Fix model operations that produce datasets for 78babab645

Should only affect unzip I think - fixes #5780 - probably need to rebuild collections though, collections built in the meantime are going to be broken in the DB.

Includes test case that fails against 18.01.

lib/galaxy/tools/actions/model_operations.py

@@ -69,5 +69,12 @@ class ModelOperationToolAction(DefaultToolAction):
 
     def _produce_outputs(self, trans, tool, out_data, output_collections, incoming, history, tags):
         tool.produce_outputs(trans, out_data, output_collections, incoming, history=history, tags=tags)
+        mapped_over_elements = output_collections.dataset_collection_elements
+        if mapped_over_elements:
+            for name, value in out_data.items():
+                if name in mapped_over_elements:
+                    value.visible = False
+                    mapped_over_elements[name].hda = value
+
         trans.sa_session.add_all(out_data.values())
         trans.sa_session.flush()

test/api/test_tools.py

@@ -168,7 +168,11 @@ class ToolsTestCase(api.ApiTestCase):
                 }
             }
             self.dataset_populator.wait_for_history(history_id, assert_ok=True)
-            self._run("__UNZIP_COLLECTION__", history_id, inputs, assert_ok=True)
+            response = self._run("__UNZIP_COLLECTION__", history_id, inputs, assert_ok=True)
+            implicit_collections = response["implicit_collections"]
+            self.assertEquals(len(implicit_collections), 2)
+            unzipped_hdca = self.dataset_populator.get_history_collection_details(history_id, hid=implicit_collections[0]["hid"])
+            assert unzipped_hdca["elements"][0]["element_type"] == "hda", unzipped_hdca
 
     def test_zip_inputs(self):
         with self.dataset_populator.test_history() as history_id: