Merge pull request #19407 from jdavcs/dev_remove_transaction_helper

Remove transaction helper

lib/galaxy/actions/library.py

@@ -17,7 +17,6 @@
     dictify_dataset_collection_instance,
 )
 from galaxy.model import LibraryFolder
-from galaxy.model.base import transaction
 from galaxy.tools.actions import upload_common
 from galaxy.tools.parameters import populate_state
 from galaxy.util.path import (
@@ -294,8 +293,7 @@ def _make_library_uploaded_dataset(self, trans, params, name, path, type, librar
         if link_data_only == "link_to_files":
             uploaded_dataset.data.link_to(path)
             trans.sa_session.add_all((uploaded_dataset.data, uploaded_dataset.data.dataset))
-            with transaction(trans.sa_session):
-                trans.sa_session.commit()
+            trans.sa_session.commit()
         return uploaded_dataset
 
     def _upload_library_dataset(self, trans, payload):
@@ -335,8 +333,7 @@ def _create_folder(self, trans, payload):
         new_folder.genome_build = trans.app.genome_builds.default_value
         parent_folder.add_folder(new_folder)
         trans.sa_session.add(new_folder)
-        with transaction(trans.sa_session):
-            trans.sa_session.commit()
+        trans.sa_session.commit()
         # New folders default to having the same permissions as their parent folder
         trans.app.security_agent.copy_library_permissions(trans, parent_folder, new_folder)
         new_folder_dict = dict(created=new_folder)

lib/galaxy/app_unittest_utils/galaxy_mock.py

@@ -36,7 +36,6 @@
 from galaxy.model.base import (
     ModelMapping,
     SharedModelMapping,
-    transaction,
 )
 from galaxy.model.mapping import GalaxyModelMapping
 from galaxy.model.scoped_session import galaxy_scoped_session
@@ -357,8 +356,7 @@ def set_user(self, user):
         if self.galaxy_session:
             self.galaxy_session.user = user
             self.sa_session.add(self.galaxy_session)
-            with transaction(self.sa_session):
-                self.sa_session.commit()
+            self.sa_session.commit()
         self.__user = user
 
     user = property(get_user, set_user)

lib/galaxy/app_unittest_utils/toolbox_support.py

@@ -8,7 +8,6 @@
 from galaxy.app_unittest_utils.tools_support import UsesTools
 from galaxy.config_watchers import ConfigWatchers
 from galaxy.model import tool_shed_install
-from galaxy.model.base import transaction
 from galaxy.model.tool_shed_install import mapping
 from galaxy.tools import ToolBox
 from galaxy.tools.cache import ToolCache
@@ -113,8 +112,7 @@ def _repo_install(self, changeset, config_filename=None):
         repository.uninstalled = False
         self.app.install_model.context.add(repository)
         session = self.app.install_model.context
-        with transaction(session):
-            session.commit()
+        session.commit()
         return repository
 
     def _setup_two_versions(self):
@@ -123,25 +121,22 @@ def _setup_two_versions(self):
         version1.tool_id = "github.com/galaxyproject/example/test_tool/0.1"
         self.app.install_model.context.add(version1)
         session = self.app.install_model.context
-        with transaction(session):
-            session.commit()
+        session.commit()
 
         self._repo_install(changeset="2")
         version2 = tool_shed_install.ToolVersion()
         version2.tool_id = "github.com/galaxyproject/example/test_tool/0.2"
         self.app.install_model.context.add(version2)
         session = self.app.install_model.context
-        with transaction(session):
-            session.commit()
+        session.commit()
 
         version_association = tool_shed_install.ToolVersionAssociation()
         version_association.parent_id = version1.id
         version_association.tool_id = version2.id
 
         self.app.install_model.context.add(version_association)
         session = self.app.install_model.context
-        with transaction(session):
-            session.commit()
+        session.commit()
 
     def _setup_two_versions_in_config(self, section=False):
         if section:

lib/galaxy/authnz/custos_authnz.py

@@ -27,7 +27,6 @@
     CustosAuthnzToken,
     User,
 )
-from galaxy.model.base import transaction
 from galaxy.model.orm.util import add_object_to_object_session
 from galaxy.util import requests
 from . import IdentityProvider
@@ -293,8 +292,7 @@ def callback(self, state_token, authz_code, trans, login_redirect_url):
             redirect_url = "/"
 
         trans.sa_session.add(custos_authnz_token)
-        with transaction(trans.sa_session):
-            trans.sa_session.commit()
+        trans.sa_session.commit()
 
         return redirect_url, custos_authnz_token.user
 
@@ -342,8 +340,7 @@ def create_user(self, token, trans, login_redirect_url):
 
         trans.sa_session.add(user)
         trans.sa_session.add(custos_authnz_token)
-        with transaction(trans.sa_session):
-            trans.sa_session.commit()
+        trans.sa_session.commit()
         return login_redirect_url, user
 
