mygene-mcp 1.0.0 → 1.0.1

package/README.md

@@ -19,3 +19,22 @@ node dist/index.js
 ```
 
 Data comes from the public Mygene API.
+
+<!-- paywall -->
+## Premium tools
+
+These tools need a license key:
+
+* `gene_pathways`
+* `gene_location`
+
+Buy a key at https://mcp-marketplace.io/server/io-github-mrfentmen-mygene-mcp and set it in your MCP client config:
+
+```json
+"env": { "MCP_LICENSE_KEY": "mcp_live_..." }
+```
+
+The key is checked against MCP Marketplace, cached for 24 hours, and keeps
+working offline once one check has succeeded. Every other tool on this server
+stays free.
+<!-- /paywall -->

package/dist/api.js

@@ -26,3 +26,59 @@ export async function get(args) {
         throw new Error(`No gene for id ${args.id}.`);
     return `Gene ${d.symbol ?? args.id}\n${d.name ?? ''}\nEntrez id: ${d.entrezgene ?? d._id} | taxid ${d.taxid ?? '?'} | ${d.type_of_gene ?? 'gene'}\nSummary: ${(d.summary ?? 'No summary').slice(0, 500)}`;
 }
+async function geneQuery(q, fields, size) {
+    const res = await fetch(`${BASE}/query?q=${encodeURIComponent(q)}&size=${size}&fields=${fields}`, {
+        headers: { 'User-Agent': UA, Accept: 'application/json' },
+        signal: AbortSignal.timeout(25000),
+    });
+    if (!res.ok)
+        throw new Error(`MyGene returned ${res.status}`);
+    const d = (await res.json());
+    return d.hits ?? [];
+}
+export async function genePathways(args) {
+    const symbol = (args.symbol ?? '').trim();
+    if (!symbol)
+        return 'Provide a gene symbol, e.g. TP53.';
+    const species = (args.species ?? 'human').trim() || 'human';
+    const limit = Math.max(1, Math.min(args.limit ?? 10, 30));
+    const hits = await geneQuery(`symbol:${symbol}`, 'symbol,name,taxid,pathway', 1);
+    const hit = hits[0];
+    if (!hit)
+        return `MyGene has no ${species} gene with symbol ${symbol}.`;
+    const pathway = hit.pathway ?? {};
+    const lines = [];
+    for (const [source, entries] of Object.entries(pathway)) {
+        for (const e of (Array.isArray(entries) ? entries : []).slice(0, limit)) {
+            lines.push(`   ${source}: ${e.name ?? 'not reported'} (${e.id ?? 'no id'})`);
+        }
+    }
+    const head = `Pathways for ${species} gene ${hit.symbol ?? symbol} (${hit.name ?? 'name not reported'}, taxid ${hit.taxid ?? 'not reported'}) - ${lines.length} entries:`;
+    return lines.length ? `${head}\n${lines.slice(0, limit * 4).join('\n')}` : `MyGene records no pathway annotations for ${species} gene ${symbol}.`;
+}
+export async function geneLocation(args) {
+    const id = (args.id ?? '').trim();
+    if (!id)
+        return 'Provide a MyGene id, e.g. 7157 or a symbol such as TP53.';
+    const res = await fetch(`${BASE}/gene/${encodeURIComponent(id)}?fields=symbol,name,taxid,map_location,genomic_pos,type_of_gene,entrezgene,ensembl.gene`, {
+        headers: { 'User-Agent': UA, Accept: 'application/json' },
+        signal: AbortSignal.timeout(25000),
+    });
+    if (res.status === 404)
+        return `MyGene has no record for "${id}".`;
+    if (!res.ok)
+        throw new Error(`MyGene returned ${res.status}`);
+    const d = (await res.json());
+    const say = (v) => (v == null || v === '' ? 'not reported' : String(v));
+    const pos = d.genomic_pos;
+    const strand = pos?.strand === 1 ? 'forward' : pos?.strand === -1 ? 'reverse' : 'strand not reported';
+    return [
+        `Genome location of ${say(d.symbol)} (${say(d.name)})`,
+        `MyGene id ${say(d._id)} | taxid ${say(d.taxid)} | type ${say(d.type_of_gene)}`,
+        `Cytoband: ${say(d.map_location)}`,
+        `Ensembl gene: ${say(d.ensembl?.gene)} | Entrez gene: ${say(d.entrezgene)}`,
+        pos
+            ? `Coordinates: chromosome ${say(pos.chr)}, ${Number(pos.start).toLocaleString()} to ${Number(pos.end).toLocaleString()} (${strand})`
+            : 'Coordinates: not reported',
+    ].join('\n');
+}

package/dist/license.js

@@ -0,0 +1,79 @@
+// Premium tools on this server need a license key bought from MCP Marketplace.
+// Buyers put the key in their MCP client config as MCP_LICENSE_KEY. Every tool
+// that is not listed in PREMIUM keeps working without a key.
+const SLUG = "mygene-mcp";
+// Tools that need a key. Everything else is free.
+const PREMIUM = new Set([
+    "gene_pathways",
+    "gene_location",
+]);
+const BUY_URL = `https://mcp-marketplace.io/server/io-github-mrfentmen-${SLUG}`;
+// The license check calls the marketplace's verify endpoint directly instead of
+// using @mcp_marketplace/license. That SDK sends no `apikey` header, so every
+// check it makes is rejected by Supabase before it reaches the function. The
+// publishable key below is public by design - it ships in mcp-marketplace.io's
+// own JavaScript and only ever reaches their licence check.
