get_molecular_profiles
Retrieve molecular profiles for a specific cancer study using pagination, sorting, and customizable parameters to analyze genomic data efficiently.
Instructions
Get a list of molecular profiles available for a specific cancer study with pagination support.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| direction | No | ASC | |
| limit | No | ||
| page_number | No | ||
| page_size | No | ||
| sort_by | No | ||
| study_id | Yes |
Input Schema (JSON Schema)
{
"additionalProperties": false,
"properties": {
"direction": {
"default": "ASC",
"title": "Direction",
"type": "string"
},
"limit": {
"anyOf": [
{
"type": "integer"
},
{
"type": "null"
}
],
"default": null,
"title": "Limit"
},
"page_number": {
"default": 0,
"title": "Page Number",
"type": "integer"
},
"page_size": {
"default": 50,
"title": "Page Size",
"type": "integer"
},
"sort_by": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null,
"title": "Sort By"
},
"study_id": {
"title": "Study Id",
"type": "string"
}
},
"required": [
"study_id"
],
"type": "object"
}
Implementation Reference
- Core implementation of the get_molecular_profiles tool: validates inputs, fetches all molecular profiles for the study from API, applies sorting and client-side pagination, returns paginated results.@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:96-132 (registration)Registers all server methods as MCP tools using FastMCP.add_tool(), including 'get_molecular_profiles' in the tool_methods list.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") async def paginate_results(
- cbioportal_mcp/server.py:292-306 (handler)Thin wrapper handler in the main CBioPortalMCPServer class that delegates the get_molecular_profiles call to the MolecularProfilesEndpoints instance.# --- Molecular Profiles endpoints (delegated to MolecularProfilesEndpoints) --- 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 )