Fix mypy errors

lib/galaxy/schema/visualization.py

@@ -3,6 +3,7 @@
     Dict,
     List,
     Optional,
+    Union,
 )
 
 from pydantic import (
@@ -357,7 +358,7 @@ class VisualizationUpdatePayload(Model):
         title="Deleted",
         description="Whether this Visualization has been deleted.",
     )
-    config: Optional[dict] = Field(
+    config: Optional[Union[dict, bytes]] = Field(
         {},
         title="Config",
         description="The config of the visualization.",

lib/galaxy/webapps/galaxy/services/visualizations.py

@@ -1,6 +1,7 @@
 import json
 import logging
 from typing import (
+    cast,
     Optional,
     Tuple,
     Union,
@@ -120,7 +121,11 @@ def show(
             "dbkey": visualization.dbkey,
             "slug": visualization.slug,
             # to_dict only the latest revision (allow older to be fetched elsewhere)
-            "latest_revision": self._get_visualization_revision_dict(visualization.latest_revision),
+            "latest_revision": (
+                self._get_visualization_revision_dict(visualization.latest_revision)
+                if visualization.latest_revision
+                else None
+            ),
             # need to encode ids in revisions as well
             # NOTE: does not encode ids inside the configs
             "revisions": [r.id for r in visualization.revisions],
@@ -136,10 +141,10 @@ def show(
         dictionary["email_hash"] = md5_hash_str(visualization.user.email)
         dictionary["tags"] = visualization.make_tag_string_list()
         dictionary["annotation"] = get_item_annotation_str(trans.sa_session, trans.user, visualization)
-        app: StructuredApp = trans.app
+        app = cast(StructuredApp, trans.app)
         if app.visualizations_registry:
-            visualizations_registry: VisualizationsRegistry = app.visualizations_registry
-            visualization_plugin: VisualizationPlugin = visualizations_registry.get_plugin(dictionary["type"])
+            visualizations_registry = cast(VisualizationsRegistry, app.visualizations_registry)
+            visualization_plugin = cast(VisualizationPlugin, visualizations_registry.get_plugin(dictionary["type"]))
             dictionary["plugin"] = visualization_plugin.to_dict()
         return VisualizationShowResponse(**dictionary)
 
@@ -157,7 +162,7 @@ def create(
         if payload.import_id:
             visualization = self._import_visualization(trans, payload.import_id)
         else:
-            payload = self._validate_and_parse_payload(payload)
+            payload = cast(VisualizationCreatePayload, self._validate_and_parse_payload(payload))
             # must have a type (I've taken this to be the visualization name)
             if not payload.type:
                 raise exceptions.RequestParameterMissingException("key/value 'type' is required")
@@ -184,9 +189,7 @@ def create(
                 with transaction(session):
                     session.commit()
 
-        rval = {"id": visualization.id}
-
-        return VisualizationCreateResponse(**rval)
+        return VisualizationCreateResponse(id=str(visualization.id))
 
     def update(
         self,
@@ -201,7 +204,7 @@ def update(
         :returns:   dictionary containing Visualization details
         """
         rval = None
-        payload = self._validate_and_parse_payload(payload)
+        payload = cast(VisualizationUpdatePayload, self._validate_and_parse_payload(payload))
 
         # there's a differentiation here between updating the visualization and creating a new revision
         # that needs to be handled clearly here or alternately, using a different controller
@@ -212,19 +215,20 @@ def update(
 
         # only update owned visualizations
         visualization = self._get_visualization(trans, visualization_id, check_ownership=True)
-        title = payload.title or visualization.latest_revision.title
-        dbkey = payload.dbkey or visualization.latest_revision.dbkey
+        latest_revision = cast(VisualizationRevision, visualization.latest_revision)
+        title = payload.title or latest_revision.title
+        dbkey = payload.dbkey or latest_revision.dbkey
         deleted = payload.deleted or visualization.deleted
-        config = payload.config or visualization.latest_revision.config
+        config = payload.config or latest_revision.config
 
-        latest_config = visualization.latest_revision.config
+        latest_config = latest_revision.config
         if (
-            (title != visualization.latest_revision.title)
-            or (dbkey != visualization.latest_revision.dbkey)
+            (title != latest_revision.title)
+            or (dbkey != latest_revision.dbkey)
             or (json.dumps(config) != json.dumps(latest_config))
         ):
             revision = self._add_visualization_revision(trans, visualization, config, title, dbkey)
-            rval = {"id": visualization_id, "revision": revision.id}
+            rval = {"id": str(visualization_id), "revision": str(revision.id)}
 
         # allow updating vis title
         visualization.title = title
@@ -346,9 +350,9 @@ def _add_visualization_revision(
         self,
         trans: ProvidesUserContext,
         visualization: Visualization,
-        config: dict,
-        title: str,
-        dbkey: str,
+        config: Optional[Union[dict, bytes]],
+        title: Optional[str],
+        dbkey: Optional[str],
     ) -> VisualizationRevision:
         """
         Adds a new `VisualizationRevision` to the given `visualization` with
@@ -376,7 +380,7 @@ def _create_visualization(
         dbkey: Optional[str] = None,
         slug: Optional[str] = None,
         annotation: Optional[str] = None,
-        save: bool = True,
+        save: Optional[bool] = True,
     ) -> Visualization:
         """Create visualization but not first revision. Returns Visualization object."""
         user = trans.get_user()