ebi-search-mcp 1.0.0 → 1.0.2

package/README.md

@@ -19,3 +19,21 @@ node dist/index.js
 ```
 
 Data comes from the public Ebi Search API.
+
+<!-- paywall -->
+## Premium tools
+
+These tools need a license key:
+
+* `domain_info`
+
+Buy a key at https://mcp-marketplace.io/server/io-github-mrfentmen-ebi-search-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

@@ -34,3 +34,80 @@ export async function entry(args) {
     const fields = (d.fields ?? []).slice(0, 15).map((f) => `* ${f.name ?? '?'}: ${(f.value ?? '').slice(0, 120)}`);
     return `Entry ${d.id} (${d.source ?? args.domain}):\n` + fields.join('\n');
 }
+async function explainFailure(res) {
+    let why = `HTTP ${res.status}`;
+    try {
+        const body = (await res.json());
+        if (body?.diagnostics?.message)
+            why = body.diagnostics.message;
+    }
+    catch {
+        // the body was not JSON, so the status code is the only reason we have
+        why = `HTTP ${res.status}`;
+    }
+    return why;
+}
+async function getEbi(url) {
+    const res = await fetch(url, {
+        headers: { 'User-Agent': UA, Accept: 'application/json' },
+        signal: AbortSignal.timeout(25000),
+    });
+    if (!res.ok)
+        throw new Error(`EBI Search said ${await explainFailure(res)}`);
+    return res.json();
+}
+export async function domainIndex(_args = {}) {
+    const data = (await getEbi(`${BASE}?format=json`));
+    const roots = data.domains ?? [];
+    if (!roots.length)
+        throw new Error('EBI Search returned no domains.');
+    const nodes = [];
+    const walk = (node, depth) => {
+        const entry = { id: node.id, name: node.name ?? '', depth, descendants: 0 };
+        nodes.push(entry);
+        for (const child of node.subdomains ?? [])
+            entry.descendants += 1 + walk(child, depth + 1);
+        return entry.descendants;
+    };
+    for (const root of roots)
+        walk(root, 0);
+    const at = (depth) => nodes.filter((n) => n.depth === depth);
+    const lines = [
+        `EBI Search holds ${nodes.length} domains in one tree, ${nodes.length - roots.length} of them below the top level.`,
+    ];
+    for (const root of at(0))
+        lines.push(`${root.id}${root.name ? ` (${root.name})` : ''}`);
+    lines.push('  the groups directly below it:');
+    for (const group of at(1)) {
+        lines.push(`    ${group.id}${group.name ? ` (${group.name})` : ''}: ${group.descendants} domain(s) inside`);
+    }
+    const deepest = nodes.reduce((max, n) => Math.max(max, n.depth), 0);
+    lines.push(`  the tree is ${deepest + 1} level(s) deep; pass any of these ids to the search or entry tool.`);
+    return lines.join('\n');
+}
+export async function domainInfo(args) {
+    const domain = (args.domain ?? '').trim().toLowerCase();
+    if (!domain)
+        throw new Error('Provide a domain id like uniprot or ensembl.');
+    const data = (await getEbi(`${BASE}/${encodeURIComponent(domain)}?format=json`));
+    const d = (data.domains ?? [])[0];
+    if (!d)
+        throw new Error(`EBI Search did not describe a domain called "${domain}".`);
+    const infos = (d.indexInfos ?? []).slice(0, 12).map((i) => `    ${i.name ?? '?'}: ${i.value ?? ''}`);
+    const fields = d.fieldInfos ?? [];
+    const searchable = fields.filter((f) => (f.options ?? []).some((o) => o.name === 'searchable' && o.value === 'true'));
+    const lines = [
+        `${d.id}${d.name ? ` - ${d.name}` : ''}`,
+        d.description ? `  ${d.description.slice(0, 300)}` : '  no description reported',
+        '  what EBI Search reports about this index:',
+        ...infos,
+        `  fields in the index: ${fields.length}, of which ${searchable.length} are marked searchable`,
+        ...searchable.slice(0, 10).map((f) => `    ${f.id ?? '?'}`),
+    ];
+    if (searchable.length > 10)
+        lines.push(`    and ${searchable.length - 10} more`);
+    if (!fields.length)
+        lines.push('  the index reported no field list.');
+    lines.push(`  query it with the search tool and the domain "${d.id}", or read one record with the entry tool.`);
+    return lines.join('\n');
+}

package/dist/license.js

@@ -0,0 +1,78 @@
+// 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 = "ebi-search-mcp";
+// Tools that need a key. Everything else is free.
+const PREMIUM = new Set([
+    "domain_info",
+]);
+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 { entry } from "./api.js";
-import { search } from "./api.js";
+import { search, domainIndex, domainInfo } 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 +35,36 @@ export function createServer() {
             return textError(error(e));
         }
     });
+    server.registerTool("domain_index", {
+        title: "Domain index",
+        description: "The whole tree of databases EBI Search can query, with how many domains sit inside each group, so a caller can see what is searchable instead of guessing a domain name.",
+        inputSchema: z.object({}),
+        annotations: READ_ONLY,
+    }, async (args) => {
+        try {
+            return text(await domainIndex());
+        }
+        catch (e) {
+            return textError(error(e));
+        }
+    });
+    server.registerTool("domain_info", {
+        title: "Domain info",
+        description: "One database's own facts: the entry count and release dates EBI Search reports for it, and which of its fields are searchable. The search tool only returns results, it never describes the domain.",
+        inputSchema: z.object({ domain: z.string().describe("A domain id from the domain index, like uniprot, ensembl or literature.") }),
+        annotations: READ_ONLY,
+    }, async (args) => {
+        // ---- paywall: domain_info ----
+        const paywallMessage = await premiumRequired("domain_info");
+        if (paywallMessage)
+            return { content: [{ type: "text", text: paywallMessage }], isError: true };
+        // ---- paywall: end ----
+        try {
+            return text(await domainInfo(args));
+        }
+        catch (e) {
+            return textError(error(e));
+        }
+    });
     return server;
 }

package/package.json

@@ -1,5 +1,5 @@
 {
-  "version": "1.0.0",
+  "version": "1.0.2",
   "type": "module",
   "repository": {
     "type": "git",

package/server.json

@@ -6,12 +6,12 @@
     "url": "https://github.com/mrfentmen/ebi-search-mcp",
     "source": "github"
   },
-  "version": "1.0.0",
+  "version": "1.0.1",
   "packages": [
     {
       "registryType": "npm",
       "identifier": "ebi-search-mcp",
-      "version": "1.0.0",
+      "version": "1.0.1",
       "transport": {
         "type": "stdio"
       }