Fix SA2.0 ORM usage in model.store

lib/galaxy/model/store/__init__.py

@@ -39,6 +39,7 @@
     WorkflowDescription,
 )
 from rocrate.rocrate import ROCrate
+from sqlalchemy import select
 from sqlalchemy.orm import joinedload
 from sqlalchemy.orm.scoping import scoped_session
 from sqlalchemy.sql import expression
@@ -466,9 +467,8 @@ def handle_dataset_object_edit(dataset_instance, dataset_attrs):
                 self.dataset_state_serialized = False
 
             if "id" in dataset_attrs and self.import_options.allow_edit and not self.sessionless:
-                dataset_instance: model.DatasetInstance = self.sa_session.query(
-                    getattr(model, dataset_attrs["model_class"])
-                ).get(dataset_attrs["id"])
+                model_class = getattr(model, dataset_attrs["model_class"])
+                dataset_instance: model.DatasetInstance = self.sa_session.get(model_class, dataset_attrs["id"])
                 attributes = [
                     "name",
                     "extension",
@@ -775,7 +775,7 @@ def import_folder(folder_attrs, root_folder=None):
                 and not self.sessionless
                 and self.import_options.allow_edit
             ):
-                library_folder = self.sa_session.query(model.LibraryFolder).get(library_attrs["id"])
+                library_folder = self.sa_session.get(model.LibraryFolder, library_attrs["id"])
                 import_folder(library_attrs, root_folder=library_folder)
             else:
                 assert self.import_options.allow_library_creation
@@ -838,7 +838,7 @@ def materialize_elements(dc):
                 dc.element_count = len(elements_attrs)
 
             if "id" in collection_attrs and self.import_options.allow_edit and not self.sessionless:
-                dc = self.sa_session.query(model.DatasetCollection).get(collection_attrs["id"])
+                dc = self.sa_session.get(model.DatasetCollection, collection_attrs["id"])
                 attributes = [
                     "collection_type",
                     "populated_state",
@@ -865,7 +865,7 @@ def materialize_elements(dc):
             if "collection" in collection_attrs:
                 dc = import_collection(collection_attrs["collection"])
                 if "id" in collection_attrs and self.import_options.allow_edit and not self.sessionless:
-                    hdca = self.sa_session.query(model.HistoryDatasetCollectionAssociation).get(collection_attrs["id"])
+                    hdca = self.sa_session.get(model.HistoryDatasetCollectionAssociation, collection_attrs["id"])
                     # TODO: edit attributes...
                 else:
                     hdca = model.HistoryDatasetCollectionAssociation(
@@ -1217,7 +1217,7 @@ def _import_jobs(self, object_import_tracker: "ObjectImportTracker", history: Op
             if "id" in job_attrs and not self.sessionless:
                 # only thing we allow editing currently is associations for incoming jobs.
                 assert self.import_options.allow_edit
-                job = self.sa_session.query(model.Job).get(job_attrs["id"])
+                job = self.sa_session.get(model.Job, job_attrs["id"])
                 self._connect_job_io(job, job_attrs, _find_hda, _find_hdca, _find_dce)  # type: ignore[attr-defined]
                 self._set_job_attributes(job, job_attrs, force_terminal=False)  # type: ignore[attr-defined]
                 # Don't edit job
@@ -2110,12 +2110,12 @@ def export_history(
         sa_session = app.model.session
 
         # Write collections' attributes (including datasets list) to file.
-        query = (
-            sa_session.query(model.HistoryDatasetCollectionAssociation)
-            .filter(model.HistoryDatasetCollectionAssociation.history == history)
-            .filter(model.HistoryDatasetCollectionAssociation.deleted == expression.false())
+        stmt = (
+            select(model.HistoryDatasetCollectionAssociation)
+            .where(model.HistoryDatasetCollectionAssociation.history == history)
+            .where(model.HistoryDatasetCollectionAssociation.deleted == expression.false())
         )
-        collections = query.all()
+        collections = sa_session.scalars(stmt)
 
         for collection in collections:
             # filter this ?
@@ -2128,15 +2128,16 @@ def export_history(
 
         # Write datasets' attributes to file.
         actions_backref = model.Dataset.actions  # type: ignore[attr-defined]
-        query = (
-            sa_session.query(model.HistoryDatasetAssociation)
-            .filter(model.HistoryDatasetAssociation.history == history)
+
+        stmt = (
+            select(model.HistoryDatasetAssociation)
+            .where(model.HistoryDatasetAssociation.history == history)
             .join(model.Dataset)
             .options(joinedload(model.HistoryDatasetAssociation.dataset).joinedload(actions_backref))
             .order_by(model.HistoryDatasetAssociation.hid)
-            .filter(model.Dataset.purged == expression.false())
+            .where(model.Dataset.purged == expression.false())
         )
-        datasets = query.all()
+        datasets = sa_session.scalars(stmt).unique()
         for dataset in datasets:
             dataset.annotation = get_item_annotation_str(sa_session, history.user, dataset)
             should_include_file = (dataset.visible or include_hidden) and (not dataset.deleted or include_deleted)

lib/galaxy/model/store/discover.py

@@ -828,7 +828,7 @@ def collect_elements_for_history(elements):
                     sa_session = (
                         model_persistence_context.sa_session or model_persistence_context.import_store.sa_session
                     )
-                    primary_dataset = sa_session.query(galaxy.model.HistoryDatasetAssociation).get(hda_id)
+                    primary_dataset = sa_session.get(galaxy.model.HistoryDatasetAssociation, hda_id)
 
                 sources = fields_match.sources
                 hashes = fields_match.hashes