From a6ed01ced84f241309b93f19e16dfd6ee3a0e210 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 9 Feb 2015 12:22:22 -0500
Subject: [PATCH 1/2] Do not import argparse unconditionally in
 lib/galaxy/tools/deps/brew_exts.py.

---
 lib/galaxy/tools/deps/brew_exts.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/tools/deps/brew_exts.py b/lib/galaxy/tools/deps/brew_exts.py
index 763bac60697..ca0cd803980 100755
--- a/lib/galaxy/tools/deps/brew_exts.py
+++ b/lib/galaxy/tools/deps/brew_exts.py
@@ -21,7 +21,10 @@
 
 from __future__ import print_function
 
-import argparse
+try:
+    import argparse
+except ImportError:
+    argparse = None
 import contextlib
 import json
 import glob

From c26c8a86cba28f339a369c8a030f93e210c377a5 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 9 Feb 2015 13:29:45 -0500
Subject: [PATCH 2/2] When copying individual collections via the GUI - copy
 HDAs by default also. We may want to be able to turn this off someday in
 certain scenarios - but usually this will result in less confusion for the
 user.

Doing this for whole histories also needs to be done - but it is a bit trickier (don't want the HDA copied twice). Might be better on the other side of eliminating the nessecity that these things have HIDs.
---
 lib/galaxy/model/__init__.py                  | 39 +++++++++++++++----
 .../webapps/galaxy/controllers/dataset.py     |  6 ++-
 2 files changed, 37 insertions(+), 8 deletions(-)

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index caa058dc507..14abe5cf0a9 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -2711,12 +2711,16 @@ class DatasetCollection( object, Dictifiable, UsesAnnotations ):
         error_message = "Dataset collection has no %s with key %s." % ( get_by_attribute, key )
         raise KeyError( error_message )
 
-    def copy( self ):
+    def copy( self, destination=None, element_destination=None ):
         new_collection = DatasetCollection(
             collection_type=self.collection_type,
         )
         for element in self.elements:
-            element.copy_to_collection( new_collection )
+            element.copy_to_collection(
+                new_collection,
+                destination=destination,
+                element_destination=element_destination,
+            )
         object_session( self ).add( new_collection )
         object_session( self ).flush()
         return new_collection
@@ -2835,20 +2839,24 @@ class HistoryDatasetCollectionAssociation( DatasetCollectionInstance, Dictifiabl
                 break
         return matching_collection
 
-    def copy( self ):
+    def copy( self, element_destination=None ):
         """
         Create a copy of this history dataset collection association. Copy
         underlying collection.
         """
         hdca = HistoryDatasetCollectionAssociation(
             hid=self.hid,
-            collection=self.collection.copy(),
+            collection=None,
             visible=self.visible,
             deleted=self.deleted,
             name=self.name,
             copied_from_history_dataset_collection_association=self,
         )
-
+        collection_copy = self.collection.copy(
+            destination=hdca,
+            element_destination=element_destination,
+        )
+        hdca.collection = collection_copy
         object_session( self ).add( hdca )
         object_session( self ).flush()
         return hdca
@@ -2957,9 +2965,26 @@ class DatasetCollectionElement( object, Dictifiable ):
         else:
             return element_object
 
-    def copy_to_collection( self, collection ):
+    def copy_to_collection( self, collection, destination=None, element_destination=None ):
+        element_object = self.element_object
+        if element_destination:
+            if self.is_collection:
+                element_object = element_object.copy(
+                    destination=destination,
+                    element_destination=element_destination
+                )
+            else:
+                new_element_object = element_object.copy( copy_children=True )
+                if destination is not None and element_object.hidden_beneath_collection_instance:
+                    new_element_object.hidden_beneath_collection_instance = destination
+                # Ideally we would not need to give the following
+                # element an HID and it would exist in the history only
+                # as an element of the containing collection.
+                element_destination.add_dataset( new_element_object )
+                element_object = new_element_object
+
         new_element = DatasetCollectionElement(
-            element=self.element_object,
+            element=element_object,
             collection=collection,
             element_index=self.element_index,
             element_identifier=self.element_identifier,
diff --git a/lib/galaxy/webapps/galaxy/controllers/dataset.py b/lib/galaxy/webapps/galaxy/controllers/dataset.py
index 66eb7f51227..071bbbf3c13 100644
--- a/lib/galaxy/webapps/galaxy/controllers/dataset.py
+++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py
@@ -1074,7 +1074,11 @@ class DatasetInterface( BaseUIController, UsesAnnotations, UsesItemRatings, Uses
                             if content.history_content_type == "dataset":
                                 hist.add_dataset( content.copy( copy_children=True ) )
                             else:
-                                hist.add_dataset_collection( content.copy( ) )
+                                copy_collected_datasets = True
+                                copy_kwds = {}
+                                if copy_collected_datasets:
+                                    copy_kwds["element_destination"] = hist
+                                hist.add_dataset_collection( content.copy( **copy_kwds ) )
                 if current_history in target_histories:
                     refresh_frames = ['history']
                 trans.sa_session.flush()