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 >= 3.8.

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