Towards SQLAlchemy 2.0: use model attributes instead of strings

lib/galaxy/managers/collections.py

@@ -829,7 +829,9 @@ def _get_collection_contents_qry(self, parent_id, limit=None, offset=None):
         DCE = model.DatasetCollectionElement
         qry = Query(DCE).filter(DCE.dataset_collection_id == parent_id)
         qry = qry.order_by(DCE.element_index)
-        qry = qry.options(joinedload("child_collection"), joinedload("hda"))
+        qry = qry.options(
+            joinedload(model.DatasetCollectionElement.child_collection), joinedload(model.DatasetCollectionElement.hda)
+        )
         if limit is not None:
             qry = qry.limit(int(limit))
         if offset is not None:

lib/galaxy/managers/history_contents.py

@@ -438,7 +438,7 @@ def _contained_id_map(self, id_list):
             .query(component_class)
             .filter(component_class.id.in_(id_list))
             .options(undefer(component_class._metadata))
-            .options(joinedload("dataset.actions"))  # TODO: use class attr after moving Dataset to declarative mapping.
+            .options(joinedload(component_class.dataset).joinedload(model.Dataset.actions))
             .options(joinedload(component_class.tags))
             .options(joinedload(component_class.annotations))  # type: ignore[attr-defined]
         )

lib/galaxy/managers/session.py

@@ -30,7 +30,7 @@ def get_session_from_session_key(self, session_key: str):
                     self.model.GalaxySession.table.c.is_valid == true(),
                 )
             )
-            .options(joinedload("user"))
+            .options(joinedload(self.model.GalaxySession.user))
             .first()
         )
         return galaxy_session

lib/galaxy/managers/sharable.py

@@ -222,7 +222,7 @@ def _query_shared_with(self, user, eagerloads=True, **kwargs):
         Return a query for this model already filtered to models shared
         with a particular user.
         """
-        query = self.session().query(self.model_class).join("users_shared_with")
+        query = self.session().query(self.model_class).join(self.model_class.users_shared_with)
         if eagerloads is False:
             query = query.enable_eagerloads(False)
         # TODO: as filter in FilterParser also

lib/galaxy/managers/workflows.py

@@ -163,10 +163,10 @@ def index_query(
             query = query.outerjoin(model.StoredWorkflow.users_shared_with)
         query = query.outerjoin(model.StoredWorkflow.tags)
 
-        latest_workflow_load = joinedload("latest_workflow")
+        latest_workflow_load = joinedload(model.StoredWorkflow.latest_workflow)
         if not payload.skip_step_counts:
             latest_workflow_load = latest_workflow_load.undefer("step_count")
-        latest_workflow_load = latest_workflow_load.lazyload("steps")
+        latest_workflow_load = latest_workflow_load.lazyload(model.Workflow.steps)
 
         query = query.options(joinedload(model.StoredWorkflow.annotations))
         query = query.options(latest_workflow_load)
@@ -268,9 +268,11 @@ def get_stored_workflow(self, trans, workflow_id, by_stored_id=True) -> StoredWo
                     )
                 )
         stored_workflow = workflow_query.options(
-            joinedload("annotations"),
-            joinedload("tags"),
-            subqueryload("latest_workflow").joinedload("steps").joinedload("*"),
+            joinedload(trans.app.model.StoredWorkflow.annotations),
+            joinedload(trans.app.model.StoredWorkflow.tags),
+            subqueryload(trans.app.model.StoredWorkflow.latest_workflow)
+            .joinedload(trans.app.model.Workflow.steps)
+            .joinedload("*"),
         ).first()
         if stored_workflow is None:
             if not by_stored_id:
@@ -366,10 +368,10 @@ def get_invocation(self, trans, decoded_invocation_id, eager=False) -> model.Wor
         if eager:
             q = q.options(
                 subqueryload(model.WorkflowInvocation.steps)
-                .joinedload("implicit_collection_jobs")
-                .joinedload("jobs")
-                .joinedload("job")
-                .joinedload("input_datasets")
+                .joinedload(model.WorkflowInvocationStep.implicit_collection_jobs)
+                .joinedload(model.ImplicitCollectionJobs.jobs)
+                .joinedload(model.ImplicitCollectionJobsJobAssociation.job)
+                .joinedload(model.Job.input_datasets)
             )
         workflow_invocation = q.get(decoded_invocation_id)
         if not workflow_invocation:

lib/galaxy/model/__init__.py

@@ -2962,10 +2962,10 @@ def active_dataset_and_roles_query(self):
             .filter(not_(HistoryDatasetAssociation.deleted))
             .order_by(HistoryDatasetAssociation.table.c.hid.asc())
             .options(
-                joinedload("dataset"),
-                joinedload("dataset.actions"),
-                joinedload("dataset.actions.role"),
-                joinedload("tags"),
+                joinedload(HistoryDatasetAssociation.dataset)
+                .joinedload(Dataset.actions)
+                .joinedload(DatasetPermissions.role),
+                joinedload(HistoryDatasetAssociation.tags),
             )
         )
 
