edencehealth / sqlalchemy_omopcdm_modelgen

code generator that powers sqlalchemy_omopcdm

sqlalchemy_omopcdm_modelgen

Repo	URL
GitHub	https://github.com/edencehealth/sqlalchemy_omopcdm_modelgen
Docker Hub	https://hub.docker.com/r/edence/sqlalchemy-omopcdm-modelgen

This repo contains the source code for the tool we use to generate the model files in our edencehealth/sqlalchemy_omopcdm repo.

The source code in this repo is a containerized Python program which:

• downloads the official OHDSI OMOP CDM DDL files
• applies the DDL files to a PostgreSQL database server
• applies edenceHealth custom DDL which adds composite primary keys to the tables that don't have a natural primary key
• uses the tool sqlacodegen to scan that database to generate a Declarative Mapping-based SQLAlchemy 2 model for each table in the OMOP CDM, including primary keys, indexes, and constraints
• rewrites the generated model using libcst to:
  • add doc comments (from the official OMOP CDM documentation website),
  • insert relevant pylint "disable" comments
  • renames the generated base class
• formats the resulting python module with the PSF tools black and isort