Fix hda_manager.copy so it doesn't flush datasets without a history_id

lib/galaxy/managers/collections.py

@@ -201,6 +201,7 @@ class DatasetCollectionManager:
         has_subcollections = collection_type_description.has_subcollections()
         # If we have elements, this is an internal request, don't need to load
         # objects from identifiers.
+        history = history or trans.history
         if elements is None:
             elements = self._element_identifiers_to_elements(trans,
                                                              collection_type_description=collection_type_description,
@@ -208,6 +209,7 @@ class DatasetCollectionManager:
                                                              hide_source_items=hide_source_items,
                                                              copy_elements=copy_elements,
                                                              history=history)
+            history.add_pending_items()
         else:
             if has_subcollections:
                 # Nested collection - recursively create collections as needed.
@@ -493,7 +495,7 @@ class DatasetCollectionManager:
             decoded_id = int(trans.app.security.decode_id(encoded_id))
             hda = self.hda_manager.get_accessible(decoded_id, trans.user)
             if copy_elements:
-                element = self.hda_manager.copy(hda, history=history or trans.history, hide_copy=True)
+                element = self.hda_manager.copy(hda, history=history or trans.history, hide_copy=True, flush=False)
             else:
                 element = hda
             if hide_source_items and self.hda_manager.get_owned(hda.id, user=trans.user, current_history=history or trans.history):

lib/galaxy/managers/hdas.py

@@ -8,6 +8,8 @@ import gettext
 import logging
 import os
 
+from sqlalchemy.orm.session import object_session
+
 from galaxy import (
     datatypes,
     exceptions,
@@ -110,26 +112,22 @@ class HDAManager(datasets.DatasetAssociationManager,
             self.session().flush()
         return hda
 
-    def copy(self, hda, history=None, hide_copy=False, **kwargs):
+    def copy(self, hda, history=None, hide_copy=False, flush=True, **kwargs):
         """
         Copy hda, including annotation and tags, add to history and return the given HDA.
         """
-        copy = hda.copy(parent_id=kwargs.get('parent_id'), copy_hid=False)
+        copy = hda.copy(parent_id=kwargs.get('parent_id'), copy_hid=False, copy_tags=hda.tags)
         if hide_copy:
             copy.visible = False
-        # add_dataset will update the hid to the next avail. in history
         if history:
-            history.add_dataset(copy)
+            history.stage_addition(copy)
 
-        copy.copied_from_history_dataset_association = hda
         copy.set_size()
 
         original_annotation = self.annotation(hda)
         self.annotate(copy, original_annotation, user=hda.history.user)
-
-        # these use a session flush
-        original_tags = self.get_tags(hda)
-        self.set_tags(copy, original_tags, user=hda.history.user)
+        if flush:
+            object_session(copy).flush()
 
         return copy