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ome / omero-py

Python project containing Ice remoting code for OMERO
https://www.openmicroscopy.org/omero
GNU General Public License v2.0
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bulk.yml depth is passed to xargs #337

Open will-moore opened 1 year ago

will-moore commented 1 year ago

When performing bulk import, any depth: 100 value added to the bulk.yml is currently ignored and you have to use --depth=100 on the command line.

This attempts to fix that issue.

This fix works, BUT it now overrides any value passed on the command-line (which probably should take precedence)? However, at this point in the code, I can't check xarg for the presence of any -Domero.import.depth command, since this is always there with the default of 4.

Not quite sure where the "right" place is to fix this?

cc @sbesson @joshmoore @dominikl

sbesson commented 1 year ago

Looking briefly at the way the API are called, either the full xargs set-up or maybe only the omero.import.depth set-up could potentially be moved under do_import so that it's only defined once?

I would also have assumed that arguments passed via the command-line would take precedence as well but looking at the implementation, it is possible that this might not be the case as the parsing of the bulk keys calls CommandArguments.add for most keys and I do not see the logic for handling existing keys. Additional unit tests might be needed to confirm this.