import axios from 'axios';
import xml2js from 'xml2js';
import { promisify } from 'util';
const parseXML = promisify(xml2js.parseString);
function generatePubMedSearchUrl(term, numResults = 10) {
const baseUrl = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi';
const encodedTerm = encodeURIComponent(term);
return `${baseUrl}?db=pubmed&term=${encodedTerm}&retmax=${numResults}&retmode=xml`;
}
async function searchPubMed(searchUrl) {
try {
const response = await axios.get(searchUrl, {
timeout: 30000,
headers: {
'User-Agent': 'PubMed-MCP-Server/1.0.0 (uh-joan@github.com)'
}
});
const result = await parseXML(response.data);
const pmids = [];
if (result?.eSearchResult?.IdList?.[0]?.Id) {
const ids = result.eSearchResult.IdList[0].Id;
for (const id of ids) {
if (typeof id === 'string') {
pmids.push(id);
} else if (id?._) {
pmids.push(id._);
}
}
}
return pmids;
} catch (error) {
console.error('Error searching PubMed:', error.message);
return [];
}
}
async function getPubMedMetadata(pmid) {
try {
const url = `https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=${pmid}&retmode=xml`;
const response = await axios.get(url, {
timeout: 30000,
headers: {
'User-Agent': 'PubMed-MCP-Server/1.0.0 (uh-joan@github.com)'
}
});
const result = await parseXML(response.data);
const article = result?.PubmedArticleSet?.PubmedArticle?.[0];
if (!article) return null;
const medlineCitation = article.MedlineCitation?.[0];
const pubmedData = article.PubmedData?.[0];
if (!medlineCitation) return null;
const title = medlineCitation.Article?.[0]?.ArticleTitle?.[0] || 'No title available';
const journal = medlineCitation.Article?.[0]?.Journal?.[0]?.Title?.[0] || 'Unknown journal';
const authors = [];
const authorList = medlineCitation.Article?.[0]?.AuthorList?.[0]?.Author;
if (authorList) {
for (const author of authorList) {
const lastName = author.LastName?.[0] || '';
const foreName = author.ForeName?.[0] || '';
if (lastName) {
authors.push(`${lastName}, ${foreName}`.trim());
}
}
}
let publicationDate = 'Unknown date';
const pubDate = medlineCitation.Article?.[0]?.Journal?.[0]?.JournalIssue?.[0]?.PubDate?.[0];
if (pubDate) {
const year = pubDate.Year?.[0] || '';
const month = pubDate.Month?.[0] || '';
const day = pubDate.Day?.[0] || '';
publicationDate = [year, month, day].filter(Boolean).join('-');
}
const abstractTexts = medlineCitation.Article?.[0]?.Abstract?.[0]?.AbstractText;
let abstract = '';
if (abstractTexts) {
abstract = abstractTexts.map(text => {
if (typeof text === 'string') return text;
if (text._) return text._;
return '';
}).join(' ');
}
let doi = '';
const articleIds = pubmedData?.ArticleIdList?.[0]?.ArticleId;
if (articleIds) {
for (const id of articleIds) {
if (id.$ && id.$.IdType === 'doi') {
doi = id._;
break;
}
}
}
let pmcid = '';
if (articleIds) {
for (const id of articleIds) {
if (id.$ && id.$.IdType === 'pmc') {
pmcid = id._;
break;
}
}
}
const meshTerms = [];
const meshHeadingList = medlineCitation.MeshHeadingList?.[0]?.MeshHeading;
if (meshHeadingList) {
for (const heading of meshHeadingList) {
const descriptorName = heading.DescriptorName?.[0]?._;
if (descriptorName) {
meshTerms.push(descriptorName);
}
}
}
const keywords = [];
const keywordList = medlineCitation.KeywordList?.[0]?.Keyword;
if (keywordList) {
for (const keyword of keywordList) {
if (typeof keyword === 'string') {
keywords.push(keyword);
} else if (keyword._) {
keywords.push(keyword._);
}
}
}
return {
pmid,
title,
authors,
journal,
publication_date: publicationDate,
abstract,
doi,
pmcid,
keywords,
mesh_terms: meshTerms,
url: `https://pubmed.ncbi.nlm.nih.gov/${pmid}/`
};
} catch (error) {
console.error(`Error fetching metadata for PMID ${pmid}:`, error.message);
return null;
}
}
async function searchKeywords(keywords, numResults = 10) {
console.log(`Generated search URL for keywords: ${keywords}`);
const searchUrl = generatePubMedSearchUrl(keywords, numResults);
const pmids = await searchPubMed(searchUrl);
const articles = [];
for (const pmid of pmids) {
const metadata = await getPubMedMetadata(pmid);
if (metadata) {
articles.push(metadata);
}
}
return articles;
}
async function searchAdvanced(params) {
let searchTerm = '';
const terms = [];
if (params.term) terms.push(params.term);
if (params.title) terms.push(`${params.title}[Title]`);
if (params.author) terms.push(`${params.author}[Author]`);
if (params.journal) terms.push(`${params.journal}[Journal]`);
if (params.start_date && params.end_date) {
terms.push(`${params.start_date}:${params.end_date}[Date - Publication]`);
} else if (params.start_date) {
terms.push(`${params.start_date}:3000[Date - Publication]`);
} else if (params.end_date) {
terms.push(`1800:${params.end_date}[Date - Publication]`);
}
searchTerm = terms.join(' AND ');
if (!searchTerm) {
throw new Error('At least one search parameter is required');
}
console.log(`Generated advanced search URL: ${searchTerm}`);
const searchUrl = generatePubMedSearchUrl(searchTerm, params.num_results || 10);
const pmids = await searchPubMed(searchUrl);
const articles = [];
for (const pmid of pmids) {
const metadata = await getPubMedMetadata(pmid);
if (metadata) {
articles.push(metadata);
}
}
return articles;
}
async function getArticleMetadata(pmid) {
const pmidStr = typeof pmid === 'number' ? pmid.toString() : pmid;
console.log(`Fetching metadata for PMID: ${pmidStr}`);
return await getPubMedMetadata(pmidStr);
}
async function downloadFullTextPdf(pmid) {
const pmidStr = typeof pmid === 'number' ? pmid.toString() : pmid;
console.log(`PDF download requested for PMID: ${pmidStr}`);
const metadata = await getPubMedMetadata(pmidStr);
if (metadata?.pmcid) {
return {
pdf_url: `https://www.ncbi.nlm.nih.gov/pmc/articles/${metadata.pmcid}/pdf/`,
message: `PDF may be available at PMC: ${metadata.pmcid}`
};
}
return {
message: `PDF not directly available for PMID ${pmidStr}. Check publisher website.`
};
}
export {
searchKeywords,
searchAdvanced,
getArticleMetadata,
downloadFullTextPdf
};
