Noctua MCP Server

Instructions

Input Schema

Input Schema (JSON Schema)

Implementation Reference

• src/noctua_mcp/mcp_server.py:570-687 (handler)

  MCP tool handler for adding an entity set (functionally interchangeable entities) to a GO-CAM model. Converts input members to Pydantic models using EntitySetMember schema, calls BaristaClient.add_entity_set, handles validation and errors, and extracts the set ID.
  async def add_entity_set( model_id: str, members: List[Dict[str, Any]], assign_var: str = "set1" ) -> Dict[str, Any]: """ Add an entity set to a GO-CAM model with validated members. Creates an entity set (CHEBI:33695 "information biomacromolecule" by default) representing functionally interchangeable entities. Links members using RO:0019003 (has substitutable entity) relation. The operation is atomic - either all members are added successfully or the entire operation is rolled back. Args: model_id: The GO-CAM model identifier members: List of member dictionaries with keys: - entity_id (required): Entity ID (e.g., "UniProtKB:P12345") - label (optional): Member label for validation - evidence_type (optional): ECO code (e.g., "ECO:0000353") - reference (optional): Source reference (e.g., "PMID:12345678") assign_var: Variable name for the set (default: "set1") Returns: Barista API response with set ID and member IDs Examples: # Create a set of functionally equivalent kinases add_entity_set( "gomodel:12345", [ {"entity_id": "UniProtKB:P31749", "label": "AKT1"}, {"entity_id": "UniProtKB:P31751", "label": "AKT2"}, {"entity_id": "UniProtKB:Q9Y243", "label": "AKT3"} ], assign_var="akt_isoforms" ) # Create set with evidence add_entity_set( "gomodel:12345", [ { "entity_id": "UniProtKB:P04637", "label": "TP53", "evidence_type": "ECO:0000314", "reference": "PMID:87654321" }, { "entity_id": "UniProtKB:P04049", "label": "RAF1", "evidence_type": "ECO:0000314", "reference": "PMID:87654321" } ], ) Notes: - All members must have entity_id specified - Label validation prevents ID hallucination - Evidence and references are optional but recommended - Uses RO:0019003 (has substitutable entity) to link members - Atomic operation with automatic rollback on failure - Entity sets represent functionally interchangeable entities """ client = get_client() # Convert member dicts to Pydantic models try: pydantic_members = [EntitySetMember(**member) for member in members] except Exception as e: return { "success": False, "error": "Invalid member structure", "reason": str(e), "hint": "Each member must have 'entity_id' field. Optional: 'label', 'evidence_type', 'reference'" } # Call the new add_entity_set method resp = client.add_entity_set( model_id, pydantic_members, assign_var=assign_var, ) if resp.validation_failed: return { "success": False, "error": "Validation failed", "reason": resp.validation_reason, "rolled_back": True, "member_count": len(members) } if resp.error: return { "success": False, "error": resp.error, "model_id": model_id, } # Get the set ID from model_vars or from the individuals list set_id = assign_var if resp.model_vars and assign_var in resp.model_vars: set_id = resp.model_vars[assign_var] elif resp.individuals and len(resp.individuals) > 0: # Find the set individual - it should be the first one created # Look for an entity set (typically CHEBI:33695 or similar) for ind in resp.individuals: if hasattr(ind, 'type') and any('CHEBI' in str(t.id) if hasattr(t, 'id') else False for t in ind.type): set_id = ind.id break return { "success": True, "set_id": set_id, "member_count": len(members), "assign_var": assign_var }