@@ -2993,7 +2993,10 @@ def active_visible_dataset_collections(self):
                 .filter(not_(HistoryDatasetCollectionAssociation.deleted))
                 .filter(HistoryDatasetCollectionAssociation.visible)
                 .order_by(HistoryDatasetCollectionAssociation.table.c.hid.asc())
-                .options(joinedload("collection"), joinedload("tags"))
+                .options(
+                    joinedload(HistoryDatasetCollectionAssociation.collection),
+                    joinedload(HistoryDatasetCollectionAssociation.tags),
+                )
             )
             self._active_visible_dataset_collections = query.all()
         return self._active_visible_dataset_collections

lib/galaxy/model/security.py

@@ -1507,12 +1507,15 @@ def check_folder_contents(self, user, roles, folder, hidden_folder_ids=""):
             return True, ""
         action = self.permitted_actions.DATASET_ACCESS
 
+        raise
         lddas = (
             self.sa_session.query(self.model.LibraryDatasetDatasetAssociation)
             .join("library_dataset")
             .filter(self.model.LibraryDataset.folder == folder)
             .join("dataset")
-            .options(joinedload("dataset").joinedload("actions"))
+            .options(
+                joinedload(self.model.LibraryDatasetDatasetAssociation.dataset).joinedload(self.model.Dataset.actions)
+            )
             .all()
         )
 

lib/galaxy/tools/actions/upload_common.py

@@ -422,10 +422,11 @@ def active_folders(trans, folder):
     # Stolen from galaxy.web.controllers.library_common (importing from which causes a circular issues).
     # Much faster way of retrieving all active sub-folders within a given folder than the
     # performance of the mapper.  This query also eagerloads the permissions on each folder.
+    raise
     return (
         trans.sa_session.query(LibraryFolder)
         .filter_by(parent=folder, deleted=False)
-        .options(joinedload("actions"))
+        .options(joinedload(LibraryFolder.actions))
         .order_by(LibraryFolder.table.c.name)
         .all()
     )

lib/galaxy/webapps/galaxy/controllers/history.py

@@ -208,7 +208,7 @@ def get_value(self, trans, grid, history):
     ]
 
     def build_initial_query(self, trans, **kwargs):
-        return trans.sa_session.query(self.model_class).join("users_shared_with")
+        return trans.sa_session.query(self.model_class).join(self.model_class.users_shared_with)
 
     def apply_query_filter(self, trans, query, **kwargs):
         return query.filter(model.HistoryUserShareAssociation.user == trans.user)

lib/galaxy/webapps/galaxy/controllers/page.py

@@ -161,7 +161,11 @@ def build_initial_query(self, trans, **kwargs):
             trans.sa_session.query(self.model_class)
             .join("user")
             .filter(model.User.deleted == false())
-            .options(joinedload("user").load_only("username"), joinedload("annotations"), undefer("average_rating"))
+            .options(
+                joinedload(self.model_class.user).load_only("username"),
+                joinedload(self.model_class.annotations),
+                undefer("average_rating"),
+            )
         )
 
     def apply_query_filter(self, trans, query, **kwargs):

lib/galaxy/webapps/galaxy/controllers/visualization.py

@@ -287,8 +287,12 @@ def build_initial_query(self, trans, **kwargs):
         # See optimization description comments and TODO for tags in matching public histories query.
         return (
             trans.sa_session.query(self.model_class)
-            .join("user")
-            .options(joinedload("user").load_only("username"), joinedload("annotations"), undefer("average_rating"))
+            .join(self.model_class.user)
+            .options(
+                joinedload(self.model_class.user).load_only("username"),
+                joinedload(self.model_class.annotations),
+                undefer("average_rating"),
+            )
         )
 
     def apply_query_filter(self, trans, query, **kwargs):

lib/galaxy/webapps/galaxy/controllers/workflow.py

@@ -163,12 +163,12 @@ def build_initial_query(self, trans, **kwargs):
         # of its steps to be eagerly loaded.
         return (
             trans.sa_session.query(self.model_class)
-            .join("user")
+            .join(self.model_class.user)
             .options(
-                lazyload("latest_workflow"),
-                joinedload("user").load_only("username"),
-                joinedload("annotations"),
-                undefer("average_rating"),
+                lazyload(self.model_class.latest_workflow),
+                joinedload(self.model_class.user).load_only(model.User.username),
+                joinedload(self.model_class.annotations),
+                undefer(self.model_class.average_rating),
             )
         )
 