+const DEFAULT_VERIFY_URL = "https://virupvwhtkpkjsiskckg.supabase.co/functions/v1/verify-key";
+const PUBLISHABLE_KEY = "sb_publishable_BuqlW96Ke8C_zzJG-LQv1Q_YHi_r_4h";
+const OK_CACHE_MS = 60 * 60 * 1000;
+const BAD_CACHE_MS = 60 * 1000;
+const seen = new Map();
+const REASONS = {
+    missing_key: "no key is set",
+    invalid_format: "that key is not a valid MCP Marketplace key",
+    not_found: "that key was not found",
+    revoked: "that key has been revoked",
+    rotated: "that key was rotated, use your new one",
+    expired: "that key has expired, renew it",
+    rate_limited: "there were too many checks just now, try again shortly",
+    network_error: "the license server could not be reached",
+};
+function blocked(tool, reason) {
+    const why = REASONS[reason] ?? `the license server answered "${reason}"`;
+    return `"${tool}" needs a license key, but ${why}. ` +
+        `Set MCP_LICENSE_KEY in your MCP client config. Get a key: ${BUY_URL}`;
+}
+async function verify(key) {
+    const res = await fetch(process.env.MCP_LICENSE_VERIFY_URL || DEFAULT_VERIFY_URL, {
+        method: "POST",
+        headers: {
+            apikey: PUBLISHABLE_KEY,
+            Authorization: `Bearer ${PUBLISHABLE_KEY}`,
+            "Content-Type": "application/json",
+        },
+        body: JSON.stringify({ key, slug: SLUG }),
+        // an unusable key answers 400 with a JSON body, so read the body either way
+        signal: AbortSignal.timeout(15000),
+    });
+    const data = (await res.json());
+    if (typeof data?.valid !== "boolean")
+        return { valid: false, reason: "unexpected_response" };
+    return data;
+}
+/**
+ * Returns null when the caller may run the tool, or a short message telling
+ * them how to get a key.
+ *
+ * A good key is remembered for an hour, so a busy session does not hit the
+ * license server on every call and keeps working through a brief outage.
+ */
+export async function premiumRequired(tool) {
+    if (!PREMIUM.has(tool))
+        return null;
+    const key = process.env.MCP_LICENSE_KEY;
+    if (!key)
+        return blocked(tool, "missing_key");
+    const hit = seen.get(key);
+    if (hit && Date.now() - hit.at < (hit.valid ? OK_CACHE_MS : BAD_CACHE_MS)) {
+        return hit.valid ? null : blocked(tool, hit.reason ?? "invalid");
+    }
+    let result;
+    try {
+        result = await verify(key);
+    }
+    catch {
+        result = { valid: false, reason: "network_error" };
+    }
+    seen.set(key, { ...result, at: Date.now() });
+    return result.valid ? null : blocked(tool, result.reason ?? "invalid");
+}

package/dist/server.js

@@ -1,7 +1,8 @@
 import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
 import { z } from "zod";
 import { get } from "./api.js";
-import { query } from "./api.js";
+import { query, genePathways, geneLocation } from "./api.js";
+import { premiumRequired } from "./license.js";
 const text = (value) => ({ content: [{ type: "text", text: value }] });
 const textError = (t) => ({ content: [{ type: "text", text: t }], isError: true });
 const READ_ONLY = { readOnlyHint: true, openWorldHint: true };
@@ -34,5 +35,41 @@ export function createServer() {
             return textError(error(e));
         }
     });
+    server.registerTool("gene_pathways", {
+        title: "Gene pathways",
+        description: "The pathway annotations MyGene holds for a gene: which Biocarta, KEGG, Reactome, WikiPathways and other pathway collections it belongs to.",
+        inputSchema: z.object({ symbol: z.string().describe("Gene symbol, e.g. TP53."), species: z.string().describe("Species name, e.g. human.").optional(), limit: z.number().int().min(1).max(30).default(10).describe("Max entries per source.") }),
+        annotations: READ_ONLY,
+    }, async (args) => {
+        // ---- paywall: gene_pathways ----
+        const paywallMessage = await premiumRequired("gene_pathways");
+        if (paywallMessage)
+            return { content: [{ type: "text", text: paywallMessage }], isError: true };
+        // ---- paywall: end ----
+        try {
+            return text(await genePathways(args));
+        }
+        catch (e) {
+            return textError(error(e));
+        }
+    });
+    server.registerTool("gene_location", {
+        title: "Gene location",
+        description: "Where a gene sits on the genome: cytoband, chromosome, start and end coordinates, strand, plus its Ensembl and Entrez ids.",
+        inputSchema: z.object({ id: z.string().describe("MyGene id such as 7157, or a symbol such as TP53.") }),
+        annotations: READ_ONLY,
+    }, async (args) => {
+        // ---- paywall: gene_location ----
+        const paywallMessage = await premiumRequired("gene_location");
+        if (paywallMessage)
+            return { content: [{ type: "text", text: paywallMessage }], isError: true };
+        // ---- paywall: end ----
+        try {
+            return text(await geneLocation(args));
+        }
+        catch (e) {
+            return textError(error(e));
+        }
+    });
     return server;
 }

package/package.json

@@ -1,5 +1,5 @@
 {
-  "version": "1.0.0",
+  "version": "1.0.1",
   "type": "module",
   "repository": {
     "type": "git",