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

Nowlan Freese created issue - 27/Mar/24 11:46 AM

Nowlan Freese made changes - 27/Mar/24 11:46 AM

Field	Original Value	New Value
Epic Link		IGBF-1765 [ 17855 ]

Nowlan Freese made changes - 27/Mar/24 11:53 AM

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} ]

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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

Nowlan Freese made changes - 27/Mar/24 11:54 AM

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.

Nowlan Freese made changes - 27/Mar/24 11:56 AM

Link

This issue relates to ~~IGBF-3490~~ [ ~~IGBF-3490~~ ]

Nowlan Freese made changes - 27/Mar/24 11:57 AM

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.

Nowlan Freese made changes - 27/Mar/24 11:57 AM

Assignee

Ann Loraine [ aloraine ]

Nowlan Freese made changes - 27/Mar/24 2:00 PM

Link

This issue relates to ~~IGBF-3671~~ [ ~~IGBF-3671~~ ]

Nowlan Freese made changes - 01/Apr/24 10:22 AM

Sprint

Spring 7 [ 191 ]

Spring 8 [ 192 ]

Nowlan Freese made changes - 15/Apr/24 10:02 AM

Sprint

Spring 8 [ 192 ]

Spring 9 [ 193 ]

Nowlan Freese made changes - 23/Apr/24 2:20 PM

Sprint

Spring 9 [ 193 ]

Spring 8 [ 192 ]

Nowlan Freese made changes - 23/Apr/24 2:23 PM

Link

This issue relates to ~~IGBF-3702~~ [ ~~IGBF-3702~~ ]

Nowlan Freese made changes - 23/Apr/24 2:24 PM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

Nowlan Freese made changes - 23/Apr/24 2:24 PM

Assignee

Nowlan Freese [ nfreese ]

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Nowlan Freese added a comment - 23/Apr/24 4:10 PM - edited

Attempting to build release-9.1.10 to compare to main branch. I'm seeing the following error:

[ERROR] Failed to execute goal org.apache.maven.plugins:maven-dependency-plugin:2.8:copy (copy) on project shared-lib-wrapper: Unable to find artifact.: The following artifacts could not be resolved: org.lorainelab.igb:org.lorainelab.igb.error.reporter.api:jar:1.0.0 (absent): org.lorainelab.igb:org.lorainelab.igb.error.reporter.api:jar:1.0.0 was not found in https://maven.bioviz.org/repo1

Ann Loraine - did we move the artifact org.lorainelab.igb.error.reporter.api out of repo1?

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Nowlan Freese added a comment - 23/Apr/24 4:10 PM - edited Attempting to build release-9.1.10 to compare to main branch. I'm seeing the following error: [ERROR] Failed to execute goal org.apache.maven.plugins:maven-dependency-plugin:2.8:copy (copy) on project shared-lib-wrapper: Unable to find artifact.: The following artifacts could not be resolved: org.lorainelab.igb:org.lorainelab.igb.error.reporter.api:jar:1.0.0 (absent): org.lorainelab.igb:org.lorainelab.igb.error.reporter.api:jar:1.0.0 was not found in https: //maven.bioviz.org/repo1 Ann Loraine - did we move the artifact org.lorainelab.igb.error.reporter.api out of repo1?

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Nowlan Freese added a comment - 23/Apr/24 9:35 PM - edited

BigWigSymLoader.java in initbbReader is making a call to SeekableStreamFactory in the HTSJDK. We didn't make any changes to BigWigSymLoader as part of the upgrade to JDK21. However, there was a commit in 2020 that changed how the handling of file paths occurred in SeekableStreamFactory.java.

2020 code:

// convert to URI in order to obtain a decoded version of the path string suitable
                    // for use with the File constructor
                    final String decodedPath = new URI(path).getPath();
                    return new SeekableFileStream(new File(decodedPath));

2016 code:

else if (path.startsWith("file:")) {
                return new SeekableFileStream(new File(new URL(path).getPath()));

It looks like the SeekableStreamFactory.java code is changed again in the most recent commit.

We may just need to re-encode the URI before we send it to the SeekableStreamFactory (works in debug mode). However, it is unclear what the most recent changes to the HTSJDK will expect, so we will need to test this again after Kaushik's changes to the HTSJDK.

From initial testing it appears that only bigWig and bigBed were affected, but may need to double-check. I'm curious as to how/if we are using other filetypes with the SeekableStreamFactory.

UPDATE - It looks like the main diff in the 2020 vs 2016 HTSJDK code is changing from a Java URL to URI. It looks like URI does not encode spaces the same way that URL does, which matches with the issue we are seeing. See this stackoverflow for more info.

UPDATE 2 - Our code (BigWigSymLoader) was using a URI, but because the 2016 HTSJDK was expecting a URL we were using GeneralUtils.URLDecode on the URI. This seems to be the issue.

