Noctua MCP Server

Instructions

# Extract specific information
model = get_model("gomodel:12345")
individuals = model["data"]["individuals"]
facts = model["data"]["facts"]

# Find all molecular functions
mfs = [i for i in individuals
       if any("GO:0003674" in str(e.id) for e in i.type if hasattr(e, 'id'))]

# Find all enabled_by relationships (facts are Pydantic objects)
enabled_by = [f for f in facts if f.property == "RO:0002333"]

# Check model state
state = model["data"].get("state")

Implementation Reference

• src/noctua_mcp/mcp_server.py:836-892 (handler)

  The primary handler function for the 'get_model' MCP tool. Decorated with @mcp.tool() for automatic registration with FastMCP. Retrieves the GO-CAM model data via BaristaClient.get_model() and formats the response with success status, model data (individuals, facts, annotations, state), and raw response.

  async def get_model(model_id: str) -> Dict[str, Any]:
      """
      Retrieve the full JSON representation of a GO-CAM model.
  
      Args:
          model_id: The GO-CAM model identifier
  
      Returns:
          Full model data including individuals and facts
  
      Examples:
          # Get a production model
          model = get_model("gomodel:5fce9b7300001215")
          # Returns complete model with:
          # - data.id: model ID
          # - data.individuals: list of all individuals
          # - data.facts: list of all relationships
          # - data.annotations: model-level annotations
  
          # Extract specific information
          model = get_model("gomodel:12345")
          individuals = model["data"]["individuals"]
          facts = model["data"]["facts"]
  
          # Find all molecular functions
          mfs = [i for i in individuals
                 if any("GO:0003674" in str(e.id) for e in i.type if hasattr(e, 'id'))]
  
          # Find all enabled_by relationships (facts are Pydantic objects)
          enabled_by = [f for f in facts if f.property == "RO:0002333"]
  
          # Check model state
          state = model["data"].get("state")
      """
      client = get_client()
      resp = client.get_model(model_id)
  
      if resp.error:
          return {
              "success": False,
              "error": resp.error,
              "model_id": model_id
          }
  
      # Return structured response with model data
      return {
          "success": True,
          "model_id": model_id,
          "data": {
              "individuals": resp.individuals,
              "facts": resp.facts,
              "annotations": resp.annotations if hasattr(resp, 'annotations') else [],
              "state": resp.model_state if hasattr(resp, 'model_state') else None
          },
          "raw": resp.raw  # Include raw for backward compatibility
      }