clean up

hdmf-dev · Sep 25, 2023 · 82b7664 · 82b7664
1 parent fb72e28
commit 82b7664
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Showing 2 changed files with 13 additions and 5 deletions.
diff --git a/src/hdmf_zarr/backend.py b/src/hdmf_zarr/backend.py
@@ -529,6 +529,8 @@ def resolve_ref(self, zarr_ref):
             try:
                 target_zarr_obj = target_zarr_obj[object_path]
             except Exception:
+                # TODO: Find why the reference includes the root object.
+                # This is a fix to allow the target object to be found
                 try:
                     object_path = pathlib.Path(object_path)
                     rel_obj_path = object_path.relative_to(*object_path.parts[:2])
@@ -1078,6 +1080,7 @@ def __read_group(self, zarr_obj, name=None):
         for sub_name, sub_group in zarr_obj.groups():
             sub_builder = self.__read_group(sub_group, sub_name)
             ret.set_group(sub_builder)
+
         # read sub datasets
         for sub_name, sub_array in zarr_obj.arrays():
             sub_builder = self.__read_dataset(sub_array, sub_name)

diff --git a/tests/unit/test_io_convert.py b/tests/unit/test_io_convert.py
@@ -184,6 +184,7 @@ def test_export_roundtrip(self):
                             self.assertEqual(exported_container.baz_data.data.__class__.__name__,
                                              'ContainerZarrReferenceDataset')
                             self.assertIs(exported_container.baz_data.data[i], exported_container.bazs[baz_name])
+
                 # assert that the roundtrip worked correctly
                 message = "Using: write_path=%s, export_path=%s" % (str(write_path), str(export_path))
                 self.assertIsNotNone(str(container), message)  # added as a test to make sure printing works
@@ -199,7 +200,6 @@ def test_export_roundtrip(self):
                                           ignore_string_to_byte=self.IGNORE_STRING_TO_BYTE,
                                           message=message)
                 self.close_files_and_ios()
-                # TODO: May need to add further asserts here
 
 
 ##########################################################
@@ -225,6 +225,7 @@ def get_manager(self):
     def roundtripExportContainer(self, container, write_path, export_path):
         with HDF5IO(write_path, manager=self.get_manager(), mode='w') as write_io:
             write_io.write(container, cache_spec=True)
+
         with HDF5IO(write_path, manager=self.get_manager(), mode='r') as read_io:
             with ZarrIO(export_path, mode='w') as export_io:
                 export_io.export(src_io=read_io, write_args={'link_data': False})
@@ -255,6 +256,7 @@ def get_manager(self):
     def roundtripExportContainer(self, container,  write_path, export_path):
         with ZarrIO(write_path, manager=self.get_manager(), mode='w') as write_io:
             write_io.write(container)
+
         with ZarrIO(write_path, manager=self.get_manager(), mode='r') as read_io:
             with HDF5IO(export_path,  mode='w') as export_io:
                 export_io.export(src_io=read_io, write_args={'link_data': False})
@@ -288,6 +290,7 @@ def get_manager(self):
     def roundtripExportContainer(self, container,  write_path, export_path):
         with ZarrIO(write_path, manager=self.get_manager(), mode='w') as write_io:
             write_io.write(container, cache_spec=True)
+
         with ZarrIO(write_path, manager=self.get_manager(), mode='r') as read_io:
             with ZarrIO(export_path,  mode='w') as export_io:
                 export_io.export(src_io=read_io, write_args={'link_data': False})
@@ -646,8 +649,8 @@ class TestZarrToHDF5Baz1(MixinTestBaz1,
                          MixinTestCaseConvert,
                          TestCase):
     """
-    Test the conversion of a simple Foo container with two buckets of datasets from Zarr to HDF5
-    See MixinTestFoo.setUpContainer for the container spec used.
+    Test the conversion of a BazBucket containing a dataset of references from Zarr to HDF5
+    See MixinTestBaz1.setUpContainer for the container spec used.
     """
     IGNORE_NAME = True
     IGNORE_HDMF_ATTRS = True
@@ -660,7 +663,8 @@ class TestHDF5toZarrBaz1(MixinTestBaz1,
                          MixinTestCaseConvert,
                          TestCase):
     """
-
+    Test the conversion of a BazBucket containing a dataset of references from HDF5 to Zarr
+    See MixinTestBaz1.setUpContainer for the container spec used.
     """
     IGNORE_NAME = True
     IGNORE_HDMF_ATTRS = True
@@ -673,7 +677,8 @@ class TestZarrtoZarrBaz1(MixinTestBaz1,
                          MixinTestCaseConvert,
                          TestCase):
     """
-
+    Test the conversion of a BazBucket containing a dataset of references from Zarr to Zarr
+    See MixinTestBaz1.setUpContainer for the container spec used.
     """
     IGNORE_NAME = True
     IGNORE_HDMF_ATTRS = True