Details
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Type:
Bug
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: 10.0.1
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Labels:None
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Story Points:2
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Epic Link:
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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
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- Closed
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- Closed
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IGBF-3707 Ensure we can still build installers for IGB 9 versions
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- Closed
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- Closed
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IGBF-3671 Update HTSJDK to newest version
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- Closed
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- Closed
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Show 1 more links (1 relates to)
Activity
PR is merged. Main branch installers are built and deployed to BioViz.org as "early access" IGB.
- Tested different scenarios as described in the notes.
- No issues found while testing. The logs are clean without any errors or exceptions.
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.
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
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.