populate metadata links file ann

[will-moore]

This change is needed to allow populate_metadata script to work with the File-picker from ome/openmicroscopy#6096
That PR passes the uploaded FileAnnotation ID to populate-metadata script, but the script expects the FileAnnotation to be linked to the selected object.
This PR links the FileAnnotation to the object, which also has the benefit of not 'losing' the new FileAnnotation with it being unlinked.

To test:

• Create or find a CSV FileAnnotation for populate metadata. E.g. https://merge-ci.openmicroscopy.org/web/webclient/?show=dataset-4919 (user-3)
• Note the FileAnnotation ID - (9987) then unlink (don't delete) the Annotation from the Dataset.
• Run populate_metadata script on the Dataset, entering the File Annotation ID.
• Check that the populate-metadata works as expected to create an OMERO.table and that the csv becomes linked to the Dataset.
• If the File_Annotation ID is filled out in the script (and the FileAnnotation is already linked to the object) then script should continue to work as before

[jburel]

• user-1 merge-ci
• project ID 5757
• Create a file using https://github.com/ome/omero-metadata/ and save locally
• Choose the local file
• Error: File does not exist.

[will-moore]

It looks like merge-ci doesn't have the latest version of the script, although it was merged in the last build at snoopycrimecop@b7de9d7

[sbesson]

I was surprised by this at first it looks consistent to the introduction of the --shallow flag in ome/devspace@9a99bf1.

[will-moore]

Does that commit need reverting, or some other fix?

[sbesson]

Reverting the commit will only apply to newly deployed devspace environment. In the case of the existing merge-ci devspace, I think you want to modify the default value of MERGE_COMMAND in the job configuration and restore the previous behavior unless @jburel remembers a reason not to revert his change.

[jburel]

I do not remember why we added the shallow flag

[joshmoore]

For what it's worth, we will very soon no longer have a submodule in ome/openmicroscopy.

[joshmoore]

Coming back to the content of the PR:

This change is needed to allow populate_metadata script to work with the File-picker from ome/openmicroscopy#6096

We might need to discuss how this type of coupling should affect the semver of these two components.

[will-moore]

Certainly we shouldn't release the change in the script dialog ome/openmicroscopy#6096 before the script changes in this PR.

There are a few places where we have a 'convention' on the naming of script Parameters. E.g. "Data_Type" and "IDs" for data input. These are quite simple convention so we haven't felt the need to define this API anywhere. The "File_Annotation" parameter is also understood by the webclient and can be auto-populated. I assumed File_Annotation would simply use the ID of a File_Annotation, but it has an additional requirement that the Annotation is linked to the Project/Screen for populate_metadata script.

Perhaps we can test and merge this PR first, then consider ome/openmicroscopy#6096

Will that be enough to ensure that user don't get the webclient dialog changes before they get the script changes?

cc @chris-allan

[pwalczysko]

We still do not have this script on the merge-ci - judging according to me getting the same result of the test as @jburel above #152 - how to improve that ?

[pwalczysko]

Uploaded the script here manually onto merge-ci. The functionality works as described.

[will-moore]

Closing until #159 is merged to avoid conflicts...

[pwalczysko]

All works fine here. Tried the suggested table as well as my own, with double columns -> parade

The unattached File is found via the ID as expected, and when one is attached there already, the script still runs as expected.

Ready to merge FMPOV

[pwalczysko]

Maybe we should test on py3-ci though ? All the tests above were run on merge-ci

[will-moore]

Uploaded and tested on py3-ci today. Will list for testing there tomorrow (will need to upload script again first). Use https://py3-ci.openmicroscopy.org/web/webclient/?show=dataset-3120 (user-3).

[pwalczysko]

Tested on py3-ci, user-3 https://py3-ci.openmicroscopy.org/web/webclient/?show=dataset-2270

All good. Ready to merge.

[joshmoore]

This change is needed to allow populate_metadata script to work with the File-picker from ome/openmicroscopy#6096

But that PR is excluded. Can you explain?

[will-moore]

ome/openmicroscopy#6096 requires this PR, so it is probably excluded until this one is merged, released etc. However, this PR doesn't require that one.