miEAA3 MCP Server

// ------------------------------------------------------ // FORCE EXTENSION ROOT AS WORKING DIRECTORY // ------------------------------------------------------ import path from "path"; import { fileURLToPath } from "url"; // Resolve the absolute path of this file (dist/server.js) const __filename = fileURLToPath(import.meta.url); const __dirname = path.dirname(__filename); // Force Node to treat /dist as current working directory process.chdir(__dirname); import { MiEAACategoriesHandler } from "./handlers/mieaa_categories_handler.js"; import { MiEAAMirnaPrecursorConverterHandler } from "./handlers/mieaa_mirna_precursor_converter_handler.js"; import { MiEAAMirBaseConverterHandler } from "./handlers/mieaa_mirbase_converter_handler.js"; import { OverRepresentationAnalysisHandler } from "./handlers/over_representation_analysis_handler.js"; console.error(">>> RUNNING dist/server.js <<<"); //------------------------------------------------------ // ERROR HANDLING //------------------------------------------------------ process.on("uncaughtException", (err) => { console.error("UNCAUGHT EXCEPTION:", err); }); process.on("unhandledRejection", (err) => { console.error("UNHANDLED REJECTION:", err); }); console.error("SERVER ENTRY REACHED"); //------------------------------------------------------ // MCP SERVER BOOTSTRAP //------------------------------------------------------ import { Server } from "@modelcontextprotocol/sdk/server/index.js"; import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js"; import { CallToolRequestSchema, ListToolsRequestSchema, InitializeRequestSchema } from "@modelcontextprotocol/sdk/types.js"; //------------------------------------------------------ // Instantiate tool handlers //------------------------------------------------------ const oraTool = new OverRepresentationAnalysisHandler(); const categoryTool = new MiEAACategoriesHandler(); const mirnaPrecursorTool = new MiEAAMirnaPrecursorConverterHandler(); const mirbaseTool = new MiEAAMirBaseConverterHandler(); //------------------------------------------------------ // CREATE MCP SERVER INSTANCE //------------------------------------------------------ const server = new Server( { name: "miEAA3_mcp", version: "1.0.0", }, { capabilities: { tools: {}, sampling: {}, roots: {}, }, } ); //------------------------------------------------------ // INITIALIZE //------------------------------------------------------ server.setRequestHandler(InitializeRequestSchema, async () => { console.error("Initialize handler invoked"); return { protocolVersion: "2025-06-18", serverInfo: { name: "miEAA3_mcp", version: "1.0.0", }, capabilities: { tools: { list: true, call: true }, sampling: {}, roots: {}, } }; }); //------------------------------------------------------ // TOOL LIST //------------------------------------------------------ server.setRequestHandler(ListToolsRequestSchema, async () => { return { tools: [ // ------------------------------------------------- // TOOL 1 — OVER-REPRESENTATION ANALYSIS (ORA) // ------------------------------------------------- { name: "over_representation_analysis", description: "Run miEAA over-representation analysis (ORA) for miRNA or precursor.", inputSchema: { type: "object", properties: { species: { type: "string" }, entity: { type: "string", enum: ["mirna", "precursor"] }, ids: { type: "array", items: { type: "string" } }, category_selection: { type: "string" }, reference_set: { type: "array", items: { type: "string" } }, p_adjust: { type: "string" }, p_scope: { type: "string" }, alpha: { type: "number" }, min_hits: { type: "number" } }, required: ["species", "entity", "ids"] } }, // ------------------------------------------------- // LIST ENRICHMENT CATEGORIES // ------------------------------------------------- { name: "list_enrichment_categories", description: "List available miEAA enrichment categories for a species.", inputSchema: { type: "object", properties: { species: { type: "string" }, entity: { type: "string", enum: ["mirna", "precursor"] } }, required: ["species", "entity"] } }, // ------------------------------------------------- // miRNA ↔ PRECURSOR CONVERTER // ------------------------------------------------- { name: "mirna_precursor_converter", description: "Convert between miRNA names and precursor names.", inputSchema: { type: "object", properties: { input: { type: "array", items: { type: "string" } }, direction: { type: "string", enum: ["mirna_to_precursor", "precursor_to_mirna"] } }, required: ["input", "direction"] } }, // ------------------------------------------------- // miRBASE VERSION CONVERTER // ------------------------------------------------- { name: "mirbase_version_converter", description: "Convert miRNA identifiers between miRBase versions.", inputSchema: { type: "object", properties: { mirnas: { type: "array", items: { type: "string" } }, source_version: { type: "string" }, target_version: { type: "string" } }, required: ["mirnas", "source_version", "target_version"] } } ] }; }); //------------------------------------------------------ // TOOL EXECUTION ROUTER //------------------------------------------------------ server.setRequestHandler(CallToolRequestSchema, async (req) => { const { name, arguments: args } = req.params as { name: string; arguments: Record<string, unknown>; }; try { if (!args || typeof args !== "object") { throw new Error("Tool arguments are required"); } // -------------------------------------------------- // ORA TOOL // -------------------------------------------------- if (name === "over_representation_analysis") { return await oraTool.run(args as any); } // -------------------------------------------------- // CATEGORY LIST // -------------------------------------------------- if (name === "list_enrichment_categories") { return await categoryTool.run(args as { species: string; entity: "mirna" | "precursor"; }); } // -------------------------------------------------- // miRNA ↔ PRECURSOR CONVERTER // -------------------------------------------------- if (name === "mirna_precursor_converter") { return await mirnaPrecursorTool.run({ ids: (args as any).input, direction: (args as any).direction }); } // -------------------------------------------------- // miRBASE VERSION CONVERTER // -------------------------------------------------- if (name === "mirbase_version_converter") { return await mirbaseTool.run({ mirnas: (args as any).mirnas, from_version: (args as any).source_version, to_version: (args as any).target_version }); } throw new Error(`Unknown tool: ${name}`); } catch (err: any) { return { isError: true, content: [ { type: "text", text: `MCP Tool Error: ${err.message || String(err)}` } ] }; } }); //------------------------------------------------------ // SERVER STARTUP //------------------------------------------------------ async function main() { const transport = new StdioServerTransport(); await server.connect(transport); console.error("MCP server connected"); } main().catch(err => { console.error("FATAL:", err); }); // KEEP NODE ALIVE setInterval(() => {}, 1 << 30);