miEAA3 MCP Server

// src/handlers/mieaa_mirna_handler.ts import { startMiEAAJob, fetchMiEAACategories, fetchMiEAAResults, MiEAAError, MiEAAStartResponse } from "../utils/mieaa.js"; export class MiEAAMirnaHandler { // ----------------------------------------------------- // VALIDATION // ----------------------------------------------------- validate(options: any): string | null { if (!options.mirnas || !Array.isArray(options.mirnas) || options.mirnas.length === 0) { return "mirnas must be a non-empty array"; } if (!["ORA", "GSEA"].includes(options.analysis_type)) { return "analysis_type must be ORA or GSEA"; } if (!options.species) { return "species is required"; } return null; } // ----------------------------------------------------- // BUILD POST BODY // ----------------------------------------------------- buildBody(options: any): any { const testset = options.analysis_type === "ORA" ? options.mirnas.join(",") : options.mirnas.map((m: string) => `${m}:1.0`).join(","); return { testset, categories: options.categories, reference: options.reference_set ?? [], p_adjust: options.p_adjust ?? "BH", adjust_scope: options.p_scope ?? "global", p_value: options.alpha ?? 0.05, min_hits: options.min_hits ?? 2 }; } // ----------------------------------------------------- // PARSE CATEGORY SELECTION // ----------------------------------------------------- parseCategorySelection(selection: string, categories: string[]): string[] { if (!selection || selection === "all") { return categories; } const chosen = new Set<string>(); const parts = selection.split(","); for (let p of parts) { p = p.trim(); if (p.includes("-")) { const [start, end] = p.split("-").map(n => parseInt(n.trim())); for (let i = start; i <= end; i++) { if (categories[i - 1]) chosen.add(categories[i - 1]); } } else { const num = parseInt(p); if (!isNaN(num) && categories[num - 1]) { chosen.add(categories[num - 1]); } } } return Array.from(chosen); } // ----------------------------------------------------- // MAIN EXECUTION // ----------------------------------------------------- async runAnalysis(options: any): Promise<any | MiEAAError> { // Validate const validationError = this.validate(options); if (validationError) return { success: false, error: validationError }; // Auto-load categories if (!options.categories || options.categories.length === 0) { const catResult = await fetchMiEAACategories(options.species, "mirna"); if ("error" in catResult) return catResult; const { ids } = catResult; options.categories = ids; } // Numerically reduce categories const selectedCategories = this.parseCategorySelection( options.category_selection ?? "all", options.categories ); options.categories = selectedCategories; // Build POST body const body = this.buildBody(options); // Start job const startJob: MiEAAStartResponse = await startMiEAAJob( body, options.species, "mirna", options.analysis_type ); if ("error" in startJob) return startJob; const jobId = startJob.job_id; // Log job metadata only to stderr (safe for MCP) console.error(`Job started: ${jobId}`); console.error( `Result URL: https://ccb-compute2.cs.uni-saarland.de/mieaa/api/v1/enrichment_analysis/results/${jobId}/` ); // Retrieve final results return await fetchMiEAAResults(jobId); } }