Fix dimension separator when downloading files

ome_zarr/utils.py

@@ -129,7 +129,9 @@ def download(input_path: str, output_dir: str = ".") -> None:
                     for dataset, data in reversed(list(zip(datasets, resolutions))):
                         LOGGER.info("resolution %s...", dataset)
                         with pbar:
-                            data.to_zarr(str(target_path / dataset))
+                            data.to_zarr(
+                                str(target_path / dataset), dimension_separator="/"
+                            )
             else:
                 # Assume a group that needs metadata, like labels
                 zarr.group(str(target_path))

tests/test_cli.py

@@ -8,6 +8,16 @@
 from ome_zarr.utils import strip_common_prefix
 
 
+def directory_items(directory: Path):
+    """
+    Get all items (files and folders) in a directory, relative to that directory.
+    """
+    if not directory.is_dir():
+        raise ValueError(f"{directory} is not a directory")
+
+    return sorted([p.relative_to(directory) for p in directory.glob("*")])
+
+
 class TestCli:
     @pytest.fixture(autouse=True)
     def initdir(self, tmpdir):
@@ -40,6 +50,24 @@ def test_astronaut_download(self, tmpdir):
         main(["download", filename, f"--output={out}"])
         main(["info", f"{out}/{basename}"])
 
+        assert directory_items(Path(out) / "data-3") == [
+            Path(".zattrs"),
+            Path(".zgroup"),
+            Path("0"),
+            Path("1"),
+            Path("2"),
+            Path("3"),
+            Path("4"),
+            Path("labels"),
+        ]
+
+        assert directory_items(Path(out) / "data-3" / "1") == [
+            Path(".zarray"),
+            Path("0"),
+            Path("1"),
+            Path("2"),
+        ]
+
     def test_s3_info(self, s3_address):
         main(["info", s3_address])