NCBI Entrez MCP Server

#!/usr/bin/env node /** * NCBI Entrez MCP Server - Quick Start Guide * * This script helps you get started with the NCBI MCP Server and test your setup. */ const NCBIRateLimitTester = require("./test-rate-limits.js"); class QuickStartGuide { constructor() { this.apiKey = process.env.NCBI_API_KEY; } async run() { console.log("🚀 NCBI Entrez MCP Server - Quick Start"); console.log("=======================================\n"); // Step 1: Check current setup await this.checkSetup(); // Step 2: Offer to run tests await this.offerTesting(); // Step 3: Next steps this.showNextSteps(); } async checkSetup() { console.log("📋 Checking Your Setup"); console.log("----------------------"); // Check API key if (this.apiKey) { console.log(`✅ NCBI API Key: Found (${this.apiKey.substring(0, 8)}...)`); console.log(` Rate Limit: 10 requests/second`); } else { console.log("⚠️ NCBI API Key: Not found"); console.log(" Rate Limit: 3 requests/second (default)"); } // Check Node.js version const nodeVersion = process.version; console.log(`✅ Node.js: ${nodeVersion}`); // Check if test file exists const fs = require("node:fs"); if (fs.existsSync("./test-rate-limits.js")) { console.log("✅ Rate limit tester: Available"); } else { console.log("❌ Rate limit tester: Missing"); } console.log(); } async offerTesting() { console.log("🧪 Testing Options"); console.log("------------------"); if (!this.apiKey) { console.log( "Since no API key is configured, we'll test the default rate limits.", ); console.log("This helps verify the server is working correctly.\n"); console.log("Running basic rate limit test...\n"); try { const tester = new NCBIRateLimitTester(); // Run a quick test without API key await tester.testRate(2, 3, false); // Conservative test console.log("\n✅ Basic functionality test passed!"); console.log(" The server is working correctly without an API key."); } catch (error) { console.log("\n❌ Test failed:", error.message); console.log(" There may be a network issue or NCBI service is down."); } } else { console.log( "API key detected! Running comprehensive rate limit tests...\n", ); try { const tester = new NCBIRateLimitTester(); // Test without API key first console.log("Testing baseline (without API key):"); const baselineResult = await tester.testRate(2, 2, false); // Test with API key console.log("\nTesting with API key:"); const apiKeyResult = await tester.testRate(8, 2, true); // Compare results if (apiKeyResult.successRate > baselineResult.successRate) { console.log("\n✅ API Key is working correctly!"); console.log( ` Improvement: ${(apiKeyResult.successRate - baselineResult.successRate).toFixed(1)}% better success rate`, ); } else { console.log("\n⚠️ API Key may not be working properly"); console.log(" Check that your API key is valid and correctly set"); } } catch (error) { console.log("\n❌ Test failed:", error.message); } } } showNextSteps() { console.log("\n🎯 Next Steps"); console.log("-------------"); if (!this.apiKey) { console.log("To get 3x better performance, set up your free API key:"); console.log( "1. Visit: https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/", ); console.log("2. Get your API key (takes 30 seconds)"); console.log('3. Set it: export NCBI_API_KEY="your_key_here"'); console.log("4. Restart and run: node quick-start.js"); console.log("5. Read API_KEY_SETUP.md for detailed instructions"); } else { console.log("Your setup is optimized! You can now:"); console.log("1. Start the server: npm start"); console.log("2. Connect to Claude Desktop or AI Playground"); console.log("3. Use the NCBI tools at full speed"); } console.log("\n📚 Available Commands:"); console.log(" npm start - Start the MCP server"); console.log(" npm run test - Run comprehensive rate limit tests"); console.log(" npm run check-setup - Quick setup check"); console.log(" npm run setup-help - Show setup instructions"); console.log("\n🔍 Available NCBI Tools:"); console.log( " - entrez_query - Unified E-utilities surface (search, summary, fetch, link)", ); console.log( " - entrez_data - Stage datasets and run SQL or smart summaries", ); console.log( " - entrez_external - PubChem + PMC helpers in one interface", ); console.log( " - entrez_capabilities - Inspect tool signatures and token profiles", ); console.log(" - system_api_key_status - Check API key configuration"); console.log("\n🎉 You're ready to go! Happy researching! 🧬"); } } // Run the quick start guide if (require.main === module) { const guide = new QuickStartGuide(); guide.run().catch(console.error); } module.exports = QuickStartGuide;