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uclh-criu / miade

A set of tools for extracting formattable data from clinical notes stored in electronic health record systems.
https://uclh-criu.github.io/miade/
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Stopwords temp fix #109

Closed jenniferjiangkells closed 11 months ago

jenniferjiangkells commented 11 months ago

Although we discussed using MiADE_CAT to implement a fix for this, I feel it's not best practice to change the internals of MedCAT through our custom class and would prefer to avoid it if we can - so I think it's best to leave the stopword loading fix in a MedCAT PR https://github.com/CogStack/MedCAT/issues/382

This temp fix is implemented on MiADE side - it reloads the spacy model and MedCAT pipe creation, which reloads the stopwords correctly (so even if the bug gets fixed this is still backwards compatible, just an extra step at initialisation).

I'm hoping that we can use this temp fix for testing in DEV only, and just update to the latest MedCAT once the fix is implemented for TEST and PROD.

jamesbrandreth commented 11 months ago

100% with you re best practice there - good quick fix too