Model edits and bug fixes

lib/galaxy/jobs/handler.py

@@ -123,7 +123,6 @@ def __init__(
         self.self_handler_tags = self_handler_tags
         self.max_grab = max_grab
         self.handler_tags = handler_tags
-        self._grab_conn_opts = {"autocommit": False}
         self._grab_query = None
         self._supports_returning = self.app.application_stack.supports_returning()
 

lib/galaxy/model/base.py

@@ -81,7 +81,7 @@ def check_database_connection(session):
 class ModelMapping(Bunch):
     def __init__(self, model_modules, engine):
         self.engine = engine
-        self._SessionLocal = sessionmaker(autoflush=False, autocommit=False, future=True)
+        self._SessionLocal = sessionmaker(autoflush=False)
         versioned_session(self._SessionLocal)
         context = scoped_session(self._SessionLocal, scopefunc=self.request_scopefunc)
         # For backward compatibility with "context.current"

lib/galaxy/model/database_utils.py

@@ -45,7 +45,7 @@ def create_database(db_url, database=None, encoding="utf8", template=None):
 
 @contextmanager
 def sqlalchemy_engine(url):
-    engine = create_engine(url, future=True)
+    engine = create_engine(url)
     try:
         yield engine
     finally:

lib/galaxy/model/migrations/__init__.py

@@ -124,10 +124,10 @@ def verify_databases_via_script(
 ) -> None:
     # This function serves a use case when an engine has not been created yet
     # (e.g. when called from a script).
-    gxy_engine = create_engine(gxy_config.url, future=True)
+    gxy_engine = create_engine(gxy_config.url)
     tsi_engine = None
     if tsi_config.url and tsi_config.url != gxy_config.url:
-        tsi_engine = create_engine(tsi_config.url, future=True)
+        tsi_engine = create_engine(tsi_config.url)
 
     verify_databases(
         gxy_engine,

lib/galaxy/model/migrations/alembic/env.py

@@ -116,7 +116,7 @@ def _configure_and_run_migrations_offline(url: str) -> None:
 
 
 def _configure_and_run_migrations_online(url) -> None:
-    engine = create_engine(url, future=True)
+    engine = create_engine(url)
     with engine.connect() as connection:
         context.configure(connection=connection, target_metadata=target_metadata)
         with context.begin_transaction():

lib/galaxy/model/migrations/scripts.py

@@ -59,7 +59,7 @@ def verify_database_is_initialized(db_url: str) -> None:
     if not database_exists(db_url):
         raise DatabaseDoesNotExistError(db_url)
 
-    engine = create_engine(db_url, future=True)
+    engine = create_engine(db_url)
     try:
         db_state = DatabaseStateCache(engine=engine)
         if db_state.is_database_empty() or db_state.contains_only_kombu_tables():
@@ -161,7 +161,7 @@ def get_gxy_db_version(self, gxy_db_url=None):
         """
         db_url = gxy_db_url or self.gxy_db_url
         try:
-            engine = create_engine(db_url, future=True)
+            engine = create_engine(db_url)
             version = self._get_gxy_alembic_db_version(engine)
             if not version:
                 version = self._get_gxy_sam_db_version(engine)
@@ -197,7 +197,7 @@ def _rename_arg(self, argv, old_name, new_name) -> None:
 
     def _upgrade(self, db_url, model):
         try:
-            engine = create_engine(db_url, future=True)
+            engine = create_engine(db_url)
             am = get_alembic_manager(engine)
             am.upgrade(model)
         finally:

lib/galaxy/model/orm/engine_factory.py

@@ -106,9 +106,9 @@ def after_cursor_execute(conn, cursor, statement, parameters, context, executema
         set_sqlite_connect_args(engine_options, url)
 
     if url.startswith("sqlite://") and url not in ("sqlite:///:memory:", "sqlite://"):
-        engine = create_engine(url, **engine_options, poolclass=NullPool, future=True)
+        engine = create_engine(url, **engine_options, poolclass=NullPool)
     else:
-        engine = create_engine(url, **engine_options, future=True)
+        engine = create_engine(url, **engine_options)
 
