@pipeworx/mcp-pride 0.1.0

package/LICENSE

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+MIT License
+
+Copyright (c) 2026 Pipeworx
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

package/README.md

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+# mcp-pride
+
+EBI PRIDE Archive MCP — proteomics (mass-spectrometry) data repository.
+
+Part of [Pipeworx](https://pipeworx.io) — an MCP gateway connecting AI agents to 823+ live data sources.
+
+## Tools
+
+| Tool | Description |
+|------|-------------|
+
+## Quick Start
+
+Add to your MCP client (Claude Desktop, Cursor, Windsurf, etc.):
+
+```json
+{
+  "mcpServers": {
+    "pride": {
+      "url": "https://gateway.pipeworx.io/pride/mcp"
+    }
+  }
+}
+```
+
+Or connect to the full Pipeworx gateway for access to all 823+ data sources:
+
+```json
+{
+  "mcpServers": {
+    "pipeworx": {
+      "url": "https://gateway.pipeworx.io/mcp"
+    }
+  }
+}
+```
+
+## Using with ask_pipeworx
+
+Instead of calling tools directly, you can ask questions in plain English:
+
+```
+ask_pipeworx({ question: "your question about Pride data" })
+```
+
+The gateway picks the right tool and fills the arguments automatically.
+
+## More
+
+- [All tools and guides](https://github.com/pipeworx-io/examples)
+- [pipeworx.io](https://pipeworx.io)
+
+## License
+
+MIT

package/package.json

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+{
+  "name": "@pipeworx/mcp-pride",
+  "version": "0.1.0",
+  "description": "EBI PRIDE Archive MCP — proteomics (mass-spectrometry) data repository.",
+  "type": "module",
+  "main": "src/index.ts",
+  "types": "src/index.ts",
+  "keywords": ["mcp", "mcp-server", "model-context-protocol", "pipeworx", "pride"],
+  "license": "MIT",
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/pipeworx-io/mcp-pride"
+  },
+  "scripts": {
+    "typecheck": "tsc --noEmit"
+  },
+  "devDependencies": {
+    "typescript": "^5.7.0"
+  }
+}

package/server.json

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+{
+  "$schema": "https://static.modelcontextprotocol.io/schemas/2025-12-11/server.schema.json",
+  "name": "io.github.pipeworx-io/pride",
+  "title": "Pride",
+  "description": "EBI PRIDE Archive MCP — proteomics (mass-spectrometry) data repository.",
+  "version": "0.1.0",
+  "websiteUrl": "https://pipeworx.io/packs/pride",
+  "repository": {
+    "url": "https://github.com/pipeworx-io/mcp-pride",
+    "source": "github"
+  },
+  "remotes": [
+    {
+      "type": "streamable-http",
+      "url": "https://gateway.pipeworx.io/pride/mcp"
+    }
+  ]
+}

