[ome-users] OMERO.qa - new comment

[Sebastien Besson]

Hi Martin,

I tried to reproduce your failures with a 5.0.8 server while performing an in-place
import of 6000 fake files but could not reproduce. I will give it another go with tiff
files tomorrow.

In the meantime, do you have access to the server logs corresponding to the failing
import? Would it be possible to upload them for our examination?

Best,
Sebastien

On 23 Feb 2015, at 20:48, Josh Moore <josh at glencoesoftware.com> wrote:

> 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
> 
> 
>>>> https://www.openmicroscopy.org/qa2/qa/feedback/10523/?token=515b9ee71de697b8f25684d282d61532
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