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Use CogStack API for deidentification #185

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merged 19 commits into from
Dec 18, 2023
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@milanmlft milanmlft commented Dec 14, 2023

Replace EHR deidentification with a call to the CogStack API.

  • Set up mock cogstack service with FastAPI for tests
  • Add PIXL_EHR_COGSTACK_REDACT_URL environment variable to configure cogstack
  • Remove old deidentification code

Closes UCLH-Foundry/the-rolling-skeleton#159

To do

  • Fix test_message_processing() unit test
  • Add documentation
  • Remove obsolete deidentification code

@milanmlft milanmlft requested a review from stefpiatek December 14, 2023 14:22
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Imagine you may be doing it already but we can remove all of the spacy and en_core_web_lg in documentation and from the ehr Dockerfile

@milanmlft milanmlft marked this pull request as ready for review December 14, 2023 17:03
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Thanks for getting this in Milan 🎉

@stefpiatek
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Tested on GAE05 and its doing what it should. Names have been replaced with [name], new fields for cogstack like HCPC number have not been redacted. Think we're good for a merge if you're happy with my Dockerfile changes

@milanmlft milanmlft merged commit f146362 into main Dec 18, 2023
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@milanmlft milanmlft deleted the milanmlft/use-cogstack-api branch December 18, 2023 11:06
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2 participants