[IGBF-3670] Fix IGB unable to load files/folders with spaces - JIRA UNCC

Details

Type: Bug
Status: Closed (View Workflow)
Priority: Major
Resolution: Done
Affects Version/s: None
Fix Version/s: 10.0.1
Labels:
None

Story Points:
2
Epic Link:
Improve IGB for users
Sprint:
Spring 8, Spring 9

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

IGBF-1471 Fix bigwig parsing code in 9.0.2

Closed

IGBF-3702 User Report: Issue loading bigWig file

Closed

IGBF-3707 Ensure we can still build installers for IGB 9 versions

Closed

IGBF-3716 Create patch fix for IGB 10.0.1

Closed

IGBF-3671 Update HTSJDK to newest version

Closed

IGBF-3490 Import HTSJDK 3.0.5 as OSGI bundle

Closed

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Nowlan Freese added a comment - 27/Mar/24 11:54 AM

Error:

11:54:11.779 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$BundleClassLoader @60df7989; com.affymetrix.genometry.quickload.QuickLoadSymLoader is in unnamed module of loader org.apache.felix.framework.BundleWiringImpl$BundleClassLoader @7be71476)
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$BundleClassLoader @60df7989; com.affymetrix.genometry.quickload.QuickLoadSymLoader is in unnamed module of loader org.apache.felix.framework.BundleWiringImpl$BundleClassLoader @7be71476)
	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)
11:54:12.198 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$BundleClassLoader @60df7989; com.affymetrix.genometry.quickload.QuickLoadSymLoader is in unnamed module of loader org.apache.felix.framework.BundleWiringImpl$BundleClassLoader @7be71476)
	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$BundleClassLoader @60df7989; com.affymetrix.genometry.quickload.QuickLoadSymLoader is in unnamed module of loader org.apache.felix.framework.BundleWiringImpl$BundleClassLoader @7be71476)
	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 11:54:15 AM com.affymetrix.genometry.quickload.QuickLoadSymLoader logException
WARNING: The input string file:/Users/lorainelab/Desktop/tmp_testFiles/ngs files/O'kli/GSM_CHIP_STAT_STUFF/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'kli/GSM_CHIP_STAT_STUFF/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'kli/GSM_CHIP_STAT_STUFF/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

11:54:15.170 ERROR c.a.igb.view.load.GeneralLoadUtils - The input string file:/Users/lorainelab/Desktop/tmp_testFiles/ngs files/O'kli/GSM_CHIP_STAT_STUFF/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'kli/GSM_CHIP_STAT_STUFF/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'kli/GSM_CHIP_STAT_STUFF/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

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Nowlan Freese added a comment - 27/Mar/24 11:54 AM Error: 11:54:11.779 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$BundleClassLoader @60df7989; com.affymetrix.genometry.quickload.QuickLoadSymLoader is in unnamed module of loader org.apache.felix.framework.BundleWiringImpl$BundleClassLoader @7be71476) 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$BundleClassLoader @60df7989; com.affymetrix.genometry.quickload.QuickLoadSymLoader is in unnamed module of loader org.apache.felix.framework.BundleWiringImpl$BundleClassLoader @7be71476) 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) 11:54:12.198 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$BundleClassLoader @60df7989; com.affymetrix.genometry.quickload.QuickLoadSymLoader is in unnamed module of loader org.apache.felix.framework.BundleWiringImpl$BundleClassLoader @7be71476) 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$BundleClassLoader @60df7989; com.affymetrix.genometry.quickload.QuickLoadSymLoader is in unnamed module of loader org.apache.felix.framework.BundleWiringImpl$BundleClassLoader @7be71476) 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 11:54:15 AM com.affymetrix.genometry.quickload.QuickLoadSymLoader logException WARNING: The input string file:/Users/lorainelab/Desktop/tmp_testFiles/ngs files/O'kli/GSM_CHIP_STAT_STUFF/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'kli/GSM_CHIP_STAT_STUFF/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'kli/GSM_CHIP_STAT_STUFF/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$DefaultSeekableStreamFactory.getStreamFor(SeekableStreamFactory.java:103) ... 17 more 11:54:15.170 ERROR c.a.igb.view.load.GeneralLoadUtils - The input string file:/Users/lorainelab/Desktop/tmp_testFiles/ngs files/O'kli/GSM_CHIP_STAT_STUFF/BigWig_HomoSapien.bigWig contains a URI scheme but is not a valid URI java.lang.IllegalArgumentException: The input string file:/Users/lorainelab/Desktop/tmp_testFiles/ngs files/O'kli/GSM_CHIP_STAT_STUFF/BigWig_HomoSapien.bigWig contains a URI scheme but is not a valid URI at htsjdk.samtools.seekablestream.SeekableStreamFactory$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'kli/GSM_CHIP_STAT_STUFF/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

