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  1. IGB
  2. IGBF-3670

Fix IGB unable to load files/folders with spaces

        Details

        • Type: Bug
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None

          Description

          Situation: A user reported an issue loading a local file in IGB 10.0.0. The issue appears to be that there was an illegal character, a space, in the name of a folder on the path to the file. The issue was not present in IGB 9.1.10. Therefore, the issue may be due to our upgrade in either the htsjdk or in Java.

          The two filetypes affected appear to be bigwig and bigbed. Example files can be found here: https://data.bioviz.org/smokeTestingQuickload/H_sapiens_Dec_2013/

          Task: Allow IGB to load bigwig and bigbed files from local paths that contain spaces.

            Attachments

              Issue Links

              relates to

              Bug - A problem which impairs or prevents the functions of the product. IGBF-1471 Fix bigwig parsing code in 9.0.2

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

              Bug - A problem which impairs or prevents the functions of the product. IGBF-3702 User Report: Issue loading bigWig file

              • Critical - Crashes, loss of data, severe memory leak.
              • Closed

              Task - A task that needs to be done. IGBF-3707 Ensure we can still build installers for IGB 9 versions

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3716 Create patch fix for IGB 10.0.1

              • Major - Major loss of function.
              • Closed

              Improvement - An improvement or enhancement to an existing feature or task. IGBF-3671 Update HTSJDK to newest version

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3490 Import HTSJDK 3.0.5 as OSGI bundle

