miEAA3 MCP Server

// // src/handlers/over_representation_analysis.ts // import { // startMiEAAJob, // fetchMiEAACategories, // fetchMiEAAResults, // MiEAAError, // MiEAAStartResponse // } from "../utils/mieaa.js"; // type Entity = "mirna" | "precursor"; // interface ORAOptions { // species: string; // entity: Entity; // ids: string[]; // category_selection?: string; // categories?: string[]; // reference_set?: string[]; // p_adjust?: string; // p_scope?: string; // alpha?: number; // min_hits?: number; // } // export class OverRepresentationAnalysisHandler { // // ----------------------------------------------------- // // VALIDATION // // ----------------------------------------------------- // validate(options: ORAOptions): string | null { // if (!options.species) { // return "species is required"; // } // if (!["mirna", "precursor"].includes(options.entity)) { // return "entity must be 'mirna' or 'precursor'"; // } // if (!options.ids || !Array.isArray(options.ids) || options.ids.length === 0) { // return "ids must be a non-empty array"; // } // return null; // } // // ----------------------------------------------------- // // BUILD POST BODY (ORA ONLY) // // ----------------------------------------------------- // buildBody(options: ORAOptions): any { // const testset = options.ids.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 run(options: ORAOptions): Promise<any | MiEAAError> { // // Validate // const validationError = this.validate(options); // if (validationError) { // return { success: false, error: validationError }; // } // // Auto-fetch categories if needed // if (!options.categories || options.categories.length === 0) { // const catRes = await fetchMiEAACategories( // options.species, // options.entity // ); // if ("error" in catRes) return catRes; // options.categories = catRes.ids; // } // // Apply numeric category selection // options.categories = this.parseCategorySelection( // options.category_selection ?? "all", // options.categories // ); // // Build ORA body // const body = this.buildBody(options); // // Start ORA job (analysis_type is FIXED to ORA) // const startJob: MiEAAStartResponse = await startMiEAAJob( // body, // options.species, // options.entity, // "ORA" // ); // if ("error" in startJob) return startJob; // const jobId = startJob.job_id; // // Log metadata to stderr (MCP-safe) // console.error(`ORA job started: ${jobId}`); // console.error( // `Result URL: https://ccb-compute2.cs.uni-saarland.de/mieaa/api/v1/enrichment_analysis/results/${jobId}/` // ); // // Fetch & return final ORA results // return await fetchMiEAAResults(jobId); // } // } // src/handlers/over_representation_analysis.ts import { startMiEAAJob, fetchMiEAACategories, fetchMiEAAResults } from "../utils/mieaa.js"; export class OverRepresentationAnalysisHandler { // ----------------------------------------------------- // VALIDATION // ----------------------------------------------------- validate(options) { if (!options.species) { return "species is required"; } if (!["mirna", "precursor"].includes(options.entity)) { return "entity must be 'mirna' or 'precursor'"; } if (!options.ids || !Array.isArray(options.ids) || options.ids.length === 0) { return "ids must be a non-empty array"; } return null; } // ----------------------------------------------------- // BUILD POST BODY (ORA ONLY) // ----------------------------------------------------- buildBody(options) { const testset = options.ids.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, categories) { if (!selection || selection === "all") { return categories; } const chosen = new Set(); 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 run(options) { // Validate const validationError = this.validate(options); if (validationError) { return { content: [ { type: "text", text: JSON.stringify({ success: false, error: validationError }) } ], structuredContent: { success: false, error: validationError } }; } // Auto-fetch categories if needed if (!options.categories || options.categories.length === 0) { const catRes = await fetchMiEAACategories(options.species, options.entity); if ("error" in catRes) { return { content: [ { type: "text", text: JSON.stringify(catRes) } ], structuredContent: catRes }; } options.categories = catRes.ids; } // Apply numeric category selection options.categories = this.parseCategorySelection(options.category_selection ?? "all", options.categories); // Build ORA body const body = this.buildBody(options); // Start ORA job (analysis_type is FIXED to ORA) const startJob = await startMiEAAJob(body, options.species, options.entity, "ORA"); if ("error" in startJob) { return { content: [ { type: "text", text: JSON.stringify(startJob) } ], structuredContent: startJob }; } const jobId = startJob.job_id; // Log metadata to stderr (MCP-safe) console.error(`ORA job started: ${jobId}`); console.error(`Result URL: https://ccb-compute2.cs.uni-saarland.de/mieaa/api/v1/enrichment_analysis/results/${jobId}/`); // Fetch final ORA results const results = await fetchMiEAAResults(jobId); // Final MCP-compliant return return { content: [ { type: "text", text: JSON.stringify(results) } ], structuredContent: results }; } } //# sourceMappingURL=over_representation_analysis_handler.js.map