[ome-users] command line import & blitz gateway

[Will Moore]

Just tried replying, but not sure it worked, Trying again....


Hi Graeme,

 Have a look at some python code we use for auto-populating omero with Projects, Datasets and importing Images.
https://github.com/ome/omero-setup/blob/master/auto_import.py

This is something we use to set-up a server for testing etc.

Since you can get the pixels ID from the import process, E.g. see:
https://github.com/openmicroscopy/openmicroscopy/blob/develop/components/tools/OmeroPy/test/integration/library.py#L161
you can get the Image ID (can't assume they're the same as in that example) then add some annotations etc (see link below).


For writing your own Python client / scripts etc, you should start
https://www.openmicroscopy.org/site/support/omero4/developers/Python.html

For more detail, try the source code of the "Blitz Gateway" - Python wrappers around the core OMERO api, which
is the 'conn' etc used in many of the starter examples.
https://github.com/openmicroscopy/openmicroscopy/blob/develop/components/tools/OmeroPy/src/omero/gateway/__init__.py


 Hope that helps,

 Let us know if you have any more questions,

  Cheers,

  Will. 



On 2 May 2013, at 15:54, Graeme Ball wrote:

> Dear OME,
> 
> I have been writing OMERO scripts to process data and re-import the results, but have hit a couple of snags with the imports.
> 
> I would like to upload results to the same dataset as the images they are derived from, and the command line importer documentation suggests this is possible using the -d option. 
> http://www.openmicroscopy.org/site/support/omero4/users/command-line-import.html
> However, if I try for example, "-d 51" I get:-
>   Unknown debug action: set(['51']) 
> which seems to agree with the contents of OMERO.server/lib/python/omero/cli.py (if that is the right file)
> 
> I would also like to attach results (text files etc.) to each image, but there is no option using the command line importer. The reason I am using the command line importer is that the results are being processed remotely (and we have not managed to set up OMERO.processor as yet). 
> 
> Should I be attempting to write our own python client? And if so, where would be a good place to start? OMERO.server/lib/python/omero/clients.py perhaps?
> 
> Thanks & Best Regards,
> 
> Graeme
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users

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