[ome-users] Problems with OMERO Imports

Thu Dec 17 16:10:38 GMT 2015

Hello,

yesterday, we have just started with OMERO production use at our
institute; and while it had worked well in our preliminary tests, we
have now seen a strange issue with importing images.

Nikon ND2 image stacks (.nd2 files) are imported using the command line
client, in ln_s mode (called by a custom OMERO.dropbox-like script,
enforcing some additional naming rules etc.).

Import proceeds like normal, and all positions are added to OMERO, but
the actual image data remains inaccessible. (Only the clock icon in
thumbnail view in the webclient).

In Blitz-0 (or similarily the individual file log file), the following
errors are visible:

(repeated for each plane)
2015-12-17 16:07:10,458 ERROR [ ome.formats.OMEROMetadataStoreClient]
(2-thread-4) Server error setting extended properties for Pixels:8145
Target file:sachs_102/2015-12/17/15-07-53.074/nd009.nd2

2015-12-17 16:07:10,536 INFO  [ o.s.b.r.ManagedImportRequestI. at 49ccbb67]
(2-thread-4) Cancelled
2015-12-17 16:07:10,536 INFO  [ o.s.b.r.ManagedImportRequestI. at 49ccbb67]
(2-thread-4) Cancelled
2015-12-17 16:07:10,536 INFO  [ org.perf4j.TimingLogger] (2-thread-4)
start[1450361363591] time[3467016] tag[omero.request.step.1]
2015-12-17 16:07:10,536 INFO  [ org.perf4j.TimingLogger] (2-thread-4)
start[1450361276527] time[3554071] tag[omero.request]
2015-12-17 16:07:10,552 INFO  [ org.perf4j.TimingLogger] (2-thread-4)
start[1450361276512] time[3554108] tag[omero.call.exception]
2015-12-17 16:07:10,552 INFO  [ ome.services.util.ServiceHandler]
(2-thread-4)  Excp: omero.cmd.HandleI$Cancel: update-log-file-size
2015-12-17 16:07:10,552 ERROR [ ome.services.util.ServiceHandler]
(2-thread-4) Method interface ome.services.util.Executor$Work.doWork
invocation took 3554108
2015-12-17 16:07:10,552 DEBUG [ o.s.b.r.ManagedImportRequestI. at 49ccbb67]
(2-thread-4) Request cancelled by Ice.ObjectNotExistException
     id.name = "0323ac63-84df-401c-9f1e-ea200690a3ddomero.api.IQuery"
     id.category = "154b6433-848c-450a-b828-799944fadc0c"
     facet = ""
     operation = "get"
2015-12-17 16:07:10,583 WARN  [ ome.formats.OMEROMetadataStoreClient]
(2-thread-4) Exception closing
154b6433-848c-450a-b828-799944fadc0c/52fc1001-0fec-4034-8a05-3ce12b5c1a01omero.api.RawFileStore
-t -e 1.1:tcp -h [IPv4] -p 62733:tcp -h "[IPv6]" -p 62733
Ice.ObjectNotExistException: null
     at IceInternal.Outgoing.invoke(Outgoing.java:158) ~[ice.jar:na]
     at omero.api._RawFileStoreDelM.close(_RawFileStoreDelM.java:459)
~[blitz.jar:na]
     at
omero.api.RawFileStorePrxHelper.close(RawFileStorePrxHelper.java:1877)
~[blitz.jar:na]
     at
omero.api.RawFileStorePrxHelper.close(RawFileStorePrxHelper.java:1839)
~[blitz.jar:na]
     at
ome.formats.OMEROMetadataStoreClient.closeQuietly(OMEROMetadataStoreClient.java:1053)
[blitz.jar:na]
     at
ome.formats.OMEROMetadataStoreClient.closeServices(OMEROMetadataStoreClient.java:1074)
[blitz.jar:na]
     at
ome.formats.OMEROMetadataStoreClient.logout(OMEROMetadataStoreClient.java:1100)
[blitz.jar:na]
     at
ome.services.blitz.repo.ManagedImportRequestI.cleanupStore(ManagedImportRequestI.java:277)
[blitz.jar:na]
     at
ome.services.blitz.repo.ManagedImportRequestI.cleanup(ManagedImportRequestI.java:362)
[blitz.jar:na]
     at
ome.services.blitz.repo.ManagedImportRequestI.getResponse(ManagedImportRequestI.java:492)
[blitz.jar:na]
     at omero.cmd.HandleI.run(HandleI.java:395) [blitz.jar:na]
     at java.util.concurrent.Executors$RunnableAdapter.call(Unknown
Source) [na:1.8.0_65]
     at ome.services.util.Executor$Impl$1.call(Executor.java:484)
[server.jar:na]
     at java.util.concurrent.FutureTask.run(Unknown Source) [na:1.8.0_65]
     at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown
Source) [na:1.8.0_65]
     at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown
