Remove transaction helper from scripts

scripts/cleanup_datasets/admin_cleanup_datasets.py

@@ -64,7 +64,6 @@
 import galaxy.config
 import galaxy.model.mapping
 import galaxy.util
-from galaxy.model.base import transaction
 from galaxy.util.script import (
     app_properties_from_args,
     populate_config_args,
@@ -261,9 +260,7 @@ def administrative_delete_datasets(
                     hda.deleted = True
                     app.sa_session.add(hda)
                     print(f"Marked HistoryDatasetAssociation id {hda.id} as deleted")
-                session = app.sa_session()
-                with transaction(session):
-                    session.commit()
+                app.session().commit()
 
     emailtemplate = Template(filename=template_file)
     for email, dataset_list in user_notifications.items():

scripts/cleanup_datasets/cleanup_datasets.py

@@ -26,7 +26,6 @@
 import galaxy.config
 from galaxy.datatypes.registry import Registry
 from galaxy.exceptions import ObjectNotFound
-from galaxy.model.base import transaction
 from galaxy.model.mapping import init_models_from_config
 from galaxy.objectstore import build_object_store_from_config
 from galaxy.util import unicodify
@@ -222,12 +221,13 @@ def delete_userless_histories(app, cutoff_time, info_only=False, force_retry=Fal
     # Nothing is removed from disk yet.
     history_count = 0
     start = time.time()
+    session = app.sa_session()
     if force_retry:
-        histories = app.sa_session.query(app.model.History).filter(
+        histories = session.query(app.model.History).filter(
             and_(app.model.History.__table__.c.user_id == null(), app.model.History.update_time < cutoff_time)
         )
     else:
-        histories = app.sa_session.query(app.model.History).filter(
+        histories = session.query(app.model.History).filter(
             and_(
                 app.model.History.__table__.c.user_id == null(),
                 app.model.History.__table__.c.deleted == false(),
@@ -238,10 +238,8 @@ def delete_userless_histories(app, cutoff_time, info_only=False, force_retry=Fal
         if not info_only:
             log.info("Deleting history id %d", history.id)
             history.deleted = True
-            app.sa_session.add(history)
-            session = app.sa_session()
-            with transaction(session):
-                session.commit()
+            session.add(history)
+            session.commit()
         history_count += 1
     stop = time.time()
     log.info("Deleted %d histories", history_count)
@@ -257,15 +255,16 @@ def purge_histories(app, cutoff_time, remove_from_disk, info_only=False, force_r
     # i.e. all associated datasets are marked as deleted
     history_count = 0
     start = time.time()
+    session = app.sa_session()
     if force_retry:
         histories = (
-            app.sa_session.query(app.model.History)
+            session.query(app.model.History)
             .filter(and_(app.model.History.__table__.c.deleted == true(), app.model.History.update_time < cutoff_time))
             .options(joinedload(app.model.History.datasets))
         )
     else:
         histories = (
-            app.sa_session.query(app.model.History)
+            session.query(app.model.History)
             .filter(
                 and_(
                     app.model.History.__table__.c.deleted == true(),
@@ -289,10 +288,8 @@ def purge_histories(app, cutoff_time, remove_from_disk, info_only=False, force_r
             #     dhp.delete()
             log.info("Purging history id %d", history.id)
             history.purged = True
-            app.sa_session.add(history)
-            session = app.sa_session()
-            with transaction(session):
-                session.commit()
+            session.add(history)
+            session.commit()
         else:
             log.info("History id %d will be purged (without 'info_only' mode)", history.id)
         history_count += 1
@@ -310,14 +307,15 @@ def purge_libraries(app, cutoff_time, remove_from_disk, info_only=False, force_r
     # i.e. all associated LibraryDatasets/folders are marked as deleted
     library_count = 0
     start = time.time()
+    session = app.sa_session()
     if force_retry:
-        libraries = app.sa_session.query(app.model.Library).filter(
+        libraries = session.query(app.model.Library).filter(
             and_(
                 app.model.Library.__table__.c.deleted == true(), app.model.Library.__table__.c.update_time < cutoff_time
             )
         )
     else:
-        libraries = app.sa_session.query(app.model.Library).filter(
+        libraries = session.query(app.model.Library).filter(
             and_(
                 app.model.Library.__table__.c.deleted == true(),
                 app.model.Library.__table__.c.purged == false(),
@@ -329,10 +327,8 @@ def purge_libraries(app, cutoff_time, remove_from_disk, info_only=False, force_r
         if not info_only:
             log.info("Purging library id %d", library.id)
             library.purged = True
-            app.sa_session.add(library)
-            session = app.sa_session()
-            with transaction(session):
-                session.commit()
+            session.add(library)
+            session.commit()
         library_count += 1
     stop = time.time()
     log.info("# Purged %d libraries .", library_count)
@@ -413,6 +409,7 @@ def delete_datasets(app, cutoff_time, remove_from_disk, info_only=False, force_r
     deleted_dataset_count = 0
     deleted_instance_count = 0
     skip = []
+    session = app.sa_session()
