smartapi-mcp 0.1.0__tar.gz

smartapi_mcp-0.1.0/LICENSE

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smartapi_mcp-0.1.0/MANIFEST.in

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+# Include package metadata and documentation files
+include README.md
+include LICENSE
+include requirements.txt
+include requirements-dev.txt
+include pyproject.toml
+
+# Include package data
+recursive-include smartapi_mcp *.py
+recursive-include smartapi_mcp py.typed
+
+# Exclude development and build files
+global-exclude *.pyc
+global-exclude __pycache__
+global-exclude *.so
+global-exclude .DS_Store
+exclude .gitignore
+exclude .github
+recursive-exclude tests *
+recursive-exclude .github *
+recursive-exclude build *
+recursive-exclude dist *
+recursive-exclude *.egg-info *

smartapi_mcp-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: smartapi-mcp
+Version: 0.1.0
+Summary: Create MCP servers for one or multiple APIs registered in SmartAPI registry
+Author-email: BioThings Team <help@biothings.io>
+Maintainer-email: BioThings Team <help@biothings.io>
+License: Apache-2.0
+Project-URL: Homepage, https://github.com/biothings/smartapi-mcp
+Project-URL: Repository, https://github.com/biothings/smartapi-mcp
+Project-URL: Issues, https://github.com/biothings/smartapi-mcp/issues
+Project-URL: Documentation, https://github.com/biothings/smartapi-mcp#readme
+Keywords: mcp,smartapi,api,server,bioinformatics
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Classifier: Topic :: Internet :: WWW/HTTP :: HTTP Servers
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: awslabs_openapi_mcp_server>=0.2.4
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0.0; extra == "dev"
+Requires-Dist: pytest-asyncio>=0.21.0; extra == "dev"
+Requires-Dist: pytest-cov>=4.0.0; extra == "dev"
+Requires-Dist: ruff>=0.1.0; extra == "dev"
+Requires-Dist: build>=0.8.0; extra == "dev"
+Requires-Dist: twine>=4.0.0; extra == "dev"
+Provides-Extra: test
+Requires-Dist: pytest>=7.0.0; extra == "test"
+Requires-Dist: pytest-asyncio>=0.21.0; extra == "test"
+Requires-Dist: pytest-cov>=4.0.0; extra == "test"
+Provides-Extra: docs
+Requires-Dist: sphinx>=5.0.0; extra == "docs"
+Requires-Dist: sphinx-rtd-theme>=1.0.0; extra == "docs"
+Dynamic: license-file
+
+# SmartAPI MCP Server
+
+Create MCP (Model Context Protocol) servers for one or multiple APIs registered in the SmartAPI registry.
+
+[![Test](https://github.com/biothings/smartapi-mcp/actions/workflows/test.yml/badge.svg)](https://github.com/biothings/smartapi-mcp/actions/workflows/test.yml)
+[![PyPI version](https://badge.fury.io/py/smartapi-mcp.svg)](https://badge.fury.io/py/smartapi-mcp)
+[![Python versions](https://img.shields.io/pypi/pyversions/smartapi-mcp.svg)](https://pypi.org/project/smartapi-mcp/)
+[![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
+
+## Overview
+
+The SmartAPI MCP Server enables integration between MCP-compatible clients and APIs registered in the SmartAPI registry. This allows for seamless discovery and interaction with bioinformatics and life sciences APIs through standardized MCP protocols.
+
+Built on top of the [AWS Labs OpenAPI MCP Server](https://github.com/awslabs/openapi-mcp-server), this project extends MCP support to the extensive collection of APIs available in the SmartAPI registry, with special focus on bioinformatics and life sciences APIs.