UPDATE 3 - See ~~IGBF-1471~~ and this commit for the last time we made a change to the above logic.

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Nowlan Freese added a comment - 23/Apr/24 9:35 PM - edited BigWigSymLoader.java in initbbReader is making a call to SeekableStreamFactory in the HTSJDK. We didn't make any changes to BigWigSymLoader as part of the upgrade to JDK21. However, there was a commit in 2020 that changed how the handling of file paths occurred in SeekableStreamFactory.java . 2020 code : // convert to URI in order to obtain a decoded version of the path string suitable // for use with the File constructor final String decodedPath = new URI(path).getPath(); return new SeekableFileStream( new File(decodedPath)); 2016 code : else if (path.startsWith( "file:" )) { return new SeekableFileStream( new File( new URL(path).getPath())); It looks like the SeekableStreamFactory.java code is changed again in the most recent commit . We may just need to re-encode the URI before we send it to the SeekableStreamFactory (works in debug mode). However, it is unclear what the most recent changes to the HTSJDK will expect, so we will need to test this again after Kaushik's changes to the HTSJDK. From initial testing it appears that only bigWig and bigBed were affected, but may need to double-check. I'm curious as to how/if we are using other filetypes with the SeekableStreamFactory. UPDATE - It looks like the main diff in the 2020 vs 2016 HTSJDK code is changing from a Java URL to URI. It looks like URI does not encode spaces the same way that URL does, which matches with the issue we are seeing. See this stackoverflow for more info. UPDATE 2 - Our code (BigWigSymLoader) was using a URI, but because the 2016 HTSJDK was expecting a URL we were using GeneralUtils.URLDecode on the URI. This seems to be the issue. UPDATE 3 - See IGBF-1471 and this commit for the last time we made a change to the above logic.

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Ann Loraine added a comment - 24/Apr/24 9:42 AM - edited

Update on build error:

I have confirmed on my fork that release-9.1.10 cannot build; I observed the same error reported by Nowlan Freese
In between release of IGB 9.1.10 and IGB 10.0.0, we moved our "legacy" maven repositories to a new host. In the process I guess that artifact was lost?
I have re-started the old host with the old data deployed. I configured the firewall to allow login from any IP address. This is so that we can retrieve the missing artifact if required.
I am looking on the old host for artifact: org.lorainelab.igb:org.lorainelab.igb.error.reporter.api:jar:1.0.0

The artifact is here:

maven.bioviz.org $ pwd
/var/www/html
maven.bioviz.org $ find . | grep .jar | grep org.lorainelab.igb.error.reporter.api
./repo2/org/lorainelab/igb/org.lorainelab.igb.error.reporter.api/1.0.0/org.lorainelab.igb.error.reporter.api-1.0.0.jar
./repo2/org/lorainelab/igb/org.lorainelab.igb.error.reporter.api/1.0.0/org.lorainelab.igb.error.reporter.api-1.0.0.jar.sha1
./repo2/org/lorainelab/igb/org.lorainelab.igb.error.reporter.api/1.0.0/org.lorainelab.igb.error.reporter.api-1.0.0.jar.md5

Show

Ann Loraine added a comment - 24/Apr/24 9:42 AM - edited Update on build error: I have confirmed on my fork that release-9.1.10 cannot build; I observed the same error reported by Nowlan Freese In between release of IGB 9.1.10 and IGB 10.0.0, we moved our "legacy" maven repositories to a new host. In the process I guess that artifact was lost? I have re-started the old host with the old data deployed. I configured the firewall to allow login from any IP address. This is so that we can retrieve the missing artifact if required. I am looking on the old host for artifact: org.lorainelab.igb:org.lorainelab.igb.error.reporter.api:jar:1.0.0 The artifact is here: maven.bioviz.org $ pwd / var /www/html maven.bioviz.org $ find . | grep .jar | grep org.lorainelab.igb.error.reporter.api ./repo2/org/lorainelab/igb/org.lorainelab.igb.error.reporter.api/1.0.0/org.lorainelab.igb.error.reporter.api-1.0.0.jar ./repo2/org/lorainelab/igb/org.lorainelab.igb.error.reporter.api/1.0.0/org.lorainelab.igb.error.reporter.api-1.0.0.jar.sha1 ./repo2/org/lorainelab/igb/org.lorainelab.igb.error.reporter.api/1.0.0/org.lorainelab.igb.error.reporter.api-1.0.0.jar.md5

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Ann Loraine added a comment - 24/Apr/24 9:54 AM

To solve this problem, we will likely need to deploy multiple artifacts. I will work on it Nowlan Freese.

