@mrfentmen/uniprot-mcp 0.0.0-stage → 1.0.0

package/README.md

@@ -1,3 +1,34 @@
-# Temporary Holding Version
+# UniProt MCP
 
-This version is a temporary placeholder for this package. An operational version to replace this has been submitted for review and is awaiting a staged release.
+Protein records from the UniProt knowledgebase, with sequences and organism names. Keyless — no signup, no API key, no environment variables.
+
+## Install
+
+```bash
+npx -y @mrfentmen/uniprot-mcp
+```
+
+Or add it to your MCP client:
+
+```json
+{
+  "mcpServers": {
+    "uniprot-mcp": { "command": "npx", "args": ["-y", "@mrfentmen/uniprot-mcp"] }
+  }
+}
+```
+
+## Tools
+
+| Tool | What it does |
+|---|---|
+| `search_proteins` | Search UniProtKB protein records |
+| `get_entry` | Full UniProt record by accession |
+
+## Notes
+
+UniProt's REST service needs no key. Search accepts the full UniProt query syntax, e.g. gene:BRCA1 or organism_id:9606.
+
+## Licence
+
+MIT

package/dist/api.d.ts

@@ -0,0 +1,4 @@
+export declare class UniProtError extends Error {
+}
+export declare function searchProteins(query: string, limit?: number): Promise<string>;
+export declare function getEntry(accession: string): Promise<string>;

package/dist/api.js

@@ -0,0 +1,80 @@
+/**
+ * UniProt — Protein records from the UniProt knowledgebase, with sequences and organism names. Keyless: no signup, no API key, no environment variables.
+ *
+ * Verified live against rest.uniprot.org.
+ */
+const API = "https://rest.uniprot.org";
+export class UniProtError extends Error {
+}
+const val = (v) => {
+    if (typeof v === "string")
+        return v;
+    if (typeof v === "number")
+        return Number.isFinite(v) ? String(v) : "";
+    if (Array.isArray(v))
+        return v.length > 0 ? val(v[0]) : "";
+    if (v && typeof v === "object") {
+        const o = v;
+        if ("en" in o)
+            return val(o.en);
+        const first = Object.values(o)[0];
+        return first === undefined ? "" : val(first);
+    }
+    return "";
+};
+const at = (o, path) => path === "" ? o : path.split(".").reduce((acc, k) => (acc && typeof acc === "object" ? acc[k] : undefined), o);
+const rows = (v) => (Array.isArray(v) ? v : []);
+async function get(url, init, timeoutMs = 25000) {
+    const ctrl = new AbortController();
+    const timer = setTimeout(() => ctrl.abort(), timeoutMs);
+    try {
+        const res = await fetch(url, {
+            ...init,
+            signal: ctrl.signal,
+            headers: { "user-agent": "uniprot-mcp", accept: "application/json", ...(init?.headers ?? {}) },
+        });
+        if (!res.ok)
+            throw new UniProtError(`UniProt returned HTTP ${res.status}`);
+        return (await res.json());
+    }
+    catch (e) {
+        if (e instanceof UniProtError)
+            throw e;
+        if (e.name === "AbortError")
+            throw new UniProtError("UniProt request timed out");
+        throw new UniProtError(`UniProt request failed: ${e.message}`);
+    }
+    finally {
+        clearTimeout(timer);
+    }
+}
+export async function searchProteins(query, limit = 5) {
+    const q = query.trim();
+    if (q === "")
+        throw new UniProtError("query must not be empty");
+    const size = Math.min(50, Math.max(1, limit));
+    const body = await get(`${API}/uniprotkb/search?query=${encodeURIComponent(q)}&size=${size}&format=json&fields=accession,protein_name,organism_name,length`);
+    const items = rows(at(body, "results"));
+    if (items.length === 0)
+        return `UniProt found nothing for "${q}".`;
+    const lines = items.map((r, i) => {
+        const name = val(at(r, "proteinDescription.recommendedName.fullName.value")) || val(at(r, "proteinDescription.submissionNames"));
+        return `${i + 1}. ${val(at(r, "primaryAccession"))} — ${name} (${val(at(r, "organism.scientificName"))}, ${val(at(r, "sequence.length"))} aa)`;
+    });
+    return [`UniProt results for "${q}" — ${items.length} shown`, "", ...lines].join("\n");
+}
+export async function getEntry(accession) {
+    const acc = accession.trim().toUpperCase();
+    if (acc === "")
+        throw new UniProtError("accession must not be empty");
+    const body = await get(`${API}/uniprotkb/${encodeURIComponent(acc)}.json`);
+    const name = val(at(body, "proteinDescription.recommendedName.fullName.value"));
+    return [
+        `${val(at(body, "primaryAccession"))} — ${name}`,
+        "",
+        `Organism: ${val(at(body, "organism.scientificName"))}`,
+        `Length: ${val(at(body, "sequence.length"))} aa`,
+        `Mass: ${val(at(body, "sequence.molWeight"))} Da`,
+        `Reviewed: ${val(at(body, "entryType"))}`,
+    ].join("\n");
+}

