[ome-devel] Calling the importer from Python

[Niko Ehrenfeuchter]

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> 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 | 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 | 
www.biozentrum.unibas.ch | www.microscopynetwork.unibas.ch