Remove more __root__ and construct calls

lib/galaxy/model/store/__init__.py

@@ -2694,14 +2694,14 @@ class BcoModelExportStore(WorkflowInvocationOnlyExportStore):
             empirical_error=export_options.override_empirical_error or {},
             algorithmic_error=export_options.override_algorithmic_error or {},
         )
-        usability_domain = UsabilityDomain(__root__=usability_domain_str)
+        usability_domain = UsabilityDomain(root=usability_domain_str)
         description_domain = DescriptionDomain(
             keywords=keywords,
             xref=export_options.override_xref or [],
             platform=["Galaxy"],
             pipeline_steps=pipeline_steps,
         )
-        parametric_domain = ParametricDomain(__root__=parametric_domain_items)
+        parametric_domain = ParametricDomain(root=parametric_domain_items)
         io_domain = InputAndOutputDomain(
             input_subdomain=input_subdomain_items,
             output_subdomain=output_subdomain_items,

lib/galaxy/webapps/galaxy/api/histories.py

@@ -391,8 +391,8 @@ class FastAPIHistories:
         use_tasks = accept == ExportTaskListResponse.__accept_type__
         exports = self.service.index_exports(trans, history_id, use_tasks, limit, offset)
         if use_tasks:
-            return ExportTaskListResponse(__root__=exports)
-        return JobExportHistoryArchiveListResponse(__root__=exports)
+            return ExportTaskListResponse(root=exports)
+        return JobExportHistoryArchiveListResponse(root=exports)
 
     @router.put(  # PUT instead of POST because multiple requests should just result in one object being created.
         "/api/histories/{history_id}/exports",

lib/galaxy/webapps/galaxy/api/roles.py

@@ -45,7 +45,7 @@ class FastAPIRoles:
     @router.get("/api/roles")
     def index(self, trans: ProvidesUserContext = DependsOnTrans) -> RoleListResponse:
         roles = self.role_manager.list_displayable_roles(trans)
-        return RoleListResponse(__root__=[role_to_model(r) for r in roles])
+        return RoleListResponse(root=[role_to_model(r) for r in roles])
 
     @router.get("/api/roles/{id}")
     def show(self, id: DecodedDatabaseIdField, trans: ProvidesUserContext = DependsOnTrans) -> RoleModelResponse:

lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py

@@ -142,9 +142,7 @@ class ToolShedRepositoriesController(BaseGalaxyAPIController):
         irm = InstallRepositoryManager(self.app)
         installed_tool_shed_repositories = irm.install(tool_shed_url, name, owner, changeset_revision, payload)
         if installed_tool_shed_repositories:
-            return InstalledToolShedRepositories(
-                __root__=list(map(self.service._show, installed_tool_shed_repositories))
-            )
+            return InstalledToolShedRepositories(root=list(map(self.service._show, installed_tool_shed_repositories)))
         message = "No repositories were installed, possibly because the selected repository has already been installed."
         return dict(status="ok", message=message)
 
@@ -245,7 +243,7 @@ class ToolShedRepositoriesController(BaseGalaxyAPIController):
                 return installed_tool_shed_repositories
             elif isinstance(installed_tool_shed_repositories, InstalledToolShedRepositories):
                 all_installed_tool_shed_repositories.extend(installed_tool_shed_repositories.__root__)
-        return InstalledToolShedRepositories(__root__=all_installed_tool_shed_repositories)
+        return InstalledToolShedRepositories(root=all_installed_tool_shed_repositories)
 
     @require_admin
     @expose_api

lib/galaxy/webapps/galaxy/api/users.py

@@ -559,7 +559,7 @@ class FastAPIUsers:
         for key, attributes in valid_dbkeys.items():
             attributes["id"] = key
             dbkey_collection.append(attributes)
-        return CustomBuildsCollection.construct(__root__=dbkey_collection)
+        return CustomBuildsCollection.model_construct(root=dbkey_collection)
 
     @router.delete(
         "/api/users/{user_id}/custom_builds/{key}", name="delete_custom_build", summary="Delete a custom build"

lib/galaxy/webapps/galaxy/services/history_contents.py

@@ -594,7 +594,7 @@ class HistoriesContentsService(ServiceBase, ServesExportStores, ConsumesModelSto
         :raises: RequestParameterInvalidException, ObjectNotFound, InsufficientPermissionsException, InternalServerError
                     RequestParameterMissingException
         """
-        payload_dict = payload.dict(by_alias=True)
+        payload_dict = payload.model_dump(by_alias=True)
         hda = self.hda_manager.get_owned(history_content_id, trans.user, current_history=trans.history, trans=trans)
         assert hda is not None
         self.history_manager.error_unless_mutable(hda.history)

lib/galaxy/webapps/galaxy/services/libraries.py

@@ -78,7 +78,7 @@ class LibrariesService(ServiceBase, ConsumesModelStores):
         for library in query:
             library_dict = self.library_manager.get_library_dict(trans, library, prefetched_ids)
             libraries.append(LibrarySummary(**library_dict))
-        return LibrarySummaryList(__root__=libraries)
+        return LibrarySummaryList(root=libraries)
 
     def show(self, trans, id: DecodedDatabaseIdField) -> LibrarySummary:
         """Returns detailed information about a library."""

