cBioPortal MCP Server

Instructions

Implementation Reference

• cbioportal_mcp/server.py:146-158 (handler)

  MCP tool handler for collect_all_results tool. Thin wrapper that injects the API client and delegates to the pagination utility.

  async def collect_all_results(
      self,
      endpoint: str,
      params: Optional[Dict[str, Any]] = None,
      method: str = "GET",
      json_data: Any = None,
      max_pages: Optional[int] = None,
      limit: Optional[int] = None,
  ) -> List[Dict[str, Any]]:
      """Delegate to utils.pagination.collect_all_results with api_client."""
      return await collect_all_results(
          self.api_client, endpoint, params, method, json_data, max_pages, limit
      )

• cbioportal_mcp/utils/pagination.py:71-107 (helper)

  Core utility implementation of collect_all_results. Uses paginate_results async generator to fetch and accumulate all pages of results, respecting limits.

  async def collect_all_results(
      api_client,
      endpoint: str,
      params: Optional[Dict[str, Any]] = None,
      method: str = "GET",
      json_data: Any = None,
      max_pages: Optional[int] = None,
      limit: Optional[int] = None,
  ) -> List[Dict[str, Any]]:
      """
      Collect all results from a paginated endpoint into a single list.
  
      Args:
          api_client: The APIClient instance to use for requests
          endpoint: API endpoint path
          params: Query parameters to include in the request
          method: HTTP method (GET or POST)
          json_data: JSON data for POST requests
          max_pages: Maximum number of pages to retrieve
          limit: Maximum number of total results to return
  
      Returns:
          List of all collected results (limited by max_pages and/or limit)
      """
      all_results = []
  
      async for page in paginate_results(
          api_client, endpoint, params, method, json_data, max_pages
      ):
          all_results.extend(page)
  
          # Stop if we've reached the specified limit
          if limit and len(all_results) >= limit:
              all_results = all_results[:limit]
              break
  
      return all_results

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

  Registration of MCP tools including collect_all_results. The tool_methods list includes it, and self.mcp.add_tool registers the handler method.

  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")