Skip to content

Bulk FHIR Gen 3 Authorization Tagging - #313

Open
dsafarian wants to merge 16 commits into
uc-cdis:masterfrom
dsafarian:fhir_transform
Open

Bulk FHIR Gen 3 Authorization Tagging #313
dsafarian wants to merge 16 commits into
uc-cdis:masterfrom
dsafarian:fhir_transform

Conversation

@dsafarian

Copy link
Copy Markdown

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

@dsafarian dsafarian changed the title Fhir transform Bulk FHIR Gen 3 Authorization Tagging Aug 19, 2026
Comment thread pyproject.toml
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"

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

why was this necessary? let's try without it

Copy link
Copy Markdown
Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

  1. Pytest version needs to be update to at least 7+
  2. If I don't pin setuptools version, and it installs version 84, I get this error:
    gen3sdk-python/tests/conftest.py'.
    tests/conftest.py:11: in
    from drsclient.client import DrsClient
    ../../../Library/Caches/pypoetry/virtualenvs/gen3-x8jGTXip-py3.13/lib/python3.13/site-packages/drsclient/init.py:1: in
    import pkg_resources
    E ModuleNotFoundError: No module named 'pkg_resources'

Copy link
Copy Markdown
Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

and in the original gen3sdk poetry lock there is this, so I think the setuptools verion has to be below 82 in the way it is written now:
[[package]]
name = "setuptools"
version = "80.9.0"
description = "Easily download, build, install, upgrade, and uninstall Python packages"
optional = false
python-versions = ">=3.9"
groups = ["main", "dev"]
files = [
{file = "setuptools-80.9.0-py3-none-any.whl", hash = "sha256:062d34222ad13e0cc312a4c02d73f059e86a4acbfbdea8f8f76b28c99f306922"},
{file = "setuptools-80.9.0.tar.gz", hash = "sha256:f36b47402ecde768dbfafc46e8e4207b4360c654f1f3bb84475f0a28628fb19c"},
]

Comment thread docs/howto/fhir.md
Comment thread docs/howto/fhir.md
Comment thread gen3/cli/fhir.py Outdated
Comment thread tests/test_data/fhir_config.yaml
Comment thread tests/test_fhir_transform.py Outdated
Comment thread gen3/fhir.py Outdated
Comment thread gen3/fhir.py Outdated
Comment thread gen3/fhir.py Outdated
Comment thread gen3/fhir.py Outdated
Comment thread gen3/fhir.py Outdated
Comment thread gen3/fhir.py Outdated
Comment thread gen3/fhir.py Outdated
Comment thread gen3/fhir.py Outdated
Comment thread gen3/fhir.py Outdated
Comment thread gen3/fhir.py Outdated
Comment thread gen3/fhir.py Outdated
Comment thread gen3/fhir.py Outdated
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

2 participants