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Nowlan Freese added a comment - 30/Apr/24 2:45 PM - edited

Branch built off of Main: https://bitbucket.org/nfreese/nowlanfork-igb/branch/IGBF-3670
Branch built off of release-10.0.0: https://bitbucket.org/nfreese/nowlanfork-igb/branch/IGBF-3670-V10.0.1

Test local files:

Download the BigWig_HomoSapien.bigWig and BigBed_HomoSapien.bigbed from https://data.bioviz.org/smokeTestingQuickload/H_sapiens_Dec_2013/
Move the files into a folder that has a name with spaces and special characters, such as "test space folder []"
Download installer or pull my branch (~~IGBF-3670~~-V10.0.1)
Start IGB
- (Not required, but I would suggest disabling UCSC REST and DAS data sources as it will speed up loading the human genome)
Go to the human genome (H_sapiens_Dec_2013)
Navigate to chr1:86,545,393-86,582,438
Add the BigWig_HomoSapien.bigWig and BigBed_HomoSapien.bigbed files to IGB (can drag and drop or use File > Open File...)
Click Load Data
Check that data load for both files, and that there are no errors in the log.

Test HTTPS files:

Download installer or pull my branch (~~IGBF-3670~~-V10.0.1)
Start IGB
- (Not required, but I would suggest disabling UCSC REST and DAS data sources as it will speed up loading the human genome)
Go to the human genome (H_sapiens_Dec_2013)
Navigate to chr1:86,545,393-86,582,438
Select File > Open URL...
Copy and paste this bigBed URL
Click OK
Select File > Open URL...
Copy and paste this bigWig URL
Click OK
Click Load Data
Check that data load for both files, and that there are no errors in the log.

Test HTTP files:

Download installer or pull my branch (~~IGBF-3670~~-V10.0.1)
Start IGB
- (Not required, but I would suggest disabling UCSC REST and DAS data sources as it will speed up loading the human genome)
Go to the human genome (H_sapiens_Dec_2013)
Navigate to chr1:86,545,393-86,582,438
Select File > Open URL...
Copy and paste this bigBed URL
Click OK
Select File > Open URL...
Copy and paste this bigWig URL
Click OK
Click Load Data
Check that data load for both files, and that there are no errors in the log.

Test Quickload:

Download installer or pull my branch (~~IGBF-3670~~-V10.0.1)
Start IGB
- (Not required, but I would suggest disabling UCSC REST and DAS data sources as it will speed up loading the human genome)
Go to the human genome (H_sapiens_Dec_2013)
Navigate to chr1:86,545,393-86,582,438
Add http://igbquickload.org/smokeTestingQuickload/ as a new quickload in the Data Sources tab of the IGB Preferences
Select the BigBed and BigWig files in the Available Data window
Click Load Data
Check that data load for both files, and that there are no errors in the log.

