Update biopython/mcp_output/mcp_plugin/mcp_service.py

biopython/mcp_output/mcp_plugin/mcp_service.py

@@ -160,42 +160,18 @@ def usage_tool(payload: dict | None = None):
         return {"success": False, "result": None, "error": str(e)}
 
 @mcp.tool(name="notepad", description="Instantiate Scripts/xbbtools/xbb_utils.NotePad")
-def notepad_tool(*args, **kwargs):
-    """NotePad class"""
+def notepad_tool(payload: dict):
+    """NotePad class - pass constructor arguments in payload"""
     try:
         NotePad = lazy_import_script("Scripts.xbbtools.xbb_utils", "NotePad")
         if NotePad is None:
             return {"success": False, "result": None, "error": "Class NotePad is not available"}
         
-        # MCP parameter type conversion
-        converted_args = []
-        converted_kwargs = kwargs.copy()
+        # Extract args and kwargs from payload
+        args = payload.get("args", [])
+        kwargs = payload.get("kwargs", {})
         
-        # Handle position argument type conversion
-        for arg in args:
-            if isinstance(arg, str):
-                try:
-                    if '.' in arg:
-                        converted_args.append(float(arg))
-                    else:
-                        converted_args.append(int(arg))
-                except ValueError:
-                    converted_args.append(arg)
-            else:
-                converted_args.append(arg)
-        
-        # Handle keyword argument type conversion
-        for key, value in converted_kwargs.items():
-            if isinstance(value, str):
-                try:
-                    if '.' in value:
-                        converted_kwargs[key] = float(value)
-                    else:
-                        converted_kwargs[key] = int(value)
-                except ValueError:
-                    pass
-        
-        instance = NotePad(*converted_args, **converted_kwargs)
+        instance = NotePad(*args, **kwargs)
         return {"success": True, "result": str(instance), "error": None}
     except Exception as e:
         return {"success": False, "result": None, "error": str(e)}
@@ -223,79 +199,35 @@ def makeTableX_tool(payload: dict):
         return {"success": False, "result": None, "error": str(e)}
 
 @mcp.tool(name="missingtable", description="Instantiate MissingTable (Scripts/xbbtools/nextorf.py)")
-def missingtable_tool(*args, **kwargs):
-    """MissingTable class"""
+def missingtable_tool(payload: dict):
+    """MissingTable class - pass constructor arguments in payload"""
     try:
         MissingTable = lazy_import_script("Scripts.xbbtools.nextorf", "MissingTable")
         if MissingTable is None:
             return {"success": False, "result": None, "error": "Class MissingTable is not available"}
         
-        # MCP parameter type conversion
-        converted_args = []
-        converted_kwargs = kwargs.copy()
-        
-        for arg in args:
-            if isinstance(arg, str):
-                try:
-                    if '.' in arg:
-                        converted_args.append(float(arg))
-                    else:
-                        converted_args.append(int(arg))
-                except ValueError:
-                    converted_args.append(arg)
-            else:
-                converted_args.append(arg)
+        # Extract args and kwargs from payload
+        args = payload.get("args", [])
+        kwargs = payload.get("kwargs", {})
         
-        for key, value in converted_kwargs.items():
-            if isinstance(value, str):
-                try:
-                    if '.' in value:
-                        converted_kwargs[key] = float(value)
-                    else:
-                        converted_kwargs[key] = int(value)
-                except ValueError:
-                    pass
-        
-        instance = MissingTable(*converted_args, **converted_kwargs)
+        instance = MissingTable(*args, **kwargs)
         return {"success": True, "result": str(instance), "error": None}
     except Exception as e:
         return {"success": False, "result": None, "error": str(e)}
 
 @mcp.tool(name="nextorf", description="Instantiate NextOrf (Scripts/xbbtools/nextorf.py)")
-def nextorf_tool(*args, **kwargs):
-    """NextOrf class"""
+def nextorf_tool(payload: dict):
+    """NextOrf class - pass constructor arguments in payload"""
     try:
         NextOrf = lazy_import_script("Scripts.xbbtools.nextorf", "NextOrf")
         if NextOrf is None:
             return {"success": False, "result": None, "error": "Class NextOrf is not available"}
         
-        # MCP parameter type conversion
-        converted_args = []
-        converted_kwargs = kwargs.copy()
-        
-        for arg in args:
-            if isinstance(arg, str):
-                try:
-                    if '.' in arg:
-                        converted_args.append(float(arg))
-                    else:
-                        converted_args.append(int(arg))
-                except ValueError:
-                    converted_args.append(arg)
-            else:
-                converted_args.append(arg)
-        
-        for key, value in converted_kwargs.items():
-            if isinstance(value, str):
-                try:
-                    if '.' in value:
-                        converted_kwargs[key] = float(value)
-                    else:
-                        converted_kwargs[key] = int(value)
-                except ValueError:
-                    pass
+        # Extract args and kwargs from payload
+        args = payload.get("args", [])
+        kwargs = payload.get("kwargs", {})
         
-        instance = NextOrf(*converted_args, **converted_kwargs)
+        instance = NextOrf(*args, **kwargs)
         return {"success": True, "result": str(instance), "error": None}
     except Exception as e:
         return {"success": False, "result": None, "error": str(e)}