omop-cdm

omop-cdm is a Python package that contains SQLAlchemy declarative table definitions of several versions of the OHDSI OMOP CDM.

Installation

omop-cdm requires Python >= 3.9.

Install from PyPI:

pip install omop-cdm

Usage

See User documentation

Supported databases

The omop-cdm table definitions are tested to be compatible with PostgreSQL.

Though not officially supported, omop-cdm doesn't use postgres-specific features of SQLAlchemy, so it can likely be used for other database types as well.

CDM versions

omop-cdm contains table defintions for the following CDM versions:

• CDM 5.4
• CDM 5.3.1
• CDM 6.0.0 (not recommended)

Development

Setup steps

• Make sure Poetry is installed.
• Install the project and dependencies via poetry install.
• Set up the pre-commit hook scripts via poetry run pre-commit install.

Nox sessions

Several developer actions (e.g. run tests, code format, lint) are available via nox sessions. For a complete list, run:

nox --list

Releasing

omop-cdm uses semantic versioning.

Releases should be made from the main branch. Before creating a release on GitHub, make sure the CHANGELOG has been updated and the version number in pyproject.toml is correct.

Once the GitHub release has been made, the package will be automatically uploaded to PyPI (via the publish.yml workflow).