Show

Nowlan Freese added a comment - 30/Apr/24 2:45 PM - edited Branch built off of Main: https://bitbucket.org/nfreese/nowlanfork-igb/branch/IGBF-3670 Branch built off of release-10.0.0: https://bitbucket.org/nfreese/nowlanfork-igb/branch/IGBF-3670-V10.0.1 Test local files: Download the BigWig_HomoSapien.bigWig and BigBed_HomoSapien.bigbed from https://data.bioviz.org/smokeTestingQuickload/H_sapiens_Dec_2013/ Move the files into a folder that has a name with spaces and special characters, such as "test space folder []" Download installer or pull my branch ( IGBF-3670 -V10.0.1) Start IGB (Not required, but I would suggest disabling UCSC REST and DAS data sources as it will speed up loading the human genome) Go to the human genome (H_sapiens_Dec_2013) Navigate to chr1:86,545,393-86,582,438 Add the BigWig_HomoSapien.bigWig and BigBed_HomoSapien.bigbed files to IGB (can drag and drop or use File > Open File...) Click Load Data Check that data load for both files, and that there are no errors in the log. Test HTTPS files: Download installer or pull my branch ( IGBF-3670 -V10.0.1) Start IGB (Not required, but I would suggest disabling UCSC REST and DAS data sources as it will speed up loading the human genome) Go to the human genome (H_sapiens_Dec_2013) Navigate to chr1:86,545,393-86,582,438 Select File > Open URL... Copy and paste this bigBed URL Click OK Select File > Open URL... Copy and paste this bigWig URL Click OK Click Load Data Check that data load for both files, and that there are no errors in the log. Test HTTP files: Download installer or pull my branch ( IGBF-3670 -V10.0.1) Start IGB (Not required, but I would suggest disabling UCSC REST and DAS data sources as it will speed up loading the human genome) Go to the human genome (H_sapiens_Dec_2013) Navigate to chr1:86,545,393-86,582,438 Select File > Open URL... Copy and paste this bigBed URL Click OK Select File > Open URL... Copy and paste this bigWig URL Click OK Click Load Data Check that data load for both files, and that there are no errors in the log. Test Quickload: Download installer or pull my branch ( IGBF-3670 -V10.0.1) Start IGB (Not required, but I would suggest disabling UCSC REST and DAS data sources as it will speed up loading the human genome) Go to the human genome (H_sapiens_Dec_2013) Navigate to chr1:86,545,393-86,582,438 Add http://igbquickload.org/smokeTestingQuickload/ as a new quickload in the Data Sources tab of the IGB Preferences Select the BigBed and BigWig files in the Available Data window Click Load Data Check that data load for both files, and that there are no errors in the log.

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Kaushik Gopu added a comment - 02/May/24 12:08 PM

Tested different scenarios as described in the notes.
No issues found while testing. The logs are clean without any errors or exceptions.

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Kaushik Gopu added a comment - 02/May/24 12:08 PM Tested different scenarios as described in the notes. No issues found while testing. The logs are clean without any errors or exceptions.

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Nowlan Freese added a comment - 02/May/24 3:07 PM

Pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1001

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Nowlan Freese added a comment - 02/May/24 3:07 PM Pull request: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1001

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Ann Loraine added a comment - 03/May/24 9:48 AM - edited

PR is merged. Main branch installers are built and deployed to BioViz.org as "early access" IGB.

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Ann Loraine added a comment - 03/May/24 9:48 AM - edited PR is merged. Main branch installers are built and deployed to BioViz.org as "early access" IGB.

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Nowlan Freese added a comment - 08/May/24 11:30 AM - edited

Tested IGB main installer on Mac, Linux, and Windows. I was able to load a bigwig and bigbed file that were located in a folder with spaces in the name.

Closing ticket.

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Nowlan Freese added a comment - 08/May/24 11:30 AM - edited Tested IGB main installer on Mac, Linux, and Windows. I was able to load a bigwig and bigbed file that were located in a folder with spaces in the name. Closing ticket.

People

Assignee:

Nowlan Freese

Reporter:

Nowlan Freese

Votes:

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Watchers:

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Dates

Created:

27/Mar/24 11:46 AM

Updated:

24/Sep/24 8:54 AM

Resolved:

08/May/24 11:31 AM