Bulk FHIR Gen 3 Authorization Tagging - #313

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dsafarian wants to merge 39 commits into

uc-cdis:masterfrom

dsafarian:fhir_transform

dsafarian commented Aug 19, 2026 •

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New Features

Bulk FHIR Gen 3 Authorization Tagging (see more details with gen3 fhir --help or in the fhir.md in docs/howto)

Dependency updates

fhirpathpy

Breaking Changes

Drop support for Python 3.9, which has been end-of-life since last year

dsafarian and others added 9 commits

August 14, 2026 08:54


          Added cli/fhir_transform.py and transform_utils.py

fdc70f1


          Add fhir_transform cli, utils, and tests

134df13


          Remove unnecessary imports

92d603e


          Add documentation, format tests, integrate into gen3 cli, add test_da…

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…ta files


          Fix and add tests, create folder even if output_file path doesn't exist

aab4d54


          Pass all tests, modify multiprocessing to not cause issues with gen3,…

c66e855

… remove unecessary dependencies


          test md

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          Add fhir.md

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          Merge branch 'uc-cdis:master' into fhir_transform

2d2e6fe

dsafarian changed the title ~~Fhir transform~~ Bulk FHIR Gen 3 Authorization Tagging

dsafarian added 2 commits

August 19, 2026 13:36


          Black formatting

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          black formatting

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docs/howto/fhir.md

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dsafarian and others added 15 commits

August 27, 2026 10:44


          Remove test outputs, fix typos, add assertions, change to SHA-256 has…

6b5f319

…h, update function descriptions


          Fix hash bug

d00ecf5


          Add unit test for global authz and fix tmp_path


          Comment out all parrallelization code

9cbf8ba


          Remove _resume_run from all code

8f5eee5


          Fix exception handling

9cdf886


          Fix resource_type check

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          Use fhirpathpy.compile instead of fhirpathpy.evaluate for speed up.

dd2abb2


          Add check for if output file exists and is not empty for _is_new.

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          Fix poetry dependencies

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          Remove all parallelization code and make fhir import optional in cli

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          Add helper function for tag_fhir_resources_with_authz and fix tmp_roo…

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…t in the unit tests


          Black formatting

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          fix(drsclient): remove dep due to out of date sub-deps, implement DRS…

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… through API instead


          Merge branch 'master' into fhir_transform

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dsafarian and others added 7 commits

September 2, 2026 17:45


          Update docs/howto/fhir.md

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Co-authored-by: Alexander VanTol <Avantol13@users.noreply.github.com>


          Update fhir.md

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          Update fhir.md

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          Update fhir.md

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          Fix commands for optional fhir import

50ae4e1


          Fix paths in .config.json for fhir unit test and the pyproject.toml

d248015


          Black formatting

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