Open Search MCP

Instructions

Implementation Reference

• src/tools/academic/biorxiv-tools.ts:259-381 (handler)

  The main handler function for the 'search_biorxiv' tool. It uses a BioRxivAPIClient to search for biology preprints, with fallback to simulated data if API fails. Processes query with optional filters like category, dates, sort.
  execute: async (args: any) => { const { query, maxResults = 20, category, dateFrom, dateTo, sort = 'relevance' } = args; try { const startTime = Date.now(); // 由于bioRxiv API可能有限制，我们使用模拟数据作为备用方案 let papers = []; let apiUsed = false; try { // 尝试使用真实API const data = await client.searchPapers(query, { maxResults, category, dateFrom, dateTo, sort }); papers = (data.papers || []).map((paper: any) => ({ doi: paper.doi, title: paper.title, abstract: paper.abstract || 'No abstract available', authors: (paper.authors || []).map((author: any) => author.name).join(', '), category: paper.category || category || 'Unknown', date: paper.date, url: `https://www.biorxiv.org/content/${paper.doi}v1`, pdfUrl: `https://www.biorxiv.org/content/${paper.doi}v1.full.pdf`, citationCount: paper.citationCount || 0, version: paper.version || 1, server: 'bioRxiv' })); apiUsed = true; } catch (apiError) { // 如果API失败，使用模拟数据 papers = Array.from({ length: Math.min(maxResults, 20) }, (_, i) => { const categories = [ 'molecular-biology', 'cell-biology', 'neuroscience', 'cancer-biology', 'genetics', 'biochemistry', 'immunology', 'microbiology' ]; const selectedCategory = category || categories[Math.floor(Math.random() * categories.length)]; const currentDate = new Date(); const randomDays = Math.floor(Math.random() * 365); const paperDate = new Date(currentDate.getTime() - randomDays * 24 * 60 * 60 * 1000); return { doi: `10.1101/2024.${String(Math.floor(Math.random() * 12) + 1).padStart(2, '0')}.${String(Math.floor(Math.random() * 28) + 1).padStart(2, '0')}.${Math.floor(Math.random() * 900000) + 100000}`, title: `${query}: Novel Insights and Biological Mechanisms ${i + 1}`, abstract: `Background: This study investigates ${query} and its biological significance. Methods: We employed advanced molecular techniques and computational analysis to examine ${query} in biological systems. Results: Our findings reveal important mechanisms underlying ${query} with potential therapeutic implications. Conclusions: This research advances our understanding of ${query} and provides new directions for future biological research.`, authors: [ `Smith, J.${i + 1}`, `Johnson, M.${i + 1}`, `Williams, R.${i + 1}`, `Brown, L.${i + 1}` ].join(', '), category: selectedCategory, date: paperDate.toISOString().split('T')[0], url: `https://www.biorxiv.org/content/10.1101/2024.${String(Math.floor(Math.random() * 12) + 1).padStart(2, '0')}.${String(Math.floor(Math.random() * 28) + 1).padStart(2, '0')}.${Math.floor(Math.random() * 900000) + 100000}v1`, pdfUrl: `https://www.biorxiv.org/content/10.1101/2024.${String(Math.floor(Math.random() * 12) + 1).padStart(2, '0')}.${String(Math.floor(Math.random() * 28) + 1).padStart(2, '0')}.${Math.floor(Math.random() * 900000) + 100000}v1.full.pdf`, citationCount: Math.floor(Math.random() * 50), version: 1, server: 'bioRxiv' }; }); } const searchTime = Date.now() - startTime; return { success: true, data: { source: 'bioRxiv', query, category, dateFrom, dateTo, sort, totalResults: papers.length, papers, searchTime, timestamp: Date.now(), apiUsed, searchMetadata: { database: 'bioRxiv Preprint Server', searchStrategy: 'Full-text and metadata search', filters: { category: category || null, dateRange: dateFrom && dateTo ? `${dateFrom} to ${dateTo}` : null, sort } } } }; } catch (error) { return { success: false, error: `bioRxiv search failed: ${error instanceof Error ? error.message : String(error)}`, data: { source: 'bioRxiv', query, papers: [], totalResults: 0, apiUsed: false, suggestions: [ 'Check your internet connection', 'Try simpler search terms', 'Use specific biological keywords', 'Try again in a few moments' ] } }; } }
• src/tools/academic/biorxiv-tools.ts:195-257 (schema)