     # Prevent sharing connection across fork: https://docs.sqlalchemy.org/en/14/core/pooling.html#using-connection-pools-with-multiprocessing-or-os-fork
     register_after_fork(engine, lambda e: e.dispose())

lib/galaxy/model/store/__init__.py

@@ -1047,7 +1047,6 @@ def _import_workflow_invocations(
         for invocation_attrs in invocations_attrs:
             assert not self.import_options.allow_edit
             imported_invocation = model.WorkflowInvocation()
-            imported_invocation.user = self.user
             imported_invocation.history = history
             ensure_object_added_to_session(imported_invocation, object_in_session=history)
             workflow_key = invocation_attrs["workflow"]

lib/galaxy/model/unittest_utils/migration_scripts_testing_utils.py

@@ -76,7 +76,7 @@ def get_db_heads(config: Config) -> Tuple[str, ...]:
     """Return revision ids (version heads) stored in the database."""
     dburl = config.get_main_option("sqlalchemy.url")
     assert dburl
-    engine = create_engine(dburl, future=True)
+    engine = create_engine(dburl)
     with engine.connect() as conn:
         context = MigrationContext.configure(conn)
         heads = context.get_current_heads()

lib/galaxy/model/unittest_utils/model_testing_utils.py

@@ -67,7 +67,7 @@ def drop_existing_database(url: DbUrl) -> Iterator[None]:
 @contextmanager
 def disposing_engine(url: DbUrl) -> Iterator[Engine]:
     """Context manager for engine that disposes of its connection pool on exit."""
-    engine = create_engine(url, future=True)
+    engine = create_engine(url)
     try:
         yield engine
     finally:
@@ -233,7 +233,7 @@ def _drop_postgres_database(url: DbUrl) -> None:
 
 
 def _drop_database(connection_url, database_name):
-    engine = create_engine(connection_url, isolation_level="AUTOCOMMIT", future=True)
+    engine = create_engine(connection_url, isolation_level="AUTOCOMMIT")
     preparer = IdentifierPreparer(engine.dialect)
     database_name = preparer.quote(database_name)
     stmt = text(f"DROP DATABASE IF EXISTS {database_name}")

lib/tool_shed/webapp/model/migrations/__init__.py

@@ -46,7 +46,7 @@ def __init__(self) -> None:
 
 def verify_database(url, engine_options=None) -> None:
     engine_options = engine_options or {}
-    engine = create_engine(url, **engine_options, future=True)
+    engine = create_engine(url, **engine_options)
     verifier = DatabaseStateVerifier(engine)
     verifier.run()
     engine.dispose()

lib/tool_shed/webapp/model/migrations/alembic/env.py

@@ -62,7 +62,7 @@ def _configure_and_run_migrations_offline(url: str) -> None:
 
 
 def _configure_and_run_migrations_online(url) -> None:
-    engine = create_engine(url, future=True)
+    engine = create_engine(url)
     with engine.connect() as connection:
         context.configure(connection=connection, target_metadata=target_metadata)
         with context.begin_transaction():

scripts/check_model.py

@@ -49,7 +49,7 @@ def load_indexes(metadata):
     # create EMPTY metadata, then load from database
     db_url = get_config(sys.argv)["db_url"]
     metadata = MetaData()
-    engine = create_engine(db_url, future=True)
+    engine = create_engine(db_url)
     metadata.reflect(bind=engine)
     indexes_in_db = load_indexes(metadata)
 

scripts/update_shed_config_path.py

@@ -46,9 +46,9 @@ def create_database(config_file):
         exit(1)
 
     # Initialize the database connection.
-    engine = create_engine(database_connection, future=True)
+    engine = create_engine(database_connection)
     MetaData(bind=engine)
-    install_session = scoped_session(sessionmaker(bind=engine, autoflush=False, autocommit=True))
+    install_session = scoped_session(sessionmaker(bind=engine, autoflush=False))
     model = mapping.init(database_connection)
     return install_session, model
 

test/unit/data/model/conftest.py

@@ -30,7 +30,7 @@ def sqlite_memory_url():
 @pytest.fixture(scope="module")
 def engine():
     db_uri = "sqlite:///:memory:"
-    return create_engine(db_uri, future=True)
+    return create_engine(db_uri)
 
 
 @pytest.fixture

test/unit/workflows/test_workflow_progress.py

@@ -100,7 +100,7 @@ def _set_previous_progress(self, outputs):
 
             workflow_invocation_step_state = model.WorkflowRequestStepState()
             workflow_invocation_step_state.workflow_step_id = step_id
-            workflow_invocation_step_state.value = True
+            workflow_invocation_step_state.value = cast(bytes, True)
             self.invocation.step_states.append(workflow_invocation_step_state)
 
     def _step(self, index):