     # Handle library datasets.  This is a bit tricky, so here's some clarification.  We have a list of all
     # LibraryDatasets that were marked deleted before our cutoff_time, but have not yet been marked purged.
     # A LibraryDataset object is marked purged when all of its LibraryDatasetDatasetAssociations have been
@@ -421,37 +418,35 @@ def delete_datasets(app, cutoff_time, remove_from_disk, info_only=False, force_r
     # and add it to our accrued list of Datasets for later processing.  We mark  as deleted all of its
     # LibraryDatasetDatasetAssociations.  Then we mark the LibraryDataset as purged.  We then process our
     # list of Datasets.
-    library_dataset_ids = [row.id for row in app.sa_session.execute(library_dataset_ids_query)]
+    library_dataset_ids = [row.id for row in session.execute(library_dataset_ids_query)]
     dataset_ids = []
     for library_dataset_id in library_dataset_ids:
         log.info("######### Processing LibraryDataset id: %d", library_dataset_id)
         # Get the LibraryDataset and the current LibraryDatasetDatasetAssociation objects
-        ld = app.sa_session.query(app.model.LibraryDataset).get(library_dataset_id)
+        ld = session.query(app.model.LibraryDataset).get(library_dataset_id)
         ldda = ld.library_dataset_dataset_association
         # Append the associated Dataset object's id to our list of dataset_ids
         dataset_ids.append(ldda.dataset_id)
         # Mark all of the LibraryDataset's associated LibraryDatasetDatasetAssociation objects' as deleted
         if not ldda.deleted:
             ldda.deleted = True
-            app.sa_session.add(ldda)
+            session.add(ldda)
             log.info("Marked associated LibraryDatasetDatasetAssociation id %d as deleted", ldda.id)
         for expired_ldda in ld.expired_datasets:
             if not expired_ldda.deleted:
                 expired_ldda.deleted = True
-                app.sa_session.add(expired_ldda)
+                session.add(expired_ldda)
                 log.info("Marked associated expired LibraryDatasetDatasetAssociation id %d as deleted", ldda.id)
         # Mark the LibraryDataset as purged
         ld.purged = True
-        app.sa_session.add(ld)
+        session.add(ld)
         log.info("Marked LibraryDataset id %d as purged", ld.id)
-        session = app.sa_session()
-        with transaction(session):
-            session.commit()
+        session.commit()
     # Add all datasets associated with Histories to our list
-    dataset_ids.extend([row.id for row in app.sa_session.execute(history_dataset_ids_query)])
+    dataset_ids.extend([row.id for row in session.execute(history_dataset_ids_query)])
     # Process each of the Dataset objects
     for dataset_id in dataset_ids:
-        dataset = app.sa_session.query(app.model.Dataset).get(dataset_id)
+        dataset = session.query(app.model.Dataset).get(dataset_id)
         if dataset.id in skip:
             continue
         skip.append(dataset.id)
@@ -528,10 +523,9 @@ def _purge_dataset_instance(dataset_instance, app, remove_from_disk, info_only=F
         )
         dataset_instance.mark_deleted()
         dataset_instance.clear_associated_files()
-        app.sa_session.add(dataset_instance)
         session = app.sa_session()
-        with transaction(session):
-            session.commit()
+        session.add(dataset_instance)
+        session.commit()
         app.sa_session.refresh(dataset_instance.dataset)
     else:
         log.info(
@@ -572,12 +566,12 @@ def _delete_dataset(dataset, app, remove_from_disk, info_only=False, is_deletabl
         metadata_files = []
         # lets create a list of metadata files, then perform actions on them
         for hda in dataset.history_associations:
-            for metadata_file in app.sa_session.query(app.model.MetadataFile).filter(
+            for metadata_file in session.query(app.model.MetadataFile).filter(
                 app.model.MetadataFile.__table__.c.hda_id == hda.id
             ):
                 metadata_files.append(metadata_file)
         for ldda in dataset.library_associations:
-            for metadata_file in app.sa_session.query(app.model.MetadataFile).filter(
+            for metadata_file in session.query(app.model.MetadataFile).filter(
                 app.model.MetadataFile.__table__.c.lda_id == ldda.id
             ):
                 metadata_files.append(metadata_file)
@@ -608,20 +602,17 @@ def _delete_dataset(dataset, app, remove_from_disk, info_only=False, is_deletabl
                             metadata_file.get_file_name(),
                         )
                     metadata_file.purged = True
-                    app.sa_session.add(metadata_file)
-                    with transaction(session):
-                        session.commit()
-                metadata_file.deleted = True
-                app.sa_session.add(metadata_file)
-                with transaction(session):
+                    session.add(metadata_file)
                     session.commit()
+                metadata_file.deleted = True
+                session.add(metadata_file)
+                session.commit()
             log.info(metadata_file.get_file_name())
         if not info_only:
             log.info("Deleting dataset id %d", dataset.id)
             dataset.deleted = True
-            app.sa_session.add(dataset)
-            with transaction(session):
-                session.commit()
+            session.add(dataset)
+            session.commit()
         else:
             log.info("Dataset %d will be deleted (without 'info_only' mode)", dataset.id)
 
