doctor

🩺 Doctor

A tool for discovering, crawl, and indexing web sites to be exposed as an MCP server for LLM agents for better and more up-to-date reasoning and code generation.

🔍 Overview

Doctor provides a complete stack for:

• Crawling web pages using crawl4ai with hierarchy tracking
• Chunking text with LangChain
• Creating embeddings with OpenAI via litellm
• Storing data in DuckDB with vector search support
• Exposing search functionality via a FastAPI web service
• Making these capabilities available to LLMs through an MCP server
• Navigating crawled sites with hierarchical site maps

🏗️ Core Infrastructure

🗄️ DuckDB

• Database for storing document data and embeddings with vector search capabilities
• Managed by unified Database class

📨 Redis

• Message broker for asynchronous task processing

🕸️ Crawl Worker

• Processes crawl jobs
• Chunks text
• Creates embeddings

🌐 Web Server

• FastAPI service exposing endpoints
• Fetching, searching, and viewing data
• Exposing the MCP server

💻 Setup

⚙️ Prerequisites

• Docker and Docker Compose
• Python 3.10+
• uv (Python package manager)
• OpenAI API key

📦 Installation

1. Clone this repository
2. Set up environment variables:

   export OPENAI_API_KEY=your-openai-key
   

3. Run the stack:

   docker compose up
   

👁 Usage

1. Go to http://localhost:9111/docs to see the OpenAPI docs
2. Look for the /fetch_url endpoint and start a crawl job by providing a URL
3. Use /job_progress to see the current job status
4. Configure your editor to use http://localhost:9111/mcp as an MCP server

☁️ Web API

Core Endpoints

• POST /fetch_url: Start crawling a URL
• GET /search_docs: Search indexed documents
• GET /job_progress: Check crawl job progress
• GET /list_doc_pages: List indexed pages
• GET /get_doc_page: Get full text of a page

Site Map Feature

The Maps feature provides a hierarchical view of crawled websites, making it easy to navigate and explore the structure of indexed sites.

Endpoints:

• GET /map: View an index of all crawled sites
• GET /map/site/{root_page_id}: View the hierarchical tree structure of a specific site
• GET /map/page/{page_id}: View a specific page with navigation (parent, siblings, children)
• GET /map/page/{page_id}/raw: Get the raw markdown content of a page

Features:

• Hierarchical Navigation: Pages maintain parent-child relationships, allowing you to navigate through the site structure
• Domain Grouping: Pages from the same domain crawled individually are automatically grouped together
• Automatic Title Extraction: Page titles are extracted from HTML or markdown content
• Breadcrumb Navigation: Easy navigation with breadcrumbs showing the path from root to current page
• Sibling Navigation: Quick access to pages at the same level in the hierarchy
• Legacy Page Support: Pages crawled before hierarchy tracking are grouped by domain for easy access
• No JavaScript Required: All navigation works with pure HTML and CSS for maximum compatibility

Usage Example:

1. Crawl a website using the /fetch_url endpoint
2. Visit /map to see all crawled sites
3. Click on a site to view its hierarchical structure
4. Navigate through pages using the provided links

🔧 MCP Integration

Ensure that your Docker Compose stack is up, and then add to your Cursor or VSCode MCP Servers configuration:

"doctor": {
    "type": "sse",
    "url": "http://localhost:9111/mcp"
}

🧪 Testing

Running Tests

To run all tests:

# Run all tests with coverage report
pytest

To run specific test categories:

# Run only unit tests
pytest -m unit

# Run only async tests
pytest -m async_test

# Run tests for a specific component
pytest tests/lib/test_crawler.py

Test Coverage

The project is configured to generate coverage reports automatically:

# Run tests with detailed coverage report
pytest --cov=src --cov-report=term-missing

Test Structure

• tests/conftest.py: Common fixtures for all tests
• tests/lib/: Tests for library components
  • test_crawler.py: Tests for the crawler module
  • test_crawler_enhanced.py: Tests for enhanced crawler with hierarchy tracking
  • test_chunker.py: Tests for the chunker module
  • test_embedder.py: Tests for the embedder module
  • test_database.py: Tests for the unified Database class
  • test_database_hierarchy.py: Tests for database hierarchy operations
• tests/common/: Tests for common modules
• tests/services/: Tests for service layer
  • test_map_service.py: Tests for the map service
• tests/api/: Tests for API endpoints
  • test_map_api.py: Tests for map API endpoints
• tests/integration/: Integration tests
  • test_processor_enhanced.py: Tests for enhanced processor with hierarchy

🐞 Code Quality

Pre-commit Hooks

The project is configured with pre-commit hooks that run automatically before each commit:

• ruff check --fix: Lints code and automatically fixes issues
• ruff format: Formats code according to project style
• Trailing whitespace removal
• End-of-file fixing
• YAML validation
• Large file checks

Setup Pre-commit

To set up pre-commit hooks:

# Install pre-commit
uv pip install pre-commit

# Install the git hooks
pre-commit install

Running Pre-commit Manually

You can run the pre-commit hooks manually on all files:

# Run all pre-commit hooks
pre-commit run --all-files

Or on staged files only:

# Run on staged files
pre-commit run

⚖️ License

This project is licensed under the MIT License - see the file for details.