pubmed-tools.ts•11.4 kB
/**
* PubMed Academic Research Tools
* 提供PubMed医学文献搜索和研究功能
*/
import { ToolRegistry } from '../tool-registry.js';
import axios from 'axios';
/**
* PubMed API客户端
*/
class PubMedAPIClient {
private baseURL = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils';
private apiKey: string | undefined;
constructor(apiKey?: string) {
this.apiKey = apiKey;
}
async makeRequest(endpoint: string, params: Record<string, any> = {}) {
try {
const requestParams = {
...params,
retmode: 'json',
retmax: Math.min(params.retmax || 20, 200),
tool: 'open-search-mcp',
email: 'support@open-search-mcp.com'
};
if (this.apiKey) {
(requestParams as any).api_key = this.apiKey;
}
const response = await axios.get(`${this.baseURL}/${endpoint}`, {
params: requestParams,
timeout: 20000,
headers: {
'User-Agent': 'Open-Search-MCP/2.0'
}
});
return response.data;
} catch (error) {
throw error;
}
}
async searchPubMed(query: string, options: any = {}) {
// 第一步：搜索获取PMID列表
const searchParams = {
db: 'pubmed',
term: query,
retmax: options.maxResults || 20,
sort: options.sort === 'date' ? 'pub_date' : 'relevance',
datetype: 'pdat'
};
// 添加日期过滤
if (options.dateRange && options.dateRange !== 'all') {
const now = new Date();
let startDate;
switch (options.dateRange) {
case '1year':
startDate = new Date(now.getFullYear() - 1, now.getMonth(), now.getDate());
break;
case '5years':
startDate = new Date(now.getFullYear() - 5, now.getMonth(), now.getDate());
break;
case '10years':
startDate = new Date(now.getFullYear() - 10, now.getMonth(), now.getDate());
break;
}
if (startDate) {
const startDateStr = startDate.toISOString().split('T')[0].replace(/-/g, '/');
const endDateStr = now.toISOString().split('T')[0].replace(/-/g, '/');
searchParams.term += ` AND ("${startDateStr}"[Date - Publication] : "${endDateStr}"[Date - Publication])`;
}
}
// 添加出版物类型过滤
if (options.publicationType && options.publicationType !== 'all') {
const typeMap: Record<string, string> = {
'review': 'Review[Publication Type]',
'clinical_trial': 'Clinical Trial[Publication Type]',
'meta_analysis': 'Meta-Analysis[Publication Type]',
'case_report': 'Case Reports[Publication Type]'
};
const pubType = options.publicationType as string;
if (typeMap[pubType]) {
searchParams.term += ` AND ${typeMap[pubType]}`;
}
}
const searchResult = await this.makeRequest('esearch.fcgi', searchParams);
if (!searchResult.esearchresult || !searchResult.esearchresult.idlist || searchResult.esearchresult.idlist.length === 0) {
return { articles: [], count: 0 };
}
const pmids = searchResult.esearchresult.idlist;
// 第二步：获取详细信息
const summaryParams = {
db: 'pubmed',
id: pmids.join(','),
retmode: 'json'
};
const summaryResult = await this.makeRequest('esummary.fcgi', summaryParams);
return {
articles: this.parseSummaryResult(summaryResult),
count: parseInt(searchResult.esearchresult.count) || 0
};
}
private parseSummaryResult(summaryResult: any): any[] {
if (!summaryResult.result) return [];
const articles = [];
const uids = summaryResult.result.uids || [];
for (const uid of uids) {
const article = summaryResult.result[uid];
if (!article) continue;
articles.push({
pmid: article.uid,
title: article.title || 'No title available',
abstract: article.abstract || 'No abstract available',
authors: (article.authors || []).map((author: any) => author.name).join(', '),
journal: article.fulljournalname || article.source || 'Unknown journal',
publicationDate: article.pubdate || 'Unknown date',
publicationType: (article.pubtype || []).join(', ') || 'Unknown type',
doi: article.elocationid && article.elocationid.includes('doi:')
? article.elocationid.replace('doi: ', '')
: null,
pmcid: article.pmcid || null,
volume: article.volume || null,
issue: article.issue || null,
pages: article.pages || null,
url: `https://pubmed.ncbi.nlm.nih.gov/${article.uid}/`,
fullTextUrl: article.pmcid ? `https://www.ncbi.nlm.nih.gov/pmc/articles/${article.pmcid}/` : null
});
}
return articles;
}
}
export function registerPubMedTools(registry: ToolRegistry): void {
const apiKey = process.env.PUBMED_API_KEY; // 可选的API密钥
const client = new PubMedAPIClient(apiKey);
// PubMed文献搜索
registry.registerTool({
name: 'search_pubmed',
description: 'Search PubMed for medical and life science literature',
category: 'academic',
source: 'PubMed',
inputSchema: {
type: 'object',
properties: {
