Mutation Clinical Trial Matching MCP

# API Improvements Plan ## Comprehensive Enhancement Strategy for Clinical Trials MCP Server ### Executive Summary This document outlines a systematic approach to enhance the API interactions in the Clinical Trials MCP Server, combining insights from code review, peer feedback, and future work considerations. The improvements are prioritized by impact and implementation effort. --- ## Current State Assessment ### ✅ **Strengths (Already Implemented)** - Comprehensive error handling for network failures - Robust input validation and parameter sanitization - Excellent test coverage with proper mocking - Clear logging strategy with appropriate levels - Consistent error response format - Proper HTTP status code validation - JSON parsing error handling ### ⚠️ **Areas for Improvement** Based on combined analysis from multiple sources: 1. **Resilience**: No retry logic for transient failures 2. **Performance**: No caching or connection reuse 3. **Configuration**: Hardcoded endpoints and missing environment documentation 4. **Monitoring**: Limited performance metrics and debugging information 5. **Standards**: Missing User-Agent headers --- ## Improvement Categories ### 🔄 **Category 1: Resilience & Reliability** **Goal**: Make API calls more robust against transient failures #### 1.1 Retry Logic with Exponential Backoff - **Files**: `clinicaltrials/query.py`, `utils/call_llm.py` - **Impact**: High - **Effort**: Medium - **Implementation**: - Add configurable retry decorator - Implement exponential backoff (1s, 2s, 4s, 8s) - Retry only on specific exceptions (timeout, connection errors) - Max retries: 3 (configurable) #### 1.2 Circuit Breaker Pattern - **Files**: New `utils/circuit_breaker.py` - **Impact**: Medium - **Effort**: Medium - **Implementation**: - Fail fast when API consistently fails - Automatic recovery after cool-down period - Configurable failure threshold ### 🚀 **Category 2: Performance Optimization** #### 2.1 HTTP Session Reuse - **Files**: `clinicaltrials/query.py`, `utils/call_llm.py` - **Impact**: Medium - **Effort**: Low - **Implementation**: - Use `requests.Session()` for connection pooling - Configure session with appropriate timeouts - Reuse connections across requests #### 2.2 Basic Caching - **Files**: `clinicaltrials/query.py` - **Impact**: High - **Effort**: Low - **Implementation**: - Use `functools.lru_cache` for recent queries - Cache size: 100 entries (configurable) - TTL: 1 hour (configurable) - Cache key: mutation + parameters hash #### 2.3 Async Support (Future) - **Files**: New `clinicaltrials/async_query.py` - **Impact**: High - **Effort**: High - **Implementation**: - Use `httpx` for async HTTP requests - Parallel API calls for multiple queries - Backward compatibility with sync interface ### ⚙️ **Category 3: Configuration & Environment** #### 3.1 Parameterized API Endpoints - **Files**: New `clinicaltrials/config.py` - **Impact**: Medium - **Effort**: Low - **Implementation**: - Move hardcoded URLs to constants - Support environment variable overrides - Default values for all endpoints #### 3.2 Enhanced Environment Documentation - **Files**: `README.md`, new `docs/environment_setup.md` - **Impact**: Medium - **Effort**: Low - **Implementation**: - Document all required environment variables - Provide example `.env` file - Add environment validation on startup #### 3.3 Configuration Validation - **Files**: New `utils/config_validator.py` - **Impact**: Medium - **Effort**: Low - **Implementation**: - Validate all environment variables on startup - Provide clear error messages for missing config - Support for development/production profiles ### 📊 **Category 4: Monitoring & Observability** #### 4.1 Enhanced Logging - **Files**: `clinicaltrials/query.py`, `utils/call_llm.py` - **Impact**: High - **Effort**: Low - **Implementation**: - Log request/response times - Add structured logging with context - Include request IDs for tracing - Exception details instead of just error strings #### 4.2 Request Metrics - **Files**: New `utils/metrics.py` - **Impact**: Medium - **Effort**: Medium - **Implementation**: - Track API call counts and latencies - Monitor success/failure rates - Cache hit/miss ratios - Export metrics for monitoring systems #### 4.3 Health Check Endpoint - **Files**: `clinicaltrials_mcp_server.py` - **Impact**: Low - **Effort**: Low - **Implementation**: - Add `/healthz` endpoint - Check API connectivity - Return service status and version ### 🔧 **Category 5: Code Quality & Standards** #### 5.1 HTTP Headers Standardization - **Files**: `clinicaltrials/query.py`, `utils/call_llm.py` - **Impact**: Low - **Effort**: Low - **Implementation**: - Add User-Agent headers - Consistent header formatting - API version headers where applicable #### 5.2 Response Validation - **Files**: `clinicaltrials/query.py` - **Impact**: Medium - **Effort**: Low - **Implementation**: - Validate API response structure - Handle API schema changes gracefully - Log warnings for unexpected response formats --- ## Implementation Roadmap ### 🎯 **Phase 1: Quick Wins (1-2 days)** **Priority**: High Impact, Low Effort 1. **HTTP Session Reuse** (2 hours) - [ ] Implement session management in `query.py` - [ ] Update `call_llm.py` to use sessions - [ ] Add session configuration 2. **Basic Caching** (3 hours) - [ ] Add `@lru_cache` decorator to `query_clinical_trials` - [ ] Implement cache invalidation strategy - [ ] Add cache statistics logging 3. **User-Agent Headers** (1 hour) - [ ] Add descriptive User-Agent strings - [ ] Include version information - [ ] Update both API clients 4. **Enhanced Logging** (2 hours) - [ ] Add request timing logs - [ ] Include structured context - [ ] Log exception details in `call_llm.py` ### 🚀 **Phase 2: Core Resilience (2-3 days)** **Priority**: High Impact, Medium Effort 1. **Retry Logic with Exponential Backoff** (4 hours) - [ ] Create retry decorator - [ ] Implement exponential backoff - [ ] Add configuration options - [ ] Update both API clients 2. **Configuration System** (3 hours) - [ ] Create `config.py` with constants - [ ] Add environment variable support - [ ] Implement configuration validation - [ ] Update documentation 3. **Environment Documentation** (2 hours) - [ ] Document all required variables - [ ] Create example `.env` file - [ ] Add setup validation script ### 🔄 **Phase 3: Advanced Features (3-5 days)** **Priority**: Medium Impact, Medium-High Effort 1. **Circuit Breaker Pattern** (6 hours) - [ ] Implement circuit breaker utility - [ ] Add failure threshold configuration - [ ] Integrate with existing API clients - [ ] Add monitoring and alerting 2. **Request Metrics** (4 hours) - [ ] Create metrics collection system - [ ] Add performance counters - [ ] Implement metrics export - [ ] Add dashboard queries 3. **Response Validation** (3 hours) - [ ] Define API response schemas - [ ] Add validation middleware - [ ] Handle schema evolution - [ ] Log validation warnings ### 🌟 **Phase 4: Future Enhancements (1-2 weeks)** **Priority**: High Impact, High Effort 1. **Async Support** (1 week) - [ ] Implement async query functions - [ ] Add parallel request capabilities - [ ] Maintain backward compatibility - [ ] Performance testing 2. **Advanced Caching** (3 days) - [ ] Implement distributed caching - [ ] Add cache warming strategies - [ ] Smart cache invalidation - [ ] Cache analytics --- ## Testing Strategy ### Unit Tests Updates - [ ] Add tests for retry logic - [ ] Test caching behavior - [ ] Validate configuration loading - [ ] Test circuit breaker states ### Integration Tests - [ ] Test with actual API endpoints - [ ] Validate error scenarios - [ ] Performance benchmarks - [ ] Cache effectiveness tests ### Performance Tests - [ ] Load testing with caching - [ ] Retry logic performance impact - [ ] Connection pooling benefits - [ ] Memory usage validation --- ## Monitoring & Success Metrics ### Key Performance Indicators - **API Success Rate**: Target >99.5% - **Average Response Time**: Target <2s - **Cache Hit Rate**: Target >60% - **Error Recovery Rate**: Target >95% ### Monitoring Dashboards - API call volume and latency - Error rates by type - Cache performance metrics - Circuit breaker state changes --- ## Configuration Examples ### Environment Variables ```bash # API Configuration CLINICALTRIALS_API_URL=https://clinicaltrials.gov/api/v2/studies ANTHROPIC_API_URL=https://api.anthropic.com/v1/messages ANTHROPIC_API_KEY=your_api_key_here # Retry Configuration MAX_RETRIES=3 RETRY_DELAY=1 BACKOFF_FACTOR=2 # Cache Configuration CACHE_SIZE=100 CACHE_TTL=3600 # Circuit Breaker Configuration FAILURE_THRESHOLD=5 RECOVERY_TIMEOUT=60 ``` ### Example `.env` File ```bash # Copy this to .env and fill in your values ANTHROPIC_API_KEY=sk-ant-api03-... ``` --- ## Risk Assessment ### Low Risk - HTTP session reuse - Basic caching - User-Agent headers - Enhanced logging ### Medium Risk - Retry logic (could increase latency) - Configuration changes (deployment impact) - Circuit breaker (could block legitimate requests) ### High Risk - Async implementation (major architectural change) - Distributed caching (infrastructure dependency) --- ## Conclusion This comprehensive improvement plan addresses all identified areas for enhancement while maintaining a systematic, risk-managed approach. The phased implementation allows for iterative improvements with continuous validation and rollback capabilities. **Immediate Next Steps**: 1. Begin with Phase 1 quick wins 2. Set up monitoring for baseline metrics 3. Create feature branches for each improvement 4. Implement comprehensive testing strategy **Success Criteria**: - Improved API reliability and performance - Better developer experience - Enhanced monitoring and debugging capabilities - Maintainable and extensible codebase --- *Document Version: 1.0* *Last Updated: 2025-01-09* *Next Review: After Phase 1 completion*