Noctua MCP Server

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Implementation Reference

• src/noctua_mcp/mcp_server.py:439-567 (handler)

  The main handler function for the 'add_protein_complex' MCP tool. It validates input components using ProteinComplexComponent models, calls the underlying BaristaClient.add_protein_complex method, handles validation and errors with rollback, and returns the complex ID and status.
  @mcp.tool() async def add_protein_complex( model_id: str, components: List[Dict[str, Any]], assign_var: str = "complex1" ) -> Dict[str, Any]: """ Add a protein complex to a GO-CAM model with validated components. Creates a protein-containing complex (GO:0032991 by default) and links all components using BFO:0000051 (has part) relation. The operation is atomic - either all components are added successfully or the entire operation is rolled back. Args: model_id: The GO-CAM model identifier components: List of component dictionaries with keys: - entity_id (required): Protein/gene product ID (e.g., "UniProtKB:P12345") - label (optional): Component 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 complex (default: "complex1") Returns: Barista API response with complex ID and component IDs Examples: # Create a simple dimer complex add_protein_complex( "gomodel:12345", [ {"entity_id": "UniProtKB:P04637", "label": "TP53"}, {"entity_id": "UniProtKB:P04637", "label": "TP53"} ], ) # Create complex with evidence add_protein_complex( "gomodel:12345", [ { "entity_id": "UniProtKB:P68400", "label": "CSNK1A1", "evidence_type": "ECO:0000353", "reference": "PMID:12345678" }, { "entity_id": "UniProtKB:P49841", "label": "GSK3B", "evidence_type": "ECO:0000353", "reference": "PMID:12345678" } ], assign_var="destruction_complex" ) # Create a complex with specific assignment variable add_protein_complex( "gomodel:12345", [ {"entity_id": "UniProtKB:P62191", "label": "PSMC1"}, {"entity_id": "UniProtKB:P62195", "label": "PSMC5"} ], assign_var="proteasome" ) Notes: - All components must have entity_id specified - Label validation prevents ID hallucination - Evidence and references are optional but recommended - Uses BFO:0000051 (has part) to link components - Atomic operation with automatic rollback on failure """ client = get_client() # Convert component dicts to Pydantic models try: pydantic_components = [ProteinComplexComponent(**comp) for comp in components] except Exception as e: return { "success": False, "error": "Invalid component structure", "reason": str(e), "hint": "Each component must have 'entity_id' field. Optional: 'label', 'evidence_type', 'reference'" } # Call the new add_protein_complex method resp = client.add_protein_complex( model_id, pydantic_components, assign_var=assign_var ) if resp.validation_failed: return { "success": False, "error": "Validation failed", "reason": resp.validation_reason, "rolled_back": True, "component_count": len(components) } if resp.error: return { "success": False, "error": resp.error, "model_id": model_id } # Get the complex ID from model_vars or from the individuals list complex_id = assign_var if resp.model_vars and assign_var in resp.model_vars: complex_id = resp.model_vars[assign_var] elif resp.individuals and len(resp.individuals) > 0: # Find the complex individual (it should be the first one created in this operation) # The complex is created first, then components are added for ind in resp.individuals: # Check if it's a protein-containing complex if hasattr(ind, 'type') and any('GO:0032991' in str(t.id) if hasattr(t, 'id') else False for t in ind.type): complex_id = ind.id break return { "success": True, "complex_id": complex_id, "component_count": len(components), "assign_var": assign_var }