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Task #12366 (closed)

Opened 10 years ago

Closed 10 years ago

Bug: DICOM failure with memoisation

Reported by: omero-qa Owned by: mlinkert
Priority: minor Milestone: 5.1.0-m3
Component: Bio-Formats Version: 5.0.2
Keywords: n.a. Cc: stephan.hahn16@…
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description (last modified by rleigh)

Can't reproduce with either dev_5_0 bioformats or today's OMERO build on octopus (both w/o memoiser). Looks like it's possibly due to a memoisation failure after upgrade from 5.0.0/5.0.1 with a bfmemo from the earlier version causing the problem?

​http://qa.openmicroscopy.org.uk/qa/feedback/9273/

java.lang.IllegalArgumentException: 0 must not be null and positive.
	at ome.xml.model.primitives.PositiveInteger.<init>(PositiveInteger.java:52)
	at loci.formats.MetadataTools.populatePixelsOnly(MetadataTools.java:277)
	at loci.formats.MetadataTools.populateMetadata(MetadataTools.java:238)
	at loci.formats.MetadataTools.populatePixels(MetadataTools.java:138)
	at loci.formats.MetadataTools.populatePixels(MetadataTools.java:97)
	at loci.formats.in.DicomReader.initFile(DicomReader.java:713)
	at loci.formats.FormatReader.setId(FormatReader.java:1315)
	at loci.formats.ImageReader.setId(ImageReader.java:753)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:259)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:270)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569)
	at loci.formats.Memoizer.setId(Memoizer.java:467)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:569)
	at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:414)
	at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:596)
	at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:371)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:229)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:180)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.getImportCandidates(OMEROGateway.java:6481)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1195)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:77)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:53)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:102)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Unknown Source)

Change History (3)

comment:1 Changed 10 years ago by rleigh

  • Component changed from from QA to Bio-Formats
  • Description modified (diff)

comment:2 Changed 10 years ago by mlinkert

  • Milestone changed from Unscheduled to 5.0.4

comment:3 Changed 10 years ago by mlinkert

  • Resolution set to worksforme
  • Status changed from new to closed

I haven't been able to reproduce this using 5.0.0, 5.0.1, or 5.0.2 files with 5.0.0, 5.0.1, 5.0.2, or current develop.

The Memoizer section of the stack trace indicates that the memo file directory is not writable, and the fact that the reader attempts to set SizeZ = 0 suggests that listing the directory containing the DICOM file silently failed. I'd strongly suspect an I/O issue with the filesystem on which /OMERO/ was mounted. A network blip with NFS could certainly cause both symptoms.

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