Merge pull request #12698 from ic4f/dev_sa20prep_1

Misc. fixes for SQLAlchemy 2.0

lib/galaxy/model/__init__.py

@@ -9025,7 +9025,7 @@ mapper_registry.map_imperatively(
 # The following statements must not precede the mapped models defined above.
 
 Job.any_output_dataset_collection_instances_deleted = column_property(
-    exists([HistoryDatasetCollectionAssociation.id], and_(
+    exists(HistoryDatasetCollectionAssociation.id).where(and_(
         Job.id == JobToOutputDatasetCollectionAssociation.job_id,
         HistoryDatasetCollectionAssociation.id == JobToOutputDatasetCollectionAssociation.dataset_collection_id,
         HistoryDatasetCollectionAssociation.deleted == true())
@@ -9033,7 +9033,7 @@ Job.any_output_dataset_collection_instances_deleted = column_property(
 )
 
 Job.any_output_dataset_deleted = column_property(
-    exists([HistoryDatasetAssociation], and_(
+    exists(HistoryDatasetAssociation).where(and_(
         Job.id == JobToOutputDatasetAssociation.job_id,
         HistoryDatasetAssociation.table.c.id == JobToOutputDatasetAssociation.dataset_id,
         HistoryDatasetAssociation.table.c.deleted == true())

lib/galaxy/model/migrate/versions/util.py

@@ -200,4 +200,6 @@ def execute_statements(engine, raw_sql):
     statements = raw_sql if isinstance(raw_sql, list) else [raw_sql]
     for sql in statements:
         cmd = DDL(sql)
-        cmd.execute(bind=engine)
+        with engine.connect() as connection:
+            with connection.begin():
+                connection.execute(cmd)

lib/galaxy/model/store/__init__.py

@@ -1394,7 +1394,7 @@ class DirectoryModelExportStore(ModelExportStore):
         # Write datasets' attributes to file.
         query = (sa_session.query(model.HistoryDatasetAssociation)
                  .filter(model.HistoryDatasetAssociation.history == history)
-                 .join("dataset")
+                 .join(model.Dataset)
                  .options(joinedload("dataset").joinedload("actions"))
                  .order_by(model.HistoryDatasetAssociation.hid)
                  .filter(model.Dataset.purged == expression.false()))

lib/galaxy/model/view/__init__.py

@@ -2,12 +2,16 @@
 Galaxy sql view models
 """
 from sqlalchemy import Integer
-from sqlalchemy.orm import mapper
+from sqlalchemy.orm import registry
 from sqlalchemy.sql import column, text
 
 from galaxy.model.view.utils import View
 
-AGGREGATE_STATE_QUERY = """
+
+class HistoryDatasetCollectionJobStateSummary(View):
+    name = 'collection_job_state_summary_view'
+
+    aggregate_state_query = """
 SELECT
     hdca_id,
     SUM(CASE WHEN state = 'new' THEN 1 ELSE 0 END) AS new,
@@ -43,11 +47,7 @@ FROM (
 GROUP BY jobstates.hdca_id
 """
 
-
-class HistoryDatasetCollectionJobStateSummary(View):
-    name = 'collection_job_state_summary_view'
-
-    __view__ = text(AGGREGATE_STATE_QUERY).columns(
+    __view__ = text(aggregate_state_query).columns(
         column('hdca_id', Integer),
         column('new', Integer),
         column('resubmitted', Integer),
@@ -67,4 +67,6 @@ class HistoryDatasetCollectionJobStateSummary(View):
     __table__ = View._make_table(name, __view__, pkeys)
 
 
-mapper(HistoryDatasetCollectionJobStateSummary, HistoryDatasetCollectionJobStateSummary.__table__)
+mapper_registry = registry()
+mapper_registry.map_imperatively(
+    HistoryDatasetCollectionJobStateSummary, HistoryDatasetCollectionJobStateSummary.__table__)

lib/galaxy/model/view/utils.py

@@ -76,5 +76,6 @@ def install_views(engine):
         # it mocks the app and CreateView will attempt to rebuild an existing
         # view in a database that is already made, the right answer is probably
         # to change the sql that gest emitted when CreateView is rendered.
-        engine.execute(DropView(view.name))
-        engine.execute(CreateView(view.name, view.__view__))
+        with engine.begin() as conn:
+            conn.execute(DropView(view.name))
+            conn.execute(CreateView(view.name, view.__view__))

test/unit/data/model/test_views.py

@@ -82,8 +82,8 @@ def make_table(metadata):
 
 def run_view_test(url, metadata, view, query):
     with sqlalchemy_engine(url) as engine:
-        with engine.connect() as conn:
+        with engine.begin() as conn:
             metadata.create_all(conn)  # create table in database
             conn.execute(CreateView(view.name, view.__view__))  # create view in database
-            result = conn.execute(query).fetchall()
+            result = conn.execute(text(query)).fetchall()
             assert len(result) == 1  # assert that view exists in database