[ome-devel] batch import into OME 5.0.2

Tue Jun 10 16:44:05 BST 2014

Server configuration: Ubuntu 12.04 VM with 3TB NFS storage attached. OME 5
is installed and the ManagedRepository is located on the 3TB NFS storage.

When using command line import tool to inject one user folder plus its
subfolders to one dataset in OME, I have got following error on certain
TIFF images (file path removed from log info)  :

Using session 0267110d-87b6-446a-92b8-0a6aa5b707f9 (acharyaj at localhost:4064).
Current group: EMLAB
2014-06-06 16:43:36,419 181        [      main] INFO
ome.formats.importer.ImportConfig - OMERO Version: 5.0.2-ice34-b26
2014-06-06 16:43:36,432 194        [      main] INFO
ome.formats.importer.ImportConfig - Bioformats version: 5.0.2-ice34-b26
revision: 0c4215a date: 27 May 2014
2014-06-06 16:43:36,440 202        [      main] INFO
formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR
OMERO.importer: INFO
2014-06-06 16:43:36,677 439        [      main] INFO
ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM
2014-06-06 16:43:37,710 1472       [      main] INFO
ome.formats.importer.ImportCandidates - 9 file(s) parsed into 8 group(s)
with 9 call(s) to setId in 1003ms. (1033ms total) [1 unknowns]
2014-06-06 16:43:39,695 3457       [      main] INFO
ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to
localhost:4064
2014-06-06 16:43:40,131 3893       [      main] INFO
ome.formats.OMEROMetadataStoreClient - Insecure connection requested,
falling back
2014-06-06 16:43:40,371 4133       [      main] INFO
ome.formats.OMEROMetadataStoreClient - Server: 5.0.2
2014-06-06 16:43:40,371 4133       [      main] INFO
ome.formats.OMEROMetadataStoreClient - Client: 5.0.2-ice34-b26
2014-06-06 16:43:40,371 4133       [      main] INFO
ome.formats.OMEROMetadataStoreClient - Java Version: 1.6.0_30
2014-06-06 16:43:40,371 4133       [      main] INFO
ome.formats.OMEROMetadataStoreClient - OS Name: Linux
2014-06-06 16:43:40,371 4133       [      main] INFO
ome.formats.OMEROMetadataStoreClient - OS Arch: amd64
2014-06-06 16:43:40,371 4133       [      main] INFO
ome.formats.OMEROMetadataStoreClient - OS Version: 3.2.0-34-generic
2014-06-06 16:43:40,509 4271       [      main] INFO
ome.formats.OMEROMetadataStoreClient - Call context: {omero.group:3}
2014-06-06 16:43:40,527 4289       [      main] INFO
ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION
2014-06-06 16:43:40,760 4522       [      main] INFO
ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START
2014-06-06 16:43:40,773 4535       [      main] INFO
ts.importer.transfers.UploadFileTransfer - Transferring /../51-11.tif...
2014-06-06 16:43:40,790 4552       [      main] INFO
ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED:
/../51-11.tif
2014-06-06 16:43:40,872 4634       [      main] ERROR
ome.formats.importer.cli.ErrorHandler - FILE_EXCEPTION: /../51-11.tif
omero.ResourceError: null
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native
Method) ~[na:1.6.0_30]
    at
sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
~[na:1.6.0_30]
    at
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
~[na:1.6.0_30]
    at java.lang.reflect.Constructor.newInstance(Constructor.java:534)
~[na:1.6.0_30]
    at java.lang.Class.newInstance(Class.java:374) ~[na:1.6.0_30]
    at
IceInternal.BasicStream$DynamicUserExceptionFactory.createAndThrow(BasicStream.java:2142)
~[ice.jar:na]
    at IceInternal.BasicStream.throwException(BasicStream.java:1564)
~[ice.jar:na]
