Merge pull request galaxyproject#16264 from jdavcs/dev_sa20_fix10

Towards SQLAlchemy 2.0 (upgrades to SA Core usage)
bgruening · Jul 21, 2023 · da965dc · da965dc
2 parents cf44aee + 00a600e
commit da965dc
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Showing 20 changed files with 418 additions and 462 deletions.
diff --git a/lib/galaxy/jobs/handler.py b/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_(
@@ -866,7 +866,7 @@ def get_user_job_count_per_destination(self, user_id):
             rval.update(cached)
             result = self.sa_session.execute(
                 select(
-                    [model.Job.table.c.destination_id, func.count(model.Job.table.c.destination_id).label("job_count")]
+                    model.Job.table.c.destination_id, func.count(model.Job.table.c.destination_id).label("job_count")
                 )
                 .where(
                     and_(
@@ -887,11 +887,9 @@ def __cache_user_job_count_per_destination(self):
             self.user_job_count_per_destination = {}
             result = self.sa_session.execute(
                 select(
-                    [
-                        model.Job.table.c.user_id,
-                        model.Job.table.c.destination_id,
-                        func.count(model.Job.table.c.user_id).label("job_count"),
-                    ]
+                    model.Job.table.c.user_id,
+                    model.Job.table.c.destination_id,
+                    func.count(model.Job.table.c.user_id).label("job_count"),
                 )
                 .where(and_(model.Job.table.c.state.in_((model.Job.states.QUEUED, model.Job.states.RUNNING))))
                 .group_by(model.Job.table.c.user_id, model.Job.table.c.destination_id)
@@ -987,7 +985,7 @@ def __cache_total_job_count_per_destination(self):
             self.total_job_count_per_destination = {}
             result = self.sa_session.execute(
                 select(
-                    [model.Job.table.c.destination_id, func.count(model.Job.table.c.destination_id).label("job_count")]
+                    model.Job.table.c.destination_id, func.count(model.Job.table.c.destination_id).label("job_count")
                 )
                 .where(and_(model.Job.table.c.state.in_((model.Job.states.QUEUED, model.Job.states.RUNNING))))
                 .group_by(model.Job.table.c.destination_id)

diff --git a/lib/galaxy/managers/hdas.py b/lib/galaxy/managers/hdas.py
@@ -360,7 +360,7 @@ 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)
@@ -385,12 +385,10 @@ def get_discarded(
     ) -> List[StoredItem]:
         stmt = (
             select(
-                [
-                    model.HistoryDatasetAssociation.id,
-                    model.HistoryDatasetAssociation.name,
-                    model.HistoryDatasetAssociation.update_time,
-                    model.Dataset.total_size,
-                ]
+                model.HistoryDatasetAssociation.id,
+                model.HistoryDatasetAssociation.name,
+                model.HistoryDatasetAssociation.update_time,
+                model.Dataset.total_size,
             )
             .select_from(model.HistoryDatasetAssociation)
             .join(model.Dataset, model.HistoryDatasetAssociation.table.c.dataset_id == model.Dataset.id)

diff --git a/lib/galaxy/managers/histories.py b/lib/galaxy/managers/histories.py
@@ -417,7 +417,7 @@ 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(),

diff --git a/lib/galaxy/managers/history_contents.py b/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"))
         )

diff --git a/lib/galaxy/managers/job_connections.py b/lib/galaxy/managers/job_connections.py
@@ -66,10 +66,8 @@ def _get_union_results(self, *selects):
     def outputs_derived_from_input_hda(self, input_hda_id: int):
         hda_select = (
             select(
-                [
-                    literal("HistoryDatasetAssociation").label("src"),
-                    model.JobToOutputDatasetAssociation.dataset_id.label("id"),
-                ]
+                literal("HistoryDatasetAssociation").label("src"),
+                model.JobToOutputDatasetAssociation.dataset_id.label("id"),
             )
             .join(
                 model.JobToInputDatasetAssociation,
@@ -80,10 +78,8 @@ def outputs_derived_from_input_hda(self, input_hda_id: int):
         )
         hdca_select = (
             select(
-                [
-                    literal("HistoryDatasetCollectionAssociation").label("src"),
-                    model.JobToOutputDatasetCollectionAssociation.dataset_collection_id.label("id"),
-                ]
+                literal("HistoryDatasetCollectionAssociation").label("src"),
+                model.JobToOutputDatasetCollectionAssociation.dataset_collection_id.label("id"),
             )
             .join(
                 model.JobToInputDatasetAssociation,
@@ -97,10 +93,8 @@ def outputs_derived_from_input_hda(self, input_hda_id: int):
     def outputs_derived_from_input_hdca(self, input_hdca_id: int):
         hda_select = (
             select(
-                [
-                    literal("HistoryDatasetAssociation").label("src"),
-                    model.JobToOutputDatasetAssociation.dataset_id.label("id"),
-                ]
+                literal("HistoryDatasetAssociation").label("src"),
+                model.JobToOutputDatasetAssociation.dataset_id.label("id"),
             )
             .join(
                 model.JobToInputDatasetCollectionAssociation,
@@ -111,10 +105,8 @@ def outputs_derived_from_input_hdca(self, input_hdca_id: int):
         )
         hdca_select = (
             select(
-                [
-                    literal("HistoryDatasetCollectionAssociation").label("src"),
-                    model.JobToOutputDatasetCollectionAssociation.dataset_collection_id.label("id"),
-                ]
+                literal("HistoryDatasetCollectionAssociation").label("src"),
+                model.JobToOutputDatasetCollectionAssociation.dataset_collection_id.label("id"),
             )
             .join(
                 model.JobToInputDatasetCollectionAssociation,
@@ -129,10 +121,8 @@ def outputs_derived_from_input_hdca(self, input_hdca_id: int):
     def inputs_for_hda(self, input_hda_id: int):
         input_hdas = (
             select(
-                [
-                    literal("HistoryDatasetAssociation").label("src"),
-                    model.JobToInputDatasetAssociation.dataset_id.label("id"),
-                ]
+                literal("HistoryDatasetAssociation").label("src"),
+                model.JobToInputDatasetAssociation.dataset_id.label("id"),
             )
             .join(
                 model.JobToOutputDatasetAssociation,
@@ -143,10 +133,8 @@ def inputs_for_hda(self, input_hda_id: int):
         )
         input_hdcas = (
             select(
-                [
-                    literal("HistoryDatasetCollectionAssociation").label("src"),
-                    model.JobToInputDatasetCollectionAssociation.dataset_collection_id.label("id"),
-                ]
+                literal("HistoryDatasetCollectionAssociation").label("src"),
+                model.JobToInputDatasetCollectionAssociation.dataset_collection_id.label("id"),
             )
             .join(
                 model.JobToOutputDatasetAssociation,
@@ -160,10 +148,8 @@ def inputs_for_hda(self, input_hda_id: int):
     def inputs_for_hdca(self, input_hdca_id: int):
         input_hdas = (
             select(
-                [
-                    literal("HistoryDatasetAssociation").label("src"),
-                    model.JobToInputDatasetAssociation.dataset_id.label("id"),
-                ]
+                literal("HistoryDatasetAssociation").label("src"),
+                model.JobToInputDatasetAssociation.dataset_id.label("id"),
             )
             .join(
                 model.JobToOutputDatasetCollectionAssociation,
@@ -174,10 +160,8 @@ def inputs_for_hdca(self, input_hdca_id: int):
         )
         input_hdcas = (
             select(
-                [
-                    literal("HistoryDatasetCollectionAssociation").label("src"),
-                    model.JobToInputDatasetCollectionAssociation.dataset_collection_id.label("id"),
-                ]
+                literal("HistoryDatasetCollectionAssociation").label("src"),
+                model.JobToInputDatasetCollectionAssociation.dataset_collection_id.label("id"),
             )
             .join(
                 model.JobToOutputDatasetCollectionAssociation,

