From c9d06aeb41d9e15c07dddf4fff67630f2ee2237d Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Wed, 22 Mar 2017 12:23:29 -0400
Subject: [PATCH] Allow collection creation API to hide original datasets
 during creation.

---
 lib/galaxy/managers/collections.py      |  8 ++++++++
 lib/galaxy/managers/collections_util.py |  2 ++
 test/api/test_history_contents.py       | 17 +++++++++++++++++
 3 files changed, 27 insertions(+)

diff --git a/lib/galaxy/managers/collections.py b/lib/galaxy/managers/collections.py
index aadaf226439..43db8c1a39d 100644
--- a/lib/galaxy/managers/collections.py
+++ b/lib/galaxy/managers/collections.py
@@ -51,6 +51,7 @@ class DatasetCollectionManager( object ):
         elements=None,
         implicit_collection_info=None,
         trusted_identifiers=None,  # Trust preloaded element objects
+        hide_source_items=False,
     ):
         """
         """
@@ -66,6 +67,7 @@ class DatasetCollectionManager( object ):
             collection_type=collection_type,
             element_identifiers=element_identifiers,
             elements=elements,
+            hide_source_items=hide_source_items,
         )
 
         if isinstance( parent, model.History ):
@@ -114,6 +116,7 @@ class DatasetCollectionManager( object ):
         collection_type,
         element_identifiers=None,
         elements=None,
+        hide_source_items=False,
     ):
         if element_identifiers is None and elements is None:
             raise RequestParameterInvalidException( ERROR_INVALID_ELEMENTS_SPECIFICATION )
@@ -133,11 +136,16 @@ class DatasetCollectionManager( object ):
                     elements = self.__load_elements(trans, element_identifier['element_identifiers'])
             if not new_collection:
                 elements = self.__load_elements( trans, element_identifiers )
+
         # else if elements is set, it better be an ordered dict!
 
         if elements is not self.ELEMENTS_UNINITIALIZED:
             type_plugin = collection_type_description.rank_type_plugin()
             dataset_collection = builder.build_collection( type_plugin, elements )
+            if hide_source_items:
+                log.debug("Hiding source items during dataset collection creation")
+                for dataset in dataset_collection.dataset_instances:
+                    dataset.visible = False
         else:
             dataset_collection = model.DatasetCollection( populated=False )
         dataset_collection.collection_type = collection_type
diff --git a/lib/galaxy/managers/collections_util.py b/lib/galaxy/managers/collections_util.py
index 16bfaee8199..a6a9571cb01 100644
--- a/lib/galaxy/managers/collections_util.py
+++ b/lib/galaxy/managers/collections_util.py
@@ -1,6 +1,7 @@
 import logging
 
 from galaxy import exceptions, model, web
+from galaxy.util import string_as_bool
 
 log = logging.getLogger( __name__ )
 
@@ -26,6 +27,7 @@ def api_payload_to_create_params( payload ):
         collection_type=payload.get( "collection_type" ),
         element_identifiers=payload.get( "element_identifiers" ),
         name=payload.get( "name", None ),
+        hide_source_items=string_as_bool( payload.get( "hide_source_items", False ) )
     )
     return params
 
diff --git a/test/api/test_history_contents.py b/test/api/test_history_contents.py
index 7ef60cb6950..89ada2cc2ce 100644
--- a/test/api/test_history_contents.py
+++ b/test/api/test_history_contents.py
@@ -161,6 +161,23 @@ class HistoryContentsApiTestCase( api.ApiTestCase, TestsDatasets ):
         dataset_collection = show_response.json()
         assert dataset_collection[ "deleted" ]
 
+    def test_dataset_collection_hide_originals( self ):
+        payload = self.dataset_collection_populator.create_pair_payload(
+            self.history_id,
+            type="dataset_collection"
+        )
+
+        payload["hide_source_items"] = True
+        dataset_collection_response = self._post( "histories/%s/contents" % self.history_id, payload )
+        self.__check_create_collection_response( dataset_collection_response )
+
+        contents_response = self._get( "histories/%s/contents" % self.history_id )
+        datasets = [d for d in contents_response.json() if d["history_content_type"] == "dataset" and d["hid"] in [1, 2]]
+        # Assert two datasets in source were hidden.
+        assert len(datasets) == 2
+        assert not datasets[0]["visible"]
+        assert not datasets[1]["visible"]
+
     def test_update_dataset_collection( self ):
         payload = self.dataset_collection_populator.create_pair_payload(
             self.history_id,