get_molecular_profiles
Retrieve molecular profiles for a cancer study with pagination support to explore genomic data types available for analysis.
Instructions
Get a list of molecular profiles available for a specific cancer study with pagination support.
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| study_id | Yes | ||
| page_number | No | ||
| page_size | No | ||
| sort_by | No | ||
| direction | No | ASC | |
| limit | No |
Implementation Reference
- Core handler function implementing the get_molecular_profiles tool logic: validates inputs, fetches data from cBioPortal API, applies client-side sorting and pagination, and formats the response.@handle_api_errors("get molecular profiles") async def get_molecular_profiles( self, study_id: str, page_number: int = 0, page_size: int = 50, sort_by: Optional[str] = None, direction: str = "ASC", limit: Optional[int] = None, ) -> Dict: """ Get a list of molecular profiles available for a specific cancer study with pagination support. """ # Input Validation validate_study_id(study_id) validate_page_params(page_number, page_size, limit) validate_sort_params(sort_by, direction) try: if limit == 0: page_size = FETCH_ALL_PAGE_SIZE profiles = await self.api_client.make_api_request( f"studies/{study_id}/molecular-profiles" ) if sort_by: reverse = direction.upper() == "DESC" profiles.sort(key=lambda p: str(p.get(sort_by, "")), reverse=reverse) total_count = len(profiles) start_idx = page_number * page_size end_idx = start_idx + page_size paginated_profiles = profiles[start_idx:end_idx] if limit and limit > 0 and len(paginated_profiles) > limit: paginated_profiles = paginated_profiles[:limit] has_more = end_idx < total_count return { "molecular_profiles": paginated_profiles, "pagination": { "page": page_number, "page_size": page_size, "total_found": total_count, "has_more": has_more, }, } except Exception as e: return { "error": f"Failed to get molecular profiles for {study_id}: {str(e)}" }
- cbioportal_mcp/server.py:294-306 (registration)Thin wrapper method on the MCP server class that delegates to the MolecularProfilesEndpoints handler. This method is registered as the MCP tool.async def get_molecular_profiles( self, study_id: str, page_number: int = 0, page_size: int = 50, sort_by: Optional[str] = None, direction: str = "ASC", limit: Optional[int] = None, ) -> Dict: """Get a list of molecular profiles available for a specific cancer study with pagination support.""" return await self.molecular_profiles.get_molecular_profiles( study_id, page_number, page_size, sort_by, direction, limit )
- cbioportal_mcp/server.py:97-131 (registration)Registers all server methods, including get_molecular_profiles, as MCP tools using FastMCP.add_tool()."""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")
- Input validation helper functions used by the get_molecular_profiles handler for study_id, pagination, and sort parameters.def validate_page_params( page_number: int, page_size: int, limit: Optional[int] = None, ) -> None: """ Validate pagination parameters. Args: page_number: Page number (0-based) page_size: Number of items per page limit: Optional limit on total results Raises: TypeError: If parameters are not the correct type ValueError: If parameters have invalid values """ if not isinstance(page_number, int): raise TypeError("page_number must be an integer") if page_number < 0: raise ValueError("page_number must be non-negative") if not isinstance(page_size, int): raise TypeError("page_size must be an integer") if page_size <= 0: raise ValueError("page_size must be positive") if limit is not None: if not isinstance(limit, int): raise TypeError("limit must be an integer if provided") if limit < 0: raise ValueError("limit must be non-negative if provided") def validate_sort_params( sort_by: Optional[str], direction: str, ) -> None: """ Validate sorting parameters. Args: sort_by: Field to sort by (optional) direction: Sort direction (ASC or DESC) Raises: TypeError: If parameters are not the correct type ValueError: If direction is not valid """ if sort_by is not None and not isinstance(sort_by, str): raise TypeError("sort_by must be a string if provided") if not isinstance(direction, str) or direction.upper() not in ["ASC", "DESC"]: raise ValueError("direction must be 'ASC' or 'DESC'") 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")