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Task #1585 (new)

Opened 10 years ago

Last modified 10 years ago

Import hung on findAll(enums)

Reported by: jamoore Owned by: jamoore
Priority: critical Milestone: Unscheduled
Component: General Version: 3.0-M1
Keywords: n.a. Cc: bwzloranger, cxallan, jburel, dzmacdonald
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description

Blocked thread below. Server doesn't have any active threads. In general, this could happen to any client. We need to come up with a solution.

"pool-2-thread-1" prio=5 tid=0x005316f0 nid=0x1a39e00 in Object.wait() [0xb1010000..0xb1010d10]
        at java.lang.Object.wait(Native Method)
        - waiting on <0x0d874bf8> (a IceInternal.Outgoing)
        at java.lang.Object.wait(Object.java:474)
        at IceInternal.Outgoing.invoke(Outgoing.java:109)
        - locked <0x0d874bf8> (a IceInternal.Outgoing)
        at omero.api._IQueryDelM.findAll(_IQueryDelM.java:90)
        at omero.api.IQueryPrxHelper.findAll(IQueryPrxHelper.java:116)
        at omero.api.IQueryPrxHelper.findAll(IQueryPrxHelper.java:88)
        at ome.formats.enums.IQueryEnumProvider.getEnumerations(IQueryEnumProvider.java:177)
        at ome.formats.enums.IQueryEnumProvider.getEnumeration(IQueryEnumProvider.java:132)
        at ome.formats.OMEROMetadataStoreClient.getEnumeration(OMEROMetadataStoreClient.java:500)
        at ome.formats.OMEROMetadataStoreClient.setPixelsPixelType(OMEROMetadataStoreClient.java:1835)
        at loci.formats.meta.FilterMetadata.setPixelsPixelType(FilterMetadata.java:1280)
        at loci.formats.MetadataTools.populatePixels(MetadataTools.java:390)
        at loci.formats.MetadataTools.populatePixels(MetadataTools.java:353)
        at loci.formats.in.APNGReader.initFile(APNGReader.java:293)
        at loci.formats.FormatReader.setId(FormatReader.java:901)
        at loci.formats.ImageReader.setId(ImageReader.java:588)
        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:448)
        at loci.formats.ChannelFiller.setId(ChannelFiller.java:179)
        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:448)
        at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:206)
        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:448)
        at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:185)
        at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:281)
        at ome.formats.importer.gui.ImportHandler.importImages(ImportHandler.java:182)
        at ome.formats.importer.gui.ImportHandler.access$100(ImportHandler.java:45)
        at ome.formats.importer.gui.ImportHandler$2.run(ImportHandler.java:97)
        at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:417)
        at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:269)
        at java.util.concurrent.FutureTask.run(FutureTask.java:123)
        at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:65)
        at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:172)
        at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:651)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:676)
        at java.lang.Thread.run(Thread.java:613)

Change History (2)

comment:1 Changed 10 years ago by jmoore

Now from CLI:

"main" prio=5 tid=0x005013d0 nid=0x1803800 in Object.wait() [0xb07ff000..0xb08000f8]
        at java.lang.Object.wait(Native Method)
        - waiting on <0x0660a520> (a IceInternal.Outgoing)
        at java.lang.Object.wait(Object.java:474)
        at IceInternal.Outgoing.invoke(Outgoing.java:109)
        - locked <0x0660a520> (a IceInternal.Outgoing)
        at omero.api._IQueryDelM.findAll(_IQueryDelM.java:90)
        at omero.api.IQueryPrxHelper.findAll(IQueryPrxHelper.java:116)
        at omero.api.IQueryPrxHelper.findAll(IQueryPrxHelper.java:88)
        at ome.formats.enums.IQueryEnumProvider.getEnumerations(IQueryEnumProvider.java:177)
        at ome.formats.enums.IQueryEnumProvider.getEnumeration(IQueryEnumProvider.java:132)
        at ome.formats.OMEROMetadataStoreClient.getEnumeration(OMEROMetadataStoreClient.java:500)
        at ome.formats.OMEROMetadataStoreClient.setPixelsPixelType(OMEROMetadataStoreClient.java:1835)
        at loci.formats.MetadataTools.populatePixels(MetadataTools.java:390)
        at loci.formats.ChannelFiller.setId(ChannelFiller.java:181)
        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:448)
        at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:206)
        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:448)
        at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:185)
        at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:281)
        at ome.formats.importer.ImportLibrary.importCandidates(ImportLibrary.java:157)
        at ome.formats.importer.cli.CommandLineImporter.start(CommandLineImporter.java:126)
        at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:334)

comment:2 Changed 10 years ago by jmoore

  • Milestone changed from OMERO-Beta4.2 to Unscheduled
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