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Core OMERO Scripts
https://pypi.org/project/omero-scripts/
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ROI export handle points whitespace #170

Closed will-moore closed 4 years ago

will-moore commented 4 years ago

Found this bug when trying Batch_ROI_Export from outreach server, using idr0022 data. Failed with float(x.strip(", ") since points string was not in the exact expected format.

I now strip whitespace before split(' ') so don't end up with empty string from trailing whitespace. Also wrap with try/except in case some other unexpected format - Don't want a single invalid points list to break the whole script.

To test:

pwalczysko commented 4 years ago

Tested on merge-ci user-3 (we have the idr0021 in full with ROIs imported there too).

All works fine, on the dataset which errored on ome-training-4 previously, as well as on the whole idr0021 project.

Ready to merge fmpov

joshmoore commented 4 years ago

The idea would be to roll this into the next release, correct? Is there anything else foreseen or shall we call this 5.6.1?

jburel commented 4 years ago

@will-moore might come back from workshop with a fix for a script :-) in that case it might be included in a 5.6.1 minor comments on this PR that will be good to have it in

jburel commented 4 years ago

I could not reproduce the error on workshop using few images from idr21 (images 9539, 9540, 9541) using the older version of the script

jburel commented 4 years ago

The handling of the string is quite fragile in a way This PR handles potential cases we have seen and it does not affect existing shapes

will-moore commented 4 years ago

No, I can't find the shapes that broke this script originally. But you only need to have Points string with trailing whitespace "1,2 3,4 " to break the script (without this PR).