              • Major - Major loss of function.
              • Closed

                Activity

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                nfreese Nowlan Freese created issue -
                nfreese Nowlan Freese made changes -
                Field Original Value New Value
                Epic Link IGBF-1765 [ 17855 ]
                nfreese Nowlan Freese made changes -
                Comment [ Error:
                {code}
                11:52:22.849 ERROR c.a.genometry.thread.CThreadWorker - class com.gene.bigwighandler.BigWigSymLoader cannot be cast to class com.affymetrix.genometry.quickload.QuickLoadSymLoader (com.gene.bigwighandler.BigWigSymLoader is in unnamed module of loader org.apache.felix.framework.BundleWiringImpl$BundleClassLoader @2dbc408c; com.affymetrix.genometry.quickload.QuickLoadSymLoader is in unnamed module of loader org.apache.felix.framework.BundleWiringImpl$BundleClassLoader @2dd8239)
                java.lang.ClassCastException: class com.gene.bigwighandler.BigWigSymLoader cannot be cast to class com.affymetrix.genometry.quickload.QuickLoadSymLoader (com.gene.bigwighandler.BigWigSymLoader is in unnamed module of loader org.apache.felix.framework.BundleWiringImpl$BundleClassLoader @2dbc408c; com.affymetrix.genometry.quickload.QuickLoadSymLoader is in unnamed module of loader org.apache.felix.framework.BundleWiringImpl$BundleClassLoader @2dd8239)
                at com.affymetrix.igb.view.load.GeneralLoadUtils$3.runInBackground(GeneralLoadUtils.java:1022)
                at com.affymetrix.igb.view.load.GeneralLoadUtils$3.runInBackground(GeneralLoadUtils.java:1001)
                at com.affymetrix.genometry.thread.CThreadWorker.doInBackground(CThreadWorker.java:73)
                at java.desktop/javax.swing.SwingWorker$1.call(SwingWorker.java:305)
                at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
                at java.desktop/javax.swing.SwingWorker.run(SwingWorker.java:342)
                at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
                at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
                at java.base/java.lang.Thread.run(Thread.java:1583)
                11:52:23.002 ERROR c.a.igb.view.load.GeneralLoadUtils - null
                java.util.concurrent.ExecutionException: java.lang.ClassCastException: class com.gene.bigwighandler.BigWigSymLoader cannot be cast to class com.affymetrix.genometry.quickload.QuickLoadSymLoader (com.gene.bigwighandler.BigWigSymLoader is in unnamed module of loader org.apache.felix.framework.BundleWiringImpl$BundleClassLoader @2dbc408c; com.affymetrix.genometry.quickload.QuickLoadSymLoader is in unnamed module of loader org.apache.felix.framework.BundleWiringImpl$BundleClassLoader @2dd8239)
                at java.base/java.util.concurrent.FutureTask.report(FutureTask.java:122)
                at java.base/java.util.concurrent.FutureTask.get(FutureTask.java:191)
                at java.desktop/javax.swing.SwingWorker.get(SwingWorker.java:612)
                at com.affymetrix.igb.view.load.GeneralLoadUtils$3.finished(GeneralLoadUtils.java:1050)
                at com.affymetrix.genometry.thread.CThreadWorker.done(CThreadWorker.java:51)
                at java.desktop/javax.swing.SwingWorker$4.run(SwingWorker.java:749)
                at java.desktop/javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.run(SwingWorker.java:847)
                at java.desktop/sun.swing.AccumulativeRunnable.run(AccumulativeRunnable.java:112)
                at java.desktop/javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.actionPerformed(SwingWorker.java:857)
                at java.desktop/javax.swing.Timer.fireActionPerformed(Timer.java:311)
                at java.desktop/javax.swing.Timer$DoPostEvent.run(Timer.java:243)
                at java.desktop/java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:318)
                at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:773)
                at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:720)
                at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:714)
                at java.base/java.security.AccessController.doPrivileged(AccessController.java:400)
                at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:87)
                at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:742)
                at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203)
                at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124)
                at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113)
                at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109)
                at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
                at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)
                Caused by: java.lang.ClassCastException: class com.gene.bigwighandler.BigWigSymLoader cannot be cast to class com.affymetrix.genometry.quickload.QuickLoadSymLoader (com.gene.bigwighandler.BigWigSymLoader is in unnamed module of loader org.apache.felix.framework.BundleWiringImpl$BundleClassLoader @2dbc408c; com.affymetrix.genometry.quickload.QuickLoadSymLoader is in unnamed module of loader org.apache.felix.framework.BundleWiringImpl$BundleClassLoader @2dd8239)
                at com.affymetrix.igb.view.load.GeneralLoadUtils$3.runInBackground(GeneralLoadUtils.java:1022)
                at com.affymetrix.igb.view.load.GeneralLoadUtils$3.runInBackground(GeneralLoadUtils.java:1001)
                at com.affymetrix.genometry.thread.CThreadWorker.doInBackground(CThreadWorker.java:73)
                at java.desktop/javax.swing.SwingWorker$1.call(SwingWorker.java:305)
                at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
                at java.desktop/javax.swing.SwingWorker.run(SwingWorker.java:342)
                at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
                at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
                at java.base/java.lang.Thread.run(Thread.java:1583)
                Mar 27, 2024 11:52:26 AM com.affymetrix.genometry.quickload.QuickLoadSymLoader logException
                WARNING: The input string file:/Users/lorainelab/Desktop/tmp_testFiles/ngs files/O'Shea/GSM4869780_ChIP_STAT3_Th1723_WT_100122L6/BigWig_HomoSapien.bigWig contains a URI scheme but is not a valid URI
                java.lang.IllegalArgumentException: The input string file:/Users/lorainelab/Desktop/tmp_testFiles/ngs files/O'Shea/GSM4869780_ChIP_STAT3_Th1723_WT_100122L6/BigWig_HomoSapien.bigWig contains a URI scheme but is not a valid URI
                at htsjdk.samtools.seekablestream.SeekableStreamFactory$DefaultSeekableStreamFactory.getStreamFor(SeekableStreamFactory.java:106)
                at htsjdk.samtools.seekablestream.SeekableStreamFactory$DefaultSeekableStreamFactory.getStreamFor(SeekableStreamFactory.java:78)
                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.loadAndAddSymmetries(QuickLoadSymLoader.java:153)
                at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadSymmetriesThread(QuickLoadSymLoader.java:139)
                at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadFeatures(QuickLoadSymLoader.java:119)
                at com.affymetrix.igb.view.load.GeneralLoadUtils.loadFeaturesForSym(GeneralLoadUtils.java:749)
                at com.affymetrix.igb.view.load.GeneralLoadUtils$2.runInBackground(GeneralLoadUtils.java:691)
                at com.affymetrix.igb.view.load.GeneralLoadUtils$2.runInBackground(GeneralLoadUtils.java:686)
                at com.affymetrix.genometry.thread.CThreadWorker.doInBackground(CThreadWorker.java:73)
                at java.desktop/javax.swing.SwingWorker$1.call(SwingWorker.java:305)
                at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
                at java.desktop/javax.swing.SwingWorker.run(SwingWorker.java:342)
                at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
                at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
                at java.base/java.lang.Thread.run(Thread.java:1583)
                Caused by: java.net.URISyntaxException: Illegal character in path at index 48: file:/Users/lorainelab/Desktop/tmp_testFiles/ngs files/O'Shea/GSM4869780_ChIP_STAT3_Th1723_WT_100122L6/BigWig_HomoSapien.bigWig
                at java.base/java.net.URI$Parser.fail(URI.java:2995)
                at java.base/java.net.URI$Parser.checkChars(URI.java:3166)
                at java.base/java.net.URI$Parser.parseHierarchical(URI.java:3248)
                at java.base/java.net.URI$Parser.parse(URI.java:3196)
                at java.base/java.net.URI.<init>(URI.java:645)
                at htsjdk.samtools.seekablestream.SeekableStreamFactory$DefaultSeekableStreamFactory.getStreamFor(SeekableStreamFactory.java:103)
                ... 17 more

