Bulk FHIR Gen 3 Authorization Tagging - #313

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dsafarian wants to merge 57 commits into

uc-cdis:masterfrom

dsafarian:fhir_transform

Commits on Aug 14, 2026

Added cli/fhir_transform.py and transform_utils.py
dsafarian
committed
fdc70f1
Add fhir_transform cli, utils, and tests
dsafarian
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134df13
Remove unnecessary imports
dsafarian
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92d603e

Commits on Aug 18, 2026

Add documentation, format tests, integrate into gen3 cli, add test_data files
dsafarian
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44940a9
Fix and add tests, create folder even if output_file path doesn't exist
dsafarian
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aab4d54

Commits on Aug 19, 2026

Pass all tests, modify multiprocessing to not cause issues with gen3, remove unecessary dependencies
dsafarian
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c66e855
test md
dsafarian
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404be39
Add fhir.md
dsafarian
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8899bef
Merge branch 'uc-cdis:master' into fhir_transform
dsafarian
authored
2d2e6fe
Black formatting
dsafarian
committed
3f861f6
black formatting
dsafarian
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80f1315

Commits on Aug 22, 2026

Fix pull request comments
dsafarian
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d8ae042
Delete test outputs
dsafarian
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76c6797
Remove setuptools dependency from pyproject.toml
dsafarian
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a34ed6c
Fix pyproject.toml dependencies and poetry.lock
dsafarian
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d929fd2
Remove FIXME
dsafarian
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8e0174c

Commits on Aug 24, 2026

Fix default working directory and directory creation, imports, renamed functions, included more details in --help
dsafarian
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6192216

Commits on Aug 27, 2026

Remove test outputs, fix typos, add assertions, change to SHA-256 hash, update function descriptions
dsafarian
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6b5f319
Fix hash bug
dsafarian
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d00ecf5
Add unit test for global authz and fix tmp_path
dsafarian
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8339418
Comment out all parrallelization code
dsafarian
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9cbf8ba
Remove _resume_run from all code
dsafarian
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8f5eee5
Fix exception handling
dsafarian
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9cdf886
Fix resource_type check
dsafarian
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818c537
Use fhirpathpy.compile instead of fhirpathpy.evaluate for speed up.
dsafarian
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dd2abb2
Add check for if output file exists and is not empty for _is_new.
dsafarian
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157eb94

Commits on Aug 28, 2026

Fix poetry dependencies
dsafarian
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d7773f6

Commits on Aug 29, 2026

Commits on Aug 31, 2026

Black formatting
dsafarian
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a9a0418
fix(drsclient): remove dep due to out of date sub-deps, implement DRS through API instead
Avantol13
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7b942b0

Commits on Sep 1, 2026

Merge branch 'master' into fhir_transform
Avantol13
authored
69279e0

Commits on Sep 2, 2026

Update docs/howto/fhir.md

dsafarian
and
Avantol13
authored
df146ee
Update fhir.md
dsafarian
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ece2a0a
Update fhir.md
dsafarian
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3d340b2
Update fhir.md
dsafarian
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8b86006
Fix commands for optional fhir import
dsafarian
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50ae4e1
Fix paths in .config.json for fhir unit test and the pyproject.toml
dsafarian
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d248015
Black formatting
dsafarian
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0591c06

Commits on Sep 16, 2026

Update tests/test_fhir_transform.py

dsafarian
and
Avantol13
authored
2cb7ec9
Update gen3/cli/fhir.py

dsafarian
and
Avantol13
authored
202bfd9
Add tagger fixture
dsafarian
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3429568
Add fixture for tagger
dsafarian
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99fef2d
Update gen3/fhir.py custom hook annotation

dsafarian
and
Avantol13
authored
bc78b45
Add more details to fhir.md
dsafarian
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b27d551
Add more details to fhir.md
dsafarian
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a4ad290
Fix ImportError in cli/__main__.py
dsafarian
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d44d5f6
Update gen3/fhir.py

dsafarian
and
Avantol13
authored
a2e9e1e
Fix quote style in test_fhir_transform.py
dsafarian
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d265955
Fix quote style in test_fhir_transform.py
dsafarian
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eb53cb9
Fix status class tests, remove __init__
dsafarian
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eb51c1c
Fix status class tests, remove __init__
dsafarian
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ae3e632
Remove pytest argument for test_merge_needed_overlap
dsafarian
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de5eab1
Add --work_dir flag to cli tests
dsafarian
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b2cd806
Fix cleanup_fhir_transform_artifacts return and doc string
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ce83e86
Fix/add hint typing and doc string where missing
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c427e80
Change version to 5.0.0 and remove python 3.9 from dependencies and tests
dsafarian
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cf86e7e