Add duplication check to check_annotations script

IDR / idr-utils

Utility scripts for managing IDR submissions

BSD 2-Clause "Simplified" License

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Add duplication check to check_annotations script #26

Closed dominikl closed 3 years ago

dominikl commented 4 years ago

Print warning if duplicated image names are found in the annotations.csv. And make sure wells without images (wellsamples) are skipped.

dominikl commented 3 years ago

Sorry, made quite an overhaul of the script now. But now using logging instead of print, and also argparse to be a bit more consistent with other scripts.

sbesson commented 3 years ago

I think I understand where my confusion comes from with respect to https://github.com/IDR/idr-utils/pull/26#pullrequestreview-496482046

The problem is that the same error messages are reported for very different checks:

missing annotation rows in the CSV for images under a Project/Screen
missing map annotation linked to images under a Project/Screen

As I will use this script to report some issues with annotations, I will look into a way to differentiate the error messages.