Fix collection operations not having a history.

Fixes #3437.

Author: jmchilton

lib/galaxy/tools/__init__.py

@@ -2352,6 +2352,8 @@ def produce_outputs( self, trans, out_data, output_collections, incoming, histor
         new_elements = odict()
         new_elements["forward"] = forward
         new_elements["reverse"] = reverse
+        history.add_dataset( forward, set_hid=False )
+        history.add_dataset( reverse, set_hid=False )
 
         output_collections.create_collection(
             next(iter(self.outputs.values())), "output", elements=new_elements
@@ -2430,7 +2432,10 @@ def produce_outputs( self, trans, out_data, output_collections, incoming, histor
         # Don't copy until we know everything is fine and we have the structure of the list ready to go.
         new_elements = odict()
         for key, value in new_element_structure.items():
-            new_elements[key] = value.copy()
+            copied_value = value.copy()
+            if getattr(copied_value, "history_content_type", None) == "dataset":
+                history.add_dataset(copied_value, set_hid=False)
+            new_elements[key] = copied_value
 
         output_collections.create_collection(
             next(iter(self.outputs.values())), "output", elements=new_elements
@@ -2465,7 +2470,10 @@ def produce_outputs( self, trans, out_data, output_collections, incoming, histor
 
             if valid:
                 element_identifier = dce.element_identifier
-                new_elements[element_identifier] = element.copy()
+                copied_value = element.copy()
+                if getattr(copied_value, "history_content_type", None) == "dataset":
+                    history.add_dataset(copied_value, set_hid=False)
+                new_elements[element_identifier] = copied_value
 
         output_collections.create_collection(
             next(iter(self.outputs.values())), "output", elements=new_elements
@@ -2488,8 +2496,9 @@ def add_elements(collection, prefix=""):
                 if dce.is_collection:
                     add_elements(dce_object, prefix=identifier)
                 else:
-                    new_elements[identifier] = dce_object.copy()
-
+                    copied_dataset = dce_object.copy()
+                    history.add_dataset(copied_dataset, set_hid=False)
+                    new_elements[identifier] = copied_dataset
         add_elements(hdca.collection)
         output_collections.create_collection(
             next(iter(self.outputs.values())), "output", elements=new_elements

lib/galaxy/tools/actions/__init__.py

@@ -679,6 +679,17 @@ def create_collection(self, output, name, **element_kwds):
 
             collection_type = input_collections[collection_type_source].collection.collection_type
 
+        if "elements" in element_kwds:
+            elements = element_kwds["elements"]
+            if hasattr(elements, "items"):  # else it is ELEMENTS_UNINITIALIZED object.
+                for key, value in elements.items():
+                    # Either a HDA (if) or a DatasetCollection (the else)
+                    if getattr(value, "history_content_type", None) == "dataset":
+                        assert value.history is not None
+                    else:
+                        for dataset in value.dataset_instances:
+                            assert dataset.history is not None
+
         if self.mapping_over_collection:
             dc = collections_manager.create_dataset_collection(
                 self.trans,

test/api/test_tools.py

@@ -166,6 +166,9 @@ def test_zip_inputs( self ):
         response = self._run( "__ZIP_COLLECTION__", history_id, inputs, assert_ok=True )
         output_collections = response[ "output_collections" ]
         self.assertEquals( len(output_collections), 1 )
+        self.dataset_populator.wait_for_job( response["jobs"][0]["id"], assert_ok=True )
+        zipped_hdca = self.dataset_populator.get_history_collection_details(history_id, hid=output_collections[0]["hid"])
+        assert zipped_hdca["collection_type"] == "paired"
 
     def test_zip_list_inputs( self ):
         history_id = self.dataset_populator.new_history()
@@ -179,6 +182,9 @@ def test_zip_list_inputs( self ):
         response = self._run( "__ZIP_COLLECTION__", history_id, inputs, assert_ok=True )
         implicit_collections = response[ "implicit_collections" ]
         self.assertEquals( len(implicit_collections), 1 )
+        self.dataset_populator.wait_for_job( response["jobs"][0]["id"], assert_ok=True )
+        zipped_hdca = self.dataset_populator.get_history_collection_details(history_id, hid=implicit_collections[0]["hid"])
+        assert zipped_hdca["collection_type"] == "list:paired"
 
     def test_filter_failed( self ):
         history_id = self.dataset_populator.new_history()

test/base/populators.py

@@ -173,19 +173,23 @@ def __history_content_id( self, history_id, wait=True, **kwds ):
         # kwds should contain a 'dataset' object response, a 'dataset_id' or
         # the last dataset in the history will be fetched.
         if "dataset_id" in kwds:
-            dataset_id = kwds[ "dataset_id" ]
+            history_content_id = kwds[ "dataset_id" ]
         elif "dataset" in kwds:
-            dataset_id = kwds[ "dataset" ][ "id" ]
+            history_content_id = kwds[ "dataset" ][ "id" ]
         else:
             hid = kwds.get( "hid", None )  # If not hid, just grab last dataset
+            history_contents = self.__get_contents_request( history_id ).json()
             if hid:
-                index = hid - 1
+                history_content_id = None
+                for history_item in history_contents:
+                    if history_item["hid"] == hid:
+                        history_content_id = history_item["id"]
+                if history_content_id is None:
+                    raise Exception("Could not find content with HID [%s] in [%s]" % (hid, history_contents))
             else:
                 # No hid specified - just grab most recent element.
-                index = -1
-            dataset_contents = self.__get_contents_request( history_id ).json()
-            dataset_id = dataset_contents[ index ][ "id" ]
-        return dataset_id
+                history_content_id = history_contents[-1]["id"]
+        return history_content_id
 
     def __get_contents_request( self, history_id, suffix=""):
         url = "histories/%s/contents" % history_id