Populate metadata example

[will-moore]

Now that the webclient will display bulk metadata for Plates #4446 (and Insight has done for some time), this gives users an example of how to use populate_metadata from within a python script to upload Table data to a plate from a csv.

To test:

• try running the code sample, then check result in webclient (using PR Bulk annotations right panel #4446)

[joshmoore]

Question: Do we want to try and provide more vanilla Python code for doing this (without using populate_metadata.py)? This will be quite a bit more complex. However, we may still want this for Matlab or Java, (E.g. users asking how to do this from IJ)?

Options I can think of:

• Turn this into a service (i.e. provide a cmd command)
• Have a script which allows doing this
• Allow use of the CLI from the client-side

[will-moore]

Test fails https://ci.openmicroscopy.org/view/Failing/job/OMERO-DEV-merge-training/227/console
because the plate only has one Well, but test code expects 3 columns: A1, A2, A3.

File "/opt/hudson/workspace/OMERO-DEV-merge-training/OMERO.py/lib/python/omero/util/populate_metadata.py", line 423, in post_process
    well = well[well_column.values[i]]
KeyError: -1L

[will-moore]

@sbesson Where can I fix the DEV-merge-training job to create a Plate with 3 columns instead of one?

@joshmoore Best solution might be to create a "Populate_Metadata.py" script, very similar to
https://github.com/ome/scripts/blob/develop/omero/import_scripts/Populate_ROI.py, which replicates the code in this PR, using a csv file that has been attached to the Plate/Screen. This would even allow regular users to run the script from Insight / Web / CLI.

[sbesson]

@will-moore the training data is all generated using the script under https://github.com/sbesson/openmicroscopy/blob/develop/examples/Training/training_setup.sh. You should be adjust the SPW fake filename to match your new requirements /cc @ximenesuk

[emilroz]

@will-moore this may be worth looking at: https://github.com/glencoesoftware/omero-user-scripts/blob/master/util_scripts/Populate_Metadata.py
It's not directly from a csv but from a File Annotation that holds a csv.

[will-moore]

Thanks @emilroz that's perfect! @joshmoore do we want to add that script into the the main OMERO release, or leave it under glencoe scripts and point users there?

[manics]

In case it's relevant there's a whole new omero metadata command on the way (e.g. #4037)

[joshmoore]

@joshmoore do we want to add that script into the the main OMERO release, or leave it under glencoe scripts and point users there?

Better to copy it over, @will-moore.

[jburel]

@will-moore: will you take care of the Java/matlab examples too?

[simleo]

Looks good. Here is what I get on the right panel for the three wells (I've merged screenshots vertically to a single image):

[joshmoore]

👍