miEAA3 MCP Server

//------------------------------------------------------------- // FORCE IPv4 DNS //------------------------------------------------------------- import dns from "dns"; dns.setDefaultResultOrder("ipv4first"); // ---------------- ERROR WRAPPER ---------------- export function formatMiEAAError(msg) { return { success: false, error: msg }; } // ============================================================= // 1. FETCH CATEGORY NAMES // ============================================================= export async function fetchMiEAACategories(species, inputType) { const url = `https://ccb-compute2.cs.uni-saarland.de/mieaa/api/v1/enrichment_categories/${species}/${inputType}/`; try { const res = await fetch(url); const json = await res.json(); if (!res.ok || !json.categories) { return formatMiEAAError("Failed to fetch categories"); } const ids = json.categories.map((pair) => pair[0]); const map = {}; ids.forEach((id, i) => { map[i + 1] = id; }); return { ids, map }; } catch (err) { return formatMiEAAError(`CATEGORY FETCH ERROR: ${err?.message}`); } } // ============================================================= // 2. START MI-EAA JOB // ============================================================= export async function startMiEAAJob(body, species, input_type, analysis_type) { const url = `https://ccb-compute2.cs.uni-saarland.de/mieaa/api/v1/enrichment_analysis/${species}/${input_type}/${analysis_type}/`; try { const res = await fetch(url, { method: "POST", headers: { "Content-Type": "application/json" }, body: JSON.stringify(body) }); const json = await res.json(); if (!res.ok || !json.job_id) { return formatMiEAAError("Failed to start job"); } return { job_id: json.job_id }; } catch (err) { return formatMiEAAError(`START FETCH ERROR: ${err?.message}`); } } // ============================================================= // 3. FETCH MI-EAA RESULTS (ORA + GSEA AUTO-DETECT) // ============================================================= export async function fetchMiEAAResults(jobId) { const url = `https://ccb-compute2.cs.uni-saarland.de/mieaa/api/v1/enrichment_analysis/results/${jobId}/`; const LIMIT = 10; // Poll results for up to 120 seconds for (let attempt = 0; attempt < 120; attempt++) { try { const res = await fetch(url); const raw = await res.json(); // Still processing → retry if (Array.isArray(raw) && raw.length === 0) { await new Promise(r => setTimeout(r, 1000)); continue; } // ------------------------------------------------------------ // ORA FORMAT → single flat array of rows // ------------------------------------------------------------ if (Array.isArray(raw)) { const grouped = {}; for (const row of raw) { if (!Array.isArray(row) || row.length < 9) continue; const category = row[0]; if (!grouped[category]) grouped[category] = []; grouped[category].push({ category: row[0], term: row[1], direction: row[2], p_value: row[3], adj_p_value: row[4], score: row[5], hits: row[7], mirnas: row[8] }); } for (const key of Object.keys(grouped)) { grouped[key] = grouped[key].slice(0, LIMIT); } return grouped; } // ------------------------------------------------------------ // OBJECT FORMAT (ORA or GSEA) // ------------------------------------------------------------ if (typeof raw === "object" && raw !== null) { // WRAPPED GSEA: { Enrichment_Results: {...} } if (raw.Enrichment_Results) { const out = {}; for (const cat of Object.keys(raw.Enrichment_Results)) { const rows = raw.Enrichment_Results[cat]; if (!Array.isArray(rows)) continue; out[cat] = rows.slice(0, LIMIT).map(r => ({ category: cat, term: r.term ?? r.name ?? "", direction: r.direction ?? "", es: r.es, nes: r.nes, p_value: r.p_value, adj_p_value: r.adj_p_value, leading_edge: r.leading_edge, mirnas: r.mirnas })); } return out; } // UNWRAPPED GSEA: { category: [ {term:...