Mark outputs skipped if necessary

lib/galaxy/model/__init__.py

@@ -152,6 +152,7 @@
 )
 from galaxy.model.orm.now import now
 from galaxy.model.orm.util import add_object_to_object_session
+from galaxy.objectstore import ObjectStorePopulator
 from galaxy.schema.invocation import (
     InvocationCancellationUserRequest,
     InvocationState,
@@ -4581,6 +4582,17 @@ def get_quota_source_label(self):
 
     quota_source_label = property(get_quota_source_label)
 
+    def set_skipped(self, object_store_populator: ObjectStorePopulator):
+        assert self.dataset
+        object_store_populator.set_object_store_id(self)
+        self.extension = "expression.json"
+        self.state = self.states.OK
+        self.blurb = "skipped"
+        self.visible = False
+        with open(self.dataset.get_file_name(), "w") as out:
+            out.write(json.dumps(None))
+        self.set_total_size()
+
     def get_file_name(self, sync_cache=True) -> str:
         if self.dataset.purged:
             return ""

lib/galaxy/tools/actions/__init__.py

@@ -675,14 +675,7 @@ def handle_output(name, output, hidden=None):
                 hdca.visible = False
             object_store_populator = ObjectStorePopulator(trans.app, trans.user)
             for data in out_data.values():
-                object_store_populator.set_object_store_id(data)
-                data.extension = "expression.json"
-                data.state = "ok"
-                data.blurb = "skipped"
-                data.visible = False
-                with open(data.dataset.get_file_name(), "w") as out:
-                    out.write(json.dumps(None))
-                data.set_total_size()
+                data.set_skipped(object_store_populator)
         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

@@ -1,6 +1,7 @@
 import logging
 from typing import TYPE_CHECKING
 
+from galaxy.objectstore import ObjectStorePopulator
 from galaxy.tools.actions import (
     DefaultToolAction,
     OutputCollections,
@@ -137,8 +138,10 @@ def _produce_outputs(
         if skip:
             for output_collection in output_collections.out_collections.values():
                 output_collection.mark_as_populated()
+            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?
-
+                # Would we also need to replace the datasets with skipped datasets?
+                for data in hdca.dataset_instances:
+                    data.set_skipped(object_store_populator)
         trans.sa_session.add_all(out_data.values())