Don't write to database operation outputs

without making a copy first. These are probably unmodified inputs.

Author: mvdbeek

lib/galaxy/model/__init__.py

@@ -4948,9 +4948,15 @@ def get_quota_source_label(self):
 
     quota_source_label = property(get_quota_source_label)
 
-    def set_skipped(self, object_store_populator: "ObjectStorePopulator") -> None:
+    def set_skipped(self, object_store_populator: "ObjectStorePopulator", replace_dataset: bool) -> None:
         assert self.dataset
         object_store_populator.set_object_store_id(self)
+        if replace_dataset:
+            replacement = Dataset(state=Dataset.states.NEW)
+            replacement.object_store_id = self.dataset.object_store_id
+            self.dataset = replacement
+            self.dataset_id = None
+            self.dataset.object_store.create(self.dataset)
         self.extension = "expression.json"
         self.state = self.states.OK
         self.blurb = "skipped"

lib/galaxy/tools/actions/__init__.py

@@ -737,7 +737,7 @@ def handle_output(name, output, hidden=None):
                 hdca.collection.mark_as_populated()
             object_store_populator = ObjectStorePopulator(trans.app, trans.user)
             for data in out_data.values():
-                data.set_skipped(object_store_populator)
+                data.set_skipped(object_store_populator, replace_dataset=False)
         job.preferred_object_store_id = preferred_object_store_id
         self._record_inputs(trans, tool, job, incoming, inp_data, inp_dataset_collections)
         self._record_outputs(job, out_data, output_collections)

lib/galaxy/tools/actions/model_operations.py

@@ -178,7 +178,6 @@ def _produce_outputs(
             object_store_populator = ObjectStorePopulator(trans.app, trans.user)
             for hdca in output_collections.out_collection_instances.values():
                 hdca.visible = False
-                # Would we also need to replace the datasets with skipped datasets?
                 for data in hdca.dataset_instances:
-                    data.set_skipped(object_store_populator)
+                    data.set_skipped(object_store_populator, replace_dataset=True)
         trans.sa_session.add_all(out_data.values())