get_dataset_info

Instructions

Implementation Reference

• src/handlers/reference-handlers.ts:445-514 (handler)

  Main handler function for 'get_dataset_info' tool. Calls API client, handles errors, and formats dataset information into a detailed markdown response.

  async getDatasetInfo(args: any) {
    const result = await this.apiClient.getDatasetInfo(args.datasetId);
  
    if (result.error) {
      return {
        content: [{
          type: "text",
          text: `Error retrieving dataset information: ${result.error}`
        }],
        isError: true
      };
    }
  
    const datasets = result.data || [];
    if (datasets.length === 0) {
      return {
        content: [{
          type: "text",
          text: "No dataset information available."
        }]
      };
    }
  
    let output = `**GTEx Dataset Information**\n\n`;
  
    datasets.forEach((dataset, index) => {
      if (datasets.length > 1) {
        output += `### Dataset ${index + 1}: ${dataset.datasetId}\n`;
      }
      
      output += `**Basic Information:**\n`;
      output += `  • ID: ${dataset.datasetId}\n`;
      output += `  • Display Name: ${dataset.displayName}\n`;
      output += `  • Organization: ${dataset.organization}\n`;
      if (dataset.description) {
        output += `  • Description: ${dataset.description}\n`;
      }
      if (dataset.dbgapId) {
        output += `  • dbGaP ID: ${dataset.dbgapId}\n`;
      }
  
      output += `\n**Genomic References:**\n`;
      output += `  • Genome Build: ${dataset.genomeBuild}\n`;
      output += `  • GENCODE Version: ${dataset.gencodeVersion}\n`;
      if (dataset.dbSnpBuild) {
        output += `  • dbSNP Build: ${dataset.dbSnpBuild}\n`;
      }
  
      output += `\n**Sample Statistics:**\n`;
      output += `  • Total subjects: ${dataset.subjectCount.toLocaleString()}\n`;
      output += `  • Total tissues: ${dataset.tissueCount}\n`;
      output += `  • RNA-seq samples: ${dataset.rnaSeqSampleCount.toLocaleString()}\n`;
      output += `  • RNA-seq + genotype samples: ${dataset.rnaSeqAndGenotypeSampleCount.toLocaleString()}\n`;
  
      output += `\n**QTL Analysis:**\n`;
      output += `  • eQTL subjects: ${dataset.eqtlSubjectCount.toLocaleString()}\n`;
      output += `  • eQTL tissues: ${dataset.eqtlTissuesCount}\n`;
  
      if (datasets.length > 1 && index < datasets.length - 1) {
        output += '\n';
      }
    });
  
    return {
      content: [{
        type: "text",
        text: output
      }]
    };
  }

• src/index.ts:763-767 (registration)

  Registration and dispatching logic in the main CallToolRequestHandler that routes 'get_dataset_info' calls to the referenceHandlers.getDatasetInfo method.

  if (name === "get_dataset_info") {
    return await referenceHandlers.getDatasetInfo({
      datasetId: args?.datasetId
    });
  }

• src/index.ts:533-543 (schema)

  Tool schema definition including name, description, and input schema for 'get_dataset_info' in the ListTools response.

  name: "get_dataset_info",
  description: "Get information about available GTEx datasets",
  inputSchema: {
    type: "object",
    properties: {
      datasetId: {
        type: "string",
        description: "Specific dataset ID (optional, returns all if not provided)"
      }
    }
  }

• src/utils/api-client.ts:133-142 (helper)

  API client helper method that makes the HTTP request to GTEx Portal API /metadata/dataset endpoint to fetch dataset information.

  async getDatasetInfo(datasetId?: string): Promise<GTExApiResponse<DatasetInfo[]>> {
    try {
      const params = datasetId ? { datasetId } : {};
      const queryParams = this.buildQueryParams(params);
      const response = await this.axiosInstance.get(`/metadata/dataset?${queryParams}`);
      return { data: response.data };
    } catch (error) {
      return error as GTExApiResponse<DatasetInfo[]>;
    }
  }

• src/types/gtex-types.ts:36-51 (schema)

  TypeScript interface defining the structure of DatasetInfo objects returned by the API, used for type safety in handlers and client.

  export interface DatasetInfo {
    datasetId: string;
    dbSnpBuild: number;
    dbgapId: string;
    description: string;
    displayName: string;
    eqtlSubjectCount: number;
    eqtlTissuesCount: number;
    gencodeVersion: string;
    genomeBuild: string;
    organization: string;
    rnaSeqAndGenotypeSampleCount: number;
    rnaSeqSampleCount: number;
    subjectCount: number;
    tissueCount: number;
  }