SQLAlchemy ORM of the OHDSI OMOP CDM
Project description
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
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
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