FastOMOP Evaluation and Monitoring

This project is a work in progress.

foem (FastOMOP Evaluation and Monitoring) is a Python toolkit for evaluating and monitoring OMOP (Observational Medical Outcomes Partnership) databases. It automates SQL test generation, template-based query construction, and result aggregation for clinical data analysis.

• Automated SQL test generation for OMOP databases
• Template-based query construction for common clinical questions
• PostgreSQL connection management
• Outputs results in JSON format
• Easily extensible with new tests and templates

• Python 3.8+
• PostgreSQL database
• Python packages: psycopg2 (or psycopg2-binary), python-dotenv

# (Optional) create & activate a virtual environment
python -m venv .venv
source .venv/bin/activate  # Windows: .venv\Scripts\activate

# Install dependencies
pip install psycopg2-binary python-dotenv

Create a .env file at the project root:

DB_CONNECTION_STRING=postgresql://USER:PASSWORD@HOST:PORT/DBNAME

Run the predefined SQL tests and write results to dataset.json:

python main.py

Extend/customize:

• Add/modify tests in validator.py
• Add/modify templates in template.py

• main.py — Entry point for running tests and writing output
• validator.py — SQL test logic and database interaction
• template.py — Query templates for OMOP concepts
• config.py — Database connection setup
• dataset.json — Results of executed tests

See LICENSE for details.