Noctua MCP Server

Instructions

Implementation Reference

• src/noctua_mcp/mcp_server.py:91-153 (handler)

  The handler function decorated with @mcp.tool() that implements the create_model tool logic. It uses BaristaClient to create a new GO-CAM model, handles responses, validation errors, and constructs editor URLs.

  @mcp.tool()
  async def create_model(
      title: Optional[str] = None
  ) -> Dict[str, Any]:
      """
      Create a new empty GO-CAM model.
  
      Args:
          title: Optional title for the model
  
      Returns:
          Barista API response containing the new model ID and editor URLs
  
      Examples:
  
      - `create_model("RAS-RAF signaling pathway")`
        
  
      Notes:
          - The returned model_id can be used with other tools like add_individual
          - Models are created in "development" state by default
          - To add taxon information, use add_individual after creating the model
      """
      client = get_client()
      resp = client.create_model(title=title)
  
      if resp.validation_failed:
          return {
              "success": False,
              "error": "Validation failed",
              "reason": resp.validation_reason,
              "rolled_back": True
          }
  
      if resp.error:
          return {
              "success": False,
              "error": "Operation failed",
              "reason": resp.error
          }
  
      # Build minimal response
      result = {
          "success": True,
          "model_id": resp.model_id,
          "created": True
      }
  
      # Add editor URLs if we have a model ID
      if resp.model_id:
          import os
          token = os.environ.get("BARISTA_TOKEN", "")
  
          # Graph editor with token
          result["graph_editor_url"] = f"http://noctua-dev.berkeleybop.org/editor/graph/{resp.model_id}?barista_token={token}"
  
          # Pathway editor without token (URL encoded model ID)
          from urllib.parse import quote
          encoded_id = quote(resp.model_id, safe="")
          result["pathway_editor_url"] = f"http://noctua-dev.berkeleybop.org/workbench/noctua-visual-pathway-editor/?model_id={encoded_id}"
  
      return result