Don't flush for inner elements

galaxyproject · May 14, 2024 · baf7fef · baf7fef
1 parent c1ce0be
commit baf7fef
Showing 1 changed file with 7 additions and 4 deletions.
diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
@@ -2681,7 +2681,7 @@ def to_text(self, value):
 
 # Code from CWL branch to massage in order to be shared across tools and workflows,
 # and for CWL artifacts as well as Galaxy ones.
-def raw_to_galaxy(app: "MinimalApp", history: "History", as_dict_value: Dict[str, Any]) -> "HistoryItem":
+def raw_to_galaxy(app: "MinimalApp", history: "History", as_dict_value: Dict[str, Any], commit=True) -> "HistoryItem":
     object_class = as_dict_value["class"]
     if object_class == "File":
         # TODO: relative_to = "/"
@@ -2728,7 +2728,8 @@ def raw_to_galaxy(app: "MinimalApp", history: "History", as_dict_value: Dict[str
         app.model.session.add(primary_data)
         history.stage_addition(primary_data)
         history.add_pending_items()
-        app.model.session.flush()
+        if commit:
+            app.model.session.commit()
         return primary_data
     else:
         name = as_dict_value.get("name")
@@ -2748,7 +2749,8 @@ def write_elements_to_collection(has_elements, collection_builder):
                 element_class = element_dict["class"]
                 identifier = element_dict["identifier"]
                 if element_class == "File":
-                    hda = raw_to_galaxy(app, history, element_dict)
+                    # Don't commit for inner elements
+                    hda = raw_to_galaxy(app, history, element_dict, commit=False)
                     collection_builder.add_dataset(identifier, hda)
                 else:
                     subcollection_builder = collection_builder.get_level(identifier)
@@ -2759,7 +2761,8 @@ def write_elements_to_collection(has_elements, collection_builder):
         collection_builder.populate()
         history.stage_addition(hdca)
         history.add_pending_items()
-        app.model.session.flush()
+        if commit:
+            app.model.session.commit()
         return hdca