ProteinAtlas MCP Server

Instructions

Implementation Reference

• src/index.ts:1099-1136 (handler)

  The handler function for 'search_cancer_markers' tool. Validates input using isValidPathologySearchArgs, constructs a search query based on cancer type and/or prognostic value, calls the shared searchProteins helper, and formats the response or error.

  private async handleSearchCancerMarkers(args: any) {
    if (!isValidPathologySearchArgs(args)) {
      throw new McpError(ErrorCode.InvalidParams, 'Invalid pathology search arguments');
    }
  
    try {
      let searchQuery = '';
      if (args.cancer) {
        searchQuery = `cancer:"${args.cancer}"`;
      }
      if (args.prognostic) {
        searchQuery += searchQuery ? ` AND prognostic:"${args.prognostic}"` : `prognostic:"${args.prognostic}"`;
      }
      if (!searchQuery) {
        searchQuery = 'prognostic:*'; // Search for any prognostic markers
      }
  
      const result = await this.searchProteins(searchQuery, args.format || 'json', undefined, args.maxResults);
      return {
        content: [
          {
            type: 'text',
            text: typeof result === 'object' ? JSON.stringify(result, null, 2) : String(result),
          },
        ],
      };
    } catch (error) {
      return {
        content: [
          {
            type: 'text',
            text: `Error searching cancer markers: ${error instanceof Error ? error.message : 'Unknown error'}`,
          },
        ],
        isError: true,
      };
    }
  }

• src/index.ts:574-587 (registration)

  Registration of the 'search_cancer_markers' tool in the tools list returned by ListToolsRequestSchema handler, including description and JSON input schema.

  {
    name: 'search_cancer_markers',
    description: 'Find proteins associated with specific cancers or with prognostic value',
    inputSchema: {
      type: 'object',
      properties: {
        cancer: { type: 'string', description: 'Cancer type (e.g., breast cancer, lung cancer)' },
        prognostic: { type: 'string', enum: ['favorable', 'unfavorable'], description: 'Prognostic filter' },
        format: { type: 'string', enum: ['json', 'tsv'], description: 'Output format (default: json)' },
        maxResults: { type: 'number', description: 'Maximum number of results (1-10000, default: 100)', minimum: 1, maximum: 10000 },
      },
      required: [],
    },
  },

• src/index.ts:160-171 (schema)

  Runtime type guard function used to validate input arguments for the search_cancer_markers handler, matching the inputSchema.

  const isValidPathologySearchArgs = (
    args: any
  ): args is { cancer?: string; prognostic?: string; format?: string; maxResults?: number } => {
    return (
      typeof args === 'object' &&
      args !== null &&
      (args.cancer === undefined || typeof args.cancer === 'string') &&
      (args.prognostic === undefined || ['favorable', 'unfavorable'].includes(args.prognostic)) &&
      (args.format === undefined || ['json', 'tsv'].includes(args.format)) &&
      (args.maxResults === undefined || (typeof args.maxResults === 'number' && args.maxResults > 0 && args.maxResults <= 10000))
    );
  };

• src/index.ts:692-693 (registration)

  Switch case in CallToolRequestSchema handler that dispatches calls to 'search_cancer_markers' to the specific handler method.

  case 'search_cancer_markers':
    return this.handleSearchCancerMarkers(args);