    at IceInternal.Outgoing.throwUserException(Outgoing.java:443)
~[ice.jar:na]
    at omero.api._RawFileStoreDelM.save(_RawFileStoreDelM.java:183)
~[blitz.jar:na]
    at omero.api.RawFileStorePrxHelper.save(RawFileStorePrxHelper.java:527)
~[blitz.jar:na]
    at omero.api.RawFileStorePrxHelper.save(RawFileStorePrxHelper.java:500)
~[blitz.jar:na]
    at
ome.formats.importer.transfers.TransferState.save(TransferState.java:113)
~[blitz.jar:na]
    at
ome.formats.importer.transfers.AbstractFileTransfer.finish(AbstractFileTransfer.java:107)
~[blitz.jar:na]
    at
ome.formats.importer.transfers.UploadFileTransfer.transfer(UploadFileTransfer.java:85)
~[blitz.jar:na]
    at
ome.formats.importer.ImportLibrary.uploadFile(ImportLibrary.java:414)
[blitz.jar:na]
    at
ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:477)
[blitz.jar:na]
    at
ome.formats.importer.ImportLibrary.importCandidates(ImportLibrary.java:271)
[blitz.jar:na]
    at
ome.formats.importer.cli.CommandLineImporter.start(CommandLineImporter.java:216)
~[blitz.jar:na]
    at
ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:721)
~[blitz.jar:na]
2014-06-06 16:43:40,879 4641       [      main] ERROR
ome.formats.importer.ImportLibrary - Error on import: Cannot find path.
Deleted? /../ManagedRepository/acharyaj_52/2014-06/06/16-43-40.589/51-11.tif
omero.ResourceError: null
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native
Method) ~[na:1.6.0_30]
    at
sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
~[na:1.6.0_30]
    at
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
~[na:1.6.0_30]
    at java.lang.reflect.Constructor.newInstance(Constructor.java:534)
~[na:1.6.0_30]
    at java.lang.Class.newInstance(Class.java:374) ~[na:1.6.0_30]
    at
IceInternal.BasicStream$DynamicUserExceptionFactory.createAndThrow(BasicStream.java:2142)
~[ice.jar:na]
    at IceInternal.BasicStream.throwException(BasicStream.java:1564)
~[ice.jar:na]
    at IceInternal.Outgoing.throwUserException(Outgoing.java:443)
~[ice.jar:na]
    at omero.api._RawFileStoreDelM.save(_RawFileStoreDelM.java:183)
~[blitz.jar:na]
    at omero.api.RawFileStorePrxHelper.save(RawFileStorePrxHelper.java:527)
~[blitz.jar:na]
    at omero.api.RawFileStorePrxHelper.save(RawFileStorePrxHelper.java:500)
~[blitz.jar:na]
    at
ome.formats.importer.transfers.TransferState.save(TransferState.java:113)
~[blitz.jar:na]
    at
ome.formats.importer.transfers.AbstractFileTransfer.finish(AbstractFileTransfer.java:107)
~[blitz.jar:na]
    at
ome.formats.importer.transfers.UploadFileTransfer.transfer(UploadFileTransfer.java:85)
~[blitz.jar:na]
    at
ome.formats.importer.ImportLibrary.uploadFile(ImportLibrary.java:414)
~[blitz.jar:na]
    at
ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:477)
~[blitz.jar:na]
    at
ome.formats.importer.ImportLibrary.importCandidates(ImportLibrary.java:271)
~[blitz.jar:na]
    at
ome.formats.importer.cli.CommandLineImporter.start(CommandLineImporter.java:216)
~[blitz.jar:na]
    at
ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:721)
~[blitz.jar:na]
2014-06-06 16:43:40,879 4641       [      main] INFO
ome.formats.importer.ImportLibrary - Exiting on error

I have verified the file 51-11.tif exists as
ManagedRepository/acharyaj_52/2014-06/06/16-43-40.589/51-11.tif. Tried run
tiffinfo tool again the image file and found no problem. Don't know why OME
report an existing file as non-exist...

Any help?

Thanks,
Yanling
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-devel/attachments/20140610/f03b950d/attachment-0001.html>