BUG: Cannot import Volocity files using Insight's importer

[mlinkert]

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.

[jmoore]

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.

[jmoore <josh@…>]

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

[jmoore <josh@…>]

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

Adds metakit dependency to romio/ivy.xml

[mlinkert]

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.

[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.

[jmoore <josh@…>]

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

[mlinkert]

Seems to be working now, thanks Josh!

[jmoore <josh@…>]

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

[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)