feedback fix

docs/source/storage.rst

@@ -282,8 +282,6 @@ region references link to subsets of another Dataset. To identify region referen
 to the ``source`` and ``path``, the  py:class:`~hdmf_zarr.utils.ZarrReference` object will also need to
 store the definition of the ``region`` that is being referenced, e.g., a slice or list on point indices.
 
-In the future, the reference resolver classes will need to be updated to implement region references
-
 .. warning::
 
     Region references are not yet fully implemented in :py:class:`~hdmf_zarr.backend.ZarrIO`.
@@ -298,7 +296,11 @@ In the future, the reference resolver classes will need to be updated to impleme
     4) :py:meth:`~hdmf_zarr.backend.ZarrIO.__read_dataset` to support reading region references,
     which may also require updates to :py:meth:`~hdmf_zarr.backend.ZarrIO.__parse_ref` and
     :py:meth:`~hdmf_zarr.backend.ZarrIO.__resolve_ref`, and
-    5) and possibly other parts of :py:class:`~hdmf_zarr.backend.ZarrIO`
+    5) and possibly other parts of :py:class:`~hdmf_zarr.backend.ZarrIO`.
+    6) The py:class:`~hdmf_zarr.zarr_utils.ContainerZarrRegionDataset` and
+    py:class:`~hdmf_zarr.zarr_utils.ContainerZarrRegionDataset` classes will also need to be finalized
+    to support region references.
+
 
 .. _sec-zarr-storage-dtypes:
 
@@ -381,7 +383,3 @@ data type. The specification of the namespace is stored in
 ``/specifications/<namespace-name>/<version>/<source-filename>``. Here ``<source-filename>`` refers to the main name
 of the source-file without file extension (e.g., the core namespace defines ``nwb.ephys.yaml`` as source which would
 be stored in ``/specifications/core/2.0.1/nwb.ecephys``).
-
-
-
-

src/hdmf_zarr/backend.py

@@ -1068,6 +1068,19 @@ def __set_built(self, zarr_obj, builder):
         path = os.path.join(fpath, path)
         self.__built.setdefault(path, builder)
 
+    @docval({'name': 'zarr_obj', 'type': (Array, Group),
+             'doc': 'the Zarr object to the corresponding Container/Data object for'})
+    def get_container(self, **kwargs):
+        """
+        Get the container for the corresponding Zarr Group or Dataset
+
+        :raises ValueError: When no builder has been constructed yet for the given h5py object
+        """
+        zarr_obj = getargs('zarr_obj', kwargs)
+        builder = self.get_builder(zarr_obj)
+        container = self.manager.construct(builder)
+        return container  # TODO: This method should be moved to HDMFIO
+
     @docval({'name': 'zarr_obj', 'type': (Array, Group),
              'doc': 'the Zarr object to the corresponding Builder object for'})
     def get_builder(self, **kwargs):  # TODO: move this to HDMFIO (define skeleton in there at least)
@@ -1226,16 +1239,3 @@ def __read_attrs(self, zarr_obj):
                 else:
                     ret[k] = v
         return ret
-
-    @docval({'name': 'zarr_obj', 'type': (Array, Group),
-             'doc': 'the Zarr object to the corresponding Container/Data object for'})
-    def get_container(self, **kwargs):
-        """
-        Get the container for the corresponding Zarr Group or Dataset
-
-        :raises ValueError: When no builder has been constructed yet for the given h5py object
-        """
-        zarr_obj = getargs('zarr_obj', kwargs)
-        builder = self.get_builder(zarr_obj)
-        container = self.manager.construct(builder)
-        return container  # TODO: This method should be moved to HDMFIO

tests/unit/utils.py

@@ -11,6 +11,7 @@
 from hdmf.utils import (docval, getargs, get_docval)
 
 CORE_NAMESPACE = 'test_core'
+ROOT_NAME = 'root'
 
 
 class CacheSpecTestHelper(object):
@@ -113,8 +114,6 @@ class FooFile(Container):
           and should be reset to 'root' when use is finished to avoid potential cross-talk between tests.
     """
 
-    ROOT_NAME = 'root'  # For HDF5 and Zarr this is the root. It should be set before use if different for the backend.
-
     @docval({'name': 'buckets', 'type': list, 'doc': 'the FooBuckets in this file', 'default': list()},
             {'name': 'foo_link', 'type': Foo, 'doc': 'an optional linked Foo', 'default': None},
             {'name': 'foofile_data', 'type': 'array_data', 'doc': 'an optional dataset', 'default': None},
@@ -123,7 +122,7 @@ class FooFile(Container):
     def __init__(self, **kwargs):
         buckets, foo_link, foofile_data, foo_ref_attr = getargs('buckets', 'foo_link', 'foofile_data',
                                                                 'foo_ref_attr', kwargs)
-        super().__init__(name=self.ROOT_NAME)  # name is not used - FooFile should be the root container
+        super().__init__(name=ROOT_NAME)  # name is not used - FooFile should be the root container
         self.__buckets = {b.name: b for b in buckets}  # note: collections of groups are unordered in HDF5
         for f in buckets:
             f.parent = self
@@ -306,9 +305,7 @@ class BazCpdData(Data):
 
 
 class BazBucket(Container):
-    ROOT_NAME = 'root'
-
-    @docval({'name': 'name', 'type': str, 'doc': 'the name of this bucket', 'default': 'root'},
+    @docval({'name': 'name', 'type': str, 'doc': 'the name of this bucket', 'default': ROOT_NAME},
             {'name': 'bazs', 'type': list, 'doc': 'the Baz objects in this bucket'},
             {'name': 'baz_data', 'type': BazData, 'doc': 'dataset of Baz references', 'default': None},
             {'name': 'baz_cpd_data', 'type': BazCpdData, 'doc': 'dataset of Baz references', 'default': None})