Fix mypy sqla errors around Dataset.transform.

lib/galaxy/model/__init__.py

@@ -208,8 +208,18 @@
 
 OPTIONAL_STR_TO_STR_DICT = Optional[Dict[str, str]]
 
+
+class TransformAction(TypedDict):
+    action: str
+
+
+TRANSFORM_ACTIONS = Optional[List[TransformAction]]
+
 mapper_registry = registry(
-    type_annotation_map={OPTIONAL_STR_TO_STR_DICT: JSONType},
+    type_annotation_map={
+        OPTIONAL_STR_TO_STR_DICT: JSONType,
+        TRANSFORM_ACTIONS: MutableJSONType,
+    },
 )
 
 # When constructing filters with in for a fixed set of ids, maximum
@@ -4354,7 +4364,7 @@ class DatasetSource(Base, Dictifiable, Serializable):
     dataset_id: Mapped[Optional[int]] = mapped_column(ForeignKey("dataset.id"), index=True)
     source_uri: Mapped[Optional[str]] = mapped_column(TEXT)
     extra_files_path: Mapped[Optional[str]] = mapped_column(TEXT)
-    transform: Mapped[Optional[bytes]] = mapped_column(MutableJSONType)
+    transform: Mapped[TRANSFORM_ACTIONS] = mapped_column(MutableJSONType)
     dataset: Mapped[Optional["Dataset"]] = relationship(back_populates="sources")
     hashes: Mapped[List["DatasetSourceHash"]] = relationship(back_populates="source")
     dict_collection_visible_keys = ["id", "source_uri", "extra_files_path", "transform"]

lib/galaxy/model/deferred.py

@@ -178,20 +178,20 @@ def ensure_materialized(
 
     def _stream_source(self, target_source: DatasetSource, datatype) -> str:
         path = stream_url_to_file(target_source.source_uri, file_sources=self._file_sources)
-        transform = target_source.transform or []  # type:ignore[var-annotated]
+        transform = target_source.transform or []
         to_posix_lines = False
         spaces_to_tabs = False
         datatype_groom = False
         for transform_action in transform:
-            action = transform_action["action"]  # type:ignore[index]
+            action = transform_action["action"]
             if action == "to_posix_lines":
                 to_posix_lines = True
             elif action == "spaces_to_tabs":
                 spaces_to_tabs = True
             elif action == "datatype_groom":
                 datatype_groom = True
             else:
-                raise Exception(f"Failed to materialize dataest, unknown transformation action {action} applied.")
+                raise Exception(f"Failed to materialize dataset, unknown transformation action {action} applied.")
         if to_posix_lines or spaces_to_tabs:
             convert_fxn = convert_function(to_posix_lines, spaces_to_tabs)
             convert_result = convert_fxn(path, False)