Migrate new command annotation code.

api/src/opentrons/protocol_engine/types.py

@@ -17,15 +17,14 @@
 )
 
 from pydantic import (
+    ConfigDict,
     BaseModel,
     Field,
     RootModel,
     StrictBool,
     StrictFloat,
     StrictInt,
     StrictStr,
-    validator,
-    Extra,
 )
 from typing_extensions import Literal, TypeGuard
 
@@ -1156,11 +1155,7 @@ class CustomCommandAnnotation(BaseCommandAnnotation):
     """Annotates a group of atomic commands in some manner that Opentrons software does not anticipate or originate."""
 
     annotationType: Literal["custom"] = "custom"
-
-    class Config:
-        """Config to allow extra, non-defined properties."""
-
-        extra = Extra.allow
+    model_config = ConfigDict(extra="allow")
 
 
 CommandAnnotation = Union[SecondOrderCommandAnnotation, CustomCommandAnnotation]

api/src/opentrons/protocol_runner/json_translator.py

@@ -38,6 +38,9 @@ class CommandTranslatorError(Exception):
 # serializer. To improve performance, TypeAdapters are instantiated once.
 # See https://docs.pydantic.dev/latest/concepts/performance/#typeadapter-instantiated-once
 LabwareLocationAdapter: TypeAdapter[LabwareLocation] = TypeAdapter(LabwareLocation)
+CommandAnnotationAdapter: TypeAdapter[CommandAnnotation] = TypeAdapter(
+    CommandAnnotation
+)
 
 
 def _translate_labware_command(
@@ -301,9 +304,8 @@ def translate_command_annotations(
             return []
         else:
             command_annotations: List[CommandAnnotation] = [
-                parse_obj_as(
-                    CommandAnnotation,  # type: ignore[arg-type]
-                    command_annotation.dict(),
+                CommandAnnotationAdapter.validate_python(
+                    command_annotation.model_dump(),
                 )
                 for command_annotation in protocol.commandAnnotations
             ]