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Task #5351 (closed)

Opened 13 years ago

Closed 13 years ago

Last modified 12 years ago

BUG: Cannot import Volocity files using Insight's importer

Reported by: mlinkert Owned by: jamoore
Priority: major Milestone: OMERO-Beta4.3
Component: General Version: n.a.
Keywords: n.a. Cc: cxallan
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: 0.0d
Sprint: 2011-05-19 (12)

Description

For example, attempting to import test_images_good/velocity/chris/Fig 4/Fig 4.mvd2 results in this:

loci.formats.MissingLibraryException: Could not find Metakit library
	at loci.formats.in.VolocityReader.initFile(VolocityReader.java:241)
	at loci.formats.FormatReader.setId(FormatReader.java:1072)
	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:247)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:394)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6132)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1088)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:84)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:55)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:105)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:274)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:636)
Caused by: Unable to retrieve constructor for class loci.formats.services.MetakitServiceImpl
	at loci.common.services.ServiceFactory.getConstructor(ServiceFactory.java:185)
	at loci.common.services.ServiceFactory.getInstance(ServiceFactory.java:156)
	at loci.formats.in.VolocityReader.initFile(VolocityReader.java:235)
	... 21 more
Caused by: java.lang.NoClassDefFoundError: ome/metakit/MetakitException
	at java.lang.Class.forName0(Native Method)
	at java.lang.Class.forName(Class.java:186)
	at loci.common.services.ServiceFactory.getConstructor(ServiceFactory.java:180)
	... 23 more
Caused by: java.lang.ClassNotFoundException: ome.metakit.MetakitException
	at java.net.URLClassLoader$1.run(URLClassLoader.java:217)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:205)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:321)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:266)
	... 26 more

	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6174)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1088)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:84)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:55)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:105)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:274)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:636)
Caused by: loci.formats.MissingLibraryException: Could not find Metakit library
	at loci.formats.in.VolocityReader.initFile(VolocityReader.java:241)
	at loci.formats.FormatReader.setId(FormatReader.java:1072)
	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:247)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:394)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.importImage(OMEROGateway.java:6132)
	... 11 more
Caused by: Unable to retrieve constructor for class loci.formats.services.MetakitServiceImpl
	at loci.common.services.ServiceFactory.getConstructor(ServiceFactory.java:185)
	at loci.common.services.ServiceFactory.getInstance(ServiceFactory.java:156)
	at loci.formats.in.VolocityReader.initFile(VolocityReader.java:235)
	... 21 more
Caused by: java.lang.NoClassDefFoundError: ome/metakit/MetakitException
	at java.lang.Class.forName0(Native Method)
	at java.lang.Class.forName(Class.java:186)
	at loci.common.services.ServiceFactory.getConstructor(ServiceFactory.java:180)
	... 23 more
Caused by: java.lang.ClassNotFoundException: ome.metakit.MetakitException
	at java.net.URLClassLoader$1.run(URLClassLoader.java:217)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:205)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:321)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:266)
	... 26 more

Not sure at the moment if this is something wrong in Bio-Formats, or just a missing JAR.

Change History (10)

comment:1 Changed 13 years ago by jmoore

  • Cc cxallan added

No metakit is available under ​http://hudson.openmicroscopy.org.uk/job/BIOFORMATS-trunk/lastBuild/artifact/trunk/artifacts/ explaining why it isn't added to git under the develop branch. Once that happens, then we can add the dependency to romio/ivy.xml (I have that local). There is a similar situation for dev_4_1 and dev_4_1_custom which we probably want to take care of.

comment:2 Changed 13 years ago by jmoore

  • Owner changed from mlinkert-x to jmoore
  • Remaining Time set to 0.25
  • Status changed from new to accepted

comment:4 Changed 13 years ago by jmoore <josh@…>

  • Remaining Time changed from 0.25 to 0
  • Resolution set to fixed
  • Status changed from accepted to closed

(In [f750f22fd79672d03a960af704bfb8376e46495a/ome.git] on branch develop) Updating to [330dd7fa929926ec071a808316392e952ea5b58e/bioformats.git] (Fix #5351)

Adds metakit dependency to romio/ivy.xml

comment:5 Changed 13 years ago by mlinkert

  • Resolution fixed deleted
  • Status changed from closed to reopened

The importer client can now import Volocity files, but Insight's importer still produces the same error message (using build 2607). metakit.jar is not included in the 'libs' directory of the Insight bundle, which is probably the cause of the error.

comment:6 Changed 13 years ago by jmoore

So apparently I fixed all the Volocity import issues other than the one you reported! Fixing insight requires running update_bioformats_jar --simple from within insight/LIBS. Doing that now.

comment:7 Changed 13 years ago by jmoore <josh@…>

(In [eec0eed9d66b01c290573ee19e64d3078cf57f58/ome.git] on branch develop) Adding metakit.jar to insight/LIB (See #5351)

comment:8 Changed 13 years ago by mlinkert

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

Seems to be working now, thanks Josh!

comment:9 Changed 13 years ago by jmoore <josh@…>

(In [33fb067547860948c31a697080e4ca0b17753126/ome.git]on branches dev_4_1, dev_4_1_custom) Adding metakit from [a363c33be1b71ff81cd452735431f1a145212768/bioformats.git] (See #5351)

comment:10 Changed 12 years ago by jmoore <josh@…>

(In [33fb067547860948c31a697080e4ca0b17753126/ome.git]on branches 4_1, dev_4_1, dev_4_1_custom) Adding metakit from [a363c33be1b71ff81cd452735431f1a145212768/bioformats.git] (See #5351)

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