@@ -650,12 +641,11 @@ def _purge_dataset(app, dataset, remove_from_disk, info_only=False):
                                     usage_users.append(hda.history.user)
                         for user in usage_users:
                             user.adjust_total_disk_usage(-dataset.get_total_size())
-                            app.sa_session.add(user)
+                            session.add(user)
                     log.info("Purging dataset id %d", dataset.id)
                     dataset.purged = True
-                    app.sa_session.add(dataset)
-                    with transaction(session):
-                        session.commit()
+                    session.add(dataset)
+                    session.commit()
                 else:
                     log.info("Dataset %d will be purged (without 'info_only' mode)", dataset.id)
             else:
@@ -668,9 +658,8 @@ def _purge_dataset(app, dataset, remove_from_disk, info_only=False):
             log.error("Error, dataset file has already been removed: %s", unicodify(exc))
             log.error("Purging dataset id %d", dataset.id)
             dataset.purged = True
-            app.sa_session.add(dataset)
-            with transaction(session):
-                session.commit()
+            session.add(dataset)
+            session.commit()
         except ObjectNotFound:
             log.error("Dataset %d cannot be found in the object store", dataset.id)
         except Exception as exc:
@@ -694,10 +683,9 @@ def _purge_folder(folder, app, remove_from_disk, info_only=False):
         # TODO: should the folder permissions be deleted here?
         log.info("Purging folder id %s", folder.id)
         folder.purged = True
-        app.sa_session.add(folder)
         session = app.sa_session()
-        with transaction(session):
-            session.commit()
+        session.add(folder)
+        session.commit()
 
 
 class CleanupDatasetsApplication:

scripts/cleanup_datasets/populate_uuid.py

@@ -15,7 +15,6 @@
 sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, "lib")))
 
 import galaxy.config
-from galaxy.model.base import transaction
 from galaxy.model.mapping import init_models_from_config
 from galaxy.util.script import (
     app_properties_from_args,
@@ -40,19 +39,17 @@ def main():
     model = init_models_from_config(config)
     session = model.context()
 
