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Task #6233 (closed)

Opened 13 years ago

Closed 13 years ago

BUG: DV import - Feedback 3871

Reported by: omero-qa Owned by: mlinkert
Priority: minor Milestone: OMERO-Beta4.3.2
Component: Bio-Formats Version: n.a.
Keywords: n.a. Cc: G.Akman@…
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description

http://qa.openmicroscopy.org.uk/qa/feedback/3871/

Comment: When these files are re-imported into the Deltavision software, softworx, they import correctly. Also, these files are part of a dataset. They represent a failure rate of approx. 40%

java.io.IOException: Data error (cyclic redundancy check)
	at sun.nio.ch.FileDispatcher.pread0(Native Method)
	at sun.nio.ch.FileDispatcher.pread(Unknown Source)
	at sun.nio.ch.IOUtil.readIntoNativeBuffer(Unknown Source)
	at sun.nio.ch.IOUtil.read(Unknown Source)
	at sun.nio.ch.FileChannelImpl.read(Unknown Source)
	at loci.common.NIOByteBufferProvider.allocateDirect(NIOByteBufferProvider.java:120)
	at loci.common.NIOByteBufferProvider.allocate(NIOByteBufferProvider.java:105)
	at loci.common.NIOFileHandle.buffer(NIOFileHandle.java:482)
	at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:103)
	at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:111)
	at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:119)
	at loci.common.Location.getHandle(Location.java:284)
	at loci.common.Location.getHandle(Location.java:255)
	at loci.formats.ImageReader.getReader(ImageReader.java:158)
	at loci.formats.ImageReader.setId(ImageReader.java:670)
	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:248)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:402)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6288)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1137)
	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(Unknown Source)

Change History (4)

comment:1 Changed 13 years ago by wmoore

http://qa.openmicroscopy.org.uk/qa/feedback/3872/ , 3873, 3874, 3875, 3876, 3877, 3878 too!

comment:2 Changed 13 years ago by mlinkert

  • Milestone changed from Unscheduled to OMERO-Beta4.3.2

comment:3 Changed 13 years ago by mlinkert

  • Component changed from from QA to Bio-Formats

comment:4 Changed 13 years ago by mlinkert

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

This error message almost always means that the file or file system (e.g. hard drive) is corrupted in some way. Some things to try:

  1. Restart the computer.
  2. Verify that the files can be opened in the original acquisition software.
  3. If the files are not on a local hard drive (e.g. they are on a DVD or tape drive), copy them to your local hard drive and then try to import them.
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