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Task #6603 (closed)

Opened 13 years ago

Closed 13 years ago

Bug: l2d import via Insight and Importer

Reported by: cblackburn Owned by: mlinkert
Priority: minor Milestone: OMERO-Beta4.3.2
Component: Import Version: n.a.
Keywords: n.a. Cc: jburel
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: 0.0d
Sprint: 2011-09-15 (5)

Description (last modified by cblackburn)

The files event.log and HSKMandmir2.l2d were both picked up as an import candidates. The first file failed (exception in first comment) the second imported okay. Should the event.log have been identified as a companion file?

(Same outcome in both Insight and Importer)

Change History (9)

comment:1 Changed 13 years ago by cblackburn 

java.lang.IllegalArgumentException
	at java.nio.Buffer.position(Buffer.java:218)
	at loci.common.NIOFileHandle.buffer(NIOFileHandle.java:513)
	at loci.common.NIOFileHandle.skipBytes(NIOFileHandle.java:375)
	at loci.common.RandomAccessInputStream.skipBytes(RandomAccessInputStream.java:387)
	at loci.formats.in.IvisionReader.initFile(IvisionReader.java:212)
	at loci.formats.FormatReader.setId(FormatReader.java:1072)
	at loci.formats.ImageReader.setId(ImageReader.java:672)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:488)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:249)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:488)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:257)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:488)
	at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:312)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:488)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6327)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importCandidates(OmeroImageServiceImpl.java:175)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1253)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:85)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:54)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:111)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:274)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:680)

	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6372)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importCandidates(OmeroImageServiceImpl.java:175)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1253)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:85)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:54)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:111)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:274)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:680)
Caused by: java.lang.IllegalArgumentException
	at java.nio.Buffer.position(Buffer.java:218)
	at loci.common.NIOFileHandle.buffer(NIOFileHandle.java:513)
	at loci.common.NIOFileHandle.skipBytes(NIOFileHandle.java:375)
	at loci.common.RandomAccessInputStream.skipBytes(RandomAccessInputStream.java:387)
	at loci.formats.in.IvisionReader.initFile(IvisionReader.java:212)
	at loci.formats.FormatReader.setId(FormatReader.java:1072)
	at loci.formats.ImageReader.setId(ImageReader.java:672)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:488)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:249)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:488)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:257)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:488)
	at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:312)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:488)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6327)
	... 12 more

comment:2 Changed 13 years ago by cblackburn

  • Description modified (diff)
  • Summary changed from Bug: l2d import via Insight to Bug: l2d import via Insight and Importer

comment:3 Changed 13 years ago by mlinkert

  • Cc mlinkert-x removed
  • Owner set to mlinkert-x

comment:4 Changed 13 years ago by Melissa Linkert <melissa@…>

  • Remaining Time set to 0
  • Resolution set to fixed
  • Status changed from new to closed

(In [84377a9326ee475a3278914d3dc8f1c72f2372c5/bioformats.git]) Add a file length check to the IVision reader.

This prevents it from incorrectly picking up Li-Cor log files.
Closes #6603.

comment:5 Changed 13 years ago by Melissa Linkert <melissa@…>

(In [84377a9326ee475a3278914d3dc8f1c72f2372c5/bioformats.git]) Add a file length check to the IVision reader.

This prevents it from incorrectly picking up Li-Cor log files.
Closes #6603.

comment:6 Changed 13 years ago by Melissa Linkert <melissa@…>

(In [8909c29bfb68c61cb9e518be1e8b4830d5e7158a/bioformats.git]) Add a file length check to the IVision reader.

This prevents it from incorrectly picking up Li-Cor log files.
Closes #6603.
(cherry picked from commit 84377a9326ee475a3278914d3dc8f1c72f2372c5)

comment:7 Changed 13 years ago by Melissa Linkert <melissa@…>

(In [8909c29bfb68c61cb9e518be1e8b4830d5e7158a/bioformats.git]) Add a file length check to the IVision reader.

This prevents it from incorrectly picking up Li-Cor log files.
Closes #6603.
(cherry picked from commit 84377a9326ee475a3278914d3dc8f1c72f2372c5)

comment:8 Changed 13 years ago by cblackburn

  • Resolution fixed deleted
  • Sprint changed from 2011-09-01 (4) to 2011-09-15 (5)
  • Status changed from closed to reopened

In #6685: phase_III-File Formats this error is still present with the latest clients and against the win2k8 server.

comment:9 Changed 13 years ago by cblackburn

  • Resolution set to fixed
  • Status changed from reopened to closed

Phase III testing was initially carried out with the wrong clients. Using the correct clients confirm Melissa's fix!

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