clean

src/hdmf_zarr/backend.py

@@ -558,7 +558,6 @@ def write_group(self, **kwargs):
         if links:
             for link_name, sub_builder in links.items():
                 # Note: sub_builder is a LinkBuilder not the builder within.
-                # HDMF: h5tools --> 1034
                 self.write_link(group, sub_builder, export_source)
 
         attributes = builder.attributes
@@ -850,7 +849,6 @@ def write_link(self, **kwargs):
 
         group_filename = self.__get_store_path(parent.store)
         if export_source is not None:
-            # HDMF: h5tools 1081
             if target_builder.source in (group_filename, export_source):
                 # Case 1:
                 # target_builder.source == export_source
@@ -1043,7 +1041,7 @@ def write_dataset(self, **kwargs):  # noqa: C901
                 # and will be refactored/removed.
                 if self.__is_ref(dts['dtype']):
                     refs.append(i)
-                    ref_tmp = self._create_ref(data[0][i], ref_link_source=self.path) # HDMF 1229
+                    ref_tmp = self._create_ref(data[0][i], ref_link_source=self.path)
                     if isinstance(ref_tmp, ZarrReference):
                         dts_str = 'object'
                     else:

tests/unit/base_tests_zarrio.py

@@ -1312,13 +1312,46 @@ def test_pop_linked_group(self):
                 with self.assertRaisesWith(OrphanContainerBuildError, msg):
                     export_io.export(src_io=read_io, container=read_foofile)
 
-    def test_soft_links_export(self):
+    def test_soft_link_data(self):
+        """
+        Test data soft links.
+        """
+        foo1 = Foo('foo1', [1, 2, 3, 4, 5], "I am foo1", 17, 3.14)
+        foobucket = FooBucket('bucket1', [foo1])
+        foofile = FooFile(buckets=[foobucket])
+
+        with ZarrIO(self.store[0], manager=get_foo_buildmanager(), mode='w') as write_io:
+            write_io.write(foofile)
+
+        with ZarrIO(self.store[0], manager=get_foo_buildmanager(), mode='r') as read_io:
+            read_foofile = read_io.read()
+
+            # create a foo with link to existing dataset my_data, add the foo to new foobucket
+            # this should make a soft link within the exported file
+            foo2 = Foo('foo2', read_foofile.buckets['bucket1'].foos['foo1'].my_data, "I am foo2", 17, 3.14)
+            foobucket2 = FooBucket('bucket2', [foo2])
+            read_foofile.add_bucket(foobucket2)
+
+            read_foofile.foofile_data = foo2.my_data
+
+            with ZarrIO(self.store[1], mode='w') as export_io:
+                export_io.export(src_io=read_io, container=read_foofile)
+
+        with ZarrIO(self.store[1], manager=get_foo_buildmanager(), mode='r') as read_io:
+            read_foofile2 = read_io.read()
+
+            # test new soft link to dataset in file
+            self.assertIs(read_foofile2.buckets['bucket1'].foos['foo1'].my_data,
+                          read_foofile2.buckets['bucket2'].foos['foo2'].my_data)
+
+            # test new soft link to new soft link to dataset in file
+            self.assertIs(read_foofile2.buckets['bucket1'].foos['foo1'].my_data, read_foofile2.foofile_data)
+
+
+    def test_soft_links_group_after_write(self):
         """
         Test that exporting a written container after adding
         groups, links, and references to it works.
-
-        This tests `builder.parent.name != parent_name:` within
-        `if data_filename != export_source or builder.parent.name != parent_name:`.
         """
         foo1 = Foo('foo1', [1, 2, 3, 4, 5], "I am foo1", 17, 3.14)
         foobucket = FooBucket('bucket1', [foo1])
@@ -1339,9 +1372,6 @@ def test_soft_links_export(self):
             # also add link from foofile to new foo2 container
             read_foofile.foo_link = foo2
 
-            # also add link from foofile to new foo2.my_data dataset which is a link to foo1.my_data dataset
-            read_foofile.foofile_data = foo2.my_data
-
             # also add reference from foofile to new foo2
             read_foofile.foo_ref_attr = foo2
 
@@ -1351,16 +1381,9 @@ def test_soft_links_export(self):
         with ZarrIO(self.store[1], manager=get_foo_buildmanager(), mode='r') as read_io:
             read_foofile2 = read_io.read()
 
-            # test new soft link to dataset in file
-            self.assertIs(read_foofile2.buckets['bucket1'].foos['foo1'].my_data,
-                          read_foofile2.buckets['bucket2'].foos['foo2'].my_data)
-
             # test new soft link to group in file
             self.assertIs(read_foofile2.foo_link, read_foofile2.buckets['bucket2'].foos['foo2'])
 
-            # test new soft link to new soft link to dataset in file
-            self.assertIs(read_foofile2.buckets['bucket1'].foos['foo1'].my_data, read_foofile2.foofile_data)
-
             # test new attribute reference to new group in file
             self.assertIs(read_foofile2.foo_ref_attr, read_foofile2.buckets['bucket2'].foos['foo2'])