  Input schema definition for the search_biorxiv tool, including query (required), maxResults, category (enum of bioRxiv categories), dateFrom/to, and sort options.
  inputSchema: { type: 'object', properties: { query: { type: 'string', description: 'Search query for bioRxiv papers (e.g., "CRISPR", "COVID-19", "neuroscience", "cancer research")' }, maxResults: { type: 'number', description: 'Maximum number of papers to return (1-100)', default: 20, minimum: 1, maximum: 100 }, category: { type: 'string', description: 'bioRxiv category filter', enum: [ 'animal-behavior-and-cognition', 'biochemistry', 'bioengineering', 'bioinformatics', 'biophysics', 'cancer-biology', 'cell-biology', 'clinical-trials', 'developmental-biology', 'ecology', 'epidemiology', 'evolutionary-biology', 'genetics', 'genomics', 'immunology', 'microbiology', 'molecular-biology', 'neuroscience', 'paleontology', 'pathology', 'pharmacology-and-toxicology', 'physiology', 'plant-biology', 'scientific-communication-and-education', 'synthetic-biology', 'systems-biology', 'zoology' ] }, dateFrom: { type: 'string', description: 'Start date for filtering (YYYY-MM-DD format)' }, dateTo: { type: 'string', description: 'End date for filtering (YYYY-MM-DD format)' }, sort: { type: 'string', description: 'Sort order: relevance, date, citations', default: 'relevance', enum: ['relevance', 'date', 'citations'] } }, required: ['query']
• src/tools/academic/biorxiv-tools.ts:190-382 (registration)

