Medical Research MCP Suite

#!/usr/bin/env node // Test the fixed XML parsing directly import axios from 'axios'; import { parseStringPromise } from 'xml2js'; async function testXMLParsing() { console.log('🔧 Testing XML parsing fix...'); const baseURL = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils'; try { // Get PMIDs const searchParams = new URLSearchParams(); searchParams.append('term', 'diabetes'); searchParams.append('db', 'pubmed'); searchParams.append('retmode', 'json'); searchParams.append('retmax', '2'); const searchResponse = await axios.get(`${baseURL}/esearch.fcgi`, { params: searchParams, }); const pmids = searchResponse.data.esearchresult.idlist; console.log('✅ PMIDs:', pmids); // Fetch XML const fetchParams = new URLSearchParams(); fetchParams.append('db', 'pubmed'); fetchParams.append('id', pmids.join(',')); fetchParams.append('rettype', 'abstract'); const fetchResponse = await axios.get(`${baseURL}/efetch.fcgi`, { params: fetchParams, }); // Parse XML const jsonData = await parseStringPromise(fetchResponse.data, { explicitArray: false, mergeAttrs: true, explicitRoot: false }); console.log('✅ XML parsed successfully'); console.log('Top-level keys:', Object.keys(jsonData)); // Handle different structures let articles = []; if (jsonData.PubmedArticleSet?.PubmedArticle) { console.log('PubmedArticleSet structure found'); articles = Array.isArray(jsonData.PubmedArticleSet.PubmedArticle) ? jsonData.PubmedArticleSet.PubmedArticle : [jsonData.PubmedArticleSet.PubmedArticle]; } else if (jsonData.PubmedArticle) { console.log('Direct PubmedArticle structure found'); articles = Array.isArray(jsonData.PubmedArticle) ? jsonData.PubmedArticle : [jsonData.PubmedArticle]; } else { console.log('❌ Unexpected structure'); console.log('Available keys:', Object.keys(jsonData)); } console.log('Articles count:', articles.length); if (articles.length > 0) { const firstArticle = articles[0]; console.log('\n📄 First article structure:'); console.log('- Has MedlineCitation:', !!firstArticle.MedlineCitation); console.log('- Has PMID:', !!firstArticle.MedlineCitation?.PMID); console.log('- PMID value:', firstArticle.MedlineCitation?.PMID); console.log('- Has ArticleTitle:', !!firstArticle.MedlineCitation?.Article?.ArticleTitle); console.log('- Title:', firstArticle.MedlineCitation?.Article?.ArticleTitle); // Test transformation const pmid = firstArticle.MedlineCitation?.PMID?._ || firstArticle.MedlineCitation?.PMID || 'Unknown'; const title = firstArticle.MedlineCitation?.Article?.ArticleTitle || 'No title available'; console.log('\n✅ Transformation test:'); console.log('- Extracted PMID:', pmid); console.log('- Extracted title:', title); } } catch (error) { console.error('❌ Error:', error.message); if (error.response) { console.error('Response status:', error.response.status); } } } testXMLParsing().catch(console.error);