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ome / omero-scripts

Core OMERO Scripts
https://pypi.org/project/omero-scripts/
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Keyval from CSV support choice of Value separator #213

Open will-moore opened 9 months ago

will-moore commented 9 months ago

Currently, if you have a value that contains ; then the value is split on this token and multiple Key:Value pairs are created from the same Key: https://github.com/ome/omero-scripts/blob/d3fb626a77a2f90f39eea6719f46bc8b49655a06/omero/annotation_scripts/KeyVal_from_csv.py#L275

However, I wanted to use this script with a csv I downloaded from https://zenodo.org/record/7308444/files/Davis%20lab%20200%20YFP%20trap%20expression.csv?download=1 which works with images from https://zenodo.org/record/7308444/files/Figures.zip?download=1 (paper at https://rupress.org/jcb/article/222/6/e202205129/214092/Systematic-analysis-of-YFP-traps-reveals-common)

That csv uses commas to separate multiplr values, e.g. "synapse, cytoplasm, plasma membrane". I manually changed the script to split on ", " and this worked great, but it would be nice to have the option to choose this separator:

Screenshot 2023-11-17 at 12 57 00

cc @Tom-TBT since I think your changes at https://github.com/German-BioImaging/omero-scripts/tree/xtnd_support_kvpairs remove this support for multiple Values?

Tom-TBT commented 9 months ago

I removed it because I considered it an "unexpected feature". Happens that there are , in a value, and I don't want the regularuser to find his values splitted.

I consider it to be an "advanced feature", so I can reintroduce it as a string parameter (can be one or more character). If left empty, no splitting is done

will-moore commented 9 months ago

Sounds good, thanks! 👍