[ome-devel] Calling the importer from Python

[Aleksandra Tarkowska (Staff)]

Hi Niko,

First looks like example in the thread was moved to
https://github.com/openmicroscopy/openmicroscopy/blob/develop/components/tests/python/library/__init__.py#L219
That may gives you a better idea ;-)

Also in the example below client object should be set using:

cli.set_client(conn.c)

Kind regards
Ola

From: William Moore <will at lifesci.dundee.ac.uk<mailto:will at lifesci.dundee.ac.uk>>
Reply-To: OME External Developer List <ome-devel at lists.openmicroscopy.org.uk<mailto:ome-devel at lists.openmicroscopy.org.uk>>
Date: Tue, 12 May 2015 10:05:34 +0100
To: OME External Developer List <ome-devel at lists.openmicroscopy.org.uk<mailto:ome-devel at lists.openmicroscopy.org.uk>>
Subject: Re: [ome-devel] Calling the importer from Python

Hi Niko,

 You should be able to use conn.c to access the underlying omero.client in the
Blitz Gateway. This client is already connected (don't need to call createClient).
So you can simply do:

cli = omero.cli.CLI()
cli.loadplugins()
cli._client = conn.c
cli.invoke(["import", path_to_file])


You might also find something useful at
https://www.openmicroscopy.org/community/viewtopic.php?f=6&t=7562&p=14258

which links to this example: https://github.com/ome/omego/blob/master/auto_import.py

Regards,

  Will.



On 12 May 2015, at 08:29, Niko Ehrenfeuchter <nikolaus.ehrenfeuchter at unibas.ch<mailto:nikolaus.ehrenfeuchter at unibas.ch>> wrote:

Hi again,

one more question regarding this: is there a way to create the CLI() object using an existing BlitzGateway connection?

I'm only asking since all the rest of my script is currently based on the conn object only, so it were very nice if I could simply re-use that.

Thanks
~Niko

On 12.05.2015 00:00, Niko Ehrenfeuchter wrote:
Hi Ola,

thanks for the quick response, I'll go for the omero.cli version then.

The example in the thread mentioned is very helpful, btw!

Best
~Niko

On 11.05.2015 23:47, Aleksandra Tarkowska (Staff) wrote:
Hi Niko,

I am affraid that is the way to do it. Please see similar thread

http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2014-September/002982.html



Kind regards
Ola

On 11 May 2015, at 21:45, Niko Ehrenfeuchter
<nikolaus.ehrenfeuchter at unibas.ch<mailto:nikolaus.ehrenfeuchter at unibas.ch>> wrote:

Hi all,

I was wondering what the best method for calling the importer from
within a Python script might be?

I've looked at uploadFile() from omero.util.script_utils, but in my
understanding that's not for images - or am I wrong here?

Delusively, the most simple thing would be to use
omero.plugins.import, but as far as I can see the plugins are not
meant as modules to be imported in other Python scripts but rather
for extending the OMERO command line interface.

Of course I could use popen() to call the "real" command line
interface directly, but it feels a bit stupid calling a Python script
from another one where all the OMERO stuff has already been set up.

My approach now would be to use the CLI class from omero.cli, but I
wanted to know if there is a better way that I am overlooking?

Many Thanks,
~Niko
--
Niko Ehrenfeuchter | Image Analysis Specialist | Biozentrum,
University of Basel | Klingelbergstr. 50/70 | CH-4056 Basel
Phone: +41 (61) 26 72673 | nikolaus.ehrenfeuchter at unibas.ch<mailto:nikolaus.ehrenfeuchter at unibas.ch> |
www.biozentrum.unibas.ch | www.microscopynetwork.unibas.ch
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--
Niko Ehrenfeuchter | Image Analysis Specialist | Biozentrum, University of Basel | Klingelbergstr. 50/70 | CH-4056 Basel
Phone: +41 (61) 26 72673 | nikolaus.ehrenfeuchter at unibas.ch<mailto:nikolaus.ehrenfeuchter at unibas.ch> | www.biozentrum.unibas.ch<http://www.biozentrum.unibas.ch> | www.microscopynetwork.unibas.ch<http://www.microscopynetwork.unibas.ch>
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