                11:52:26.214 ERROR c.a.igb.view.load.GeneralLoadUtils - The input string file:/Users/lorainelab/Desktop/tmp_testFiles/ngs files/O'Shea/GSM4869780_ChIP_STAT3_Th1723_WT_100122L6/BigWig_HomoSapien.bigWig contains a URI scheme but is not a valid URI
                java.lang.IllegalArgumentException: The input string file:/Users/lorainelab/Desktop/tmp_testFiles/ngs files/O'Shea/GSM4869780_ChIP_STAT3_Th1723_WT_100122L6/BigWig_HomoSapien.bigWig contains a URI scheme but is not a valid URI
                at htsjdk.samtools.seekablestream.SeekableStreamFactory$DefaultSeekableStreamFactory.getStreamFor(SeekableStreamFactory.java:106)
                at htsjdk.samtools.seekablestream.SeekableStreamFactory$DefaultSeekableStreamFactory.getStreamFor(SeekableStreamFactory.java:78)
                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.loadAndAddSymmetries(QuickLoadSymLoader.java:153)
                at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadSymmetriesThread(QuickLoadSymLoader.java:139)
                at com.affymetrix.genometry.quickload.QuickLoadSymLoader.loadFeatures(QuickLoadSymLoader.java:119)
                at com.affymetrix.igb.view.load.GeneralLoadUtils.loadFeaturesForSym(GeneralLoadUtils.java:749)
                at com.affymetrix.igb.view.load.GeneralLoadUtils$2.runInBackground(GeneralLoadUtils.java:691)
                at com.affymetrix.igb.view.load.GeneralLoadUtils$2.runInBackground(GeneralLoadUtils.java:686)
                at com.affymetrix.genometry.thread.CThreadWorker.doInBackground(CThreadWorker.java:73)
                at java.desktop/javax.swing.SwingWorker$1.call(SwingWorker.java:305)
                at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:317)
                at java.desktop/javax.swing.SwingWorker.run(SwingWorker.java:342)
                at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1144)
                at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:642)
                at java.base/java.lang.Thread.run(Thread.java:1583)
                Caused by: java.net.URISyntaxException: Illegal character in path at index 48: file:/Users/lorainelab/Desktop/tmp_testFiles/ngs files/O'Shea/GSM4869780_ChIP_STAT3_Th1723_WT_100122L6/BigWig_HomoSapien.bigWig
                at java.base/java.net.URI$Parser.fail(URI.java:2995)
                at java.base/java.net.URI$Parser.checkChars(URI.java:3166)
                at java.base/java.net.URI$Parser.parseHierarchical(URI.java:3248)
                at java.base/java.net.URI$Parser.parse(URI.java:3196)
                at java.base/java.net.URI.<init>(URI.java:645)
                at htsjdk.samtools.seekablestream.SeekableStreamFactory$DefaultSeekableStreamFactory.getStreamFor(SeekableStreamFactory.java:103)
                ... 17 common frames omitted

