[ome-users] Problems with OMERO Imports

[Josh Moore]

Hi Christian,

On Thu, Dec 17, 2015 at 5:10 PM, Christian Carsten Sachs
<c.sachs at fz-juelich.de> wrote:
> 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.).

Is the script available somewhere?


> 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

Is there any stack trace above this line? Perhaps send the whole log (dir)?


> 2015-12-17 16:07:10,536 INFO  [ o.s.b.r.ManagedImportRequestI. at 49ccbb67]
> (2-thread-4) Cancelled

 I'd guess the above exception is leading to the import being cancelled.


> 2015-12-17 16:07:10,552 DEBUG [ o.s.b.r.ManagedImportRequestI. at 49ccbb67]
> ome.services.blitz.repo.ManagedImportRequestI.cleanup(ManagedImportRequestI.java:362)

This is all secondary after the import has died (or been killed).


> 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?

The fact that this is happening for each plane makes me think that
somehow the fileset detection on the production system differs from
the test system. Could you use `bin\omero import -f YOURDATAHERE` on
both the test and the production system and send us the logs?

Thanks,
~Josh.


> 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