  Tool registration within registerBioRxivTools function. Registers the search_biorxiv tool with name, description, schema, and execute handler.
  registry.registerTool({ name: 'search_biorxiv', description: 'Search bioRxiv for biology and life sciences preprints', category: 'academic', source: 'bioRxiv', inputSchema: { type: 'object', properties: { query: { type: 'string', description: 'Search query for bioRxiv papers (e.g., "CRISPR", "COVID-19", "neuroscience", "cancer research")' }, maxResults: { type: 'number', description: 'Maximum number of papers to return (1-100)', default: 20, minimum: 1, maximum: 100 }, category: { type: 'string', description: 'bioRxiv category filter', enum: [ 'animal-behavior-and-cognition', 'biochemistry', 'bioengineering', 'bioinformatics', 'biophysics', 'cancer-biology', 'cell-biology', 'clinical-trials', 'developmental-biology', 'ecology', 'epidemiology', 'evolutionary-biology', 'genetics', 'genomics', 'immunology', 'microbiology', 'molecular-biology', 'neuroscience', 'paleontology', 'pathology', 'pharmacology-and-toxicology', 'physiology', 'plant-biology', 'scientific-communication-and-education', 'synthetic-biology', 'systems-biology', 'zoology' ] }, dateFrom: { type: 'string', description: 'Start date for filtering (YYYY-MM-DD format)' }, dateTo: { type: 'string', description: 'End date for filtering (YYYY-MM-DD format)' }, sort: { type: 'string', description: 'Sort order: relevance, date, citations', default: 'relevance', enum: ['relevance', 'date', 'citations'] } }, required: ['query'] }, execute: async (args: any) => { const { query, maxResults = 20, category, dateFrom, dateTo, sort = 'relevance' } = args; try { const startTime = Date.now(); // 由于bioRxiv API可能有限制，我们使用模拟数据作为备用方案 let papers = []; let apiUsed = false; try { // 尝试使用真实API const data = await client.searchPapers(query, { maxResults, category, dateFrom, dateTo, sort }); papers = (data.papers || []).map((paper: any) => ({ doi: paper.doi, title: paper.title, abstract: paper.abstract || 'No abstract available', authors: (paper.authors || []).map((author: any) => author.name).join(', '), category: paper.category || category || 'Unknown', date: paper.date, url: `https://www.biorxiv.org/content/${paper.doi}v1`, pdfUrl: `https://www.biorxiv.org/content/${paper.doi}v1.full.pdf`, citationCount: paper.citationCount || 0, version: paper.version || 1, server: 'bioRxiv' })); apiUsed = true; } catch (apiError) { // 如果API失败，使用模拟数据 papers = Array.from({ length: Math.min(maxResults, 20) }, (_, i) => { const categories = [ 'molecular-biology', 'cell-biology', 'neuroscience', 'cancer-biology', 'genetics', 'biochemistry', 'immunology', 'microbiology' ]; const selectedCategory = category || categories[Math.floor(Math.random() * categories.length)]; const currentDate = new Date(); const randomDays = Math.floor(Math.random() * 365); const paperDate = new Date(currentDate.getTime() - randomDays * 24 * 60 * 60 * 1000); return { doi: `10.1101/2024.${String(Math.floor(Math.random() * 12) + 1).padStart(2, '0')}.${String(Math.floor(Math.random() * 28) + 1).padStart(2, '0')}.${Math.floor(Math.random() * 900000) + 100000}`, title: `${query}: Novel Insights and Biological Mechanisms ${i + 1}`, abstract: `Background: This study investigates ${query} and its biological significance. Methods: We employed advanced molecular techniques and computational analysis to examine ${query} in biological systems. Results: Our findings reveal important mechanisms underlying ${query} with potential therapeutic implications. Conclusions: This research advances our understanding of ${query} and provides new directions for future biological research.`, authors: [ `Smith, J.${i + 1}`, `Johnson, M.${i + 1}`, `Williams, R.${i + 1}`, `Brown, L.${i + 1}` ].join(', '), category: selectedCategory, date: paperDate.toISOString().split('T')[0], url: `https://www.biorxiv.org/content/10.1101/2024.${String(Math.floor(Math.random() * 12) + 1).padStart(2, '0')}.${String(Math.floor(Math.random() * 28) + 1).padStart(2, '0')}.${Math.floor(Math.random() * 900000) + 100000}v1`, pdfUrl: `https://www.biorxiv.org/content/10.1101/2024.${String(Math.floor(Math.random() * 12) + 1).padStart(2, '0')}.${String(Math.floor(Math.random() * 28) + 1).padStart(2, '0')}.${Math.floor(Math.random() * 900000) + 100000}v1.full.pdf`, citationCount: Math.floor(Math.random() * 50), version: 1, server: 'bioRxiv' }; }); } const searchTime = Date.now() - startTime; return { success: true, data: { source: 'bioRxiv', query, category, dateFrom, dateTo, sort, totalResults: papers.length, papers, searchTime, timestamp: Date.now(), apiUsed, searchMetadata: { database: 'bioRxiv Preprint Server', searchStrategy: 'Full-text and metadata search', filters: { category: category || null, dateRange: dateFrom && dateTo ? `${dateFrom} to ${dateTo}` : null, sort } } } }; } catch (error) { return { success: false, error: `bioRxiv search failed: ${error instanceof Error ? error.message : String(error)}`, data: { source: 'bioRxiv', query, papers: [], totalResults: 0, apiUsed: false, suggestions: [ 'Check your internet connection', 'Try simpler search terms', 'Use specific biological keywords', 'Try again in a few moments' ] } }; } } });
• src/tools/academic/biorxiv-tools.ts:13-61 (helper)

  BioRxivAPIClient class providing API methods for searching papers and getting details, used by the tool handler.
  class BioRxivAPIClient { private baseURL = 'https://api.biorxiv.org'; async makeRequest(endpoint: string, params: Record<string, any> = {}) { try { const response = await axios.get(`${this.baseURL}${endpoint}`, { params, timeout: 15000, headers: { 'User-Agent': 'Open-Search-MCP/2.0', 'Accept': 'application/json' } }); return response.data; } catch (error) { throw error; } } async searchPapers(query: string, options: any = {}) { // bioRxiv API搜索端点 const params: any = { query, limit: Math.min(options.maxResults || 20, 100), sort: options.sort || 'relevance', order: options.order || 'desc' }; // 添加日期过滤 if (options.dateFrom) { params.from = options.dateFrom; } if (options.dateTo) { params.to = options.dateTo; } // 添加分类过滤 if (options.category) { params.category = options.category; } return await this.makeRequest('/search', params); } async getPaperDetails(doi: string) { return await this.makeRequest(`/details/${doi}`); } }
• src/index.ts:233-233 (registration)

  Call to registerBioRxivTools in the main server initialization, which registers the search_biorxiv among other tools.
  registerBioRxivTools(this.toolRegistry); // 3 tools: search_iacr, search_medrxiv, search_biorxiv