add basic io testing

src/ngio/io/zarr_group_utils.py

@@ -1,15 +1,23 @@
 """Collection of helper functions to work with Zarr groups."""
 
 from pathlib import Path
+from typing import Literal
 
 import zarr
-from zarr.core.common import AccessModeLiteral, StoreLike, ZarrFormat
+import zarr.store
+from zarr.core.common import ZarrFormat
+from zarr.store.common import StoreLike
+
+ReadOrEdirLiteral = Literal["r", "r+"]
 
 
 def _open_group(
-    store: StoreLike, mode: AccessModeLiteral, zarr_version: ZarrFormat = 2
-) -> zarr.hierarchy.Group:
+    store: StoreLike, mode: ReadOrEdirLiteral, zarr_format: ZarrFormat = 2
+) -> zarr.Group:
     """Wrapper around zarr.open_group with some additional checks."""
+    assert mode in ["r", "r+"], f"Invalid mode: {mode}. Must be 'r' or 'r+'."
+    assert zarr_format in [2, 3], f"Invalid zarr_format: {zarr_format}. Must be 2 or 3."
+
     if isinstance(store, str):
         store = Path(store)
 
@@ -22,42 +30,52 @@ def _open_group(
             raise FileNotFoundError(
                 f"Path {store.root} does not exist. Cannot open group."
             )
+
+        if store.mode == "r" and mode == "r+":
+            raise PermissionError(
+                "Store is opened in read-only mode. Cannot open be edited."
+            )
+
+        elif store.mode == "r+" and mode == "r":
+            # Reopen the store in read only mode to avoid failing in the zarr.open_group
+            store = zarr.store.LocalStore(str(store.root), mode="r")
+
     elif isinstance(store, zarr.store.RemoteStore):
         raise NotImplementedError(
             "RemoteStore is not yet supported. Please use LocalStore."
         )
 
-    return zarr.open_group(store=store, mode=mode, zarr_version=zarr_version)
+    return zarr.open_group(store=store, mode=mode, zarr_format=zarr_format)
 
 
-def read_group_attrs(store: StoreLike, zarr_version: ZarrFormat = 2) -> dict:
+def read_group_attrs(store: StoreLike, zarr_format: ZarrFormat = 2) -> dict:
     """Simple helper function to read the attributes of a Zarr group."""
-    group = _open_group(store=store, mode="r", zarr_version=zarr_version)
-    return group.attrs.asdict()
+    group = _open_group(store=store, mode="r", zarr_format=zarr_format)
+    return dict(group.attrs)
 
 
-def update_group_attrs(store: StoreLike, attrs: dict, zarr_version: ZarrFormat) -> None:
+def update_group_attrs(store: StoreLike, attrs: dict, zarr_format: ZarrFormat) -> None:
     """Simple helper function to update the attributes of a Zarr group."""
-    group = _open_group(store=store, mode="a", zarr_version=zarr_version)
+    group = _open_group(store=store, mode="r+", zarr_format=zarr_format)
     group.attrs.update(attrs)
 
 
 def overwrite_group_attrs(
-    store: StoreLike, attrs: dict, zarr_version: ZarrFormat
+    store: StoreLike, attrs: dict, zarr_format: ZarrFormat
 ) -> None:
     """Simple helper function to overwrite the attributes of a Zarr group."""
-    group = _open_group(store=store, mode="a", zarr_version=zarr_version)
+    group = _open_group(store=store, mode="r+", zarr_format=zarr_format)
     group.attrs.clear()
     group.attrs.update(attrs)
 
 
-def list_group_arrays(store: StoreLike, zarr_version: ZarrFormat = 2) -> list:
+def list_group_arrays(store: StoreLike, zarr_format: ZarrFormat = 2) -> list:
     """Simple helper function to list the arrays in a Zarr group."""
-    group = _open_group(store, mode="r", zarr_version=zarr_version)
-    return group.list_arrays()
+    group = _open_group(store, mode="r", zarr_format=zarr_format)
+    return list(group.array_keys())
 
