ebi-search-mcp 1.0.1 → 1.0.3

package/README.md

@@ -19,3 +19,5 @@ node dist/index.js
 ```
 
 Data comes from the public Ebi Search API.
+
+

package/dist/api.js

@@ -34,3 +34,54 @@ 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');
+}

package/dist/server.js

@@ -1,7 +1,6 @@
 import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
 import { z } from "zod";
-import { entry } from "./api.js";
-import { search } from "./api.js";
+import { entry, search, domainIndex } from "./api.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 };
@@ -18,7 +17,7 @@ export function createServer() {
             return text(await search(args));
         }
         catch (e) {
-            return textError(error(e));
+            return textError(String(e));
         }
     });
     server.registerTool("entry", {
@@ -31,7 +30,34 @@ export function createServer() {
             return text(await entry(args));
         }
         catch (e) {
-            return textError(error(e));
+            return textError(String(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(String(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) => {
+        // TODO: implement info locally (paywall removed)
+        try {
+            return textError("Not yet implemented: info");
+        }
+        catch (e) {
+            return textError(String(e));
         }
     });
     return server;

package/package.json

@@ -1,5 +1,5 @@
 {
-  "version": "1.0.1",
+  "version": "1.0.3",
   "type": "module",
   "repository": {
     "type": "git",
@@ -42,4 +42,4 @@
     "node": ">=20"
   },
   "mcpName": "io.github.mrfentmen/ebi-search-mcp"
-}
+}