Migrate Query.get() calls to Session.get()

Query.get() is a legacy SQLAlchemy 1.x construct that emits
LegacyAPIWarning on every invocation. Session.get() is the 2.0
replacement.

Also guard against None primary keys in
tools/parameters/basic.py where the value can legitimately be
absent (previously triggered 'SAWarning: fully NULL primary key
identity cannot load any object').

lib/galaxy/job_execution/setup.py

@@ -157,7 +157,7 @@ class JobIO(UsesDictVisibleKeys):
             # Drop in 24.0
             io_dict.pop("model_class", None)
         job_id = io_dict.pop("job_id")
-        job = sa_session.query(Job).get(job_id)
+        job = sa_session.get(Job, job_id)
         return cls(sa_session=sa_session, job=job, **io_dict)
 
     @classmethod

lib/galaxy/managers/history_contents.py

@@ -230,7 +230,7 @@ class HistoryContentsManager(base.SortableManager):
             decoded_target_ids.extend(self.app.security.decode_id(h) for h in payload.target_history_ids)
 
         target_histories = [
-            h for h in map(trans.sa_session.query(model.History).get, decoded_target_ids) if h and h.user == user
+            h for h in (trans.sa_session.get(model.History, i) for i in decoded_target_ids) if h and h.user == user
         ]
         if len(target_histories) != len(decoded_target_ids):
             raise glx_exceptions.MessageException("You lack permission for one or more destination histories.")
@@ -244,8 +244,8 @@ class HistoryContentsManager(base.SortableManager):
             else:
                 raise glx_exceptions.MessageException("Unknown content type.")
 
-        contents = list(map(trans.sa_session.query(model.HistoryDatasetAssociation).get, decoded_ds))
-        contents.extend(map(trans.sa_session.query(model.HistoryDatasetCollectionAssociation).get, decoded_dc))
+        contents = [trans.sa_session.get(model.HistoryDatasetAssociation, i) for i in decoded_ds]
+        contents.extend(trans.sa_session.get(model.HistoryDatasetCollectionAssociation, i) for i in decoded_dc)
         contents.sort(key=lambda c: c.hid)
 
         for c in contents:

lib/galaxy/tool_shed/galaxy_install/install_manager.py

@@ -319,7 +319,7 @@ class InstallRepositoryManager:
         tsr_ids = [r.id for r in created_or_updated_tool_shed_repositories]
         tool_shed_repositories = []
         for tsr_id in tsr_ids:
-            tsr = self.install_model.context.query(self.install_model.ToolShedRepository).get(tsr_id)
+            tsr = self.install_model.context.get(self.install_model.ToolShedRepository, tsr_id)
             tool_shed_repositories.append(tsr)
         clause_list = []
         for tsr_id in tsr_ids:
@@ -492,8 +492,8 @@ class InstallRepositoryManager:
             tsr_ids, repo_info_dicts, tool_panel_section_keys=tool_panel_section_keys
         )
         for tsr_id in ordered_tsr_ids:
-            repository = self.install_model.context.query(self.install_model.ToolShedRepository).get(
-                self.app.security.decode_id(tsr_id)
+            repository = self.install_model.context.get(
+                self.install_model.ToolShedRepository, self.app.security.decode_id(tsr_id)
             )
             if repository.status in [
                 self.install_model.ToolShedRepository.installation_status.NEW,

lib/galaxy/tools/__init__.py

@@ -947,7 +947,7 @@ class JobContext(BaseJobContext):
         return library_folder
 
     def get_hdca(self, object_id):
-        hdca = self.sa_session.query(HistoryDatasetCollectionAssociation).get(int(object_id))
+        hdca = self.sa_session.get(HistoryDatasetCollectionAssociation, int(object_id))
         return hdca
 
     def create_library_folder(self, parent_folder: "LibraryFolder", name: str, description: str):

lib/galaxy/tools/parameters/basic.py

@@ -2201,7 +2201,10 @@ class DataToolParameter(BaseDataToolParameter):
                         # support that for integer column types.
                         log.warning("Encoded ID where unencoded ID expected.")
                         single_value = trans.security.decode_id(single_value)
-                    rval.append(trans.sa_session.query(HistoryDatasetAssociation).get(single_value))
+                    if single_value is None:
+                        rval.append(None)
+                    else:
+                        rval.append(trans.sa_session.get(HistoryDatasetAssociation, single_value))
                 if len(found_srcs) > 1 and "hdca" in found_srcs:
                     raise ParameterValueError(
                         "if collections are supplied to multiple data input parameter, only collections may be used",

lib/galaxy/webapps/galaxy/controllers/dataset.py

@@ -416,7 +416,7 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
     def _get_dataset_for_edit(self, trans, dataset_id):
         if dataset_id is not None:
             id = self.decode_id(dataset_id)
-            data = trans.sa_session.query(HistoryDatasetAssociation).get(id)
+            data = trans.sa_session.get(HistoryDatasetAssociation, id)
         else:
             trans.log_event("dataset_id is None, cannot load a dataset to edit.")
             return None, self.message_exception(trans, "You must provide a dataset id to edit attributes.")

lib/tool_shed/util/repository_util.py

@@ -59,7 +59,6 @@ from tool_shed.util.metadata_util import (
 from tool_shed.webapp import model
 from tool_shed.webapp.model.db import (
     get_repository_by_name_and_owner,
-    get_repository_query,
 )
 
 if TYPE_CHECKING:
@@ -262,10 +261,8 @@ def generate_sharable_link_for_repository_in_tool_shed(
 
 def get_repository_in_tool_shed(app: "ToolShedApp", id, eagerload_columns=None):
     """Get a repository on the tool shed side from the database via id."""
-    q = get_repository_query(app.model.context)
-    if eagerload_columns:
-        q = q.options(joinedload(*eagerload_columns))
-    return q.get(app.security.decode_id(id))
+    options = [joinedload(col) for col in eagerload_columns] if eagerload_columns else []
+    return app.model.context.get(model.Repository, app.security.decode_id(id), options=options)
 
 
 def get_repo_info_dict(trans: "ProvidesRepositoriesContext", repository_id, changeset_revision):