Source) [na:1.8.0_65]
     at java.lang.Thread.run(Unknown Source) [na:1.8.0_65]
2015-12-17 16:07:10,583 WARN  [ ome.formats.OMEROMetadataStoreClient]
(2-thread-4) Exception closing
154b6433-848c-450a-b828-799944fadc0c/5cc66418-40b8-42f0-b380-e71f89804298omero.api.RawPixelsStore
-t -e 1.1:tcp -h [IPv4] -p 62733:tcp -h "[IPv6]" -p 62733
Ice.ObjectNotExistException: null
     at IceInternal.Outgoing.invoke(Outgoing.java:158) ~[ice.jar:na]
     at
omero.api._RawPixelsStoreDelM.close(_RawPixelsStoreDelM.java:2003)
~[blitz.jar:na]
     at
omero.api.RawPixelsStorePrxHelper.close(RawPixelsStorePrxHelper.java:9946)
~[blitz.jar:na]
     at
omero.api.RawPixelsStorePrxHelper.close(RawPixelsStorePrxHelper.java:9908)
~[blitz.jar:na]
     at
ome.formats.OMEROMetadataStoreClient.closeQuietly(OMEROMetadataStoreClient.java:1053)
[blitz.jar:na]
     at
ome.formats.OMEROMetadataStoreClient.closeServices(OMEROMetadataStoreClient.java:1077)
[blitz.jar:na]
     at
ome.formats.OMEROMetadataStoreClient.logout(OMEROMetadataStoreClient.java:1100)
[blitz.jar:na]
     at
ome.services.blitz.repo.ManagedImportRequestI.cleanupStore(ManagedImportRequestI.java:277)
[blitz.jar:na]
     at
ome.services.blitz.repo.ManagedImportRequestI.cleanup(ManagedImportRequestI.java:362)
[blitz.jar:na]
     at
ome.services.blitz.repo.ManagedImportRequestI.getResponse(ManagedImportRequestI.java:492)
[blitz.jar:na]
     at omero.cmd.HandleI.run(HandleI.java:395) [blitz.jar:na]
     at java.util.concurrent.Executors$RunnableAdapter.call(Unknown
Source) [na:1.8.0_65]
     at ome.services.util.Executor$Impl$1.call(Executor.java:484)
[server.jar:na]
     at java.util.concurrent.FutureTask.run(Unknown Source) [na:1.8.0_65]
     at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown
Source) [na:1.8.0_65]
     at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown
Source) [na:1.8.0_65]
     at java.lang.Thread.run(Unknown Source) [na:1.8.0_65]
2015-12-17 16:07:10,583 WARN  [ ome.formats.OMEROMetadataStoreClient]
(2-thread-4) Exception closing
154b6433-848c-450a-b828-799944fadc0c/cd4f1f13-0b9a-411c-bb33-b25f7320a0d3omero.api.ThumbnailStore
-t -e 1.1:tcp -h [IPv4] -p 62733:tcp -h "[IPv6]" -p 62733
Ice.ObjectNotExistException: null
     at IceInternal.Outgoing.invoke(Outgoing.java:158) ~[ice.jar:na]
     at omero.api._ThumbnailStoreDelM.close(_ThumbnailStoreDelM.java:74)
~[blitz.jar:na]
     at
omero.api.ThumbnailStorePrxHelper.close(ThumbnailStorePrxHelper.java:356) ~[blitz.jar:na]
     at
omero.api.ThumbnailStorePrxHelper.close(ThumbnailStorePrxHelper.java:318) ~[blitz.jar:na]
     at
ome.formats.OMEROMetadataStoreClient.closeQuietly(OMEROMetadataStoreClient.java:1053)
[blitz.jar:na]
     at
ome.formats.OMEROMetadataStoreClient.closeServices(OMEROMetadataStoreClient.java:1080)
[blitz.jar:na]
     at
ome.formats.OMEROMetadataStoreClient.logout(OMEROMetadataStoreClient.java:1100)
[blitz.jar:na]
     at
ome.services.blitz.repo.ManagedImportRequestI.cleanupStore(ManagedImportRequestI.java:277)
[blitz.jar:na]
     at
ome.services.blitz.repo.ManagedImportRequestI.cleanup(ManagedImportRequestI.java:362)
[blitz.jar:na]
     at
ome.services.blitz.repo.ManagedImportRequestI.getResponse(ManagedImportRequestI.java:492)
[blitz.jar:na]
     at omero.cmd.HandleI.run(HandleI.java:395) [blitz.jar:na]
     at java.util.concurrent.Executors$RunnableAdapter.call(Unknown
Source) [na:1.8.0_65]
     at ome.services.util.Executor$Impl$1.call(Executor.java:484)
[server.jar:na]
     at java.util.concurrent.FutureTask.run(Unknown Source) [na:1.8.0_65]
     at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown
Source) [na:1.8.0_65]
     at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown
Source) [na:1.8.0_65]
     at java.lang.Thread.run(Unknown Source) [na:1.8.0_65]
2015-12-17 16:07:10,599 WARN  [ ome.formats.OMEROMetadataStoreClient]
(2-thread-4) Exception closing