+
+## Requirements
+
+- Python 3.10 or higher
+- Network access to SmartAPI registry (https://smart-api.info)
+- Dependencies: `awslabs_openapi_mcp_server>=0.2.4`
+
+## Features
+
+- 🔍 **SmartAPI Integration**: Direct integration with the SmartAPI registry for API discovery
+- 🏗️ **MCP Protocol Support**: Full MCP (Model Context Protocol) server implementation
+- 🔄 **Async Architecture**: Built with modern Python async/await patterns for high performance
+- 📖 **OpenAPI Validation**: Automatic OpenAPI specification parsing and validation
+- 🛠️ **CLI Interface**: Easy-to-use command-line interface with multiple configuration options
+- 🧬 **Bioinformatics Focus**: Pre-configured API sets for bioinformatics and life sciences
+- 🎯 **Flexible Configuration**: Support for environment variables, arguments, and configuration files
+- 🚀 **Multiple Transport Modes**: Support for both stdio and HTTP transport protocols
+- 🧪 **Comprehensive Testing**: Full test suite with 99% code coverage
+
+## Installation
+
+### From PyPI (recommended)
+
+```bash
+pip install smartapi-mcp
+```
+
+### From Source
+
+```bash
+git clone https://github.com/biothings/smartapi-mcp.git
+cd smartapi-mcp
+pip install -e .
+```
+
+### Development Installation
+
+```bash
+git clone https://github.com/biothings/smartapi-mcp.git
+cd smartapi-mcp
+pip install -e ".[dev]"
+```
+
+## Quick Start
+
+### Command Line Usage
+
+#### Start with a predefined API set (recommended)
+
+```bash
+# Use BioThings core APIs (MyGene, MyVariant, MyChem, MyDisease)
+smartapi-mcp --api_set biothings_core
+
+# Use all BioThings APIs (with some exclusions)
+smartapi-mcp --api_set biothings_all
+```
+
+#### Start with specific SmartAPI IDs
+
+```bash
+# Single API
+smartapi-mcp --smartapi_id 59dce17363dce279d389100834e43648
+
+# Multiple APIs
+smartapi-mcp --smartapi_ids "59dce17363dce279d389100834e43648,09c8782d9f4027712e65b95424adba79"
+```
+
+#### Start with HTTP transport (instead of stdio)
+
+```bash
+# HTTP mode on localhost:8000 (default)
+smartapi-mcp --api_set biothings_core --transport http
+
+# Custom host and port
+smartapi-mcp --api_set biothings_core --transport http --host 0.0.0.0 --port 9000
+```
+
+#### Advanced options
+
+```bash
+# Custom logging level
+smartapi-mcp --api_set biothings_core --log-level DEBUG
+
+# Custom server name
+smartapi-mcp --api_set biothings_core --server_name "My Custom MCP Server"
+
+# Query-based API discovery
+smartapi-mcp --smartapi_q "tags.name=biothings"
+
+# Exclude specific APIs
+smartapi-mcp --api_set biothings_all --smartapi_exclude_ids "api_id_1,api_id_2"
+```
+
+### Python API Usage
+
+```python
+import asyncio
+from smartapi_mcp import (
+    get_smartapi_ids,
+    load_api_spec,
+    get_mcp_server,
+    get_merged_mcp_server,
+    PREDEFINED_API_SETS
+)
+
+async def main():
+    # Get SmartAPI IDs using a query
+    smartapi_ids = await get_smartapi_ids("tags.name=biothings")
+    print(f"Found {len(smartapi_ids)} APIs matching the query")
+    
+    # Load API specification for a specific SmartAPI
+    api_spec = load_api_spec("59dce17363dce279d389100834e43648")  # MyGene.info
+    print(f"Loaded API: {api_spec.get('info', {}).get('title', 'Unknown')}")
+    
+    # Create MCP server for a single API
+    server = await get_mcp_server(
+        smartapi_id="59dce17363dce279d389100834e43648",
+        server_name="MyGene MCP Server"
+    )
+    
+    # Create merged MCP server for multiple APIs (recommended approach)
+    merged_server = await get_merged_mcp_server(
