Paper Search MCP

Instructions

Implementation Reference

• src/mcp/handleToolCall.ts:128-151 (handler)

  Handler logic for executing the 'search_pubmed' MCP tool: destructures args, performs search via searchers.pubmed.search(), retrieves rate limit status, and returns formatted JSON response with paper details.

  case 'search_pubmed': {
    const { query, maxResults, year, author, journal, publicationType, sortBy } = args;
  
    const results = await searchers.pubmed.search(query, {
      maxResults,
      year,
      author,
      journal,
      publicationType,
      sortBy
    });
  
    const rateStatus = searchers.pubmed.getRateLimiterStatus();
    const apiKeyStatus = searchers.pubmed.hasApiKey() ? 'configured' : 'not configured';
    const rateLimit = searchers.pubmed.hasApiKey() ? '10 requests/second' : '3 requests/second';
  
    return jsonTextResponse(
      `Found ${results.length} PubMed papers.\n\nAPI Status: ${apiKeyStatus} (${rateLimit})\nRate Limiter: ${rateStatus.availableTokens}/${rateStatus.maxTokens} tokens available\n\n${JSON.stringify(
        results.map((paper: Paper) => PaperFactory.toDict(paper)),
        null,
        2
      )}`
    );
  }

• src/mcp/schemas.ts:69-79 (schema)

  Zod schema definition (SearchPubMedSchema) for input validation of the 'search_pubmed' tool parameters.

  export const SearchPubMedSchema = z
    .object({
      query: z.string().min(1),
      maxResults: z.number().int().min(1).max(100).optional().default(10),
      year: z.string().optional(),
      author: z.string().optional(),
      journal: z.string().optional(),
      publicationType: z.array(z.string()).optional(),
      sortBy: z.enum(['relevance', 'date']).optional()
    })
    .strip();

• src/mcp/tools.ts:131-160 (registration)

  MCP tool registration in TOOLS array, including name, description, and JSON inputSchema matching the Zod schema.

  {
    name: 'search_pubmed',
    description: 'Search biomedical literature from PubMed/MEDLINE database using NCBI E-utilities API',
    inputSchema: {
      type: 'object',
      properties: {
        query: { type: 'string', description: 'Search query string' },
        maxResults: {
          type: 'number',
          minimum: 1,
          maximum: 100,
          description: 'Maximum number of results to return'
        },
        year: { type: 'string', description: 'Publication year filter (e.g., "2023", "2020-2023")' },
        author: { type: 'string', description: 'Author name filter' },
        journal: { type: 'string', description: 'Journal name filter' },
        publicationType: {
          type: 'array',
          items: { type: 'string' },
          description: 'Publication type filter (e.g., ["Journal Article", "Review"])'
        },
        sortBy: {
          type: 'string',
          enum: ['relevance', 'date'],
          description: 'Sort results by relevance or date'
        }
      },
      required: ['query']
    }
  },

• src/mcp/schemas.ts:238-239 (schema)

  Schema parsing logic in parseToolArgs function for 'search_pubmed' tool.

  case 'search_pubmed':
    return SearchPubMedSchema.parse(args);