[ome-devel] CLI render

[Damir Sudar]

Hi Josh and all,

On 7/10/2017 6:45, Josh Moore wrote:
> Rather than trying more of this, I thought to check with you first 
> whether I'm missing something fundamental.
> 5.3 :) (or the upcoming 5.4)
>
> Fundamentally, the plugin is not production quality and has only been
> used in isolated situations. We certainly intend to get it into the
> testing pipeline for 5.4 but that's not likely to uncover what's going
> on with 5.2. If you or anyone on your side wants to continue digging,
> we're happy to evaluate your changes, but there's a question of how
> far you want to go in modifying your local installation.
>
> Cheers,
> ~Josh.
Thanks. For now I'll refrain from delving any deeper into this. Simon 
had warned me that this was very early code and not tested extensively. 
I look forward to it appearing in full glory in a future version.

Meanwhile, I had kludged together a regular OMERO script 
(HCS_Render_Settings.py) that does a number of the things that the 
render.py plugin does but much much less elegantly and very slowly. I'll 
use that for now. That script is on: https://github.com/dsudar/OMEROscripts

Cheers,
- Damir
>> On 6/2/2017 2:35, Simon Li wrote:
>>
>> The render plugin (not tested on 5.3):
>> https://github.com/openmicroscopy/openmicroscopy/blob/metadata53/components/tools/OmeroPy/src/omero/plugins/render.py
>> Try dropping this into OMERO.server/lib/python/omero/plugins/
>>
>> Example YAML render settings file:
>> https://github.com/IDR/idr-metadata/blob/master/idr0015-UNKNOWN-taraoceans/screenA/idr0015-screenA-renderdef.yml
>>
>> omero render edit --help
>> omero render edit --copy Plate:1 renderdef.yml
>> omero render copy Image:SrcID Plate:TargetID
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-- 
Damir Sudar - Affiliate Scientist
Lawrence Berkeley Natl Laboratory / MBIB
One Cyclotron Road, MS 977, Berkeley, CA 94720, USA
T: 510/486-5346 - F: 510/486-5586 - E: DSudar at lbl.gov
http://biosciences.lbl.gov/profiles/damir-sudar-2/

Visiting Scientist, Oregon Health & Science University