clean up/adjust resolve_ref

hdmf-dev · Sep 28, 2023 · 862db84 · 862db84
1 parent 13387a3
commit 862db84
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Showing 3 changed files with 6 additions and 13 deletions.
diff --git a/src/hdmf_zarr/backend.py b/src/hdmf_zarr/backend.py
@@ -5,7 +5,6 @@
 import numpy as np
 import tempfile
 import logging
-import pathlib
 
 # Zarr imports
 import zarr
@@ -550,14 +549,7 @@ 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])
-                    target_zarr_obj = target_zarr_obj[rel_obj_path]
-                except Exception:
-                    raise ValueError("Found bad link to object %s in file %s" % (object_path, source_file))
+                raise ValueError("Found bad link to object %s in file %s" % (object_path, source_file))
         # Return the create path
         return target_name, target_zarr_obj
 

diff --git a/tests/unit/base_tests_zarrio.py b/tests/unit/base_tests_zarrio.py
@@ -228,7 +228,7 @@ def test_write_compound(self, test_data=None):
                      {'name': 'name', 'dtype': str}]
         self.__dataset_builder = DatasetBuilder('my_data', data, dtype=data_type)
         self.createGroupBuilder()
-        writer = ZarrIO(self.store, manager=self.manager, mode='a')
+        writer = ZarrIO(self.store, manager=self.manager, mode='w')
         writer.write_builder(self.builder)
         writer.close()
 

diff --git a/tests/unit/test_io_convert.py b/tests/unit/test_io_convert.py
@@ -706,7 +706,7 @@ def test_export_cpd_dset_refs(self):
             bazs.append(b)
             baz_pairs.append((i, b))
         baz_cpd_data = BazCpdData(name='baz_cpd_data1', data=baz_pairs)
-        bucket = BazBucket(name='bucket1', bazs=bazs.copy(), baz_cpd_data=baz_cpd_data)
+        bucket = BazBucket(name='root', bazs=bazs.copy(), baz_cpd_data=baz_cpd_data)
 
         with HDF5IO(self.path[0], manager=get_baz_buildmanager(), mode='w') as write_io:
             write_io.write(bucket)
@@ -751,7 +751,7 @@ def test_export_cpd_dset_refs(self):
             bazs.append(b)
             baz_pairs.append((i, b))
         baz_cpd_data = BazCpdData(name='baz_cpd_data1', data=baz_pairs)
-        bucket = BazBucket(name='bucket1', bazs=bazs.copy(), baz_cpd_data=baz_cpd_data)
+        bucket = BazBucket(name='root', bazs=bazs.copy(), baz_cpd_data=baz_cpd_data)
 
         with ZarrIO(self.path[0], manager=get_baz_buildmanager(), mode='w') as write_io:
             write_io.write(bucket)
@@ -797,12 +797,13 @@ def test_export_cpd_dset_refs(self):
             bazs.append(b)
             baz_pairs.append((i, b))
         baz_cpd_data = BazCpdData(name='baz_cpd_data1', data=baz_pairs)
-        bucket = BazBucket(name='bucket1', bazs=bazs.copy(), baz_cpd_data=baz_cpd_data)
+        bucket = BazBucket(name='root', bazs=bazs.copy(), baz_cpd_data=baz_cpd_data)
 
         with ZarrIO(self.path[0], manager=get_baz_buildmanager(), mode='w') as write_io:
             write_io.write(bucket)
         with ZarrIO(self.path[0], manager=get_baz_buildmanager(), mode='r') as read_io:
             read_bucket1 = read_io.read()
+            read_bucket1.baz_cpd_data.data[0][0]
             # NOTE: reference IDs might be the same between two identical files
             # adding a Baz with a smaller name should change the reference IDs on export
             new_baz = Baz(name='baz000')