package/dist/index.d.ts

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+#!/usr/bin/env node
+export {};

package/dist/index.js

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+#!/usr/bin/env node
+import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js";
+import { createServer } from "./server.js";
+async function main() {
+    const server = createServer();
+    const transport = new StdioServerTransport();
+    await server.connect(transport);
+    console.error("uniprot-mcp running on stdio");
+}
+main().catch((err) => {
+    console.error("Fatal error:", err);
+    process.exit(1);
+});

package/dist/server.d.ts

@@ -0,0 +1,2 @@
+import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+export declare function createServer(): McpServer;

package/dist/server.js

@@ -0,0 +1,26 @@
+import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+import { z } from "zod";
+import { searchProteins, getEntry } from "./api.js";
+const text = (t) => ({ content: [{ type: "text", text: t }] });
+const fail = (t) => ({ content: [{ type: "text", text: t }], isError: true });
+const errorMessage = (e) => `Error: ${e instanceof Error ? e.message : String(e)}`;
+export function createServer() {
+    const server = new McpServer({ name: "uniprot-mcp", version: "1.0.0" });
+    server.tool("search_proteins", "Search UniProtKB protein records", { query: z.string().min(1).describe("UniProt query, e.g. insulin or gene:BRCA1"), limit: z.number().int().min(1).max(50).default(5).describe("How many records") }, async ({ query, limit }) => {
+        try {
+            return text(await searchProteins(query, limit));
+        }
+        catch (e) {
+            return fail(errorMessage(e));
+        }
+    });
+    server.tool("get_entry", "Full UniProt record by accession", { accession: z.string().min(1).describe("UniProt accession, e.g. P01308") }, async ({ accession }) => {
+        try {
+            return text(await getEntry(accession));
+        }
+        catch (e) {
+            return fail(errorMessage(e));
+        }
+    });
+    return server;
+}

package/package.json

@@ -1,6 +1,44 @@
 {
   "name": "@mrfentmen/uniprot-mcp",
-  "version": "0.0.0-stage",
-  "stub": true,
-  "description": "Temporary package placeholder for staged publishing"
-}
+  "version": "1.0.0",
+  "description": "UniProt: protein records, sequences and organism names from the UniProtKB - keyless.",
+  "type": "module",
+  "mcpName": "io.github.mrfentmen/uniprot-mcp",
+  "repository": {
+    "type": "git",
+    "url": "git+https://github.com/mrfentmen/awesome-servers.git"
+  },
+  "bin": {
+    "uniprot-mcp": "./dist/index.js"
+  },
+  "main": "./dist/index.js",
+  "files": [
+    "dist"
+  ],
+  "scripts": {
+    "build": "tsc -p tsconfig.json",
+    "start": "node dist/index.js",
+    "test": "node tests/smoke.mjs"
+  },
+  "keywords": [
+    "mcp",
+    "uniprot",
+    "protein",
+    "biology",
+    "sequences",
+    "science",
+    "keyless"
+  ],
+  "license": "MIT",
+  "dependencies": {
+    "@modelcontextprotocol/sdk": "^1.0.4",
+    "zod": "^3.23.8"
+  },
+  "devDependencies": {
+    "@types/node": "^22.0.0",
+    "typescript": "^5.6.0"
+  },
+  "engines": {
+    "node": ">=20"
+  }
+}