lib/galaxy/webapps/galaxy/services/notifications.py

@@ -92,9 +92,9 @@ class NotificationService(ServiceBase):
         """
         self.notification_manager.ensure_notifications_enabled()
         if user_context.anonymous:
-            return UserNotificationListResponse(__root__=[])
+            return UserNotificationListResponse(root=[])
         user_notifications = self._get_user_notifications(user_context, limit, offset)
-        return UserNotificationListResponse(__root__=user_notifications)
+        return UserNotificationListResponse(root=user_notifications)
 
     def get_broadcasted_notification(
         self, user_context: ProvidesUserContext, notification_id: int
@@ -118,7 +118,7 @@ class NotificationService(ServiceBase):
         self.notification_manager.ensure_notifications_enabled()
         active_only = not user_context.user_is_admin
         broadcasted_notifications = self._get_all_broadcasted(active_only=active_only)
-        return BroadcastNotificationListResponse(__root__=broadcasted_notifications)
+        return BroadcastNotificationListResponse(root=broadcasted_notifications)
 
     def get_user_notification(self, user: User, notification_id: int) -> UserNotificationResponse:
         """Gets the information of the notification received by the user with the given ID."""

lib/galaxy/webapps/galaxy/services/pages.py

@@ -74,9 +74,7 @@ class PagesService(ServiceBase):
 
         pages, total_matches = self.manager.index_query(trans, payload, include_total_count)
         return (
-            PageSummaryList.construct(
-                __root__=[trans.security.encode_all_ids(p.to_dict(), recursive=True) for p in pages]
-            ),
+            PageSummaryList.construct(root=[trans.security.encode_all_ids(p.to_dict(), recursive=True) for p in pages]),
             total_matches,
         )
 

lib/tool_shed/test/base/populators.py

@@ -229,7 +229,7 @@ class ToolShedPopulator:
                 assert_msg = f"Updating repository [{repository}] with path [{path}] and commit_message {commit_message} failed to update repository contents, no changes found. Response: [{response_json}]"
                 raise AssertionError(assert_msg)
             api_asserts.assert_status_code_is_ok(response)
-        return RepositoryUpdate(__root__=response.json())
+        return RepositoryUpdate(root=response.json())
 
     def new_repository(self, category_ids: Union[List[str], str], prefix: str = DEFAULT_PREFIX) -> Repository:
         name = random_name(prefix=prefix)
@@ -293,7 +293,7 @@ class ToolShedPopulator:
             "repositories/get_ordered_installable_revisions", params=request.dict()
         )
         api_asserts.assert_status_code_is_ok(revisions_response)
-        return OrderedInstallableRevisions(__root__=revisions_response.json())
+        return OrderedInstallableRevisions(root=revisions_response.json())
 
     def assert_has_n_installable_revisions(self, repository: Repository, n: int):
         revisions = self.get_ordered_installable_revisions(repository.owner, repository.name)
@@ -312,7 +312,7 @@ class ToolShedPopulator:
     def repository_index(self, request: Optional[RepositoryIndexRequest]) -> RepositoryIndexResponse:
         repository_response = self._api_interactor.get("repositories", params=(request.dict() if request else {}))
         api_asserts.assert_status_code_is_ok(repository_response)
-        return RepositoryIndexResponse(__root__=repository_response.json())
+        return RepositoryIndexResponse(root=repository_response.json())
 
     def get_usernames_allowed_to_push(self, repository: HasRepositoryId) -> List[str]:
         repository_id = self._repository_id(repository)
@@ -373,7 +373,7 @@ class ToolShedPopulator:
             f"repositories/{repository_id}/metadata?downloadable_only={downloadable_only}"
         )
         api_asserts.assert_status_code_is_ok(metadata_response)
-        return RepositoryMetadata(__root__=metadata_response.json())
+        return RepositoryMetadata(root=metadata_response.json())
 
     def reset_metadata(self, repository: HasRepositoryId) -> ResetMetadataOnRepositoryResponse:
         repository_id = self._repository_id(repository)

test/unit/data/test_bco_utils.py

@@ -54,7 +54,7 @@ def example_bc_core_object() -> BioComputeObjectCore:
         email="normal@example.com",
         orcid="http://orcid.org/0000-0002-1825-0097",
     )
-    parametric_domain = ParametricDomain(__root__=[])
+    parametric_domain = ParametricDomain(root=[])
     provenance_domain = ProvenanceDomain(
         name="workflow_name",
         version="workflow_version.0",
@@ -64,7 +64,7 @@ def example_bc_core_object() -> BioComputeObjectCore:
         contributors=[contributor],
         license="MIT",
     )
-    usability_domain = UsabilityDomain(__root__=["workflow annotation"])
+    usability_domain = UsabilityDomain(root=["workflow annotation"])
     gx_extension_domains = extension_domains(
         galaxy_url="https://usegalaxy.org",
         galaxy_version="22.05.0",