added link_data --> clear_cache relationship to support repacking zar…

…r nwbfiles (#215)

CHANGELOG.md

@@ -6,6 +6,7 @@
 * NWBZarrIO load_namespaces=True by default. @mavaylon1 [#204](https://github.com/hdmf-dev/hdmf-zarr/pull/204)
 * Added test for opening file with consolidated metadata from DANDI. @mavaylon1 [#206](https://github.com/hdmf-dev/hdmf-zarr/pull/206)
 * Add dimension labels compatible with xarray. @mavaylon1 [#207](https://github.com/hdmf-dev/hdmf-zarr/pull/207)
+* Added link_data --> clear_cache relationship to support repacking zarr nwbfiles: [#215](https://github.com/hdmf-dev/hdmf-zarr/pull/215)
 
 ## 0.8.0 (June 4, 2024)
 ### Bug Fixes

src/hdmf_zarr/backend.py

@@ -362,6 +362,8 @@ def export(self, **kwargs):
         write_args['export_source'] = src_io.source  # pass export_source=src_io.source to write_builder
         ckwargs = kwargs.copy()
         ckwargs['write_args'] = write_args
+        if not write_args.get('link_data', True):
+            ckwargs['clear_cache'] = True
         super().export(**ckwargs)
         if cache_spec:
             self.__cache_spec()
@@ -1305,6 +1307,13 @@ def __list_fill__(self, parent, name, data, options=None):  # noqa: C901
             except ValueError:
                 for i in range(len(data)):
                     dset[i] = data[i]
+            except TypeError: # If data is an h5py.Dataset with strings, they may need to be decoded
+                for c in np.ndindex(data_shape):
+                    o = data
+                    for i in c:
+                        o = o[i]
+                    # bytes are not JSON serializable
+                    dset[c] = o if not isinstance(o, (bytes, np.bytes_)) else o.decode("utf-8")
         return dset
 
     def __scalar_fill__(self, parent, name, data, options=None):

tests/unit/test_io_convert.py

@@ -949,7 +949,7 @@ def __get_data_array(self, foo_container):
 
     def test_maxshape(self):
         """test when maxshape is set for the dataset"""
-        data = H5DataIO(data=list(range(5)), maxshape=(None,))
+        data = H5DataIO(data=list(range(5)), maxshape=(5,))
         self.__roundtrip_data(data=data)
         self.assertContainerEqual(self.out_container, self.read_container, ignore_hdmf_attrs=True)