Packages we will likely need to build IGB 9:

maven.bioviz.org $ ls org.lorainelab.igb.remote.*
org.lorainelab.igb.remote.services.commons:
1.0.0  maven-metadata.xml  maven-metadata.xml.md5  maven-metadata.xml.sha1

org.lorainelab.igb.remote.services.discovery.provider.configured:
1.0.0  maven-metadata.xml  maven-metadata.xml.md5  maven-metadata.xml.sha1

org.lorainelab.igb.remote.services.distribution.provider.http:
1.0.0  maven-metadata.xml  maven-metadata.xml.md5  maven-metadata.xml.sha1

org.lorainelab.igb.remote.services.parent:
1.0.0  maven-metadata.xml  maven-metadata.xml.md5  maven-metadata.xml.sha1

org.lorainelab.igb.remote.services.topology.manager:
1.0.0  maven-metadata.xml  maven-metadata.xml.md5  maven-metadata.xml.sha1
maven.bioviz.org $ ls org.lorainelab.igb.remote.*
org.lorainelab.igb.remote.services.commons:
1.0.0  maven-metadata.xml  maven-metadata.xml.md5  maven-metadata.xml.sha1

org.lorainelab.igb.remote.services.discovery.provider.configured:
1.0.0  maven-metadata.xml  maven-metadata.xml.md5  maven-metadata.xml.sha1

org.lorainelab.igb.remote.services.distribution.provider.http:
1.0.0  maven-metadata.xml  maven-metadata.xml.md5  maven-metadata.xml.sha1

org.lorainelab.igb.remote.services.parent:
1.0.0  maven-metadata.xml  maven-metadata.xml.md5  maven-metadata.xml.sha1

org.lorainelab.igb.remote.services.topology.manager:
1.0.0  maven-metadata.xml  maven-metadata.xml.md5  maven-metadata.xml.sha1

Show

Ann Loraine added a comment - 24/Apr/24 9:54 AM To solve this problem, we will likely need to deploy multiple artifacts. I will work on it Nowlan Freese . Packages we will likely need to build IGB 9: maven.bioviz.org $ ls org.lorainelab.igb.remote.* org.lorainelab.igb.remote.services.commons: 1.0.0 maven-metadata.xml maven-metadata.xml.md5 maven-metadata.xml.sha1 org.lorainelab.igb.remote.services.discovery.provider.configured: 1.0.0 maven-metadata.xml maven-metadata.xml.md5 maven-metadata.xml.sha1 org.lorainelab.igb.remote.services.distribution.provider.http: 1.0.0 maven-metadata.xml maven-metadata.xml.md5 maven-metadata.xml.sha1 org.lorainelab.igb.remote.services.parent: 1.0.0 maven-metadata.xml maven-metadata.xml.md5 maven-metadata.xml.sha1 org.lorainelab.igb.remote.services.topology.manager: 1.0.0 maven-metadata.xml maven-metadata.xml.md5 maven-metadata.xml.sha1 maven.bioviz.org $ ls org.lorainelab.igb.remote.* org.lorainelab.igb.remote.services.commons: 1.0.0 maven-metadata.xml maven-metadata.xml.md5 maven-metadata.xml.sha1 org.lorainelab.igb.remote.services.discovery.provider.configured: 1.0.0 maven-metadata.xml maven-metadata.xml.md5 maven-metadata.xml.sha1 org.lorainelab.igb.remote.services.distribution.provider.http: 1.0.0 maven-metadata.xml maven-metadata.xml.md5 maven-metadata.xml.sha1 org.lorainelab.igb.remote.services.parent: 1.0.0 maven-metadata.xml maven-metadata.xml.md5 maven-metadata.xml.sha1 org.lorainelab.igb.remote.services.topology.manager: 1.0.0 maven-metadata.xml maven-metadata.xml.md5 maven-metadata.xml.sha1

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Ann Loraine added a comment - 24/Apr/24 10:38 AM

Update:

I deployed the missing "error reporting" artifacts to "repo2" on our newer legacy maven repository host available at maven.bioviz.org
I confirmed that my fork can build release-9.1.10

Thank you Nowlan Freese for bringing this error to my attention.

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Ann Loraine added a comment - 24/Apr/24 10:38 AM Update: I deployed the missing "error reporting" artifacts to "repo2" on our newer legacy maven repository host available at maven.bioviz.org I confirmed that my fork can build release-9.1.10 Thank you Nowlan Freese for bringing this error to my attention.

Ann Loraine made changes - 24/Apr/24 12:03 PM

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This issue relates to ~~IGBF-3707~~ [ ~~IGBF-3707~~ ]

Nowlan Freese made changes - 24/Apr/24 2:21 PM

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This issue relates to ~~IGBF-1471~~ [ ~~IGBF-1471~~ ]

Ann Loraine made changes - 28/Apr/24 5:01 PM

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Spring 8, Spring 9 [ 192, 193 ]

Ann Loraine made changes - 28/Apr/24 5:01 PM

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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.

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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.

Nowlan Freese made changes - 02/May/24 11:35 AM

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This issue relates to ~~IGBF-3716~~ [ ~~IGBF-3716~~ ]

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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