package/src/index.ts

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+interface McpToolDefinition {
+  name: string;
+  description: string;
+  inputSchema: {
+    type: 'object';
+    properties: Record<string, unknown>;
+    required?: string[];
+  };
+}
+
+interface McpToolExport {
+  tools: McpToolDefinition[];
+  callTool: (name: string, args: Record<string, unknown>) => Promise<unknown>;
+  meter?: { credits: number };
+  cost?: Record<string, unknown>;
+  provider?: string;
+}
+
+/**
+ * EBI PRIDE Archive MCP — proteomics (mass-spectrometry) data repository.
+ * Keyless. Wraps the public PRIDE Archive REST API (v3).
+ */
+
+
+const BASE = 'https://www.ebi.ac.uk/pride/ws/archive/v3';
+const UA = 'pipeworx/1.0 (+https://pipeworx.io)';
+
+const tools: McpToolExport['tools'] = [
+  {
+    name: 'search_projects',
+    description:
+      'Search EBI PRIDE Archive — the largest public proteomics/mass-spectrometry dataset repository — for projects by keyword (disease, organism, technique, protein, instrument). Returns matching project accessions with title, organisms, diseases, and instruments. Keyless.',
+    inputSchema: {
+      type: 'object',
+      properties: {
+        keyword: { type: 'string', description: 'Free-text search term, e.g. "breast cancer", "SARS-CoV-2", "TMT".' },
+        limit: { type: 'number', description: 'Max results per page (default 20, max 100).' },
+        page: { type: 'number', description: 'Zero-based page index (default 0).' },
+      },
+      required: ['keyword'],
+    },
+  },
+  {
+    name: 'get_project',
+    description:
+      'Get full metadata for one PRIDE Archive proteomics project by accession (e.g. "PXD000001"): title, description, sample-processing and data-processing protocols, organisms, organism parts, diseases, instruments, keywords, and DOI.',
+    inputSchema: {
+      type: 'object',
+      properties: {
+        accession: { type: 'string', description: 'PRIDE project accession, e.g. "PXD000001".' },
+      },
+      required: ['accession'],
+    },
+  },
+];
+
+async function callTool(name: string, args: Record<string, unknown>): Promise<unknown> {
+  try {
+    switch (name) {
+      case 'search_projects':
+        return await searchProjects(args);
+      case 'get_project':
+        return await getProject(args);
+      default:
+        return { error: `Unknown tool: ${name}` };
+    }
+  } catch (err) {
+    return { error: err instanceof Error ? err.message : String(err) };
+  }
+}
+
+async function searchProjects(args: Record<string, unknown>): Promise<unknown> {
+  const keyword = reqStr(args, 'keyword');
+  const limit = clampNum(args.limit, 20, 1, 100);
+  const page = clampNum(args.page, 0, 0, 1_000_000);
+  const url = `${BASE}/search/projects?keyword=${encodeURIComponent(keyword)}&pageSize=${limit}&page=${page}`;
+  const res = await fetch(url, { headers: { Accept: 'application/json', 'User-Agent': UA } });
+  if (!res.ok) return { error: `PRIDE search failed: ${res.status}`, keyword };
+  const data = await safeJson(res);
+  const list = asProjectArray(data);
+  const projects = list.map((p) => ({
+    accession: p.accession ?? null,
+    title: p.title ?? null,
+    submission_date: p.submissionDate ?? null,
+    organisms: nameList(p.organisms),
+    diseases: nameList(p.diseases),
+    instruments: nameList(p.instruments),
+  }));
+  return { count: projects.length, projects };
+}
+
+async function getProject(args: Record<string, unknown>): Promise<unknown> {
+  const accession = reqStr(args, 'accession');
+  const url = `${BASE}/projects/${encodeURIComponent(accession)}`;
+  const res = await fetch(url, { headers: { Accept: 'application/json', 'User-Agent': UA } });
+  if (!res.ok) return { error: 'project not found', accession };
+  const p = await safeJson(res);
+  if (!p || typeof p !== 'object') return { error: 'project not found', accession };
+  const o = p as Record<string, unknown>;
+  return {
+    accession: o.accession ?? accession,
+    title: o.title ?? null,
+    description: o.projectDescription ?? null,
+    sample_protocol: truncate(o.sampleProcessingProtocol),
+    data_protocol: truncate(o.dataProcessingProtocol),
+    submission_date: o.submissionDate ?? null,
+    publication_date: o.publicationDate ?? null,
+    organisms: nameList(o.organisms),
+    organism_parts: nameList(o.organismParts ?? o.organismsPart),
+    diseases: nameList(o.diseases),
+    instruments: nameList(o.instruments),
+    keywords: nameList(o.keywords),
+    doi: o.doi || null,
+  };
+}
+
+/** PRIDE returns either a bare array or (rarely) a HAL-wrapped object. Prefer the array. */
+function asProjectArray(data: unknown): Record<string, unknown>[] {
+  if (Array.isArray(data)) return data as Record<string, unknown>[];
+  if (data && typeof data === 'object') {
+    const embedded = (data as Record<string, unknown>)._embedded;
+    if (embedded && typeof embedded === 'object') {
+      const vals = Object.values(embedded as Record<string, unknown>);
+      const arr = vals.find((v) => Array.isArray(v));
+      if (Array.isArray(arr)) return arr as Record<string, unknown>[];
+    }
+  }
+  return [];
+}
+
+/**
+ * Normalize an organisms/diseases/instruments/keywords field to a string[].
+ * Search returns plain strings; project detail returns CvParam objects with a `name`.
+ */
+function nameList(v: unknown): string[] {
+  if (!Array.isArray(v)) return [];
+  const out: string[] = [];
+  for (const item of v) {
+    if (typeof item === 'string') {
+      if (item.trim()) out.push(item);
+    } else if (item && typeof item === 'object') {
+      const name = (item as Record<string, unknown>).name;
+      if (typeof name === 'string' && name.trim()) out.push(name);
+    }
+  }
+  return out;
+}
+
+function truncate(v: unknown, max = 600): string | null {
+  if (typeof v !== 'string') return null;
+  return v.length > max ? `${v.slice(0, max)}…` : v;
+}
+
+async function safeJson(res: Response): Promise<unknown> {
+  try {
+    return await res.json();
+  } catch {
+    return null;
+  }
+}
+
+function clampNum(v: unknown, def: number, min: number, max: number): number {
+  const n = typeof v === 'number' ? v : typeof v === 'string' ? Number(v) : NaN;
+  if (!Number.isFinite(n)) return def;
+  return Math.min(max, Math.max(min, Math.floor(n)));
+}
+
+function reqStr(args: Record<string, unknown>, key: string): string {
+  const v = args[key];
+  if (typeof v !== 'string' || !v.trim()) throw new Error(`Required argument "${key}" is missing.`);
+  return v.trim();
+}
+
+export default { tools, callTool, meter: { credits: 1 } } satisfies McpToolExport;

package/tsconfig.json

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+{
+  "compilerOptions": {
+    "target": "ES2022",
+    "module": "ESNext",
+    "moduleResolution": "bundler",
+    "strict": true,
+    "esModuleInterop": true,
+    "skipLibCheck": true,
+    "outDir": "dist",
+    "rootDir": "src",
+    "declaration": true
+  },
+  "include": ["src"]
+}