Assay MCP Server

Connect Claude Desktop to your Assay document library. Search, explore, and extract knowledge from your research documents directly from Claude conversations.

Overview

The Assay MCP Server provides Claude Desktop with access to your Assay document library through the Model Context Protocol (MCP). It enables Claude to:

• Search your library by themes, keywords, authors, and titles
• Retrieve document summaries (comprehensive, casual, and FAQs)
• Discover related documents using Jaccard similarity
• Explore themes and generate insights
• Compare documents and synthesize FAQs across multiple sources

All tools search both your private and public document collections, giving Claude access to your entire research library.

Features

• 🔍 13 powerful tools for document exploration and analysis
• 🎯 Jaccard similarity scoring for intelligent document matching
• 🔐 Secure authentication via Firebase ID tokens
• 📊 Theme-based organization with 180+ canonical themes
• 🚀 Zero GenAI costs - tools only retrieve data, Claude does the synthesis (or optional server-side synthesis with your API key)
• 🌐 Public + Private - searches across both collections

Installation

Prerequisites

• Node.js 18+
• An Assay account (sign up here)
• Claude Desktop installed

Install from Source

git clone https://github.com/cirruslycurious/assay-mcp-server.git
cd assay-mcp-server
npm install
npm run build

Global Installation (After Publishing)

npm install -g @assay/mcp-server

Quick Start

New to Assay MCP? See the Complete Setup Guide for detailed instructions on:

• Getting your Firebase token
• Optional: Setting up server-side synthesis with Claude API key

Getting Your Firebase Token

1. Visit Assay Dashboard
2. Sign in with Google (if not already signed in)
3. Click the "Get MCP Token" button in the header
4. Copy the token from the dialog

Note: Tokens expire after 1 hour. Generate a new token when needed.

Claude Desktop Configuration

Add the MCP server to your Claude Desktop configuration:

macOS: ~/Library/Application Support/Claude/claude_desktop_config.json
Windows: %APPDATA%\Claude\claude_desktop_config.json
Linux: ~/.config/Claude/claude_desktop_config.json

For Local Installation

{
  "mcpServers": {
    "assay": {
      "command": "node",
      "args": [
        "/absolute/path/to/assay-mcp-server/dist/index.js",
        "--token",
        "YOUR_FIREBASE_TOKEN_HERE"
      ]
    }
  }
}

Replace /absolute/path/to/assay-mcp-server with your actual path, e.g.:

• macOS: /Users/yourname/Documents/assay-mcp-server/dist/index.js
• Linux: /home/yourname/assay-mcp-server/dist/index.js
• Windows: C:\\Users\\yourname\\Documents\\assay-mcp-server\\dist\\index.js

For Global Installation

{
  "mcpServers": {
    "assay": {
      "command": "assay-mcp-server",
      "args": ["--token", "YOUR_FIREBASE_TOKEN_HERE"]
    }
  }
}

Using Environment Variable

{
  "mcpServers": {
    "assay": {
      "command": "assay-mcp-server",
      "env": {
        "ASSAY_FIREBASE_TOKEN": "YOUR_FIREBASE_TOKEN_HERE",
        "CLAUDE_API_KEY": "YOUR_CLAUDE_API_KEY_HERE"
      }
    }
  }
}

Optional Environment Variables:

• FIREBASE_API_KEY - Override Firebase Web API key (default: Assay service key)
  • Only needed if you want to use your own Firebase project
  • Get from: Firebase Console > Project Settings > General > Your apps
• ASSAY_FUNCTIONS_BASE_URL - Override Cloud Functions endpoint (default: https://us-east4-pdfsummaries.cloudfunctions.net)
• CLAUDE_API_KEY - For optional server-side synthesis

⚠️ Optional: Server-Side Synthesis

Server-side synthesis is optional. The MCP server works great without it!

Without API key (Default):

• Tools return raw data from your collection
• Claude Desktop synthesizes responses using the retrieved data
• Zero additional costs - you're already using Claude Desktop

With API key (Optional):

• Tools can return pre-synthesized responses using Claude API
• Requires your own Anthropic API key (set spending limits for safety)
• Add CLAUDE_API_KEY to your config (see Setup Guide)
• Falls back to raw data if API key is missing or invalid

See the Complete Setup Guide for detailed instructions on optional server-side synthesis.