+        api_set="biothings_core",  # Use predefined set
+        server_name="BioThings Core MCP Server"
+    )
+    
+    # Or with specific SmartAPI IDs
+    merged_server = await get_merged_mcp_server(
+        smartapi_ids=[
+            "59dce17363dce279d389100834e43648",  # MyGene.info
+            "09c8782d9f4027712e65b95424adba79",  # MyVariant.info
+        ],
+        server_name="Custom MCP Server"
+    )
+    
+    # Show available predefined API sets
+    print(f"Available API sets: {PREDEFINED_API_SETS}")
+    
+    # Run server with stdio transport (default for MCP)
+    merged_server.run()
+    
+    # Or run with HTTP transport
+    # merged_server.run(transport="http", host="localhost", port=8000)
+
+if __name__ == "__main__":
+    asyncio.run(main())
+```
+
+## API Examples
+
+### BioThings Core APIs
+
+When you use `--api_set biothings_core`, you get access to these powerful bioinformatics APIs:
+
+1. **MyGene.info** (`59dce17363dce279d389100834e43648`): Gene annotation and information
+2. **MyVariant.info** (`09c8782d9f4027712e65b95424adba79`): Variant annotation and information  
+3. **MyChem.info** (`8f08d1446e0bb9c2b323713ce83e2bd3`): Chemical and drug information
+4. **MyDisease.info** (`671b45c0301c8624abbd26ae78449ca2`): Disease information and associations
+
+### Usage with MCP Clients
+
+Once the server is running, MCP-compatible clients can discover and use the available tools. Each API endpoint becomes an available MCP tool with:
+
+- **Tool discovery**: Clients can list all available API endpoints
+- **Parameter validation**: Automatic parameter validation based on OpenAPI specs
+- **Rich descriptions**: Each tool includes detailed descriptions from the API documentation
+- **Error handling**: Proper error responses for invalid requests
+
+## Configuration
+
+The server supports multiple configuration methods:
+
+### Environment Variables
+
+```bash
+# SmartAPI configuration
+export SMARTAPI_ID="59dce17363dce279d389100834e43648"
+export SMARTAPI_IDS="id1,id2,id3"
+export SMARTAPI_Q="tags.name=biothings"
+export SMARTAPI_API_SET="biothings_core"
+export SMARTAPI_EXCLUDE_IDS="exclude_id1,exclude_id2"
+
+# Server configuration
+export SERVER_NAME="My SmartAPI MCP Server"
+export TRANSPORT="http"
+export HOST="localhost"
+export PORT="8000"
+
+# Then run without arguments
+smartapi-mcp
+```
+
+### Command Line Arguments
+
+All configuration can be provided via command line arguments (see Quick Start section above).
+
+### Predefined API Sets
+
+The following predefined API sets are available:
+
+- **`biothings_core`**: Core BioThings APIs (MyGene, MyVariant, MyChem, MyDisease)
+- **`biothings_test`**: Core APIs plus SemmedDB (useful for testing)
+- **`biothings_all`**: All BioThings APIs (with some exclusions for stability)
+
+### Configuration Priority
+
+1. Command line arguments (highest priority)
+2. Environment variables
+3. Default values (lowest priority)
+
+## Development
+
+### Setting up Development Environment
+
+```bash
+# Clone the repository
+git clone https://github.com/biothings/smartapi-mcp.git
+cd smartapi-mcp
+
+# Install development dependencies
+pip install -e ".[dev]"
+```
+
+### Running Tests
+
+```bash
+# Run all tests
+pytest
+
+# Run with coverage
+pytest --cov=smartapi_mcp --cov-report=html
+
+# Run specific test file
+pytest tests/test_basic.py
+```
+
+### Code Quality
+
+```bash
+# Check and fix linting issues
+ruff check .
+ruff check . --fix
+
+# Format code
+ruff format .
