Fix: resolve complex OpenAPI reference chains with inline definitions

server.py

@@ -4,4 +4,4 @@
 from src.server import main
 
 if __name__ == "__main__":
-    main()
+    main()

src/components/customizers.py

@@ -51,6 +51,18 @@ def customize_components(
         # Hide this fully for now.
         component.output_schema = None
 
+        # SCHEMA REFERENCE HANDLING:
+        # OpenAPI-generated MCP tool schemas contain $defs with nested $ref references
+        # (e.g., $ref -> $defs -> $ref chains).
+        # FastMCP cannot resolve these complex reference chains.
+        #
+        # The following code strips $defs from MCP tool input/output schemas generated by OpenAPI docs.
+        # However, stripping $defs still resulted in "PointerToNowhere" errors due to input schemas
+        # containing nested $ref references failing to resolve.
+        #
+        # Openapi_resolver script replaces ALL $ref with inline schema definitions, and eliminates the need for $defs entirely.
+        # Keep this code to prevent any remaining $defs from breaking MCP clients.
+        #
         if hasattr(component, 'parameters') and isinstance(component.parameters, dict):
             if "$defs" in component.parameters:
                 logger.debug(f"  Found $defs with {len(component.parameters['$defs'])} definitions")

src/server.py

@@ -9,6 +9,7 @@
 from .config import Config
 from .routes.mappers import custom_route_mapper
 from .utils.logging import setup_logging
+from .utils.openapi_resolver import resolve_refs
 
 logger = setup_logging()
 
@@ -38,6 +39,11 @@ def create_mcp_server() -> FastMCP:
 
     openapi_spec = load_openapi_spec()
 
+    # Workaround to resolve all $ref references since FastMCP cannot resolve complex reference chains
+    logger.info("Resolving OpenAPI $ref references...")
+    openapi_spec = resolve_refs(openapi_spec)
+    logger.info("OpenAPI $ref references resolved")
+
     client = create_cortex_client()
 
     mcp_server = FastMCP.from_openapi(

src/utils/openapi_resolver.py

@@ -0,0 +1,136 @@
+"""
+OpenAPI $ref resolver for FastMCP compatibility.
+
+FastMCP cannot resolve complex reference chains (e.g., $ref -> $defs -> $ref chains).
+This script replaces ALL $ref in the entire OpenAPI spec with inline schema definitions.
+
+Since customizers.py currently hides output schemas, $ref resolutions are only visible in INPUT schemas.
+
+Performance note: Currently processes all ~800 endpoints but only ~20 become MCP tools.
+The dereferencing work is only visible in PointInTimeMetrics tool, since it's the only
+MCP-enabled endpoint with $ref chains in its input schema (output schemas are hidden).
+
+TODO: Optimize to only process MCP-enabled paths
+"""
+
+from typing import Any
+
+
+def resolve_refs(spec: dict[str, Any]) -> dict[str, Any]:
+    """
+    Recursively resolve all $ref references in an OpenAPI specification.
+
+    This is a workaround for FastMCP's issue with $ref handling where it
+    doesn't properly include schema definitions when creating tool input schemas.
+
+    Args:
+        spec: OpenAPI specification dictionary
+
+    Returns:
+        Modified spec with all $refs resolved inline
+    """
+    # Create a copy to avoid modifying the original
+    spec = spec.copy()
+
+    # Get the components/schemas section for reference resolution
+    schemas = spec.get("components", {}).get("schemas", {})
+
+    def resolve_schema(obj: Any, visited: set[str] | None = None) -> Any:
+        """Recursively resolve $ref in an object."""
+        if visited is None:
+            visited = set()
+
+        if isinstance(obj, dict):
+            # Check if this is a $ref
+            if "$ref" in obj and len(obj) == 1:
+                ref_path = obj["$ref"]
+
+                # Prevent infinite recursion
+                if ref_path in visited:
+                    # Return the ref as-is to avoid infinite loop
+                    return obj
+
+                visited.add(ref_path)
+
+                # Extract schema name from reference
+                if ref_path.startswith("#/components/schemas/"):
+                    schema_name = ref_path.split("/")[-1]
+                    if schema_name in schemas:
+                        # Recursively resolve the referenced schema
+                        resolved = resolve_schema(schemas[schema_name].copy(), visited)
+                        visited.remove(ref_path)
+                        return resolved
+
+                # If we can't resolve, return as-is
+                visited.remove(ref_path)
+                return obj
+            else:
+                # Recursively process all values in the dict
+                result = {}
+                for key, value in obj.items():
+                    result[key] = resolve_schema(value, visited)
+                return result
+
+        elif isinstance(obj, list):
+            # Recursively process all items in the list
+            return [resolve_schema(item, visited) for item in obj]
+        else:
+            # Return primitive values as-is
+            return obj
+
+    # Resolve refs in all paths
+    if "paths" in spec:
+        spec["paths"] = resolve_schema(spec["paths"])
+
+    return spec
+
+
+# Use if context becomes too large for inline definitions
+def resolve_refs_with_defs(spec: dict[str, Any]) -> dict[str, Any]:
+    """
+    Alternative approach: Keep $refs but ensure $defs section is populated.
+
+    This transforms OpenAPI $refs to JSON Schema format and includes
+    all referenced schemas in a $defs section at the root level.
+
+    Args:
+        spec: OpenAPI specification dictionary
+
+    Returns:
+        Modified spec with $refs pointing to $defs and all definitions included
+    """
+    # Create a copy to avoid modifying the original
+    spec = spec.copy()
+
+    # Get the components/schemas section
+    schemas = spec.get("components", {}).get("schemas", {})
+
+    # Create $defs section at root level
+    if schemas:
+        spec["$defs"] = schemas.copy()
+
+    def transform_refs(obj: Any) -> Any:
+        """Transform OpenAPI $refs to JSON Schema $refs."""
+        if isinstance(obj, dict):
+            result = {}
+            for key, value in obj.items():
+                if key == "$ref" and isinstance(value, str):
+                    # Transform the reference format
+                    if value.startswith("#/components/schemas/"):
+                        schema_name = value.split("/")[-1]
+                        result[key] = f"#/$defs/{schema_name}"
+                    else:
+                        result[key] = value
+                else:
+                    result[key] = transform_refs(value)
+            return result
+        elif isinstance(obj, list):
+            return [transform_refs(item) for item in obj]
+        else:
+            return obj
+
+    # Transform all refs in paths
+    if "paths" in spec:
+        spec["paths"] = transform_refs(spec["paths"])
+
+    return spec