154b6433-848c-450a-b828-799944fadc0c/0323ac63-84df-401c-9f1e-ea200690a3ddomero.api.MetadataStore
-t -e 1.1:tcp -h [IPv4] -p 62733:tcp -h "[IPv6]" -p 62733
Ice.ObjectNotExistException: null
     at IceInternal.Outgoing.invoke(Outgoing.java:158) ~[ice.jar:na]
     at omero.api._MetadataStoreDelM.close(_MetadataStoreDelM.java:412)
~[blitz.jar:na]
     at
omero.api.MetadataStorePrxHelper.close(MetadataStorePrxHelper.java:1560)
~[blitz.jar:na]
     at
omero.api.MetadataStorePrxHelper.close(MetadataStorePrxHelper.java:1522)
~[blitz.jar:na]
     at
ome.formats.OMEROMetadataStoreClient.closeQuietly(OMEROMetadataStoreClient.java:1053)
[blitz.jar:na]
     at
ome.formats.OMEROMetadataStoreClient.closeServices(OMEROMetadataStoreClient.java:1083)
[blitz.jar:na]
     at
ome.formats.OMEROMetadataStoreClient.logout(OMEROMetadataStoreClient.java:1100)
[blitz.jar:na]
     at
ome.services.blitz.repo.ManagedImportRequestI.cleanupStore(ManagedImportRequestI.java:277)
[blitz.jar:na]
     at
ome.services.blitz.repo.ManagedImportRequestI.cleanup(ManagedImportRequestI.java:362)
[blitz.jar:na]
     at
ome.services.blitz.repo.ManagedImportRequestI.getResponse(ManagedImportRequestI.java:492)
[blitz.jar:na]
     at omero.cmd.HandleI.run(HandleI.java:395) [blitz.jar:na]
     at java.util.concurrent.Executors$RunnableAdapter.call(Unknown
Source) [na:1.8.0_65]
     at ome.services.util.Executor$Impl$1.call(Executor.java:484)
[server.jar:na]
     at java.util.concurrent.FutureTask.run(Unknown Source) [na:1.8.0_65]
     at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown
Source) [na:1.8.0_65]
     at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown
Source) [na:1.8.0_65]
     at java.lang.Thread.run(Unknown Source) [na:1.8.0_65]
2015-12-17 16:07:10,599 INFO  [ o.s.blitz.repo.ManagedImportRequestI]
(2-thread-4) Finalizing log file.
2015-12-17 16:07:10,599 INFO  [ o.s.blitz.repo.ManagedImportRequestI]
(2-thread-4) Auto-closing...
2015-12-17 16:07:10,599 ERROR [ o.s.blitz.repo.ManagedImportRequestI]
(2-thread-4) Failed to close handle on autoClose
Ice.ObjectNotExistException: null
     at IceInternal.Outgoing.invoke(Outgoing.java:158) ~[ice.jar:na]
     at omero.cmd._HandleDelM.close(_HandleDelM.java:124) ~[blitz.jar:na]
     at omero.cmd.HandlePrxHelper.close(HandlePrxHelper.java:467)
~[blitz.jar:na]
     at omero.cmd.HandlePrxHelper.close(HandlePrxHelper.java:436)
~[blitz.jar:na]
     at
ome.services.blitz.repo.ManagedImportRequestI.autoClose(ManagedImportRequestI.java:340)
[blitz.jar:na]
     at
ome.services.blitz.repo.ManagedImportRequestI.cleanup(ManagedImportRequestI.java:376)
[blitz.jar:na]
     at
ome.services.blitz.repo.ManagedImportRequestI.getResponse(ManagedImportRequestI.java:492)
[blitz.jar:na]
     at omero.cmd.HandleI.run(HandleI.java:395) [blitz.jar:na]
     at java.util.concurrent.Executors$RunnableAdapter.call(Unknown
Source) [na:1.8.0_65]
     at ome.services.util.Executor$Impl$1.call(Executor.java:484)
[server.jar:na]
     at java.util.concurrent.FutureTask.run(Unknown Source) [na:1.8.0_65]
     at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown
Source) [na:1.8.0_65]
     at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown
Source) [na:1.8.0_65]
     at java.lang.Thread.run(Unknown Source) [na:1.8.0_65]

I will start trying to reproduce this with another test installation;
but maybe a dev could quickly point me into the right direction what the
problem might be?

We're using OMERO 5.2.0 on a Windows server (which has - to my knowledge
- been upgraded multiple times from earlier versions).
As of the last three files imported, none was imported properly, we have
told our users to stop imports till the problem is resolved.

Thank you,
best regards

Christian Sachs

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Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt
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