Don't open with consolidated metadata in mode r+ (#193)

CHANGELOG.md

@@ -1,7 +1,8 @@
 # HDMF-ZARR Changelog
 
-## 0.7.0 (May 2, 2024)
+## 0.8.0 (Upcoming)
 ### Bug Fixes
+* Fixed bug when opening a file in with `mode=r+`. The file will open without using the consolidated metadata. @mavaylon1 [#182](https://github.com/hdmf-dev/hdmf-zarr/issues/182)
 * Fixed bug on how we access scalar arrays. Added warning filter for Zarr deprecation of NestedDirectoryStore. Fixed bug on how we write a dataset of references. @mavaylon1 [#195](https://github.com/hdmf-dev/hdmf-zarr/pull/195)
 
 ## 0.7.0 (May 2, 2024)

src/hdmf_zarr/backend.py

@@ -160,7 +160,10 @@ def open(self):
         if self.__file is None:
             # Within zarr, open_consolidated only allows the mode to be 'r' or 'r+'.
             # As a result, when in other modes, the file will not use consolidated metadata.
-            if self.__mode not in ['r', 'r+']:
+            if self.__mode != 'r':
+                # When we consolidate metadata, we use ConsolidatedMetadataStore.
+                # This interface does not allow for setting items.
+                # In the doc string, it says it is "read only". As a result, we cannot use r+ with consolidate_metadata.
                 # r- is only an internal mode in ZarrIO to force the use of regular open. For Zarr we need to
                 # use the regular mode r when r- is specified
                 mode_to_use = self.__mode if self.__mode != 'r-' else 'r'
@@ -1453,6 +1456,7 @@ def __read_dataset(self, zarr_obj, name):
         # Read scalar dataset
         if dtype == 'scalar':
             data = zarr_obj[()]
+
         if isinstance(dtype, list):
             # Check compound dataset where one of the subsets contains references
             has_reference = False