After updating the config file, restart Claude Desktop to load the MCP server.

Available Tools

Search Tools

1. search_documents

Search your library by theme name, author, or document title. Searches both private and public collections.

Example prompts:

• "Search for documents about AI safety"
• "Find papers on zero trust architecture"
• "Show me documents by Anthropic researchers"

2. search_by_author

Search specifically by author name.

Example prompts:

• "Find all documents by Brian Singer"
• "Show me papers from OpenAI researchers"

3. search_by_title

Search by document title keywords.

Example prompts:

• "Find documents with 'red team' in the title"
• "Search for papers titled 'LLM safety'"

4. search_by_keywords

Search in document keywords, key concepts, and key phrases.

Example prompts:

• "Find documents about 'machine learning' and 'neural networks'"
• "Search for 'zero trust' and 'confidential computing'"

Document Retrieval

5. get_document_summary

Get comprehensive, casual, or FAQ summaries for a specific document.

Parameters:

• documentId: The document ID
• summaryType: "comprehensive", "casual", or "faq"

Example prompts:

• "Get the comprehensive summary of document abc123"
• "What's the casual summary for the governance paper?"
• "Show me FAQs for document xyz789"

6. get_similar_documents

Find documents similar to a given document using Jaccard similarity based on theme overlap.

Returns: Similar documents with similarity scores (High ≥35%, Moderate ≥20%, Low <20%)

Example prompts:

• "What documents are similar to document abc123?"
• "Find related papers to the prompt injection document"

Exploration Tools

7. browse_themes

Browse the canonical theme taxonomy. Without a domain, returns all L0 domains with document counts. With a domain, returns L1 themes within that domain.

Example prompts:

• "What themes do I have documents in?"
• "Show me all themes under Cybersecurity"
• "Browse themes in the Artificial Intelligence domain"

8. get_library_insight

Get your AI-generated personalized insight about your research profile.

Example prompts:

• "What does my document collection say about my research interests?"
• "Get my library insight"

Advanced Analysis

9. ask_question

Ask a question about your library. The tool searches for relevant documents and returns their summaries for Claude to synthesize an answer.

With Claude API key: Returns a synthesized answer (server-side).
Without API key: Returns raw document summaries for Claude Desktop to synthesize.

Example prompts:

• "If I wanted to automate Red Team exercises, what should I consider?"
• "What are the key considerations for implementing zero trust?"
• "What do my documents say about AI safety frameworks?"

10. compare_documents

Compare up to 25 documents selected by themes, keywords, or authors. Returns documents sorted by relevance score.

With Claude API key: Returns a synthesized comparison (server-side).
Without API key: Returns raw document summaries for Claude Desktop to synthesize.

Parameters:

• themes: Array of theme IDs (e.g., ["CYBERSECURITY", "ARTIFICIAL_INTELLIGENCE.AI_ARCHITECTURES"])
• keywords: Array of keywords
• authors: Array of author names

Example prompts:

• "Compare documents about AI safety and cybersecurity"
• "Compare papers by Anthropic and OpenAI on AI alignment"

11. produce_faq

Generate FAQs from up to 25 documents selected by themes, keywords, or authors.

With Claude API key: Returns a synthesized FAQ (server-side).
Without API key: Returns raw document FAQs for Claude Desktop to synthesize.

Parameters: Same as compare_documents

Example prompts:

• "Generate FAQs about AI architectures and cybersecurity"
• "Create FAQs from documents about zero trust by these authors"

How It Compares

The Assay MCP Server offers unique advantages over traditional RAG systems and file-based AI assistants:

| Feature | Assay MCP | Traditional RAG | ChatGPT with Files | |---------|-----------|-----------------|-------------------| | Pre-processed summaries | ✅ 3 formats (comprehensive, casual, FAQs) | ❌ Processes on-the-fly | ❌ Processes on-the-fly | | Theme-based organization | ✅ 180 canonical themes | ❌ No structured taxonomy | ❌ No structured taxonomy | | Similarity algorithm | ✅ Jaccard (theme overlap) | Vector embeddings | Vector embeddings | | Multi-format summaries | ✅ Comprehensive, Casual, FAQs | Single format | Single format | | Cost per query | ✅ $0 (Firestore only) | $0.01-0.10 (embeddings + LLM) | Included in subscription | | Conversational interface | ✅ Via Claude Desktop | ✅ Via chat interface | ✅ Native | | Public + Private collections | ✅ Both searchable | ❌ Single collection | ❌ Single collection | | Cross-document analysis | ✅ Compare, synthesize FAQs | Limited | Limited | | Structured metadata | ✅ Authors, dates, keywords | ❌ Unstructured | ❌ Unstructured | | No document storage | ✅ Summaries only | ❌ Stores full documents | ❌ Stores full documents |

