NCBI Entrez MCP Server

# Entrez MCP Server - Project Status Report **Date**: 2025-12-02 **Status**: ✅ **Production Ready** ## Executive Summary The Entrez MCP Server has been successfully upgraded to achieve **100% compliance** with the Model Context Protocol (MCP) specification version 2025-11-25. All tools have been updated, the SDK has been upgraded to the latest version (1.24.0), and comprehensive testing confirms everything is working correctly. ## Completed Work ### 1. MCP 2025-11-25 Specification Compliance ✅ All aspects of the MCP specification have been implemented: - ✅ **Content Types**: Full support for text, image, audio, resource_link, resource - ✅ **Annotations**: Support for audience, priority, lastModified metadata - ✅ **Error Handling**: Proper use of `isError` flag for tool execution errors - ✅ **Input Schemas**: All tools use valid JSON Schema (proper empty schema for no-parameter tools) - ✅ **Output Schemas**: All 6 tools declare comprehensive output schemas - ✅ **Tool Titles**: Human-readable titles for all tools - ✅ **Tool Name Validation**: Enforcement of MCP naming rules (1-128 chars, valid characters) - ✅ **Structured Content**: Backwards-compatible responses with both text and structuredContent - ✅ **Capabilities Declaration**: Server properly declares tools.listChanged: true **Documentation**: See `MCP_SPEC_COMPLIANCE.md` for complete details. ### 2. SDK Update to 1.24.0 ✅ Successfully upgraded to the latest MCP SDK: - ✅ **Package Updated**: `@modelcontextprotocol/sdk` from previous version to 1.24.0 - ✅ **Breaking Changes Addressed**: Fixed `Implementation.description` → `Implementation.title` - ✅ **registerTool() Fix**: Corrected tool registration to use proper SDK method with full feature support - ✅ **Build Size**: Increased to 3715.22 KiB (expected with newer SDK features) **Location**: `package.json`, `src/index.ts`, `src/tools/base.ts` ### 3. All Tools Updated ✅ Six tools have been completely migrated to the new patterns: 1. **EntrezQueryTool** (`entrez_query`) - Title: "NCBI Entrez E-utilities Gateway" - Comprehensive outputSchema - 15+ error cases converted to errorResult() - Actionable suggestions for every error 2. **DataManagerTool** (`entrez_data`) - Title: "NCBI Data Staging & SQL Query Manager" - outputSchema covers all 4 operations - Full error handling migration - Contextual help for staging and queries 3. **ExternalAPIsTool** (`entrez_external`) - Title: "External APIs Gateway (PubChem & PMC)" - Refactored validation logic - Service-specific error context - Comprehensive outputSchema 4. **CapabilitiesTool** (`entrez_capabilities`) - Title: "Tool Capabilities Inspector" - outputSchema for tool metadata - Error handling with suggestions 5. **ToolInfoTool** (`entrez_tool_info`) - Title: "Tool Metadata Inspector" - Detailed outputSchema - Improved error messages 6. **ApiKeyStatusTool** (`system_api_key_status`) - Title: "NCBI API Key Status Reporter" - Reference implementation - Complete compliance example **Documentation**: See individual tool files in `src/tools/` ### 4. Code Execution Support ✅ Full support for both direct MCP tool calling and code execution: - ✅ **JavaScript/TypeScript SDK**: Complete with type definitions - ✅ **Python SDK**: Full async/await implementation - ✅ **Integration Tests**: 100% pass rate for both SDKs - ✅ **Documentation**: Comprehensive API reference and examples - ✅ **Helper Classes**: DataStaging for automatic ID management **Documentation**: See `CODE_EXECUTION_IMPROVEMENTS.md` and `sdk/README.md` ### 5. Verification & Testing ✅ All verification checks pass: ```bash ✅ TypeScript Compilation: No errors ✅ Build Process: Success (3715.22 KiB) ✅ IDE Diagnostics: No issues ✅ registerTool() Functionality: Verified working ✅ JavaScript SDK Tests: 100% pass rate ✅ Python SDK Tests: 100% pass rate ``` **Commands to verify**: ```bash npm run type-check # TypeScript compilation npm run build # Production build npm run test-sdk-all # SDK integration tests npm run test-all # Complete test suite ``` ## Architecture Overview ### Core Components - **Server**: McpServer with dual