Obsidian Vectorize MCP

A modern, serverless solution for indexing Obsidian notes using Cloudflare's official OAuth 2.1 pattern, Vectorize, and Workers AI, with native Model Context Protocol (MCP) support.

🚀 Key Features

• Cost Effective: ~$0-10/month for typical personal use (250 - 2.5k Notes)

• Affordable Embedding Costs: Workers AI embedding models used - no OpenAI API fees needed

• Official Cloudflare OAuth 2.1: Uses @cloudflare/workers-oauth-provider

• Standards Compliant: Follows MCP v2025-03-26 specification with Streamable HTTP transport

• Global Edge Performance: 300+ locations worldwide

• Serverless Simplicity: No infrastructure management required

• 15-Minute Setup: Get running quickly with simple commands

Related MCP server: MCP Obsidian

🚀 Quick Start

1. Clone & Setup

Note: This project requires git clone to access all necessary configuration files and source code for deployment. Runtime: Node.js 20.3.0 or newer is required because the project now pins Wrangler 4.80.0.

# Clone the repository
git clone https://github.com/ben-vargas/obsidian-vectorize-mcp.git
cd obsidian-vectorize-mcp

# Use the repo's Node version
nvm use || nvm install

# Install dependencies
npm ci

# Optional: install obvec CLI globally
npm install -g .

# Copy and configure your deployable Wrangler config
cp wrangler.toml.example wrangler.toml

# Login to Cloudflare
obvec login

# Create KV namespaces
wrangler kv:namespace create kv
wrangler kv:namespace create oauth_tokens
# Update wrangler.toml with the returned namespace IDs

# Create R2 bucket
wrangler r2 bucket create obsidian-vectorize

# Set your password
wrangler secret put MCP_PASSWORD

2. Deploy & Index

Option A: Deploy to Cloudflare (Recommended)

# Deploy your MCP server
obvec deploy

# Create and configure .env file (required)
cp .env.example .env
# Edit .env with:
# WORKER_URL=https://obvec.<your-cloudflare-subdomain>.workers.dev
# MCP_PASSWORD=your-secure-password-here
# OBSIDIAN_VAULT_PATH=/path/to/your/vault

# Index your vault
obvec index

Option B: Local Development

# Create .dev.vars for local Worker environment
echo "MCP_PASSWORD=your-local-password" > .dev.vars

# Create .env for CLI scripts
cp .env.example .env
# Edit .env with:
# WORKER_URL=http://localhost:8787
# MCP_PASSWORD=your-local-password
# OBSIDIAN_VAULT_PATH=/path/to/vault

# Start local development server
obvec dev

# In another terminal, index your vault
obvec index

3. Connect to MCP Clients

Note about Connectors: Claude.ai uses "Connectors" to integrate with MCP servers. If you add a Connector on claude.ai (Web), it will also appear in Claude Desktop - no additional configuration needed. However, Claude Code requires separate MCP configuration.

claude.ai (Web) & Claude Desktop

On claude.ai, add a custom MCP Connector:

1. Go to Settings → Connectors

2. Click "Add Custom Connector"

3. Enter your MCP endpoint:

   • Streamable HTTP: https://obvec.<account_subdomain>.workers.dev/mcp (recommended - current MCP spec)

   • SSE: https://obvec.<account_subdomain>.workers.dev/sse (deprecated - only use if required)

Note: The MCP specification deprecated SSE on March 26, 2025. We recommend using the Streamable HTTP endpoint.

When you first connect, a browser window will open for OAuth authentication. Enter your password to authorize access. This Connector will automatically sync to your Claude Desktop app.

Claude Code (CLI)

Add via command line:

claude mcp add -s user -t http obvec https://obvec.<account_subdomain>.workers.dev/mcp

Breaking this down:

• claude mcp add - The command to add an MCP server

• -s user - Scope set to "user" (applies to all your projects, not just the current one)

• -t http - Transport type for the new Streamable HTTP protocol

• obvec - The name you want to give the server

• https://obvec.<account_subdomain>.workers.dev/mcp - The URL of your MCP endpoint

Note for Claude Code users: OAuth tokens now default to 30 days to prevent frequent re-authentication. If you still experience timeouts, see troubleshooting.

Manual Claude Desktop Configuration (Optional)

If you prefer to configure Claude Desktop directly instead of using Connectors, add to your claude_desktop_config.json:

{
  "mcpServers": {
    "obvec": {
      "type": "http",
      "url": "https://obvec.<account_subdomain>.workers.dev/mcp"
    }
  }
}

Replace <account_subdomain> with your actual Cloudflare Workers subdomain in all examples.

