Fix select([foo]) SA2.0 warnings

lib/galaxy/jobs/handler.py

@@ -123,7 +123,7 @@ def __init__(
 
     def setup_query(self):
         subq = (
-            select([self.grab_this.id])
+            select(self.grab_this.id)
             .where(
                 and_(
                     self.grab_this.table.c.handler.in_(self.self_handler_tags),
@@ -817,7 +817,7 @@ def get_user_job_count(self, user_id):
         rval = self.user_job_count.get(user_id, 0)
         if not self.app.config.cache_user_job_count:
             result = self.sa_session.execute(
-                select([func.count(model.Job.table.c.id)]).where(
+                select(func.count(model.Job.table.c.id)).where(
                     and_(
                         model.Job.table.c.state.in_(
                             (model.Job.states.QUEUED, model.Job.states.RUNNING, model.Job.states.RESUBMITTED)
@@ -836,7 +836,7 @@ def __cache_user_job_count(self):
         if self.user_job_count is None and self.app.config.cache_user_job_count:
             self.user_job_count = {}
             query = self.sa_session.execute(
-                select([model.Job.table.c.user_id, func.count(model.Job.table.c.user_id)])
+                select(model.Job.table.c.user_id, func.count(model.Job.table.c.user_id))
                 .where(
                     and_(
                         model.Job.table.c.state.in_(

lib/galaxy/managers/hdas.py

@@ -359,7 +359,7 @@ def __init__(self, hda_manager: HDAManager, dataset_manager: datasets.DatasetMan
 
     def get_discarded_summary(self, user: model.User) -> CleanableItemsSummary:
         stmt = (
-            select([func.sum(model.Dataset.total_size), func.count(model.HistoryDatasetAssociation.id)])
+            select(func.sum(model.Dataset.total_size), func.count(model.HistoryDatasetAssociation.id))
             .select_from(model.HistoryDatasetAssociation)
             .join(model.Dataset, model.HistoryDatasetAssociation.table.c.dataset_id == model.Dataset.id)
             .join(model.History, model.HistoryDatasetAssociation.table.c.history_id == model.History.id)

lib/galaxy/managers/histories.py

@@ -382,7 +382,7 @@ def __init__(self, history_manager: HistoryManager):
         }
 
     def get_discarded_summary(self, user: model.User) -> CleanableItemsSummary:
-        stmt = select([func.sum(model.History.disk_size), func.count(model.History.id)]).where(
+        stmt = select(func.sum(model.History.disk_size), func.count(model.History.id)).where(
             model.History.user_id == user.id,
             model.History.deleted == true(),
             model.History.purged == false(),

lib/galaxy/managers/history_contents.py

@@ -180,7 +180,7 @@ def state_counts(self, history):
         ]
         contents_subquery = self._union_of_contents_query(history, filters=filters).subquery()
         statement = (
-            sql.select([sql.column("state"), func.count("*")])
+            sql.select(sql.column("state"), func.count("*"))
             .select_from(contents_subquery)
             .group_by(sql.column("state"))
         )

lib/galaxy/managers/jobs.py

@@ -416,7 +416,7 @@ def replace_dataset_ids(path, key, value):
                     c = aliased(model.HistoryDatasetAssociation)
                     d = aliased(model.JobParameter)
                     e = aliased(model.HistoryDatasetAssociationHistory)
-                    stmt = select([model.HistoryDatasetAssociation.id]).where(
+                    stmt = select(model.HistoryDatasetAssociation.id).where(
                         model.HistoryDatasetAssociation.id == e.history_dataset_association_id
                     )
                     name_condition = []
@@ -789,7 +789,7 @@ def summarize_jobs_to_dict(sa_session, jobs_source):
                 model.ImplicitCollectionJobsJobAssociation.table.join(model.Job)
             )
             statement = (
-                select([model.Job.state, func.count("*")])
+                select(model.Job.state, func.count("*"))
                 .select_from(join)
                 .where(model.ImplicitCollectionJobs.id == jobs_source.id)
                 .group_by(model.Job.state)

lib/galaxy/managers/notification.py

@@ -184,7 +184,7 @@ def get_user_total_unread_notification_count(self, user: User) -> int:
         Only published and not expired notifications are accounted.
         """
         stmt = (
-            select([func.count(UserNotificationAssociation.id)])
+            select(func.count(UserNotificationAssociation.id))
             .select_from(UserNotificationAssociation)
             .join(
                 Notification,

lib/galaxy/model/__init__.py

@@ -3263,7 +3263,7 @@ def disk_size(cls):
         distinct_datasets_alias = aliased(distinct_datasets.subquery(), name="datasets")
         # then, bind as property of history using the cls.id
         size_query = (
-            select([func.coalesce(func.sum(distinct_datasets_alias.c.dataset_size), 0)])
+            select(func.coalesce(func.sum(distinct_datasets_alias.c.dataset_size), 0))
             .select_from(distinct_datasets_alias)
             .where(distinct_datasets_alias.c.history_id == cls.id)
         )
@@ -8544,7 +8544,7 @@ class WorkflowInvocationStep(Base, Dictifiable, Serializable):
         viewonly=True,
     )
     order_index = column_property(
-        select([WorkflowStep.order_index]).where(WorkflowStep.id == workflow_step_id).scalar_subquery()
+        select(WorkflowStep.order_index).where(WorkflowStep.id == workflow_step_id).scalar_subquery()
     )
 
     subworkflow_invocation_id: column_property

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

@@ -857,7 +857,7 @@ def per_user(self, trans, **kwd):
         q_time.stop()
         query1time = q_time.time_elapsed()
 
-        users = sa.select([model.User.table.c.email], from_obj=[model.User.table])
+        users = sa.select(model.User.table.c.email).select_from(model.User.table)
 
         all_jobs_per_user = sa.select(
             (