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hdmf-dev · Dec 13, 2023 · 005bfbc · 005bfbc
1 parent 9692a98
commit 005bfbc
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Showing 3 changed files with 33 additions and 10 deletions.
diff --git a/src/hdmf_zarr/backend.py b/src/hdmf_zarr/backend.py
@@ -1018,11 +1018,20 @@ def write_dataset(self, **kwargs):  # noqa: C901
                                               **options['io_settings'])
                 self._written_builders.set_written(builder)  # record that the builder has been written
                 dset.attrs['zarr_dtype'] = type_str
+                new_items = []
                 for j, item in enumerate(data):
                     new_item = list(item)
                     for i in refs:
                         new_item[i] = self.__get_ref(item[i], export_source=export_source)
-                    dset[j] = new_item
+                    new_items.append(tuple(new_item))
+                    # dset[j] = new_item
+
+                generated_dtype = []
+                for item in builder.dtype:
+                    if item['dtype'] == type('string'):
+                        item['dtype'] = 'U25'
+                    generated_dtype.append((item['name'], item['dtype']))
+                dset[...] = np.array(new_items, dtype=generated_dtype)
             else:
                 # write a compound datatype
                 dset = self.__list_fill__(parent, name, data, options)

diff --git a/src/hdmf_zarr/zarr_utils.py b/src/hdmf_zarr/zarr_utils.py
@@ -151,7 +151,8 @@ def dtype(self):
         return self.__dtype
 
     def __getitem__(self, arg):
-        rows = copy(super().__getitem__(arg))
+        rows = list(copy(super().__getitem__(arg)))
+        # breakpoint()
         if np.issubdtype(type(arg), np.integer):
             self.__swap_refs(rows)
         else:

diff --git a/tests/unit/base_tests_zarrio.py b/tests/unit/base_tests_zarrio.py
@@ -426,20 +426,33 @@ def test_read_reference(self):
         builder = self.createReferenceBuilder()['ref_dataset']
         read_builder = self.root['ref_dataset']
         # Load the linked arrays and confirm we get the same data as we had in the original builder
-        for i, v in enumerate(read_builder['data']):
-            self.assertTrue(np.all(builder['data'][i]['builder']['data'] == v['data'][:]))
+        breakpoint()
+        # for i, v in enumerate(read_builder['data']):
+        #     self.assertTrue(np.all(builder['data'][i]['builder']['data'] == v['data'][:]))
 
     def test_read_reference_compound(self):
         self.test_write_reference_compound()
         self.read()
         builder = self.createReferenceCompoundBuilder()['ref_dataset']
         read_builder = self.root['ref_dataset']
-        # Load the elements of each entry in the compound dataset and compar the index, string, and referenced array
-        for i, v in enumerate(read_builder['data']):
-            self.assertEqual(v[0], builder['data'][i][0])  # Compare index value from compound tuple
-            self.assertEqual(v[1], builder['data'][i][1])  # Compare string value from compound tuple
-            self.assertTrue(np.all(v[2]['data'][:] == builder['data'][i][2]['builder']['data'][:]))  # Compare ref array
-        # print(read_builder)
+        read_builder['data'][0]
+        #Load the elements of each entry in the compound dataset and compare the index, string, and referenced array
+        breakpoint()
+        # for i, v in enumerate(read_builder['data']):
+        #     # self.assertEqual(v[0], builder['data'][i][0])  # Compare index value from compound tuple
+        #     self.assertEqual(v[1], builder['data'][i][1])  # Compare string value from compound tuple
+        # self.assertTrue(np.all(v[2]['data'][:] == builder['data'][i][2]['builder']['data'][:]))  # Compare ref array
+
+        # self.assertEqual(read_builder['data'].dataset[0][0], builder['data'][0][0])
+        # self.assertEqual(read_builder['data'].dataset[0][0], builder['data'][1][0])
+        # self.assertEqual(read_builder['data'].dataset[0][1], 'dataset_1')
+        # self.assertEqual(read_builder['data'].dataset[1][1], 'dataset_2')
+        # self.assertEqual(read_builder['data'].dataset[0][1], '/dataset_1')
+        # self.assertEqual(read_builder['data'].dataset[1][1], '/dataset_2')
+
+            # self.assertEqual(v[1], builder['data'][i][1])  # Compare string value from compound tuple
+            # self.assertTrue(np.all(v[2]['data'][:] == builder['data'][i][2]['builder']['data'][:]))  # Compare ref array
+
 
     def test_read_reference_compound_buf(self):
         data_1 = np.arange(100, 200, 10).reshape(2, 5)