                {code} ]
                nfreese Nowlan Freese made changes -
                Description Situation: A user reported an issue loading a local file in IGB 10.0.0. The issue appears to be that there was an illegal character, a space, in the name of a folder on the path to the file. The issue was not present in IGB 9.1.10. Therefore, the issue may be due to our upgrade in either the htsjdk or in Java.

                The two filetypes affected appear to be bigwig and bigbed.

                Task: Allow IGB to load bigwig and bigbed files from local paths that contain spaces.                 		Situation: A user reported an issue loading a local file in IGB 10.0.0. The issue appears to be that there was an illegal character, a space, in the name of a folder on the path to the file. The issue was not present in IGB 9.1.10. Therefore, the issue may be due to our upgrade in either the htsjdk or in Java.

                The two filetypes affected appear to be *bigwig* and *bigbed*.

                Task: Allow IGB to load bigwig and bigbed files from local paths that contain spaces.
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-3490 [ IGBF-3490 ]
                nfreese Nowlan Freese made changes -
                Description Situation: A user reported an issue loading a local file in IGB 10.0.0. The issue appears to be that there was an illegal character, a space, in the name of a folder on the path to the file. The issue was not present in IGB 9.1.10. Therefore, the issue may be due to our upgrade in either the htsjdk or in Java.

                The two filetypes affected appear to be *bigwig* and *bigbed*.

                Task: Allow IGB to load bigwig and bigbed files from local paths that contain spaces.                 		Situation: A user reported an issue loading a local file in IGB 10.0.0. The issue appears to be that there was an illegal character, a space, in the name of a folder on the path to the file. The issue was not present in IGB 9.1.10. Therefore, the issue may be due to our upgrade in either the htsjdk or in Java.

                The two filetypes affected appear to be *bigwig* and *bigbed*. Example files can be found here: https://data.bioviz.org/smokeTestingQuickload/H_sapiens_Dec_2013/

                Task: Allow IGB to load bigwig and bigbed files from local paths that contain spaces.
                nfreese Nowlan Freese made changes -
                Assignee Ann Loraine [ aloraine ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-3671 [ IGBF-3671 ]
                nfreese Nowlan Freese made changes -
                Sprint Spring 7 [ 191 ] Spring 8 [ 192 ]
                nfreese Nowlan Freese made changes -
                Sprint Spring 8 [ 192 ] Spring 9 [ 193 ]
                nfreese Nowlan Freese made changes -
                Sprint Spring 9 [ 193 ] Spring 8 [ 192 ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-3702 [ IGBF-3702 ]
                nfreese Nowlan Freese made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-3707 [ IGBF-3707 ]
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-1471 [ IGBF-1471 ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 8 [ 192 ] Spring 8, Spring 9 [ 192, 193 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-3716 [ IGBF-3716 ]
                nfreese Nowlan Freese made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                nfreese Nowlan Freese made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                nfreese Nowlan Freese made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                nfreese Nowlan Freese made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ]
                ann.loraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                ann.loraine Ann Loraine made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                nfreese Nowlan Freese made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                nfreese Nowlan Freese made changes -
                Story Points 3 2
                nfreese Nowlan Freese made changes -
                Assignee Nowlan Freese [ nfreese ]
                nfreese Nowlan Freese made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]

                  People

                  • Assignee:
                    nfreese Nowlan Freese
                    Reporter:
                    nfreese Nowlan Freese
                  • Votes:
                    0 Vote for this issue
                    Watchers:
                    3 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: