[ome-devel] CLI render

[Josh Moore]

On Fri, Jul 7, 2017 at 7:31 PM, Damir Sudar <dsudar at lbl.gov> wrote:
> Hi team,

Hi Damir,


> At the OME meeting, I spoke with Simon about the CLI render function that he
> had written primarily for IDR but it's a great capability that I was hoping
> to use as well. Below is Simon's message telling me where to find the code.
> After a few weeks of vacation after the OME meeting and now trying to get
> back into the groove, I had a quick look at it. My server is still at 5.2.8
> so I had hope to get it going quickly. Alas, I ran into a few snags and was
> hoping you had some wise words.
>
> First one was relatively easy: the render plugin wants to import
> pydict_text_io and that wasn't there in the vanilla 5.2.8. I found a
> pydict_text_io.py in 5.3.3 so copied that into the util directory of my
> 5.2.8 server since it didn't look like that was specific to the 5.3.x line.

Yes, it's mostly a collection of utilities, so that seems fine.



> Next I tried a few of the basic commands of the render plugin:
> 1 ---
...
>   File "/home/omero_user/OMERO.server/lib/python/omero/plugins/render.py",
> line 117, in init_from_channel
>     self.min = channel.getWindowMin()
...
> omero.UnloadedEntityException: Object unloaded:object #0

Vanilla 5.2 is not loading the necessary metadata for the plugin to
work. Unfortunately, solving this isn't as simple as copying a new
file into your installation. In fact, I haven't yet found a smoking
gun between the versions.


> 2---

> AttributeError: 'ImageI' object has no attribute '_closeRE'
> ---

Here again, changes from 5.3 are not available in your version, though
at least these I know where they come from.


> 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,
> - 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