pyomop
Verified Safeby dermatologist
Overview
Facilitates OHDSI OMOP Common Data Model (CDM) database interactions, including schema management, data loading (FHIR, Eunomia), querying, and export, with optional LLM-based natural language interfaces.
Installation
pyomop-mcp-serverEnvironment Variables
- PYOMOP_DB
- PYOMOP_HOST
- PYOMOP_PORT
- PYOMOP_USER
- PYOMOP_PW
- PYOMOP_SCHEMA
- EUNOMIA_DATA_FOLDER
- PYHEALTH_DATA_FOLDER
- GOOGLE_GENAI_API_KEY
Security Notes
The system uses default database credentials (e.g., 'root/pass' for MySQL, 'postgres/mypass' for PostgreSQL) if environment variables are not set. These are suitable for development/testing but pose a significant risk in production. The 'run_sql' MCP tool executes raw SQL generated by an LLM agent; while 'sqlalchemy.text()' is used to mitigate basic SQL injection, it trusts the LLM's output, creating an inherent risk if the LLM or its input is compromised.
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