[ome-users] Fwd: OMERO.qa - new comment

[Josh Moore]

Forwarding conversation to the list.


---------- Forwarded message ----------
From: Martin Schorb <martin.schorb at embl.de>
Date: Mon, Feb 23, 2015 at 9:45 PM
Subject: Re: OMERO.qa - new comment
To: Josh Moore <josh at glencoesoftware.com>


I have a set of ~6000 tif files from a FIB-SEM. 15 MB each that I try
to import using
OMERO.server/bin/omero -s localhost -u $user import -- -d 1
--transfer=ln_s $imagedir

It manages to do so for part of the files but randomly exits with the
following complaint (first line shows last successful import):
2015-02-20 17:41:53,539 3097900 [l.Client-0] INFO
ormats.importer.cli.LoggingImportMonitor - IMPORT_DONE Imported file:
/home/emcf/images/MB1-ROI9-FIBSEM-AliCropAli-InvCLAHE/MB1-ROI9-FIBSEM_s1000-1999_InvCLAHE0781.tif
Imported pixels:
3197
Other imported objects:
Fileset:3198
Image:3197

...

2015-02-20 17:41:53,539 3097900 [l.Client-0] INFO
ome.formats.importer.cli.ErrorHandler - Number of errors: 0
2015-02-20 17:41:53,558 3097919 [ main] INFO
ome.formats.OMEROMetadataStoreClient - Call context: {omero.group:3}
2015-02-20 17:41:53,565 3097926 [ main] INFO
ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION
2015-02-20 17:41:53,689 3098050 [ main] INFO
ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START
2015-02-20 17:41:53,690 3098051 [ main] INFO
s.importer.transfers.SymlinkFileTransfer - Transferring
/home/emcf/images/MB1-ROI9-FIBSEM-AliCropAli-InvCLAHE/MB1-ROI9-FIBSEM_s1000-1999_InvCLAHE0764.tif...
2015-02-20 17:41:53,707 3098068 [ main] INFO
ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED:
/home/emcf/images/MB1-ROI9-FIBSEM-AliCropAli-InvCLAHE/MB1-ROI9-FIBSEM_s1000-1999_InvCLAHE0764.tif
2015-02-20 17:41:53,813 3098174 [ main] ERROR
ome.formats.importer.cli.ErrorHandler - FILE_EXCEPTION:
/home/emcf/images/MB1-ROI9-FIBSEM-AliCropAli-InvCLAHE/MB1-ROI9-FIBSEM_s1000-1999_InvCLAHE0764.tif
omero.ResourceError: null
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native
Method) ~[na:1.7.0_75]

....

I run the import command as the omero system user on the actual server
(thru ssh). It succeeds with 3197 files and then causes the problem. The
target dir in ManagedRepositories is empty and writable, there is no
quota and plenty of free disk space.

Martin


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