Merge pull request #18970 from arash77/optimize_history_create

Optimize to_history_dataset_association in create_datasets_from_library_folder
galaxyproject · Oct 11, 2024 · 1eac67a · 1eac67a
2 parents 6dc681d + 4bf029b
commit 1eac67a
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Showing 2 changed files with 22 additions and 11 deletions.
diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
@@ -6048,7 +6048,9 @@ def __init__(
         self.library_dataset = library_dataset
         self.user = user
 
-    def to_history_dataset_association(self, target_history, parent_id=None, add_to_history=False, visible=None):
+    def to_history_dataset_association(
+        self, target_history, parent_id=None, add_to_history=False, visible=None, commit=True
+    ):
         sa_session = object_session(self)
         hda = HistoryDatasetAssociation(
             name=self.name,
@@ -6072,9 +6074,12 @@ def to_history_dataset_association(self, target_history, parent_id=None, add_to_
         sa_session.add(hda)
         hda.metadata = self.metadata
         if add_to_history and target_history:
-            target_history.add_dataset(hda)
-        with transaction(sa_session):
-            sa_session.commit()
+            target_history.stage_addition(hda)
+            if commit:
+                target_history.add_pending_items()
+        if commit:
+            with transaction(sa_session):
+                sa_session.commit()
         return hda
 
     def copy(self, parent_id=None, target_folder=None, flush=True):

diff --git a/lib/galaxy/webapps/galaxy/services/history_contents.py b/lib/galaxy/webapps/galaxy/services/history_contents.py
@@ -1172,22 +1172,28 @@ def traverse(folder):
                         rval.append(ld)
                 return rval
 
-            for ld in traverse(folder):
-                hda = ld.library_dataset_dataset_association.to_history_dataset_association(
-                    history, add_to_history=True
+            hdas = [
+                ld.library_dataset_dataset_association.to_history_dataset_association(
+                    history, add_to_history=True, commit=False
                 )
+                for ld in traverse(folder)
+            ]
+            history.add_pending_items()
+
+            with transaction(trans.sa_session):
+                trans.sa_session.commit()
+
+            for hda in hdas:
                 hda_dict = self.hda_serializer.serialize_to_view(
                     hda, user=trans.user, trans=trans, encode_id=False, **serialization_params.model_dump()
                 )
                 rval.append(hda_dict)
+            return rval
+
         else:
             message = f"Invalid 'source' parameter in request: {source}"
             raise exceptions.RequestParameterInvalidException(message)
 
-        with transaction(trans.sa_session):
-            trans.sa_session.commit()
-        return rval
-
     def __create_dataset(
         self,
         trans,