@@ -487,7 +487,7 @@ def editor(self, trans, id=None, workflow_id=None, version=None):
             trans.sa_session.query(model.StoredWorkflow)
             .filter_by(user=trans.user, deleted=False, hidden=False)
             .order_by(desc(model.StoredWorkflow.table.c.update_time))
-            .options(joinedload("latest_workflow").joinedload("steps"))
+            .options(joinedload(model.StoredWorkflow.latest_workflow).joinedload(model.Workflow.steps))
             .all()
         )
         if version is None:

lib/galaxy/webapps/reports/controllers/system.py

@@ -115,7 +115,7 @@ def deleted_histories(self, trans, **kwd):
                         model.History.update_time < cutoff_time,
                     )
                 )
-                .options(joinedload("datasets"))
+                .options(joinedload(model.History.datasets))
             )
 
             for history in histories:

lib/tool_shed/webapp/api/repositories.py

@@ -50,6 +50,7 @@
     repository_util,
     tool_util,
 )
+from tool_shed.webapp import model
 from tool_shed.webapp.search.repo_search import RepoSearch
 
 log = logging.getLogger(__name__)
@@ -118,7 +119,7 @@ def get_ordered_installable_revisions(self, trans, name=None, owner=None, **kwd)
         if owner is None:
             owner = kwd.get("owner", None)
         tsr_id = kwd.get("tsr_id", None)
-        eagerload_columns = ["downloadable_revisions"]
+        eagerload_columns = [model.Repository.downloadable_revisions]
         if None not in [name, owner]:
             # Get the repository information.
             repository = repository_util.get_repository_by_name_and_owner(
@@ -217,7 +218,7 @@ def get_repository_revision_install_info(self, trans, name, owner, changeset_rev
         if name and owner and changeset_revision:
             # Get the repository information.
             repository = repository_util.get_repository_by_name_and_owner(
-                self.app, name, owner, eagerload_columns=["downloadable_revisions"]
+                self.app, name, owner, eagerload_columns=[model.Repository.downloadable_revisions]
             )
             if repository is None:
                 log.debug(f"Cannot locate repository {name} owned by {owner}")
@@ -284,7 +285,7 @@ def get_installable_revisions(self, trans, **kwd):
         tsr_id = kwd.get("tsr_id", None)
         if tsr_id is not None:
             repository = repository_util.get_repository_in_tool_shed(
-                self.app, tsr_id, eagerload_columns=["downloadable_revisions"]
+                self.app, tsr_id, eagerload_columns=[model.Repository.downloadable_revisions]
             )
         else:
             error_message = "Error in the Tool Shed repositories API in get_ordered_installable_revisions: "
@@ -737,7 +738,7 @@ def updates(self, trans, **kwd):
         changeset_revision = kwd.get("changeset_revision", None)
         hexlify_this = util.asbool(kwd.get("hexlify", True))
         repository = repository_util.get_repository_by_name_and_owner(
-            trans.app, name, owner, eagerload_columns=["downloadable_revisions"]
+            trans.app, name, owner, eagerload_columns=[model.Repository.downloadable_revisions]
         )
         if repository and repository.downloadable_revisions:
             repository_metadata = metadata_util.get_repository_metadata_by_changeset_revision(
@@ -837,7 +838,7 @@ def metadata(self, trans, id, **kwd):
         downloadable_only = util.asbool(kwd.get("downloadable_only", "True"))
         all_metadata = {}
         repository = repository_util.get_repository_in_tool_shed(
-            self.app, id, eagerload_columns=["downloadable_revisions"]
+            self.app, id, eagerload_columns=[model.Repository.downloadable_revisions]
         )
         for changeset, changehash in metadata_util.get_metadata_revisions(
             self.app, repository, sort_revisions=True, downloadable=downloadable_only