Key Advantages

1. Zero-cost queries

• Traditional RAG requires embedding generation and LLM calls for every query
• Assay MCP only queries Firestore (no AI costs)
• Claude does the synthesis (you're already paying for Claude)

2. Pre-processed intelligence

• Documents are analyzed once during upload
• Multiple summary formats available instantly
• No waiting for processing during queries

3. Structured discovery

• 180 canonical themes enable precise filtering
• Jaccard similarity finds documents with shared research areas
• Not just keyword matching - semantic theme understanding

4. Multi-collection access

• Search both your private documents and public collection
• Discover research from other users
• Privacy-respecting (only shows what you have access to)

How It Works

Relevance Scoring

All tools use Jaccard similarity for relevance scoring:

• Themes: Weighted Jaccard (L1 themes = 0.8, L0 domains = 0.2)
• Keywords: Standard Jaccard similarity
• Authors: Standard Jaccard similarity
• Combined: Weighted average (themes = 0.6, keywords = 0.25, authors = 0.15)

Similarity Levels:

• High: ≥35% similarity
• Moderate: ≥20% similarity
• Low: <20% similarity

Data Flow

1. Tool Call: Claude calls an MCP tool with parameters
2. Authentication: Server verifies Firebase ID token
3. Query: Searches Firestore for matching documents
4. Scoring: Calculates Jaccard similarity scores
5. Retrieval: Fetches document summaries and metadata
6. Return: Structured JSON with documents and summaries
7. Synthesis: Claude uses the data to answer questions or generate insights

Privacy & Security

• Token-based authentication: Each request requires a valid Firebase ID token
• User-scoped queries: Only returns documents the user has access to
• Private + Public: Searches both collections but respects visibility settings
• No document storage: Tools only retrieve summaries, not full document content

Development

Setup

# Install dependencies
npm install

# Build TypeScript
npm run build

# Run in development mode
npm run dev -- --token <your-token>

Project Structure

assay-mcp-server/
├── src/
│   ├── index.ts              # Main MCP server entry point
│   ├── firebase.ts           # Firebase REST API integration (no Admin SDK needed!)
│   └── tools/                # Individual tool implementations
│       ├── searchDocuments.ts
│       ├── getDocumentSummary.ts
│       ├── getSimilarDocuments.ts
│       ├── searchByAuthor.ts
│       ├── searchByTitle.ts
│       ├── searchByKeywords.ts
│       ├── getLibraryInsight.ts
│       ├── browseThemes.ts
│       ├── askQuestion.ts
│       ├── compareDocuments.ts
│       ├── produceFaq.ts
│       └── scoringUtils.ts   # Shared scoring functions
├── dist/                     # Compiled JavaScript
└── package.json

Adding New Tools

1. Create a new file in src/tools/
2. Export a Tool definition and implementation function
3. Import and register in src/index.ts
4. Rebuild: npm run build

Troubleshooting

Server Disconnects

• Token expired: Generate a new token from the Assay dashboard (tokens expire after 1 hour)
• Invalid token: Make sure you copied the full token without extra characters
• Path issues: Verify the absolute path in Claude Desktop config is correct

No Results Returned

• Check authentication: Ensure you're signed in to Assay
• Verify documents: Make sure you have documents uploaded and processed
• Check visibility: Public documents are searchable, private documents only by owner

Build Errors

• Node version: Ensure Node.js 18+ is installed
• Dependencies: Run npm install to ensure all packages are installed
• TypeScript: Check tsconfig.json is properly configured

Contributing

Contributions welcome! Please open an issue or submit a pull request.

License

MIT License - see LICENSE file for details

Links

• Assay Web App: https://assay.cirrusly-clever.com
• MCP Documentation: https://modelcontextprotocol.io

Support

For issues, questions, or feature requests:

• Open an issue on GitHub
• Contact: [email protected]

Made with ❤️ by Cirrusly Clever