Merge remote-tracking branch 'upstream/release_16.07' into release_16.10

lib/galaxy/tools/parameters/output_collect.py

@@ -205,6 +205,9 @@ class JobContext( object ):
         else:
             primary_data.init_meta()
 
+        primary_data.set_meta()
+        primary_data.set_peek()
+
         return primary_data
 
 

test/api/test_tools.py

@@ -464,10 +464,14 @@ class ToolsTestCase( api.ApiTestCase ):
         output_collection = get_collection_response.json()
         self._assert_has_keys( output_collection, "id", "name", "elements", "populated" )
         assert output_collection[ "populated" ]
-        assert len( output_collection[ "elements" ] ) == 2
         self.assertEquals( output_collection[ "name" ], "Table split on first column" )
 
-        # TODO: verify element identifiers
+        assert len( output_collection[ "elements" ] ) == 2
+        output_element_0 = output_collection["elements"][0]
+        assert output_element_0["element_index"] == 0
+        assert output_element_0["element_identifier"] == "samp1"
+        output_element_hda_0 = output_element_0["object"]
+        assert output_element_hda_0["metadata_column_types"] is not None
 
     @skip_without_tool( "cat1" )
     def test_run_cat1_with_two_inputs( self ):

tox.ini

@@ -43,7 +43,7 @@ whitelist_externals = bash
 skip_install = True
 deps =
     flake8
-    flake8-import-order>=0.9
+    flake8-import-order==0.9
 
 [testenv:py27-lint-imports-include-list]
 commands = bash .ci/flake8_wrapper_imports.sh