ChatGPT Integration

Connect your Obsidian vault to ChatGPT as a searchable knowledge source:

1. Add as ChatGPT Connector:

   • Go to ChatGPT Settings → Connectors

   • Add connector with URL: https://obvec.<account_subdomain>.workers.dev/chatgpt/mcp

   • Authenticate via OAuth when prompted

   • Select the connector in any chat where Connectors are supported

2. Basic Configuration:

   # In wrangler.toml
   OBSIDIAN_VAULT_NAME = "YourVaultName"  # For proper Obsidian URL generation
   CHATGPT_MIN_SCORE = "0.3"              # Result threshold (lower = more results)

3. Works with all ChatGPT features where Connectors are available (except GPT-5 Pro mode)

📚 For advanced configuration, QDF support, and troubleshooting, see docs/chatgpt-integration.md

🔐 Authentication & Security

OAuth 2.1 Flow

• Standards Compliant: Uses Cloudflare's official OAuth Provider Library

• PKCE Security: Proof Key for Code Exchange for enhanced security

• Simple Setup: One password via wrangler secret put MCP_PASSWORD

• MCP Compatible: Works with claude.ai, Claude Desktop, Cursor, Windsurf out of the box

For Repository Cloners/Forkers

Each person who clones this repo gets:

• Their own Worker deployment and URL

• Their own password protection (MCP_PASSWORD secret)

• Their own OAuth KV namespace

• Complete isolation from other deployments

📁 Project Structure

obvec/
├── bin/
│   └── obvec.js                     # CLI executable
├── docs/                            # Documentation
│   ├── advanced-configuration.md    # Smart re-indexing and OAuth setup
│   ├── architecture.md              # Technical architecture details
│   ├── mcp-implementation.md        # MCP protocol details
│   ├── pricing-and-performance.md   # Cost analysis and performance info
│   └── troubleshooting.md           # Common issues and diagnostics
├── scripts/
│   ├── index-vault.ts               # Vault indexing script
│   ├── search-notes.ts              # CLI search utility
│   ├── get-stats.ts                 # Index statistics
│   ├── reset-index.ts               # Clear all indexed data
│   └── cleanup-orphaned.ts          # Remove deleted notes
├── src/
│   ├── api/                         # API endpoints
│   │   ├── cleanup.ts               # Cleanup orphaned notes
│   │   ├── index.ts                 # Index management
│   │   ├── list-indexed.ts          # List indexed notes
│   │   ├── router.ts                # API router
│   │   ├── search.ts                # Search functionality
│   │   ├── stats.ts                 # Statistics endpoint
│   │   └── test-mcp.ts              # MCP testing utilities
│   ├── auth/                        # Authentication UI
│   │   └── app.ts                   # OAuth app handler
│   ├── mcp/                         # MCP server implementations
│   │   ├── server.ts                # Standard MCP server (full tools)
│   │   └── server-chatgpt.ts        # ChatGPT-specific server (search/fetch only)
│   ├── types/                       # TypeScript types
│   │   └── index.ts                 # Type definitions
│   ├── utils/                       # Utility functions
│   │   ├── auth.ts                  # Authentication utilities
│   │   ├── embeddings.ts            # Embedding generation
│   │   ├── formatting.ts            # Text formatting
│   │   ├── hash.ts                  # Hashing utilities
│   │   ├── security.ts              # Security utilities
│   │   └── validation.ts            # Input validation
│   └── index.ts                     # Main Worker entry
├── .env.example                     # Environment variables template
├── .gitignore                       # Git ignore patterns
├── .mcp.json.example                # MCP configuration example
├── LICENSE                          # MIT License
├── README.md                        # This file
├── package.json                     # NPM package config
├── tsconfig.json                    # TypeScript config
└── wrangler.toml.example            # Cloudflare Worker config template

🛠️ CLI Commands

Core Operations

obvec login        # Login to Cloudflare (alias for wrangler login)
obvec deploy       # Deploy to production (alias for wrangler deploy)
obvec dev          # Start local development (alias for wrangler dev)
npm run build      # Build with the checked-in build-only Wrangler config

Vault Management

obvec index        # Index your Obsidian vault
obvec search "AI"  # Search your notes from CLI
obvec reset        # Clear and reset the entire index
obvec cleanup      # Remove orphaned notes (deleted from vault)
obvec info         # Show MCP connection information

Search Options

# Basic search
obvec search "machine learning"

# Limit results
obvec search "productivity" --limit 20

# JSON output for scripting
obvec search "meetings" --json

# Verbose mode (includes up to 1000 chars from vectorize index)
obvec search "projects" --verbose

Authentication

# Set your MCP password
wrangler secret put MCP_PASSWORD

# Create OAuth KV namespace  
wrangler kv:namespace create oauth_tokens

# View deployment logs
wrangler tail

🔍 Troubleshooting

For common issues and debugging tips, see docs/troubleshooting.md.

📊 Performance & Costs

For detailed pricing information, free tier limits, and cost scenarios, see docs/pricing-and-performance.md.

☁️ Cloudflare Resources Overview

This project automatically creates and configures the following Cloudflare resources:

• Vectorize Index: obsidian-notes (1024 dimensions, cosine similarity)

• KV Namespaces: OAuth token storage and caching

• R2 Bucket: Full note content storage and retrieval

• Workers AI: Embedding generation (included with Workers subscription)

These resources are created during the setup process and work together to provide semantic search across your Obsidian vault.

🔧 Advanced Configuration

For advanced features like smart re-indexing, timestamp queries, custom embedding models, and OAuth configuration, see docs/advanced-configuration.md.

📚 Documentation

For detailed guides, see:

• ChatGPT Integration - ChatGPT connector setup and configuration

• Architecture - Technical implementation details

• Advanced Configuration - Power user features

• Pricing & Performance - Cost analysis and limits

• Troubleshooting - Common issues and debugging

• MCP Implementation - MCP protocol details

🤝 Contributing

1. Fork the repository

2. Create a feature branch

3. Test with your own Obsidian vault

4. Submit a pull request

📄 License

MIT License - see LICENSE file for details