+```
+
+### Building the Package
+
+```bash
+# Build source and wheel distributions
+python -m build
+
+# Check the built package
+twine check dist/*
+```
+
+## Publishing to PyPI
+
+### Manual Publishing
+
+```bash
+# Build the package
+python -m build
+
+# Upload to Test PyPI (optional)
+twine upload --repository testpypi dist/*
+
+# Upload to PyPI
+twine upload dist/*
+```
+
+### Automated Publishing
+
+This repository includes GitHub Actions workflows for automated testing and publishing:
+
+- **Test Workflow** (`.github/workflows/test.yml`): Runs on every push and pull request
+- **Publish Workflow** (`.github/workflows/publish.yml`): Publishes to PyPI on release
+
+To publish a new version:
+
+1. Update the version in `pyproject.toml` and `smartapi_mcp/__init__.py`
+2. Commit the version changes
+3. Create and push a git tag: `git tag v0.1.0 && git push origin v0.1.0`
+4. Create a new release on GitHub
+5. The publish workflow will automatically build and upload to PyPI
+
+### Manual Workflow Trigger
+
+You can also manually trigger the publish workflow to upload to Test PyPI:
+
+1. Go to the Actions tab in your GitHub repository
+2. Select "Publish Python Package"
+3. Click "Run workflow"
+4. Choose "Publish to Test PyPI" option
+
+## Contributing
+
+We welcome contributions! Please see our contributing guidelines for details.
+
+1. Fork the repository
+2. Create a feature branch (`git checkout -b feature/amazing-feature`)
+3. Make your changes
+4. Add tests for your changes
+5. Ensure tests pass (`pytest`)
+6. Commit your changes (`git commit -m 'Add amazing feature'`)
+7. Push to the branch (`git push origin feature/amazing-feature`)
+8. Open a Pull Request
+
+## Troubleshooting
+
+### Common Issues
+
+#### No tools or resources registered
+
+```
+WARNING: No tools or resources were registered. This might indicate an issue with the API specification or authentication.
+```
+
+**Solution**: This usually happens when:
+- The SmartAPI ID is invalid or the API is down
+- The OpenAPI specification has validation errors
+- Network connectivity issues
+
+Try with a known working API set: `smartapi-mcp --api_set biothings_core`
+
+#### Server fails to start
+
+**Check your Python version**: Requires Python 3.10+
+```bash
+python --version
+```
+
+**Verify installation**:
+```bash
+pip show smartapi-mcp
+```
+
+#### HTTP mode connection issues
+
+If using HTTP transport mode and clients can't connect:
+- Check if the port is available: `netstat -an | grep :8000`
+- Try binding to all interfaces: `--host 0.0.0.0`
+- Check firewall settings
+
+### Getting Help
+
+1. Enable debug logging: `--log-level DEBUG`
+2. Check the [GitHub Issues](https://github.com/biothings/smartapi-mcp/issues)
+3. Contact us at help@biothings.io
+
+## License
+
+This project is licensed under the Apache License 2.0 - see the [LICENSE](LICENSE) file for details.
+
+## Related Projects
+
+- **[SmartAPI Registry](https://smart-api.info/)** - Registry of biomedical and life sciences APIs
+- **[Model Context Protocol (MCP)](https://modelcontextprotocol.io/)** - Standard protocol for AI model-tool integration
+- **[BioThings APIs](https://biothings.io/)** - High-performance bioinformatics APIs
+- **[AWS Labs OpenAPI MCP Server](https://github.com/awslabs/openapi-mcp-server)** - Base MCP server framework
+
+## Citation
+
+If you use SmartAPI MCP Server in your research or applications, please cite:
+
+```
+SmartAPI MCP Server: Bridging Bioinformatics APIs with Model Context Protocol
+BioThings Team. (2024). https://github.com/biothings/smartapi-mcp
+```
+
+## Support
+
+For questions and support:
+
+- 📖 **Documentation**: [README](https://github.com/biothings/smartapi-mcp#readme)
+- 🐛 **Bug Reports**: [GitHub Issues](https://github.com/biothings/smartapi-mcp/issues)
+- 💬 **Questions**: [GitHub Discussions](https://github.com/biothings/smartapi-mcp/discussions)
+- 📧 **Email**: help@biothings.io
+
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+**SmartAPI MCP Server** is developed and maintained by the [BioThings Team](https://biothings.io) at The Scripps Research Institute.