[ome-users] Import error
Douglas Russell
douglas_russell at hms.harvard.edu
Wed Dec 20 01:25:05 GMT 2017
Has anyone seen this import error? It's pretty vague. I imported a test jpg
to make sure import was working in general and it was fine. I updated to
the latest OMERO and still seeing the problem.
Any ideas?
Thanks
*Import attempt:*
bash-4.2$ /opt/omero/server/OMERO.server/bin/omero import -g "public-group"
-- --transfer=ln_s /OMERO/data/ss240_802/2017-04/10/07-20-11.268/130722.nd
Using session 69309e1b-15bb-4eef-80ef-62018c661a28 (root at localhost:4064).
Idle timeout: 10 min. Current group: public-group
2017-12-19 23:46:10,097 202 [ main] INFO
ome.formats.importer.ImportConfig - OMERO Version: 5.4.1-ice36-b75
2017-12-19 23:46:10,109 214 [ main] INFO
ome.formats.importer.ImportConfig - Bioformats version: 5.7.2 revision:
6909f51c1786b58fe5a0765cea2ad6a278ebc1c2 date: 21 November 2017
2017-12-19 23:46:10,146 251 [ main] INFO
formats.importer.cli.CommandLineImporter - Setting transfer to ln_s
2017-12-19 23:46:10,149 254 [ main] INFO
formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats:
ERROR OMERO.importer: INFO
2017-12-19 23:46:10,449 554 [ main] INFO
ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM
2017-12-19 23:46:25,767 15872 [ main] INFO
ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s)
with 1 call(s) to setId in 978ms. (15317ms total) [0 unknowns]
2017-12-19 23:46:26,655 16760 [ main] INFO
ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection
to localhost:4064
2017-12-19 23:46:27,008 17113 [ main] INFO
ome.formats.OMEROMetadataStoreClient - Insecure connection requested,
falling back
2017-12-19 23:46:27,303 17408 [ main] INFO
ome.formats.OMEROMetadataStoreClient - Server: 5.4.1
2017-12-19 23:46:27,303 17408 [ main] INFO
ome.formats.OMEROMetadataStoreClient - Client: 5.4.1-ice36-b75
2017-12-19 23:46:27,303 17408 [ main] INFO
ome.formats.OMEROMetadataStoreClient - Java Version: 1.8.0_151
2017-12-19 23:46:27,303 17408 [ main] INFO
ome.formats.OMEROMetadataStoreClient - OS Name: Linux
2017-12-19 23:46:27,303 17408 [ main] INFO
ome.formats.OMEROMetadataStoreClient - OS Arch: amd64
2017-12-19 23:46:27,303 17408 [ main] INFO
ome.formats.OMEROMetadataStoreClient - OS Version:
4.4.51-40.58.amzn1.x86_64
2017-12-19 23:46:27,387 17492 [ main] INFO
ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION
2017-12-19 23:46:34,669 24774 [ main] ERROR
ome.formats.importer.ImportLibrary - Error on import
Ice.UnknownLocalException: null
at IceInternal.AsyncResultI.__wait(AsyncResultI.java:276) ~[ice.jar:na]
at
omero.grid.ManagedRepositoryPrxHelper.end_importFileset(ManagedRepositoryPrxHelper.java:171)
~[blitz.jar:na]
at
omero.grid.ManagedRepositoryPrxHelper.importFileset(ManagedRepositoryPrxHelper.java:46)
~[blitz.jar:na]
at
omero.grid.ManagedRepositoryPrxHelper.importFileset(ManagedRepositoryPrxHelper.java:33)
~[blitz.jar:na]
at ome.formats.importer.ImportLibrary.createImport(ImportLibrary.java:374)
~[blitz.jar:na]
at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:499)
~[blitz.jar:na]
at
ome.formats.importer.ImportLibrary.importCandidates(ImportLibrary.java:289)
~[blitz.jar:na]
at
ome.formats.importer.cli.CommandLineImporter.start(CommandLineImporter.java:289)
[blitz.jar:na]
at
ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:958)
[blitz.jar:na]
2017-12-19 23:46:34,679 24784 [ main] INFO
ome.formats.importer.ImportLibrary - Exiting on error
==> Summary
0 files uploaded, 0 filesets created, 0 images imported, 0 errors in
0:00:07.297
2017-12-19 23:46:34,702 24807 [ main] WARN
