Add extinfo command

[dominikl]

This command will automatically set the ExternalInfo for ome.zarr images imported using the omero-zarr-pixel-buffer.

I takes the path from the Fileset "usedFiles", which is assumed to only have one entry ..../SOME.ome.zarr/OME/METADATA.ome.xml and then set the ExternalInfo lsid to the full path of the multiscale 5d image; ..../SOME.ome.zarr/0 for an image ..../SOME.ome.zarr/A/1/1 etc. for plates.

Limitations: Only works for ome.zarr imported from the filesystem. And it's expected that the ome.zarr is a series with only that one image (/0) or a plate which path structure <row>/<column>/<field index>

[joshmoore]

💯 As a part of this I can imagine wanting to get and to reset as well.

[will-moore]

$ omero login
Error loading: /Users/wmoore/Desktop/ZARR/omero-cli-zarr/src/omero/plugins/zarr.py
Traceback (most recent call last):
  File "/Users/wmoore/Desktop/PY/omero-py/target/omero/cli.py", line 1677, in loadpath
    exec(f.read(), loc)
  File "<string>", line 1, in <module>
  File "/Users/wmoore/Desktop/ZARR/omero-cli-zarr/src/omero_zarr/cli.py", line 32, in <module>
    from .extinfo import external_info_str, get_extinfo, get_images, set_external_info
  File "/Users/wmoore/Desktop/ZARR/omero-cli-zarr/src/omero_zarr/extinfo.py", line 92, in <module>
    ) -> tuple[ImageWrapper, str | None, int | None]:
TypeError: unsupported operand type(s) for |: 'type' and 'NoneType'

[dominikl]

Interesting... is this a python version thing? I use 3.12.9.

[will-moore]

It could be, I'm on an old env python 3.9.15.

[dominikl]

Yes, looks like it's supported from 3.10 on. As we still recommend 3.9 I'll remove that stuff again.

[will-moore]

In think this needs to be a cross-group query findByQuery(query, params, conn.SERVICE_OPTS) otherwise you won't see it if the extinfo isn't in your default group.

[will-moore]

cross-group query here too

[will-moore]

Get or set...

[dominikl]

Get, because that's the default action.

[will-moore]

I was trying to test this on a non-zarr image, by specifying the --path but...

$ omero zarr extinfo Image:2856 --set --path test_extinfo_path
Previous session expired for will on localhost:4064
Server: [localhost:4064]
Username: [will]
Password:
Created session for will@localhost:4064. Idle timeout: 10 min. Current group: Swedlow Lab
Failed to set external info for image (2856) 438CTR_01_4_R3D_D3D.dv_1: Doesn't seem to be an ome.zarr: Users/wmoore/Desktop/images/DVs/438CTR_01_4_R3D_D3D.dv

It seems that there's something strange about --path, like it's being swallowed / overwritten somehow so that args.path was always None. Renaming this argument to anything else seemed to fix it. I suggest using lsid since that corresponds to the field in the extInfo.

[dominikl]

There's a check if it is a ome.zarr: https://github.com/ome/omero-cli-zarr/pull/167/files#diff-2d64f99479103ff3050c633344ddf895f61491094e9dab65218a3ec17cbfcb59R177 As that's actually only intended to be used with zarr. Otherwise it wouldn't make sense to have it as omero-cli-zarr plugin!?

[will-moore]

The point is that you have a --path argument for...

help="Use a specific path (default: Determine from clientPath) (only used in combination with --set)",

but it doesn't work for me. Does it work for you?