CU-8693v3tt6 SOMED opcs refset selection #402
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antsh3k
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Feb 16, 2024
mart-r
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Feb 28, 2024
* Cu 8693u6b4u tests continue on fail (#400) * CU-8693u6b4u: Make sure failed/errored tests fail the main workflow * CU-8693u6b4u: Attempt to fix deid multiprocessing, at least for GHA * CU-8693u6b4u: Fix small docstring issue * CU-8693v3tt6 SOMED opcs refset selection (#402) * CU-8693v3tt6: Update refset ID for OPCS4 mappings in newer SNOMED releases * CU-8693v3tt6: Add method to get direct refset mappings * CU-8693v3tt6: Add tests to direct refset mappings method * CU-8693v3tt6: Fix OPCS4 refset ID selection logic * CU-8693v3tt6: Add test for OPCS4 refset ID selection * CU-8693v6epd: Move typing imports away from pydantic (#403) * CU-8693qx9yp Deid chunking - hugging face pipeline approach (#405) * Pushing chunking update * Update transformers_ner.py * Pushing update to config Added NER config in cat load function * Update cat.py * Updating chunking overlap * CU-8693qx9yp: Add warning for deid multiprocessing with (potentially) non-functioning chunking window * CU-8693qx9yp: Fix linting issue --------- Co-authored-by: mart-r <mart.ratas@gmail.com> --------- Co-authored-by: Shubham Agarwal <66172189+shubham-s-agarwal@users.noreply.github.com>
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The OPCS4 refset ID in the current version is
1126441000000105. However, in SNOMED2024 it seems to be1382401000000109.So this PR changes the behaviour of the snomed preprocessor.
It also adds a method to convert the ICD10/OPCS4 mappings to direct mapping.
And adds some tests as well.