler.BigWigSymLoader.init(BigWigSymLoader.java:62)
                at com.gene.bigwighandler.BigWigSymLoader.getChromosomeList(BigWigSymLoader.java:106)
                at com.affymetrix.genometry.quickload.QuickLoadSymLoader.getChromosomeList(QuickLoadSymLoader.java:254)
                at com.affymetrix.igb.view.load.GeneralLoadUtils$3.runInBackground(GeneralLoadUtils.java:1002)
                at com.affymetrix.igb.view.load.GeneralLoadUtils$3.runInBackground(GeneralLoadUtils.java:996)
                at com.affymetrix.genometry.thread.CThreadWorker.doInBackground(CThreadWorker.java:73)
                at javax.swing.SwingWorker$1.call(Unknown Source)
                at java.util.concurrent.FutureTask.run(Unknown Source)
                at javax.swing.SwingWorker.run(Unknown Source)
                at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
                at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
                at java.lang.Thread.run(Unknown Source)

                Show
                nfreese Nowlan Freese added a comment - - edited Windows 8.1 IGB 9.0.2 release Java 1.8.0_191 Exception when loading test.bigWig: Nov 29, 2018 9:47:28 AM com.affymetrix.genometry.quickload.QuickLoadSymLoader logException WARNING: Provider "C" not found java.nio.file.ProviderNotFoundException: Provider "C" not found at java.nio.file.FileSystems.newFileSystem(Unknown Source) at htsjdk.samtools.util.IOUtil.getPath(IOUtil.java:1126) at htsjdk.samtools.seekablestream.SeekableStreamFactory$DefaultSeekableStreamFactory.getStreamFor(SeekableStreamFactory.java:101) at htsjdk.samtools.seekablestream.SeekableStreamFactory$DefaultSeekableStreamFactory.getStreamFor(SeekableStreamFactory.java:77) at com.gene.bigwighandler.BigWigSymLoader.initbbReader(BigWigSymLoader.java:89) at com.gene.bigwighandler.BigWigSymLoader.init(BigWigSymLoader.java:62) at com.gene.bigwighandler.BigWigSymLoader.getChromosomeList(BigWigSymLoader.java:106) at com.affymetrix.genometry.quickload.QuickLoadSymLoader.getChromosomeList(QuickLoadSymLoader.java:254) at com.affymetrix.igb.view.load.GeneralLoadUtils$3.runInBackground(GeneralLoadUtils.java:1002) at com.affymetrix.igb.view.load.GeneralLoadUtils$3.runInBackground(GeneralLoadUtils.java:996) at com.affymetrix.genometry.thread.CThreadWorker.doInBackground(CThreadWorker.java:73) at javax.swing.SwingWorker$1.call(Unknown Source) at java.util.concurrent.FutureTask.run(Unknown Source) at javax.swing.SwingWorker.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.lang.Thread.run(Unknown Source)
                nfreese Nowlan Freese made changes -
                Link This issue relates to HELP-316 [ HELP-316 ]
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                stiwari8 Srishti Tiwari (Inactive) added a comment - - edited

                on IGB release 9.0.2 when loading test.bigWig (Windows 10, Java 1.8.0_181), I am getting this exception:

                Nov 29, 2018 9:51:11 AM com.affymetrix.genometry.quickload.QuickLoadSymLoader logException
                WARNING: Provider "E" not found
                java.nio.file.ProviderNotFoundException: Provider "E" not found
                at java.nio.file.FileSystems.newFileSystem(Unknown Source)
                at htsjdk.samtools.util.IOUtil.getPath(IOUtil.java:1126)
                at htsjdk.samtools.seekablestream.SeekableStreamFactory$DefaultSeekableStreamFactory.getStreamFor(SeekableStreamFactory.java:101)
                at htsjdk.samtools.seekablestream.SeekableStreamFactory$DefaultSeekableStreamFactory.getStreamFor(SeekableStreamFactory.java:77)
                at com.gene.bigwighandler.BigWigSymLoader.initbbReader(BigWigSymLoader.java:89)
                at com.gene.bigwighandler.BigWigSymLoader.init(BigWigSymLoader.java:62)
                at com.gene.bigwighandler.BigWigSymLoader.getChromosomeList(BigWigSymLoader.java:106)
                at com.affymetrix.genometry.quickload.QuickLoadSymLoader.getChromosomeList(QuickLoadSymLoader.java:254)
                at com.affymetrix.igb.view.load.GeneralLoadUtils$3.runInBackground(GeneralLoadUtils.java:1002)
                at com.affymetrix.igb.view.load.GeneralLoadUtils$3.runInBackground(GeneralLoadUtils.java:996)
                at com.affymetrix.genometry.thread.CThreadWorker.doInBackground(CThreadWorker.java:73)
                at javax.swing.SwingWorker$1.call(Unknown Source)
                at java.util.concurrent.FutureTask.run(Unknown Source)
                at javax.swing.SwingWorker.run(Unknown Source)
                at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
                at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
                at java.lang.Thread.run(Unknown Source)