     def disconnect(self, provider, trans, disconnect_redirect_url=None, email=None, association_id=None):
@@ -360,8 +357,7 @@ def disconnect(self, provider, trans, disconnect_redirect_url=None, email=None,
                     if id_token_decoded["email"] == email:
                         index = idx
             trans.sa_session.delete(provider_tokens[index])
-            with transaction(trans.sa_session):
-                trans.sa_session.commit()
+            trans.sa_session.commit()
             return True, "", disconnect_redirect_url
         except Exception as e:
             return False, f"Failed to disconnect provider {provider}: {util.unicodify(e)}", None

lib/galaxy/authnz/psa_authnz.py

@@ -25,7 +25,6 @@
     PSAPartial,
     UserAuthnzToken,
 )
-from galaxy.model.base import transaction
 from galaxy.util import (
     DEFAULT_SOCKET_TIMEOUT,
     requests,
@@ -494,5 +493,4 @@ def disconnect(
     sa_session.delete(user_authnz)
     # option B
     # user_authnz.extra_data = None
-    with transaction(sa_session):
-        sa_session.commit()
+    sa_session.commit()

lib/galaxy/celery/base_task.py

@@ -13,7 +13,6 @@
 from sqlalchemy.exc import IntegrityError
 
 from galaxy.model import CeleryUserRateLimit
-from galaxy.model.base import transaction
 from galaxy.model.scoped_session import galaxy_scoped_session
 
 
@@ -83,25 +82,24 @@ class GalaxyTaskBeforeStartUserRateLimitPostgres(GalaxyTaskBeforeStartUserRateLi
     def calculate_task_start_time(
         self, user_id: int, sa_session: galaxy_scoped_session, task_interval_secs: float, now: datetime.datetime
     ) -> datetime.datetime:
-        with transaction(sa_session):
-            update_stmt = (
-                update(CeleryUserRateLimit)
-                .where(CeleryUserRateLimit.user_id == user_id)
-                .values(last_scheduled_time=text("greatest(last_scheduled_time + ':interval second', :now)"))
+        update_stmt = (
+            update(CeleryUserRateLimit)
+            .where(CeleryUserRateLimit.user_id == user_id)
+            .values(last_scheduled_time=text("greatest(last_scheduled_time + ':interval second', :now)"))
+            .returning(CeleryUserRateLimit.last_scheduled_time)
+        )
+        result = sa_session.execute(update_stmt, {"interval": task_interval_secs, "now": now}).all()
+        if not result:
+            sched_time = now + datetime.timedelta(seconds=task_interval_secs)
+            upsert_stmt = (
+                ps_insert(CeleryUserRateLimit)  # type:ignore[attr-defined]
+                .values(user_id=user_id, last_scheduled_time=now)
                 .returning(CeleryUserRateLimit.last_scheduled_time)
+                .on_conflict_do_update(index_elements=["user_id"], set_=dict(last_scheduled_time=sched_time))
             )
-            result = sa_session.execute(update_stmt, {"interval": task_interval_secs, "now": now}).all()
-            if not result:
-                sched_time = now + datetime.timedelta(seconds=task_interval_secs)
-                upsert_stmt = (
-                    ps_insert(CeleryUserRateLimit)  # type:ignore[attr-defined]
-                    .values(user_id=user_id, last_scheduled_time=now)
-                    .returning(CeleryUserRateLimit.last_scheduled_time)
-                    .on_conflict_do_update(index_elements=["user_id"], set_=dict(last_scheduled_time=sched_time))
-                )
-                result = sa_session.execute(upsert_stmt).all()
-            sa_session.commit()
-            return result[0][0]
+            result = sa_session.execute(upsert_stmt).all()
+        sa_session.commit()
+        return result[0][0]
 