ome.formats.OMEROMetadataStoreClient - Exception closing
69309e1b-15bb-4eef-80ef-62018c661a28/83ca5b32-2fa1-4771-a6bb-d52e794fa9c8omero.api.RawFileStore
-t -e 1.0:tcp -h 172.17.0.9 -p 44181 -t 60000
Ice.UnknownLocalException: null
at IceInternal.AsyncResultI.__wait(AsyncResultI.java:276) ~[ice.jar:na]
at
omero.api.RawFileStorePrxHelper.end_close(RawFileStorePrxHelper.java:1842)
~[blitz.jar:na]
at omero.api.RawFileStorePrxHelper.close(RawFileStorePrxHelper.java:1733)
~[blitz.jar:na]
at omero.api.RawFileStorePrxHelper.close(RawFileStorePrxHelper.java:1720)
~[blitz.jar:na]
at
ome.formats.OMEROMetadataStoreClient.closeQuietly(OMEROMetadataStoreClient.java:1035)
[blitz.jar:na]
at
ome.formats.OMEROMetadataStoreClient.closeServices(OMEROMetadataStoreClient.java:1056)
[blitz.jar:na]
at
ome.formats.OMEROMetadataStoreClient.logout(OMEROMetadataStoreClient.java:1082)
[blitz.jar:na]
at
ome.formats.importer.cli.CommandLineImporter.cleanup(CommandLineImporter.java:335)
[blitz.jar:na]
at
ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:964)
[blitz.jar:na]
*Diagnostics:*
================================================================================
OMERO Diagnostics (admin) 5.4.1-ice36-b75
================================================================================
Commands: java -version 1.8.0 (/usr/bin/java)
Commands: python -V 2.7.5 (/usr/bin/python)
Commands: icegridnode --version 3.6.4 (/usr/bin/icegridnode)
Commands: icegridadmin --version 3.6.4 (/usr/bin/icegridadmin)
Commands: psql --version 9.4.15 (/usr/bin/psql)
Server: icegridnode running
Server: Blitz-0 active (pid = 2558, enabled)
Server: DropBox active (pid = 956, enabled)
Server: FileServer active (pid = 957, enabled)
Server: Indexer-0 active (pid = 960, enabled)
Server: MonitorServer active (pid = 959, enabled)
Server: OMERO.Glacier2 active (pid = 961, enabled)
Server: OMERO.IceStorm active (pid = 970, enabled)
Server: PixelData-0 active (pid = 979, enabled)
Server: Processor-0 active (pid = 981, enabled)
Server: Tables-0 active (pid = 982, enabled)
Server: TestDropBox inactive (enabled)
Log dir: /opt/omero/server/OMERO.server/var/log exists
Log files: Blitz-0.log 3.0 MB errors=0
warnings=11
Log files: DropBox.log 1.0 KB
Log files: FileServer.log 0.0 KB
Log files: Indexer-0.log 2.0 KB
Log files: MonitorServer.log 1.0 KB
Log files: PixelData-0.log 2.0 KB
Log files: Processor-0.log 246.0 KB errors=0
warnings=2
Log files: Tables-0.log 2.0 KB errors=0
warnings=2
Log files: TestDropBox.log n/a
Log files: master.err 3.0 KB errors=0
warnings=10
Log files: master.out 0.0 KB
Log files: Total size 3.84 MB
Environment:OMERO_HOME=(unset)
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:OMERO_USERDIR=(unset)
Environment:OMERO_TMPDIR=(unset)
Environment:PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
Environment:PYTHONPATH=(unset)
Environment:ICE_HOME=(unset)
Environment:LD_LIBRARY_PATH=(unset)
Environment:DYLD_LIBRARY_PATH=(unset)
OMERO SSL port:4064
OMERO TCP port:4063
OMERO data dir:'/OMERO' Exists? True Is writable? True
OMERO temp dir:'/opt/omero/server/omero/tmp' Exists? True Is writable?
True (Size: 0)
JVM settings: Blitz-${index} -Xmx5061m -XX:MaxPermSize=1g
-XX:+IgnoreUnrecognizedVMOptions
JVM settings: Indexer-${index} -Xmx3374m -XX:MaxPermSize=1g
-XX:+IgnoreUnrecognizedVMOptions
JVM settings: PixelData-${index} -Xmx5061m -XX:MaxPermSize=1g
-XX:+IgnoreUnrecognizedVMOptions
JVM settings: Repository-${index} -Xmx3374m -XX:MaxPermSize=1g
-XX:+IgnoreUnrecognizedVMOptions
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