pyomop
by dermatologist
Overview
A Python library providing tools for managing OMOP Common Data Model databases, including LLM-powered natural language querying, FHIR-to-OMOP data conversion, and PyHealth/PLP compatibility for machine learning pipelines.
Installation
pyomop-mcp-serverEnvironment Variables
- GOOGLE_API_KEY
- OPENAI_API_KEY
- ANTHROPIC_API_KEY
- OPENROUTER_API_KEY
- EUNOMIA_DATA_FOLDER
- PYOMOP_DB
- PYOMOP_HOST
- PYOMOP_PORT
- PYOMOP_USER
- PYOMOP_PW
- PYOMOP_SCHEMA
- PYHEALTH_DATA_FOLDER
- EUNOMIA_DATASETS_URL
- DOCKER_NETWORK
- WEBAPI_HOST_PORT
Security Notes
The MCP server exposes a 'run_sql' tool that directly executes arbitrary SQL statements provided by the client, which is a significant SQL injection vulnerability if the client/agent is not trusted or the server is exposed inappropriately. The 'docker-compose.yml' includes a hardcoded PostgreSQL password ('mypass'), posing a security risk for non-development deployments. The system fetches SQL query examples from external GitHub repositories ('OHDSI/QueryLibrary'), which carries a minor risk if the external source is compromised. Database operations like 'SET FOREIGN_KEY_CHECKS=0' and 'SET session_replication_role = replica' are used for performance during bulk loading; while common, they could lead to data integrity issues if input data is not thoroughly validated.
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