assay-mcp-server 1.0.0

package/LICENSE

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+MIT License
+
+Copyright (c) 2026 Cirrusly Clever
+
+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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+# Assay MCP Server
+
+Connect Claude Desktop to your [Assay](https://assay.cirrusly-clever.com) 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](https://assay.cirrusly-clever.com))
+- Claude Desktop installed
+
+### Install from Source
+
+```bash
+git clone https://github.com/cirruslycurious/assay-mcp-server.git
+cd assay-mcp-server
+npm install
+npm run build
+```
+
+### Global Installation (After Publishing)
+
+```bash
+npm install -g @assay/mcp-server
+```
+
+## Quick Start
+
+**New to Assay MCP?** See the [Complete Setup Guide](./SETUP_GUIDE.md) 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](https://assay.cirrusly-clever.com/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
+
+```json
+{
+  "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
+
+```json
+{
+  "mcpServers": {
+    "assay": {
+      "command": "assay-mcp-server",
+      "args": ["--token", "YOUR_FIREBASE_TOKEN_HERE"]
+    }
+  }
+}
+```
+
+### Using Environment Variable
+
+```json
+{
+  "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](./SETUP_GUIDE.md))
+- Falls back to raw data if API key is missing or invalid
+
+**See the [Complete Setup Guide](./SETUP_GUIDE.md) 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
+
+```bash
+# 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: support@cirrusly-clever.com
+
+---
+
+**Made with ❤️ by [Cirrusly Clever](https://cirrusly-clever.com)**

package/dist/firebase.d.ts

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+/**
+ * Firebase integration using Cloud Function proxies
+ * MCP server is now a thin client that calls Assay Cloud Functions
+ * No Firestore access needed - all handled by backend!
+ */
+/**
+ * Verify Firebase ID token using Firebase Auth REST API
+ */
+export declare function verifyToken(token: string): Promise<{
+    uid: string;
+    email?: string;
+}>;
+/**
+ * Get Claude API key from environment
+ */
+export declare function getClaudeApiKey(): string | undefined;
+/**
+ * Call a Cloud Function with user's ID token
+ */
+export declare function callCloudFunction(functionName: string, data: any, token: string): Promise<any>;
+/**
+ * Firestore wrapper that calls Cloud Functions instead
+ * This maintains the same API so existing code doesn't break
+ */
+export declare function getFirestore(token: string): {
+    collection: (collectionName: string) => {
+        where: (field: string, operator: string, value: any) => {
+            where: (field2: string, operator2: string, value2: any) => {
+                get: () => Promise<{
+                    docs: never[];
+                }>;
+            };
+            get: () => Promise<{
+                docs: never[];
+            }>;
+        };
+        doc: (docId: string) => {
+            get: () => Promise<{
+                exists: boolean;
+                id: string;
+                data: () => {};
+            }>;
+        };
+        get: () => Promise<{
+            docs: never[];
+        }>;
+    };
+};
+/**
+ * Initialize Firebase (no-op for this approach)
+ */
+export declare function initializeFirebase(): void;
+//# sourceMappingURL=firebase.d.ts.map