} ] } const looksLikeGSEA = Object.values(raw).some(v => Array.isArray(v) && typeof v[0] === "object"); const out = {}; for (const cat of Object.keys(raw)) { const rows = raw[cat]; if (!Array.isArray(rows)) continue; // GSEA object rows if (looksLikeGSEA && typeof rows[0] === "object") { out[cat] = rows.slice(0, LIMIT).map(r => ({ category: cat, term: r.term ?? r.name ?? "", direction: r.direction ?? "", es: r.es, nes: r.nes, p_value: r.p_value, adj_p_value: r.adj_p_value, leading_edge: r.leading_edge, mirnas: r.mirnas })); } // ORA object-format rows else { out[cat] = rows.slice(0, LIMIT).map(row => ({ category: row[0], term: row[1], direction: row[2], p_value: row[3], adj_p_value: row[4], score: row[5], hits: row[7], mirnas: row[8] })); } } return out; } } catch { // ignore errors and retry } await new Promise(r => setTimeout(r, 1000)); } return formatMiEAAError("Timeout: results never became available."); } // ============================================================= // 4. LIST ENRICHMENT CATEGORIES (DISCOVERY TOOL) // ============================================================= export async function listMiEAACategories(species, entity) { const url = `https://ccb-compute2.cs.uni-saarland.de/mieaa/api/v1/enrichment_categories/${species}/${entity}/`; try { const res = await fetch(url); const json = await res.json(); if (!res.ok) { return formatMiEAAError("Failed to list enrichment categories"); } if (!Array.isArray(json.categories)) { return formatMiEAAError("Invalid category response format"); } return { species, entity, categories: json.categories.map((c, idx) => ({ index: idx + 1, id: c[0], name: c[1] })) }; } catch (err) { return formatMiEAAError(`CATEGORY LIST ERROR: ${err?.message}`); } } // ============================================================= // 5. miRBASE VERSION CONVERTER // ============================================================= export async function convertMiRBaseVersion(args) { const url = "https://ccb-compute2.cs.uni-saarland.de/mieaa/api/v1/mirbase_converter/"; try { const res = await fetch(url, { method: "POST", headers: { "Content-Type": "application/json" }, body: JSON.stringify(args) }); const json = await res.json(); if (!res.ok) { return formatMiEAAError("miRBase conversion failed"); } return json; } catch (err) { return formatMiEAAError(`MIRBASE CONVERTER ERROR: ${err?.message}`); } } // ============================================================= // 6. miRNA ↔ PRECURSOR CONVERTER // ============================================================= export async function convertMirnaPrecursor(args) { const url = "https://ccb-compute2.cs.uni-saarland.de/mieaa/api/v1/mirna_precursor_converter/"; try { const res = await fetch(url, { method: "POST", headers: { "Content-Type": "application/json" }, body: JSON.stringify(args) }); const json = await res.json(); if (!res.ok) { return formatMiEAAError("miRNA/Precursor conversion failed"); } return json; } catch (err) { return formatMiEAAError(`CONVERTER ERROR: ${err?.message}`); } } // ============================================================= // 7. FETCH JOB STATUS // ============================================================= export async function fetchMiEAAJobStatus(jobId) { const url = `https://ccb-compute2.cs.uni-saarland.de/mieaa/api/v1/job_status/${jobId}/`; try { const res = await fetch(url); const json = await res.json(); if (!res.ok) { return formatMiEAAError("Failed to fetch job status"); } return json; } catch (err) { return formatMiEAAError(`JOB STATUS ERROR: ${err?.message}`); } } // ============================================================= // 8. FETCH JOB RESULTS (DIRECT) // ============================================================= export async function fetchMiEAAJobResultsDirect(jobId) { const url = `https://ccb-compute2.cs.uni-saarland.de/mieaa/api/v1/enrichment_analysis/results/${jobId}/`; try { const res = await fetch(url); const json = await res.json(); if (!res.ok) { return formatMiEAAError("Failed to fetch job results"); } return json; } catch (err) { return formatMiEAAError(`JOB RESULT ERROR: ${err?.message}`); } } //# sourceMappingURL=mieaa.js.map