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import an image after fresh install on Ubuntu 14.04 Not work

https://www.openmicroscopy.org/community/viewtopic.php?f=5&t=8154

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import an image after fresh install on Ubuntu 14.04 Not work

PostPosted: Wed Nov 16, 2016 2:13 pm
by saleht
Hi all,
i installed on Ubuntu 14.04 LTS omero.server, and everything goes ok
but i tried to import an image, i was not able to import even with root user
i got this message
same issue when i tried to import from local-host"server" using cli
java.lang.NullPointerException
at loci.formats.in.OMETiffReader.close(OMETiffReader.java:407)
at loci.formats.ImageReader.close(ImageReader.java:581)
at loci.formats.ReaderWrapper.close(ReaderWrapper.java:366)
at loci.formats.ReaderWrapper.close(ReaderWrapper.java:366)
at loci.formats.ChannelSeparator.close(ChannelSeparator.java:246)
at loci.formats.ReaderWrapper.close(ReaderWrapper.java:366)
at loci.formats.Memoizer.close(Memoizer.java:632)
at loci.formats.MinMaxCalculator.close(MinMaxCalculator.java:278)
at ome.formats.importer.OMEROWrapper.close(OMEROWrapper.java:255)
at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:437)
at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:566)
at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:367)
at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:222)
at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:174)
at org.openmicroscopy.shoola.env.data.OMEROGateway.getImportCandidates(OMEROGateway.java:5955)
at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1036)
at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:73)
at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:48)
at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:97)
at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
at java.lang.Thread.run(Thread.java:745)

at org.openmicroscopy.shoola.env.data.util.StatusLabel.update(StatusLabel.java:671)
at ome.formats.importer.ImportCandidates.safeUpdate(ImportCandidates.java:526)
at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:461)
at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:566)
at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:367)
at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:222)
at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:174)
at org.openmicroscopy.shoola.env.data.OMEROGateway.getImportCandidates(OMEROGateway.java:5955)
at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1036)
at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:73)
at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:48)
at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:97)
at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.NullPointerException
at loci.formats.in.OMETiffReader.close(OMETiffReader.java:407)
at loci.formats.ImageReader.close(ImageReader.java:581)
at loci.formats.ReaderWrapper.close(ReaderWrapper.java:366)
at loci.formats.ReaderWrapper.close(ReaderWrapper.java:366)
at loci.formats.ChannelSeparator.close(ChannelSeparator.java:246)
at loci.formats.ReaderWrapper.close(ReaderWrapper.java:366)
at loci.formats.Memoizer.close(Memoizer.java:632)
at loci.formats.MinMaxCalculator.close(MinMaxCalculator.java:278)
at ome.formats.importer.OMEROWrapper.close(OMEROWrapper.java:255)
at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:437)
... 16 more

Re: import an image after fresh install on Ubuntu 14.04

PostPosted: Wed Nov 16, 2016 2:16 pm
by saleht
i got this logs when i tried using Cli
2016-11-15 12:06:40,362 4345 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:4064
2016-11-15 12:06:41,443 5426 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back
2016-11-15 12:06:42,694 6677 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.2.6
2016-11-15 12:06:42,694 6677 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.2.6-ice36-b35
2016-11-15 12:06:42,694 6677 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 1.7.0_111
2016-11-15 12:06:42,695 6678 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux
2016-11-15 12:06:42,695 6678 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64
2016-11-15 12:06:42,695 6678 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 4.4.0-47-generic

Re: import an image after fresh install on Ubuntu 14.04 Not

PostPosted: Wed Nov 16, 2016 3:28 pm
by kennethgillen
Hi,

To see if this is a problem with the particular image, or OMERO itself, could you please upload the file you're trying to upload via our QA system by following to https://www.openmicroscopy.org/qa2/qa/upload/

You could also try uploading a sample image, such as: http://downloads.openmicroscopy.org/ima ... es.ome.tif

Could you please also provide (here, or via the QA system as above)

  • Output of bin/omero admin diagnostics
  • Output of bin/omero config get --hide-password (Blank out any passwords)
  • OMERO.server logs: ${OMERO_SERVER}/var/log
(in particlar Blitz-0.log)

Many thanks,

Kenny

Re: import an image after fresh install on Ubuntu 14.04 Not

PostPosted: Thu Nov 17, 2016 8:08 am
by saleht
Hi,
first i would thank you for the answer,
in fact i have tried another image *.jpg and also the photo which you attached both are working fine
and i upload my image which has the problem to your QA team.
pls tell me if i have to upload logs or not :)

Re: import an image after fresh install on Ubuntu 14.04 Not

PostPosted: Fri Nov 18, 2016 11:46 am
by dgault
Hi,

Thank you for uploading the files to QA for testing. This is an issue which we have previously encountered and infact a fix was put in place recently which should prevent the Null Pointer Exception which you are seeing -
https://github.com/openmicroscopy/bioformats/pull/2438
https://github.com/openmicroscopy/biofo ... 6dc9aa23f1

You could try upgrading to the latest release to pick up the recent bug fixes which have been integrated. That should hopefully resolve the issues you have been seeing.

With Thanks,
David Gault
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