 
 class GalaxyTaskBeforeStartUserRateLimitStandard(GalaxyTaskBeforeStartUserRateLimit):
@@ -130,26 +128,23 @@ def calculate_task_start_time(
         self, user_id: int, sa_session: galaxy_scoped_session, task_interval_secs: float, now: datetime.datetime
     ) -> datetime.datetime:
         last_scheduled_time = None
-        with transaction(sa_session):
-            last_scheduled_time = sa_session.scalars(self._select_stmt, {"userid": user_id}).first()
-            if last_scheduled_time:
-                sched_time = last_scheduled_time + datetime.timedelta(seconds=task_interval_secs)
-                if sched_time < now:
-                    sched_time = now
-                sa_session.execute(self._update_stmt, {"userid": user_id, "sched_time": sched_time})
-            sa_session.commit()
+        last_scheduled_time = sa_session.scalars(self._select_stmt, {"userid": user_id}).first()
+        if last_scheduled_time:
+            sched_time = last_scheduled_time + datetime.timedelta(seconds=task_interval_secs)
+            if sched_time < now:
+                sched_time = now
+            sa_session.execute(self._update_stmt, {"userid": user_id, "sched_time": sched_time})
+        sa_session.commit()
         if not last_scheduled_time:
             try:
-                with transaction(sa_session):
-                    sched_time = now
-                    sa_session.execute(self._insert_stmt, {"userid": user_id, "sched_time": sched_time})
-                    sa_session.commit()
+                sched_time = now
+                sa_session.execute(self._insert_stmt, {"userid": user_id, "sched_time": sched_time})
+                sa_session.commit()
             except IntegrityError:
                 #  Row was inserted by another thread since we tried the update above.
-                with transaction(sa_session):
-                    sched_time = now + datetime.timedelta(seconds=task_interval_secs)
-                    result = sa_session.execute(self._update_stmt, {"userid": user_id, "sched_time": sched_time})
-                    if result.rowcount == 0:
-                        raise Exception(f"Failed to update a celery_user_rate_limit row for user id {user_id}")
-                    sa_session.commit()
+                sched_time = now + datetime.timedelta(seconds=task_interval_secs)
+                result = sa_session.execute(self._update_stmt, {"userid": user_id, "sched_time": sched_time})
+                if result.rowcount == 0:
+                    raise Exception(f"Failed to update a celery_user_rate_limit row for user id {user_id}")
+                sa_session.commit()
         return sched_time

lib/galaxy/celery/tasks.py

@@ -41,7 +41,6 @@
     Job,
     User,
 )
-from galaxy.model.base import transaction
 from galaxy.model.scoped_session import galaxy_scoped_session
 from galaxy.objectstore import BaseObjectStore
 from galaxy.objectstore.caching import check_caches
@@ -157,8 +156,7 @@ def change_datatype(
         path = dataset_instance.dataset.get_file_name()
         datatype = sniff.guess_ext(path, datatypes_registry.sniff_order)
     datatypes_registry.change_datatype(dataset_instance, datatype)
-    with transaction(sa_session):
-        sa_session.commit()
+    sa_session.commit()
     set_metadata(hda_manager, ldda_manager, sa_session, dataset_id, model_class)
 
 
@@ -174,8 +172,7 @@ def touch(
     stmt = select(model.HistoryDatasetCollectionAssociation).filter_by(id=item_id)
     item = sa_session.execute(stmt).scalar_one()
     item.touch()
-    with transaction(sa_session):
-        sa_session.commit()
+    sa_session.commit()
 
 
 @galaxy_task(action="set dataset association metadata")
@@ -209,8 +206,7 @@ def set_metadata(
     except Exception as e:
         log.info(f"Setting metadata failed on {model_class} {dataset_instance.id}: {str(e)}")
         dataset_instance.state = dataset_instance.states.FAILED_METADATA
-    with transaction(sa_session):
-        sa_session.commit()
+    sa_session.commit()
 
 
 def _get_dataset_manager(

lib/galaxy/job_execution/output_collect.py

@@ -24,7 +24,6 @@
     JobToOutputDatasetAssociation,
     LibraryDatasetDatasetAssociation,
 )
-from galaxy.model.base import transaction
 from galaxy.model.dataset_collections import builder
 from galaxy.model.dataset_collections.structure import UninitializedTree
 from galaxy.model.dataset_collections.type_description import COLLECTION_TYPE_DESCRIPTION_FACTORY
@@ -302,8 +301,7 @@ def persist_object(self, obj):
         self.sa_session.add(obj)
 
     def flush(self):
-        with transaction(self.sa_session):
-            self.sa_session.commit()
+        self.sa_session.commit()
 
     def get_library_folder(self, destination):
         app = self.app
@@ -343,8 +341,7 @@ def add_library_dataset_to_folder(self, library_folder, ld):
         trans = self.work_context
         trans.app.security_agent.copy_library_permissions(trans, library_folder, ld)
         trans.sa_session.add(ld)
-        with transaction(trans.sa_session):
-            trans.sa_session.commit()
+        trans.sa_session.commit()
 
         # Permissions must be the same on the LibraryDatasetDatasetAssociation and the associated LibraryDataset
         trans.app.security_agent.copy_library_permissions(trans, ld, ldda)
@@ -354,12 +351,10 @@ def add_library_dataset_to_folder(self, library_folder, ld):
         )
         library_folder.add_library_dataset(ld, genome_build=ldda.dbkey)
         trans.sa_session.add(library_folder)
-        with transaction(trans.sa_session):
-            trans.sa_session.commit()
+        trans.sa_session.commit()
 
         trans.sa_session.add(ld)
-        with transaction(trans.sa_session):
-            trans.sa_session.commit()
+        trans.sa_session.commit()
 
     def add_datasets_to_history(self, datasets, for_output_dataset=None):
         sa_session = self.sa_session