feat: Complete Docker MySQL integration with enhanced database utilities and comprehensive setup

[Copilot]

This PR implements complete Docker support for LeanRAG's MySQL backend, making the framework more robust, scalable, and easier to deploy while maintaining backward compatibility.

🚀 New Features

Docker MySQL Integration

• Complete Docker setup with docker-compose.yml for one-command MySQL deployment
• Custom Dockerfile (Dockerfile.mysql) optimized for LeanRAG's database requirements
• Automated initialization via mysql-init/01-init.sql that sets up databases and permissions
• Management script (mysql-docker.sh) providing easy container operations:

  ./mysql-docker.sh start    # Start MySQL container
  ./mysql-docker.sh status   # Check container status  
  ./mysql-docker.sh connect  # Connect to MySQL shell
  ./mysql-docker.sh reset    # Reset all data

Enhanced Database Utilities

The database_utils.py module now includes significant improvements:

• Database name validation with validate_database_name() function that sanitizes names for MySQL compatibility
• Improved connection handling via get_mysql_connection() with comprehensive error handling and automatic database creation
• Enhanced logging throughout all database operations for better debugging and monitoring
• File existence checks before processing to prevent runtime errors
• Better error recovery with proper rollback mechanisms

🔧 Technical Improvements

Configuration Management

• Added PyMySQL dependency to pyproject.toml for proper package management
• CommonKG configuration templates with examples for different use cases:
  • create_kg_conf_example.yaml - Full configuration template
  • create_kg_conf_test_small.yaml - Lightweight testing setup
  • test_entities_small.txt - Small-scale entity list for testing

Code Quality & Reliability

• Comprehensive error handling with descriptive error messages and logging
• Path handling improvements for cross-platform compatibility
• Database connection pooling and proper resource cleanup
• Input validation to prevent SQL injection and invalid database operations

Development Experience

• Comprehensive documentation in MYSQL_DOCKER_README.md with setup guides and troubleshooting
• Test validation script (test_docker_setup.sh) for end-to-end verification
• Enhanced logging structure for CommonKG knowledge graph creation process

📊 Performance & Scalability

The new Docker setup provides:

• Persistent data storage via Docker volumes to preserve data across container restarts
• Configurable MySQL settings optimized for knowledge graph workloads
• Health checks to ensure database availability before processing
• Resource isolation through containerization

🛠️ Usage Example

After this PR, setting up LeanRAG's MySQL backend is simplified to:

# Start MySQL with all required configurations
./mysql-docker.sh start

# Verify setup
./test_docker_setup.sh

# Run knowledge graph creation
python CommonKG/create_kg.py

# Build and query the graph
python build_graph.py
python query_graph.py

🔍 Testing

All changes have been validated with:

• ✅ Docker configuration validation
• ✅ Python syntax and import testing
• ✅ MySQL initialization script verification
• ✅ CommonKG configuration file validation
• ✅ Cross-platform compatibility checks

This implementation maintains full backward compatibility while providing a modern, containerized deployment option that significantly improves the developer and user experience.

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