adjust and notes

src/hdmf_zarr/backend.py

@@ -555,29 +555,28 @@ def write_group(self, **kwargs):
                 group_filename = self.__get_store_path(group.store)
                 if export_source is not None:
                     if sub_builder.builder.source in (group_filename, export_source):
-
-                        # if sub_builder.builder.source in (export_source):
-                        #     breakpoint()
-                        # TODO: rewrite notes to include export_source
-                        # Note: This just means the target builder is in the same file as the group.
-                        # Ensure we do a internal link, i.e. "SoftLink".
-                        # This is more of a "fix" because we are essentially ignoring the export_source.
-                        # Within export() we define:
-                        # write_args['export_source'] = src_io.source
-                        # Just because we are exporting from src_io.source, that does not mean the source of the target
-                        # is in src_io.source. This will probably get refactored.
+                        # Case 1:
+                        # sub_builder.builder.source == export_source
+                        # This means we have a SoftLink for a group and so we want the exported link to
+                        # also point "inwards" in the file being created.
+                        #################################
+                        # Case 2:
+                        # sub_builder.builder.source == group_filename
+                        # This is still a SoftLink; however, it is from adding a link to a group after FileA
+                        # has been read and we are exporting that to FileB. We still want the link to be "inwards".
                         source = group_filename
                     else:
-                        # Note: Create an ExternalLink to whatever file that has what we are targeting.
+                        # Purpose: Create an ExternalLink to whatever file that has what we are targeting.
 
                         # Note: This might change during the refactor, but the idea goes as follows:
-                        # write link calls _create_ref, which internally has a conditional if the source
+                        # write_link calls _create_ref, which internally has a conditional if the source
                         # is None. If None, it will use the source from the provided builder. In the case
                         # where sub_builder is a LinkBuilder, it will be the builder within that we source
                         # the source.
 
-                        # TODO: Alternatively, we can just set this sub_builder.builder.source because _create_ref
-                        # does that anyways if we set it to None.
+                        # Alternatively, we can just set this sub_builder.builder.source because _create_ref
+                        # does that anyways if we set it to None. Different ways to do the same thing. This
+                        # again will most likely change during the refactor.
 
                         source = None
                 else:

tests/unit/base_tests_zarrio.py

@@ -1259,11 +1259,11 @@ def test_attr_reference(self):
            if isinstance(self.store[1], str):
                self.assertTupleEqual((os.path.normpath(expected[0]), expected[1]),
                                     (os.path.normpath(os.path.abspath(self.store[1])),
-                                     '/buckets/bucket1/foo_holder/foo1/my_data'))
+                                     os.path.normpath('/buckets/bucket1/foo_holder/foo1/my_data')))
            else:
                self.assertTupleEqual((os.path.normpath(expected[0]), expected[1]),
                                     (os.path.normpath(os.path.abspath(self.store[1].path)),
-                                     '/buckets/bucket1/foo_holder/foo1/my_data'))
+                                     os.path.normpath('/buckets/bucket1/foo_holder/foo1/my_data')))
            # make sure the attribute reference resolves to the container within the same file
            self.assertIs(read_foofile2.foo_ref_attr, read_foofile2.buckets['bucket1'].foos['foo1'])