query: {
type: 'string',
description: 'Search query for medical literature (e.g., "COVID-19 treatment", "cancer immunotherapy", "diabetes management")'
},
maxResults: {
type: 'number',
description: 'Maximum number of articles to return (1-200)',
default: 20,
minimum: 1,
maximum: 200
},
sort: {
type: 'string',
description: 'Sort order: relevance, date',
default: 'relevance',
enum: ['relevance', 'date']
},
publicationType: {
type: 'string',
description: 'Filter by publication type: all, review, clinical_trial, meta_analysis, case_report',
default: 'all',
enum: ['all', 'review', 'clinical_trial', 'meta_analysis', 'case_report']
},
dateRange: {
type: 'string',
description: 'Date range filter: all, 1year, 5years, 10years',
default: 'all',
enum: ['all', '1year', '5years', '10years']
}
},
required: ['query']
},
execute: async (args: any) => {
const { query, maxResults = 20, sort = 'relevance', publicationType = 'all', dateRange = 'all' } = args;
try {
const startTime = Date.now();
// 使用真正的PubMed API
const result = await client.searchPubMed(query, {
maxResults,
sort,
publicationType,
dateRange
});
const searchTime = Date.now() - startTime;
return {
success: true,
data: {
source: 'PubMed API',
query,
sort,
publicationType,
dateRange,
totalResults: result.count,
articles: result.articles,
searchTime,
timestamp: Date.now(),
apiUsed: true,
searchMetadata: {
database: 'PubMed',
searchStrategy: 'E-utilities API',
filters: {
publicationType: publicationType !== 'all' ? publicationType : null,
dateRange: dateRange !== 'all' ? dateRange : null,
sort
}
}
}
};
} catch (error) {
// 如果API失败，提供有用的错误信息
return {
success: false,
error: `PubMed search failed: ${error instanceof Error ? error.message : String(error)}`,
data: {
source: 'PubMed',
query,
articles: [],
totalResults: 0,
apiUsed: false,
suggestions: [
'Check your internet connection',
'Try simpler search terms',
'Use medical subject headings (MeSH terms)',
'Try again in a few moments'
]
}
};
}
}
});
// PubMed文章详情获取
registry.registerTool({
name: 'pubmed_article_details',
description: 'Get detailed information about a specific PubMed article',
category: 'academic',
source: 'PubMed',
inputSchema: {
type: 'object',
properties: {
pmid: {
type: 'string',
description: 'PubMed ID (PMID) of the article'
}
},
required: ['pmid']
},
execute: async (args: any) => {
const { pmid } = args;
try {
// 获取文章摘要信息
const summaryParams = {
db: 'pubmed',
id: pmid,
retmode: 'json'
};
const summaryResult = await client.makeRequest('esummary.fcgi', summaryParams);
if (!summaryResult.result || !summaryResult.result[pmid]) {
return {
success: false,
error: `Article with PMID ${pmid} not found`
};
}
const article = summaryResult.result[pmid];
// 尝试获取全文摘要
let fullAbstract = null;
try {
const fetchParams = {
db: 'pubmed',
id: pmid,
retmode: 'xml',
rettype: 'abstract'
};
const fetchResult = await client.makeRequest('efetch.fcgi', fetchParams);
// 这里可以解析XML获取完整摘要，暂时使用summary中的摘要
fullAbstract = article.abstract || 'No abstract available';
} catch (fetchError) {
fullAbstract = article.abstract || 'No abstract available';
}
const articleDetails = {
pmid: article.uid,
title: article.title || 'No title available',
abstract: fullAbstract,
authors: (article.authors || []).map((author: any) => ({
name: author.name,
affiliation: author.affiliation || null
})),
journal: {
name: article.fulljournalname || article.source || 'Unknown journal',
abbreviation: article.source || null,
volume: article.volume || null,
issue: article.issue || null,
pages: article.pages || null
},
publicationDate: article.pubdate || 'Unknown date',
publicationType: (article.pubtype || []).join(', ') || 'Unknown type',
doi: article.elocationid && article.elocationid.includes('doi:')
? article.elocationid.replace('doi: ', '')
: null,
pmcid: article.pmcid || null,
meshTerms: article.keywords || [],
url: `https://pubmed.ncbi.nlm.nih.gov/${article.uid}/`,
fullTextUrl: article.pmcid ? `https://www.ncbi.nlm.nih.gov/pmc/articles/${article.pmcid}/` : null,
citationCount: null, // PubMed API不直接提供引用数
source: 'PubMed'
};
return {
success: true,
data: {
source: 'PubMed API',
article: articleDetails,
timestamp: Date.now(),
apiUsed: true
}
};
} catch (error) {
return {
success: false,
error: `Failed to get PubMed article details: ${error instanceof Error ? error.message : String(error)}`
};
}
}
});
}