Add example stdio wrapper and config to be able to test the MCP server

Author: armish

inst/examples/server_config.json

@@ -0,0 +1,9 @@
+{
+  "mcpServers": {
+    "plumber2mcp": {
+      "command": "python3",
+      "args": ["stdio-wrapper.py"],
+      "cwd": "."
+    }
+  }
+}

inst/examples/stdio-wrapper.py

@@ -0,0 +1,108 @@
+#!/usr/bin/env python3
+"""
+Final production wrapper for plumber2mcp
+Handles all R jsonlite serialization quirks
+"""
+
+import sys
+import json
+import urllib.request
+import urllib.error
+
+MCP_ENDPOINT = "http://localhost:8000/mcp/messages"
+
+def fix_r_json(obj):
+    """Fix all R jsonlite serialization issues"""
+    if obj is None:
+        return None
+    elif isinstance(obj, list):
+        if len(obj) == 1:
+            # Convert single-element arrays to scalars
+            return fix_r_json(obj[0])
+        else:
+            # Process array elements
+            return [fix_r_json(item) for item in obj]
+    elif isinstance(obj, dict):
+        if len(obj) == 0:
+            # Empty dict - context dependent
+            return None  # Most cases empty dict should be None
+        
+        # Process dictionary recursively
+        fixed = {}
+        for k, v in obj.items():
+            if k == "id" and isinstance(v, dict) and len(v) == 0:
+                # Empty dict for id should be null
+                fixed[k] = None
+            elif k == "id" and isinstance(v, list) and len(v) == 1:
+                # Single element array for id should be scalar
+                fixed[k] = v[0]
+            elif k == "tools" and isinstance(v, list) and len(v) == 0:
+                # Empty tools array should be empty object for capabilities
+                fixed[k] = {}
+            elif k == "properties" and isinstance(v, list) and len(v) == 0:
+                # Empty properties array should be empty object
+                fixed[k] = {}
+            elif k == "required" and isinstance(v, dict) and len(v) == 0:
+                # Empty required dict should be empty array
+                fixed[k] = []
+            elif k == "content" and isinstance(v, list):
+                # content is already an array, just fix nested arrays
+                fixed[k] = [fix_r_json(item) for item in v]
+            elif k == "error" and isinstance(v, dict):
+                # Process error object specially
+                error_fixed = {}
+                for ek, ev in v.items():
+                    if isinstance(ev, list) and len(ev) == 1:
+                        error_fixed[ek] = ev[0]
+                    else:
+                        error_fixed[ek] = ev
+                fixed[k] = error_fixed
+            else:
+                # Recursive fix
+                fixed[k] = fix_r_json(v)
+        return fixed
+    else:
+        return obj
+
+def main():
+    while True:
+        try:
+            line = sys.stdin.readline()
+            if not line:
+                break
+                
+            request = json.loads(line.strip())
+            
+            # Forward to HTTP endpoint
+            data = json.dumps(request).encode('utf-8')
+            req = urllib.request.Request(MCP_ENDPOINT, 
+                                       data=data,
+                                       headers={'Content-Type': 'application/json'})
+            
+            with urllib.request.urlopen(req) as response:
+                result = json.loads(response.read().decode('utf-8'))
+            
+            # Fix R serialization issues
+            fixed_result = fix_r_json(result)
+            
+            # Send response
+            print(json.dumps(fixed_result))
+            sys.stdout.flush()
+            
+        except KeyboardInterrupt:
+            break
+        except Exception as e:
+            # Send error response
+            error_response = {
+                "jsonrpc": "2.0",
+                "id": request.get("id") if 'request' in locals() else None,
+                "error": {
+                    "code": -32603,
+                    "message": f"Internal error: {str(e)}"
+                }
+            }
+            print(json.dumps(error_response))
+            sys.stdout.flush()
+
+if __name__ == "__main__":
+    main()