clean up

src/hdmf_zarr/backend.py

@@ -738,7 +738,7 @@ def resolve_ref(self, zarr_ref):
         # Return the create path
         return target_name, target_zarr_obj
 
-    def __get_ref(self, ref_object, path=None, source_file=None, export_source=None):
+    def __get_ref(self, ref_object, source_file=None, export_source=None):
         """
         Create a ZarrReference object that points to the given container
         If source_file is not None, use it to get the source_object_id.
@@ -758,10 +758,9 @@ def __get_ref(self, ref_object, path=None, source_file=None, export_source=None)
             builder = ref_object.builder
         else:
             builder = self.manager.build(ref_object)
-        if path is None:
-            path = self.__get_path(builder)
-        else:
-            path = path
+
+        path = self.__get_path(builder)
+
         # TODO Add to get region for region references.
         #      Also add  {'name': 'region', 'type': (slice, list, tuple),
         #      'doc': 'the region reference indexing object',  'default': None},

src/hdmf_zarr/zarr_utils.py

@@ -82,11 +82,8 @@ def append(self, arg):
         f_builder = self.invert().io.read_builder()
         source_file = self.invert().io.manager.construct(f_builder)
 
-        # Get path
-        path = self.dataset[0]['path']
-
         # Create ZarrReference
-        ref = self.invert().io._ZarrIO__get_ref(builder,path=path, source_file=source_file)
+        ref = self.invert().io._ZarrIO__get_ref(builder, source_file=source_file)
         append_data(self.dataset, ref)
 
 

tests/unit/test_zarrio.py

@@ -205,7 +205,7 @@ def tearDown(self):
                 else:
                     warnings.warn("Could not remove: %s" % path)
 
-    def test_append_references_roundtrip(self):
+    def test_append_references(self):
         # Setup a file container with references
         num_bazs = 10
         bazs = []  # set up dataset of references
@@ -218,16 +218,13 @@ def test_append_references_roundtrip(self):
         with ZarrIO(self.store, manager=manager, mode='w') as writer:
             writer.write(container=container)
         # read from file and validate references
-        with ZarrIO(self.store, manager=manager, mode='a') as append_io:
+        with ZarrIO(self.store, manager=manager, mode='r+') as append_io:
             read_container = append_io.read()
-            new_baz = Baz(name='baz0')
             DoR = read_container.baz_data.data
-            DoR.append(new_baz)
+            DoR.append(DoR[0])
 
-        with ZarrIO(self.store, manager=manager, mode='a') as reader:
-            read_container = reader.read()
             expected =  {'source': '.', 'path': '/bazs/baz0',
-                         'object_id': new_baz.object_id,
+                         'object_id': DoR[0].object_id,
                          'source_object_id': container.object_id}
 
             self.assertEqual(len(read_container.baz_data.data), 11)