get_cancer_studies
Retrieve and paginate through cancer studies in cBioPortal, enabling users to explore and analyze genomic data with customizable sorting and filtering options.
Instructions
Get a list of cancer studies in cBioPortal with pagination support.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| direction | No | ASC | |
| limit | No | ||
| page_number | No | ||
| page_size | No | ||
| sort_by | No |
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"
}
},
"type": "object"
}
Implementation Reference
- Primary handler implementing the tool logic: performs a paginated GET request to the cBioPortal 'studies' endpoint using the inherited paginated_request method.@handle_api_errors("get cancer studies") @validate_paginated_params async def get_cancer_studies( self, page_number: int = 0, page_size: int = 50, sort_by: Optional[str] = None, direction: str = "ASC", limit: Optional[int] = None, ) -> Dict[str, Any]: """ Get a list of cancer studies in cBioPortal with pagination support. Args: page_number: Page number to retrieve (0-based) page_size: Number of items per page sort_by: Field to sort by direction: Sort direction (ASC or DESC) limit: Maximum number of items to return across all pages (None for no limit) Returns: Dictionary containing list of studies and metadata """ return await self.paginated_request( endpoint="studies", page_number=page_number, page_size=page_size, sort_by=sort_by, direction=direction, limit=limit, data_key="studies" )
- cbioportal_mcp/server.py:96-131 (registration)Registers 'get_cancer_studies' (and other methods) as MCP tools by calling self.mcp.add_tool on the server instance methods.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/server.py:167-178 (handler)Thin wrapper method on the server instance that delegates to StudiesEndpoints.get_cancer_studies; this is the method directly registered as the MCP tool.async def get_cancer_studies( self, page_number: int = 0, page_size: int = 50, sort_by: Optional[str] = None, direction: str = "ASC", limit: Optional[int] = None, ) -> Dict[str, Any]: """Get a list of cancer studies in cBioPortal with pagination support.""" return await self.studies.get_cancer_studies( page_number, page_size, sort_by, direction, limit )
- cbioportal_mcp/server.py:47-47 (helper)Instantiates the StudiesEndpoints instance (self.studies) with the API client, enabling delegation to study-specific handlers.self.studies = StudiesEndpoints(self.api_client)