batch_article_lookup

Instructions

Implementation Reference

• src/index.ts:808-847 (handler)

  Handler function for batch_article_lookup. Validates input (non-empty array, max 200 PMIDs, valid PMID format), processes in chunks of 50 via eutilsClient.getArticlesBatch, and returns articles with counts.

  async function handleBatchArticleLookup(args: any) {
    const { pmids } = args;
  
    if (!Array.isArray(pmids) || pmids.length === 0) {
      throw new Error('pmids must be a non-empty array');
    }
  
    if (pmids.length > 200) {
      throw new Error('Maximum 200 PMIDs allowed per batch');
    }
  
    // Validate all PMIDs
    for (const pmid of pmids) {
      if (!isValidPMID(pmid)) {
        throw new Error(`Invalid PMID format: ${pmid}`);
      }
    }
  
    // Process in chunks of 50
    const chunks = chunkArray(pmids, 50);
    const allArticles = [];
  
    for (const chunk of chunks) {
      const articles = await eutilsClient.getArticlesBatch(chunk);
      allArticles.push(...articles);
    }
  
    return {
      content: [
        {
          type: 'text',
          text: JSON.stringify({
            totalRequested: pmids.length,
            totalRetrieved: allArticles.length,
            articles: allArticles
          }, null, 2)
        }
      ]
    };
  }

• src/index.ts:296-310 (schema)

  Tool schema/definition registered in ListToolsRequestSchema handler. Defines the input schema requiring a 'pmids' array of strings (max 200 items).

  {
    name: 'batch_article_lookup',
    description: 'Retrieve multiple articles efficiently (up to 200 PMIDs)',
    inputSchema: {
      type: 'object',
      properties: {
        pmids: {
          type: 'array',
          items: { type: 'string' },
          description: 'Array of PubMed IDs',
          maxItems: 200
        }
      },
      required: ['pmids']
    }

• src/index.ts:467-468 (registration)

  Tool execution registration in CallToolRequestSchema handler. Routes the tool name 'batch_article_lookup' to the handleBatchArticleLookup function.

  case 'batch_article_lookup':
    return await handleBatchArticleLookup(args);

• src/api/eutils.ts:346-365 (helper)

  Helper method on EUtilsClient that fetches multiple articles by PMIDs from NCBI E-utilities, parses XML response, and returns PubMedArticle objects.

  async getArticlesBatch(pmids: string[]): Promise<PubMedArticle[]> {
    if (pmids.length === 0) {
      return [];
    }
  
    const result = await this.fetch({
      db: 'pubmed',
      id: pmids,
      retmode: 'xml',
      rettype: 'abstract'
    });
  
    const articleSet = result.PubmedArticleSet?.PubmedArticle || result.PubmedArticle;
    if (!articleSet) {
      return [];
    }
  
    const articles = Array.isArray(articleSet) ? articleSet : [articleSet];
    return articles.map(article => this.parseArticle(article));
  }

• src/api/utils.ts:203-209 (helper)

  Generic utility function that splits an array into smaller chunks of a given size. Used by handleBatchArticleLookup to process PMIDs in chunks of 50.

  export function chunkArray<T>(array: T[], size: number): T[][] {
    const chunks: T[][] = [];
    for (let i = 0; i < array.length; i += size) {
      chunks.push(array.slice(i, i + size));
    }
    return chunks;
  }