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ome / omero-scripts

Core OMERO Scripts
https://pypi.org/project/omero-scripts/
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WIP: Add scripts for bulk annotation #191

Closed CFGrote closed 2 years ago

CFGrote commented 2 years ago

This PR adds scripts originally maintained by @evenhuis to support bulk annotation via csv files and dataset descriptions. The original code was ported to python3, bugs fixed and rudimentary tests added.

Marked as Draft here and seeking feedback and contributions from @will-moore , @ahamacher and others as discussed in this images.sc thread.

Update: Please see #193

joshmoore commented 2 years ago

Since it's happened to me on other repos, I took the time to at least explore saving the history in https://github.com/ome/omero-scripts/pull/192

will-moore commented 2 years ago

@CFGrote Just looking to test the various scripts added here, using your blog at https://mpievolbio-scicomp.pages.gwdg.de/blog/post/2020-09-03_omerobulkannotation/ as a guide. I notice that doesn't mention KeyVal from Description, KeyVal from Filename or Remove KeyVal and I can't guess from the script dialog description how to use them. Do you use these scripts? I'm wondering if we really want to include them here; Is the cost of maintenance, testing etc justified?

CFGrote commented 2 years ago

yes, sorry, those scripts are not mentioned.

https://github.com/mpievolbio-scicomp/ometa/blob/master/readme.orig.md has more information and links to more detailed documentation at https://code.research.uts.edu.au/MIF/OMERO-instructions.

KeyVal_from_Description: Parses the Description field of a Dataset and converts "key: val" strings to key-value annotations of the same Dataset (if I remember correctly). We used this for a little while before getting KeyVal_from_csv to work for us. I'd say it can be removed.

KeyVal_from_Filename: Never used it. It should tokenize image filenames into key-value pairs based on a pattern defined again in the Dataset description. Can be removed because that functionality is provided in Insight (correct?).

RemoveKeyVal: Strips off all key-val pairs in the special namespace from selected items. Issue is that it does not really remove the annotations (as in "delete from the database") but somehow hides from the view. They resurface under certain conditions like applying KeyVal_from_csv again. This one should stay and be debugged IMHO.

Hope that helps.

Thanks and best regards, Carsten

joshmoore commented 2 years ago

Closing in favor of #193

will-moore commented 2 years ago

@CFGrote I think KeyVal_from_Filename functionality is provided by the auto-tagging omero.web plugin to create Tags rather than KV pairs. Certainly if you've never used it then let's keep thing simpler by not including it.

I've created an issue for RemoveKeyVal https://github.com/ome/omero-scripts/issues/194

Moving this discussion to #193...

CFGrote commented 2 years ago

yes, you're right. sorry for the confusion.