transport support (Streamable HTTP + SSE) - **Protocol**: MCP 2025-11-25 compliant - **SDK Version**: @modelcontextprotocol/sdk 1.24.0 - **Tools**: 6 consolidated tools covering 20+ NCBI/external API operations - **Rate Limiting**: 3/sec default, 10/sec with API key - **Data Staging**: SQLite-based Durable Objects for complex queries ### Tool Registration Pattern All tools use the updated `registerTool()` method with: - Input schema (JSON Schema) - Output schema (JSON Schema) - Title (human-readable name) - Handler (async function) - Optional annotations ### Error Handling Pattern Tools use **result-based error handling**: - Validation errors → `errorResult()` with suggestions - Tool execution errors → `errorResult()` with context - Protocol errors → Thrown exceptions - All errors include actionable guidance ## File Changes Summary ### Modified Files (14) - `CLAUDE.md` - Updated documentation - `package.json` - SDK version bump - `package-lock.json` - Dependencies updated - `quick-start.js` - Minor updates - `sdk/javascript/entrez-sdk.js` - SDK improvements - `src/index.ts` - Server initialization fix - `src/tools/api-key-status.ts` - Reference implementation - `src/tools/base.ts` - Core infrastructure updates - `src/tools/capabilities.ts` - Updated tool - `src/tools/consolidated-data.ts` - Updated tool - `src/tools/consolidated-entrez.ts` - Updated tool - `src/tools/consolidated-external.ts` - Updated tool - `src/tools/tool-info.ts` - Updated tool - `worker-configuration.d.ts` - Type updates ### New Files (2) - `MCP_SPEC_COMPLIANCE.md` - Comprehensive compliance documentation - `CODE_EXECUTION_IMPROVEMENTS.md` - Code execution support summary ## Production Readiness Checklist - [x] MCP 2025-11-25 specification compliance - [x] Latest SDK version (1.24.0) - [x] All tools updated and tested - [x] TypeScript compilation passes - [x] Production build succeeds - [x] No IDE diagnostics warnings - [x] Integration tests pass (100%) - [x] Documentation complete and accurate - [x] Error handling provides actionable guidance - [x] Backwards compatibility maintained - [x] Code execution support verified ## Known Considerations ### Build Size - **Previous**: ~2429 KiB - **Current**: 3715.22 KiB (+53%) - **Reason**: SDK 1.24.0 includes additional features - **Impact**: Expected and acceptable for production use ### Breaking Changes - **SDK 1.24.0**: `Implementation.description` removed, use `title` instead - **Impact**: Already fixed in codebase - **Location**: `src/index.ts` line 19 ## Next Steps (Optional) While the server is production-ready, potential future enhancements include: 1. **Advanced Features** - Retry logic for transient failures - Client-side caching - Progress callbacks for long operations - Streaming support for large responses 2. **Developer Tools** - CLI tool using the SDKs - Interactive documentation - Performance monitoring dashboard 3. **Testing** - Load testing for rate limits - Stress testing for Durable Objects - End-to-end integration tests with real clients ## Deployment The server is ready for deployment to Cloudflare Workers: ```bash # Deploy to production npm run deploy # Verify deployment curl https://your-worker.workers.dev/mcp \ -H "Content-Type: application/json" \ -d '{"jsonrpc":"2.0","id":1,"method":"initialize",...}' ``` ## Support & Documentation - **MCP Specification**: [modelcontextprotocol.io/specification/2025-11-25](https://modelcontextprotocol.io/specification/2025-11-25) - **SDK Documentation**: [github.com/modelcontextprotocol/typescript-sdk](https://github.com/modelcontextprotocol/typescript-sdk) - **Project Documentation**: See `CLAUDE.md`, `MCP_SPEC_COMPLIANCE.md`, `CODE_EXECUTION_IMPROVEMENTS.md` - **API Reference**: See `sdk/README.md` ## Conclusion ✅ **All requested work completed successfully** The Entrez MCP Server is now: - Fully compliant with MCP 2025-11-25 specification - Using the latest SDK (1.24.0) - Production-ready with comprehensive testing - Well-documented with examples and guides - Supporting both direct tool calls and code execution **Status**: Ready for production deployment and use.