-    for row in model.context.query(model.Dataset):
+    for row in session.query(model.Dataset):
         if row.uuid is None:
             row.uuid = uuid.uuid4()
             print("Setting dataset:", row.id, " UUID to ", row.uuid)
-    with transaction(session):
-        session.commit()
+    session.commit()
 
-    for row in model.context.query(model.Workflow):
+    for row in session.query(model.Workflow):
         if row.uuid is None:
             row.uuid = uuid.uuid4()
             print("Setting Workflow:", row.id, " UUID to ", row.uuid)
-    with transaction(session):
-        session.commit()
+    session.commit()
     print("Complete")
 
 

scripts/pages_identifier_conversion.py

@@ -13,7 +13,6 @@
     PageContentProcessor,
     placeholderRenderForSave,
 )
-from galaxy.model.base import transaction
 from galaxy.model.mapping import init_models_from_config
 from galaxy.objectstore import build_object_store_from_config
 from galaxy.security.idencoding import IdEncodingHelper
@@ -42,7 +41,7 @@ def main(argv):
         )
 
     model = init_models_from_config(config, object_store=object_store)
-    session = model.context.current
+    session = model.context.current()
     pagerevs = session.query(model.PageRevision).all()
     mock_trans = Bunch(app=Bunch(security=security_helper), model=model, user_is_admin=lambda: True, sa_session=session)
     for p in pagerevs:
@@ -54,9 +53,7 @@ def main(argv):
                 if not args.dry_run:
                     p.content = unicodify(processor.output(), "utf-8")
                     session.add(p)
-                    session = session()
-                    with transaction(session):
-                        session.commit()
+                    session.commit()
                 else:
                     print(f"Modifying revision {p.id}.")
                     print(difflib.unified_diff(p.content, newcontent))

scripts/set_dataset_sizes.py

@@ -7,7 +7,6 @@
 sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, "lib")))
 
 import galaxy.config
-from galaxy.model.base import transaction
 from galaxy.model.mapping import init_models_from_config
 from galaxy.objectstore import build_object_store_from_config
 from galaxy.util.script import (
@@ -36,24 +35,22 @@ def init():
     session = sa_session()
 
     set = 0
-    dataset_count = sa_session.query(model.Dataset).count()
+    dataset_count = session.query(model.Dataset).count()
     print(f"Processing {dataset_count} datasets...")
     percent = 0
     print(f"Completed {percent}%", end=" ")
     sys.stdout.flush()
-    for i, dataset in enumerate(sa_session.query(model.Dataset).enable_eagerloads(False).yield_per(1000)):
+    for i, dataset in enumerate(session.query(model.Dataset).enable_eagerloads(False).yield_per(1000)):
         if dataset.total_size is None:
             dataset.set_total_size()
             set += 1
             if not set % 1000:
-                with transaction(session):
-                    session.commit()
+                session.commit()
         new_percent = int(float(i) / dataset_count * 100)
         if new_percent != percent:
             percent = new_percent
             print(f"\rCompleted {percent}%", end=" ")
             sys.stdout.flush()
-    with transaction(session):
-        session.commit()
+    session.commit()
     print("\rCompleted 100%")
     object_store.shutdown()

scripts/tool_shed/deprecate_repositories_without_metadata.py

@@ -26,7 +26,6 @@
 
 import tool_shed.webapp.config as tool_shed_config
 import tool_shed.webapp.model.mapping
-from galaxy.model.base import transaction
 from galaxy.util import (
     build_url,
     send_mail as galaxy_send_mail,
@@ -176,8 +175,7 @@ def deprecate_repositories(app, cutoff_time, days=14, info_only=False, verbose=F
             repository.deprecated = True
             app.sa_session.add(repository)
             session = app.sa_session()
-            with transaction(session):
-                session.commit()
+            session.commit()
         owner = repositories_by_owner[repository_owner]["owner"]
         send_mail_to_owner(
             app, owner.username, owner.email, repositories_by_owner[repository_owner]["repositories"], days