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Standalone MCP server (FastMCP) exposing PhenEx cohort-building tools to AI agents. Ported from ____OLD____MCP____PHENEX with protocol drafting functionality removed — cohort tools only. 15 tools: phenotype registry (list/spec derived from class introspection), codelist browsing (configurable CSV directory), cohort validation/ translation/execution, and Snowflake data exploration (7 tools). 3 prompts: explore_phenotypes, explore_snowflake_data, design_cohort. Includes launch scripts (stdio + HTTP), mcp.json config, LLM instructions with self-learning guidance, and .env.example template.
get_phenotype_spec now includes full dict schemas for supporting classes (filters, values, date helpers, Codelist) directly inline on each parameter that references them. Recursively resolves the full construction tree so LLMs can build valid serialized objects without cross-referencing separate documentation. Also fixes _extract_parameters to handle factory functions (DateFilter is a function, not a class).
Document how to copy llm-instructions.md into each client's system prompt (Claude Desktop, VS Code Copilot, Cursor).
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MCP server for phenex for use with coding clients.