                Show
                stiwari8 Srishti Tiwari (Inactive) added a comment - - edited on IGB release 9.0.2 when loading test.bigWig (Windows 10, Java 1.8.0_181), I am getting this exception: Nov 29, 2018 9:51:11 AM com.affymetrix.genometry.quickload.QuickLoadSymLoader logException WARNING: Provider "E" not found java.nio.file.ProviderNotFoundException: Provider "E" not found at java.nio.file.FileSystems.newFileSystem(Unknown Source) at htsjdk.samtools.util.IOUtil.getPath(IOUtil.java:1126) at htsjdk.samtools.seekablestream.SeekableStreamFactory$DefaultSeekableStreamFactory.getStreamFor(SeekableStreamFactory.java:101) at htsjdk.samtools.seekablestream.SeekableStreamFactory$DefaultSeekableStreamFactory.getStreamFor(SeekableStreamFactory.java:77) at com.gene.bigwighandler.BigWigSymLoader.initbbReader(BigWigSymLoader.java:89) at com.gene.bigwighandler.BigWigSymLoader.init(BigWigSymLoader.java:62) at com.gene.bigwighandler.BigWigSymLoader.getChromosomeList(BigWigSymLoader.java:106) at com.affymetrix.genometry.quickload.QuickLoadSymLoader.getChromosomeList(QuickLoadSymLoader.java:254) at com.affymetrix.igb.view.load.GeneralLoadUtils$3.runInBackground(GeneralLoadUtils.java:1002) at com.affymetrix.igb.view.load.GeneralLoadUtils$3.runInBackground(GeneralLoadUtils.java:996) at com.affymetrix.genometry.thread.CThreadWorker.doInBackground(CThreadWorker.java:73) at javax.swing.SwingWorker$1.call(Unknown Source) at java.util.concurrent.FutureTask.run(Unknown Source) at javax.swing.SwingWorker.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.lang.Thread.run(Unknown Source)
                pbole Pawan Bole (Inactive) made changes -
                Assignee Pawan Bole [ pbole ] Ann Loraine [ aloraine ]
                pbole Pawan Bole (Inactive) made changes -
                Assignee Ann Loraine [ aloraine ]
                stiwari8 Srishti Tiwari (Inactive) made changes -
                Assignee Srishti Tiwari [ stiwari8 ]
                Hide
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                stiwari8 Srishti Tiwari (Inactive) added a comment - - edited

                Fixed the issue and tested on windows 10, ubuntu and mac.
                Please review the changes:
                https://bitbucket.org/srishtitiwari/integrated-genome-browser/commits/67a5b9879c243289f1fcd9e81041a4701ae79069?at=release-9.0.2

                Show
                stiwari8 Srishti Tiwari (Inactive) added a comment - - edited Fixed the issue and tested on windows 10, ubuntu and mac. Please review the changes: https://bitbucket.org/srishtitiwari/integrated-genome-browser/commits/67a5b9879c243289f1fcd9e81041a4701ae79069?at=release-9.0.2
                stiwari8 Srishti Tiwari (Inactive) made changes -
                Status Open [ 1 ] Needs 1st Level Review [ 10005 ]
                Hide
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                stiwari8 Srishti Tiwari (Inactive) added a comment -

                Pull request submitted:

                https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/651/igbf-1471-fix-for-bigwig-file-parsing/diff

                Show
                stiwari8 Srishti Tiwari (Inactive) added a comment - Pull request submitted: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/651/igbf-1471-fix-for-bigwig-file-parsing/diff
                stiwari8 Srishti Tiwari (Inactive) made changes -
                Status Needs 1st Level Review [ 10005 ] Pull Request Submitted [ 10101 ]
                ann.loraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Needs Testing [ 10002 ]
                Hide
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                ann.loraine Ann Loraine added a comment -

                merged into release-9.0.2

                Show
                ann.loraine Ann Loraine added a comment - merged into release-9.0.2
                ann.loraine Ann Loraine made changes -
                Resolution Done [ 10000 ]
                Status Needs Testing [ 10002 ] Closed [ 6 ]
                Hide
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                ann.loraine Ann Loraine added a comment - - edited
                • tested on Windows, Mac, Linux: bigwig, bigbed files loaded locally, from Quickload
                • deployed to Bioviz.org
                Show
                ann.loraine Ann Loraine added a comment - - edited tested on Windows, Mac, Linux: bigwig, bigbed files loaded locally, from Quickload deployed to Bioviz.org
                ann.loraine Ann Loraine made changes -
                Workflow Loraine Lab Workflow [ 18186 ] Fall 2019 Workflow Update [ 19985 ]
                ann.loraine Ann Loraine made changes -
                Workflow Fall 2019 Workflow Update [ 19985 ] Revised Fall 2019 Workflow Update [ 22107 ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-2217 [ IGBF-2217 ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to HELP-327 [ HELP-327 ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to HELP-328 [ HELP-328 ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to HELP-324 [ HELP-324 ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-3670 [ IGBF-3670 ]

                  People

                  • Assignee:
                    stiwari8 Srishti Tiwari (Inactive)
                    Reporter:
                    ann.loraine Ann Loraine
                  • Votes:
                    0 Vote for this issue
                    Watchers:
                    3 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: