[ome-users] OMERO Figure Download

[Stephen Taylor]

Hi,

Ah. Spoke to soon.

Got an new error when I set a batch job to run multiple figures.

Waiting....
Traceback (most recent call last):
  File "figure2png.py", line 88, in <module>
    while proc.poll() is None:
  File "/opt/OMERO.py-5.3.5-ice35-b73/lib/python/omero_Scripts_ice.py", line 691, in poll
    return _M_omero.grid.Process._op_poll.invoke(self, ((), _ctx))
Ice.UnknownLocalException: exception ::Ice::UnknownLocalException
{
    unknown = Network.cpp:2381: Ice::ConnectionRefusedException:
connection refused: Connection refused
}

Any idea?

Steve

From: ome-users [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] On Behalf Of Stephen Taylor
Sent: 20 October 2017 14:04
To: OME User Support List <ome-users at lists.openmicroscopy.org.uk>
Subject: Re: [ome-users] OMERO Figure Download

Hi Will,

Thanks! This seems to fix things.

Steve

From: ome-users [mailto:ome-users-bounces at lists.openmicroscopy.org.uk] On Behalf Of William Moore (Staff)
Sent: 17 October 2017 11:37
To: OME User Support List <ome-users at lists.openmicroscopy.org.uk<mailto:ome-users at lists.openmicroscopy.org.uk>>
Subject: Re: [ome-users] OMERO Figure Download

Hi Steve,

 I think you must have also updated OMERO.figure too, since the return key changed in OMERO.figure 3.1.0:
https://github.com/ome/omero-figure/commit/6d07fc88

You now need to use “New_Figure” everywhere instead of “File_Annotation”).
Apologies for not anticipating that this would be a breaking change.

I’ll update the gist.

 Hope that works,

 Regards,

   Will.



On 17 Oct 2017, at 08:27, Stephen Taylor <stephen.taylor at imm.ox.ac.uk<mailto:stephen.taylor at imm.ox.ac.uk>> wrote:

Hi,

Earlier this year Will kindly helped me write a script to download data from OMERO figure (see https://gist.github.com/will-moore/d448a7abd57425734aba426f0952eff6).

Our OMERO server just got updated to version 5.3.5.  Now line 53, if rv.get('File_Annotation'):, returns None so it never gets to the download step. Please can someone advise how I can debug this because AFAIK the figures look ok and I am a bit stuck what to do next.

I am using running the script on Ubuntu and using the OMERO.py-5.3.5-ice35-b73 libs.

Kind regards and thanks,

Steve
----------------------------------
Head of Computational Biology Research Group
MRC Weatherall Institute of Molecular Medicine
Oxford
www.cbrg.ox.ac.uk<http://www.cbrg.ox.ac.uk>

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