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package/dist/firebase.js

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+/**
+ * Firebase integration using Cloud Function proxies
+ * MCP server is now a thin client that calls Assay Cloud Functions
+ * No Firestore access needed - all handled by backend!
+ */
+const ASSAY_FUNCTIONS_BASE_URL = process.env.ASSAY_FUNCTIONS_BASE_URL ||
+    'https://us-east4-pdfsummaries.cloudfunctions.net';
+// Firebase Web API key for token verification
+// This is a PUBLIC API key (Firebase Web API keys are designed to be public)
+// Security is provided by API restrictions in Google Cloud Console, not by keeping it secret
+// Users can override with FIREBASE_API_KEY env var if they want to use their own Firebase project
+const FIREBASE_API_KEY = process.env.FIREBASE_API_KEY ||
+    'AIzaSyBBq7eyl1vvcZWTdM1CmnPjlcX0OEsr5Ws';
+/**
+ * Verify Firebase ID token using Firebase Auth REST API
+ */
+export async function verifyToken(token) {
+    try {
+        const response = await fetch(`https://identitytoolkit.googleapis.com/v1/accounts:lookup?key=${FIREBASE_API_KEY}`, {
+            method: 'POST',
+            headers: {
+                'Content-Type': 'application/json',
+            },
+            body: JSON.stringify({ idToken: token }),
+        });
+        if (!response.ok) {
+            const errorData = (await response.json().catch(() => ({})));
+            throw new Error(`Token verification failed: ${errorData.error?.message || response.statusText}`);
+        }
+        const data = (await response.json());
+        if (!data.users || data.users.length === 0) {
+            throw new Error('Invalid token: no user found');
+        }
+        const user = data.users[0];
+        return {
+            uid: user.localId,
+            email: user.email,
+        };
+    }
+    catch (error) {
+        throw new Error(`Token verification failed: ${error instanceof Error ? error.message : String(error)}`);
+    }
+}
+/**
+ * Get Claude API key from environment
+ */
+export function getClaudeApiKey() {
+    return process.env.CLAUDE_API_KEY || process.env.ANTHROPIC_API_KEY;
+}
+/**
+ * Call a Cloud Function with user's ID token
+ */
+export async function callCloudFunction(functionName, data, token) {
+    // Include Claude API key if available
+    const claudeApiKey = getClaudeApiKey();
+    if (claudeApiKey) {
+        data.claudeApiKey = claudeApiKey;
+    }
+    const url = `${ASSAY_FUNCTIONS_BASE_URL}/${functionName}`;
+    const response = await fetch(url, {
+        method: 'POST',
+        headers: {
+            'Authorization': `Bearer ${token}`,
+            'Content-Type': 'application/json',
+        },
+        body: JSON.stringify({ data }),
+    });
+    if (!response.ok) {
+        const errorText = await response.text();
+        let errorData;
+        try {
+            errorData = JSON.parse(errorText);
+        }
+        catch {
+            errorData = { error: { message: errorText } };
+        }
+        throw new Error(`Cloud Function ${functionName} failed: ${errorData.error?.message || response.statusText} (${response.status})`);
+    }
+    const result = (await response.json());
+    // Firebase Callable Functions return { result: ... } or { error: ... }
+    if (result.error) {
+        throw new Error(`Cloud Function error: ${result.error.message || JSON.stringify(result.error)}`);
+    }
+    return result.result;
+}
+/**
+ * Firestore wrapper that calls Cloud Functions instead
+ * This maintains the same API so existing code doesn't break
+ */
+export function getFirestore(token) {
+    return {
+        collection: (collectionName) => ({
+            where: (field, operator, value) => ({
+                where: (field2, operator2, value2) => ({
+                    get: async () => {
+                        // This is a simplified wrapper - actual queries go through Cloud Functions
+                        // For now, return empty - individual tools will call Cloud Functions directly
+                        return { docs: [] };
+                    },
+                }),
+                get: async () => {
+                    return { docs: [] };
+                },
+            }),
+            doc: (docId) => ({
+                get: async () => {
+                    return { exists: false, id: docId, data: () => ({}) };
+                },
+            }),
+            get: async () => {
+                return { docs: [] };
+            },
+        }),
+    };
+}
+// callCloudFunction is already exported above
+/**
+ * Initialize Firebase (no-op for this approach)
+ */
+export function initializeFirebase() {
+    // No initialization needed - we use Cloud Functions
+}
+//# sourceMappingURL=firebase.js.map

package/dist/firebase.js.map

@@ -0,0 +1 @@
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package/dist/index.d.ts

@@ -0,0 +1,3 @@
+#!/usr/bin/env node
+export {};
+//# sourceMappingURL=index.d.ts.map

package/dist/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":""}