cBioPortal MCP Server

Instructions

Implementation Reference

• cbioportal_mcp/endpoints/studies.py:163-182 (handler)

  Core handler function that performs input validation, makes the API request to fetch study details from 'studies/{study_id}', and handles errors.

  @handle_api_errors("get study details")
  async def get_study_details(self, study_id: str) -> Dict[str, Any]:
      """
      Get detailed information for a specific cancer study.
  
      Args:
          study_id: The ID of the cancer study
  
      Returns:
          Dictionary containing study details
      """
      # Input Validation
      validate_study_id(study_id)
  
      endpoint = f"studies/{study_id}"
      try:
          study = await self.api_client.make_api_request(endpoint)
          return {"study": study}
      except Exception as e:
          return {"error": f"Failed to get study details for {study_id}: {str(e)}"}

• cbioportal_mcp/server.py:207-209 (handler)

  Proxy handler method on the main server class that delegates to the StudiesEndpoints implementation; this is the method registered as the MCP tool.

  async def get_study_details(self, study_id: str) -> Dict[str, Any]:
      """Get detailed information for a specific cancer study."""
      return await self.studies.get_study_details(study_id)

• cbioportal_mcp/server.py:96-131 (registration)

  Registers all MCP tools, including 'get_study_details', by dynamically adding the server instance methods to FastMCP.

  def _register_tools(self):
      """Register tool methods as MCP tools."""
      # List of methods to register as tools (explicitly defined)
      tool_methods = [
          # Pagination utilities
          "paginate_results",
          "collect_all_results",
          # Studies endpoints
          "get_cancer_studies",
          "get_cancer_types",
          "search_studies",
          "get_study_details",
          "get_multiple_studies",
          # Genes endpoints
          "search_genes",
          "get_genes",
          "get_multiple_genes",
          "get_mutations_in_gene",
          # Samples endpoints
          "get_samples_in_study",
          "get_sample_list_id",
          # Molecular profiles endpoints
          "get_molecular_profiles",
          "get_clinical_data",
          "get_gene_panels_for_study",
          "get_gene_panel_details",
      ]
  
      for method_name in tool_methods:
          if hasattr(self, method_name):
              method = getattr(self, method_name)
              self.mcp.add_tool(method)
              logger.debug(f"Registered tool: {method_name}")
          else:
              logger.warning(f"Method {method_name} not found for tool registration")

• cbioportal_mcp/utils/validation.py:66-80 (schema)

  Input validation function for the study_id parameter, ensuring it is a non-empty string. Called within the handler.

  def validate_study_id(study_id: str) -> None:
      """
      Validate study ID parameter.
  
      Args:
          study_id: Study identifier
  
      Raises:
          TypeError: If study_id is not a string
          ValueError: If study_id is empty
      """
      if not isinstance(study_id, str):
          raise TypeError("study_id must be a string")
      if not study_id:
          raise ValueError("study_id cannot be empty")