diff --git a/lib/galaxy/managers/jobs.py b/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 = []
@@ -614,11 +614,9 @@ def invocation_job_source_iter(sa_session, invocation_id):
     join = model.WorkflowInvocationStep.table.join(model.WorkflowInvocation)
     statement = (
         select(
-            [
-                model.WorkflowInvocationStep.job_id,
-                model.WorkflowInvocationStep.implicit_collection_jobs_id,
-                model.WorkflowInvocationStep.state,
-            ]
+            model.WorkflowInvocationStep.job_id,
+            model.WorkflowInvocationStep.implicit_collection_jobs_id,
+            model.WorkflowInvocationStep.state,
         )
         .select_from(join)
         .where(model.WorkflowInvocation.id == invocation_id)
@@ -789,7 +787,7 @@ 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)

diff --git a/lib/galaxy/managers/notification.py b/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,

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
@@ -3296,12 +3296,10 @@ def disk_size(cls):
         )
         distinct_datasets = (
             select(
-                [
-                    # use labels here to better access from the query above
-                    HistoryDatasetAssociation.table.c.history_id.label("history_id"),
-                    Dataset.total_size.label("dataset_size"),
-                    Dataset.id.label("dataset_id"),
-                ]
+                # use labels here to better access from the query above
+                HistoryDatasetAssociation.table.c.history_id.label("history_id"),
+                Dataset.total_size.label("dataset_size"),
+                Dataset.id.label("dataset_id"),
             )
             .where(HistoryDatasetAssociation.table.c.purged != true())
             .where(Dataset.table.c.purged != true())
@@ -3313,7 +3311,7 @@ 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)
         )
@@ -8595,7 +8593,7 @@ 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

diff --git a/lib/galaxy/model/tags.py b/lib/galaxy/model/tags.py
@@ -95,19 +95,17 @@ def get_community_tags(self, item=None, limit=None):
         if not item_tag_assoc_class:
             return []
         # Build select statement.
-        cols_to_select = [item_tag_assoc_class.table.c.tag_id, func.count("*")]
         from_obj = item_tag_assoc_class.table.join(item_class.table).join(galaxy.model.Tag.table)
         where_clause = self.get_id_col_in_item_tag_assoc_table(item_class) == item.id
-        order_by = [func.count("*").desc()]
         group_by = item_tag_assoc_class.table.c.tag_id
         # Do query and get result set.
-        query = select(
-            columns=cols_to_select,
-            from_obj=from_obj,
-            whereclause=where_clause,
-            group_by=group_by,
-            order_by=order_by,
-            limit=limit,
+        query = (
+            select(item_tag_assoc_class.table.c.tag_id, func.count())
+            .select_from(from_obj)
+            .where(where_clause)
+            .group_by(group_by)
+            .order_by(func.count().desc())
+            .limit(limit)
         )
         result_set = self.sa_session.execute(query)
         # Return community tags.
@@ -118,9 +116,7 @@ def get_community_tags(self, item=None, limit=None):
         return community_tags
 
     def get_tool_tags(self):
-        query = select(
-            columns=[galaxy.model.ToolTagAssociation.table.c.tag_id], from_obj=galaxy.model.ToolTagAssociation.table
-        ).distinct()
+        query = select(galaxy.model.ToolTagAssociation.table.c.tag_id).distinct()
         result_set = self.sa_session.execute(query)
 
         tags = []