Bulk FHIR Gen 3 Authorization Tagging by dsafarian · Pull Request #313 · uc-cdis/gen3sdk-python

dsafarian · 2026-08-19T18:22:38Z

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

…ta files

… remove unecessary dependencies

Avantol13 · 2026-08-20T16:26:02Z

 cdisutilstest = { git = "https://github.com/uc-cdis/cdisutils-test.git", tag = "2.0.0" }
 indexd = { git = "https://github.com/uc-cdis/indexd.git", tag = "5.0.4" }
 deptry = "^0.23.1"
+setuptools = "<82"


why was this necessary? let's try without it

Avantol13 · 2026-08-20T16:27:10Z

+
+`gen3 fhir --help`
+
+For example, the following tags the 'Patient.ndjson' file with Gen3 authorization and outputs 'gen3_Patient.ndjson' using the authorization rules from 'config.yaml'


can you add some more details about the configuration and how to configure different rules?

Avantol13 · 2026-08-20T16:33:08Z

let's add a README.md to this test_data directory that explains that this is all synthetic data generated

and clarify which FHIR implementation guide / model. I assume this is the default FHIR model. Did you use a specific FHIR version?

Avantol13 · 2026-08-20T16:40:43Z

+        #                return rule["authz"]
+        for rule in self.rules:
+            match = evaluate(resource, rule["condition"])
+            if match and match[0] is True:  # FIXME: what if multiple conditions match?


for the FIXME: we should maybe log a warning

Avantol13 · 2026-08-20T16:44:33Z

+            resource["meta"]["security"] = []
+
+        gen3_security_tag = {
+            "system": "http://gen3.org/authz",


this path should be configuration or at least a global variable at the top of this file

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…

44940a9

…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

404be39

Add fhir.md

8899bef

Merge branch 'uc-cdis:master' into fhir_transform

2d2e6fe

dsafarian changed the title ~~Fhir transform~~ Bulk FHIR Gen 3 Authorization Tagging Aug 19, 2026

dsafarian added 2 commits August 19, 2026 13:36

Black formatting

3f861f6

black formatting

80f1315