Improve Drop T dimension task

[jluethi]

Main improvements:

• Add support for tables: Copy tables from old Zarr to new Zarr
• Add support for labels (also with dimensionality dropping)?
• Add support for overwrite_input

In Fractal V2:
Correctly update the image list

[BioinfoTongLI]

Hi @jluethi, I am trying to wrap some tasks into Nextflow and wondering how should I run this drop_T task via CLI?
I see that you've got this section for naive run. But I couldn't figure out what are the expected args

usage: drop_t_dimension.py [-h] --args-json ARGS_JSON --out-json OUT_JSON

I tried to give the img_list.json from the import_ome_zarr task and it said

zarr_url
  field required (type=value_error.missing)

Whic is expected I'd say since it's the arg in the function. But when I add that arg with or without flag, it said:

drop_t_dimension.py: error: unrecognized arguments:  [zarr_url]

I've actually managed to run it without your main section but a bespoke one. But I do think it's better to be in line with your canonical version.

[jluethi]

Hey @BioinfoTongLI

Using these tasks directly via Python seems like a totally fine way to go to me, unless you want to run them through Fractal server or a nextflow command of course. To be able to use it through the CLI, you'll need to provide the following as an ARGS_JSON:

{
  "zarr_url": "/path/to/zarr/file/myplate.zarr/B/03/0"
}

The zarr_url should be one of the contents of img_list.json, but it's formatted differently. e.g. it can contain a list of all the zarr_urls after the import task, while Drop T dimension is meant to be run per zarr_url.

And if you want to set any of the other arguments of that task (e.g. to set overwrite_input to True), also add this to that json

[BioinfoTongLI]

Hi Joel, I've noticed that the original metadata is parsed but not updated.
https://github.com/jluethi/fractal-helper-tasks/blob/main/src/fractal_helper_tasks/drop_t_dimension.py#L70
I am not sure if you've intentionally left the MD untouched to keep the raw. Or if it's just an overlook.
If it's the later, I can help adding this.