 
-def list_group_groups(store: StoreLike, zarr_version: ZarrFormat = 2) -> list:
+def list_group_groups(store: StoreLike, zarr_format: ZarrFormat = 2) -> list:
     """Simple helper function to list the groups in a Zarr group."""
-    group = _open_group(store, mode="r", zarr_version=zarr_version)
-    return group.list_groups()
+    group = _open_group(store, mode="r", zarr_format=zarr_format)
+    return list(group.group_keys())

src/ngio/ngff_meta/v04/zarr_utils.py

@@ -26,7 +26,7 @@
 
 def check_ngff_image_meta_v04(zarr_path: str) -> bool:
     """Check if a Zarr Group contains the OME-NGFF v0.4."""
-    group = open_group(store=zarr_path, mode="r", zarr_version=2)
+    group = open_group(store=zarr_path, mode="r", zarr_format=2)
     multiscales = group.attrs.get("multiscales", None)
     if multiscales is None:
         return False
@@ -46,7 +46,7 @@ def check_ngff_image_meta_v04(zarr_path: str) -> bool:
 
 def load_vanilla_ngff_image_meta_v04(zarr_path: str) -> NgffImageMeta04:
     """Load the OME-NGFF 0.4 image meta model."""
-    group = open_group(store=zarr_path, mode="r", zarr_version=2)
+    group = open_group(store=zarr_path, mode="r", zarr_format=2)
     return NgffImageMeta04(**group.attrs)
 
 

tests/io/conftest.py

@@ -0,0 +1,40 @@
+from pathlib import Path
+
+import zarr
+import zarr.store
+from pytest import fixture
+
+
+def _create_zarr(tempdir, zarr_format=2):
+    zarr_path = Path(tempdir) / f"test_group_v{2}.zarr"
+    group = zarr.open_group(store=zarr_path, mode="w", zarr_format=zarr_format)
+
+    for i in range(3):
+        group.create_array(f"array_{i}", shape=(10, 10), dtype="i4")
+
+    for i in range(3):
+        group.create_group(f"group_{i}")
+
+    return zarr_path
+
+
+@fixture
+def local_zarr_path_v2(tmpdir) -> tuple[Path, int]:
+    zarr_path = _create_zarr(tmpdir, zarr_format=2)
+    return zarr_path, 2
+
+
+@fixture
+def local_zarr_path_v3(tmpdir) -> tuple[Path, int]:
+    zarr_path = _create_zarr(tmpdir, zarr_format=3)
+    return zarr_path, 3
+
+
+@fixture(
+    params=[
+        "local_zarr_path_v2",
+        "local_zarr_path_v3",
+    ]
+)
+def store_fixture(request):
+    return request.getfixturevalue(request.param)

tests/io/test_zarr_group_utils.py

@@ -0,0 +1,51 @@
+class TestGroupUtils:
+    @property
+    def test_attrs(self) -> dict:
+        return {"a": 1, "b": 2, "c": 3}
+
+    def test_update_group_attrs(self, store_fixture):
+        from ngio.io.zarr_group_utils import (
+            read_group_attrs,
+            update_group_attrs,
+        )
+
+        store, zarr_format = store_fixture
+
+        update_group_attrs(store=store, attrs=self.test_attrs, zarr_format=zarr_format)
+        attrs = read_group_attrs(store=store, zarr_format=zarr_format)
+        assert attrs == self.test_attrs, "Attributes were not written correctly."
+
+        update_group_attrs(store=store, attrs={"new": 1}, zarr_format=zarr_format)
+        attrs = read_group_attrs(store=store, zarr_format=zarr_format)
+        expected = {**self.test_attrs, "new": 1}
+        assert attrs == expected, "Attributes were not written correctly."
+
+    def test_overwrite_group_attrs(self, store_fixture):
+        from ngio.io.zarr_group_utils import (
+            overwrite_group_attrs,
+            read_group_attrs,
+        )
+
+        store, zarr_format = store_fixture
+
+        overwrite_group_attrs(
+            store=store, attrs=self.test_attrs, zarr_format=zarr_format
+        )
+        attrs = read_group_attrs(store=store, zarr_format=zarr_format)
+        assert attrs == self.test_attrs, "Attributes were not written correctly."
+
+    def test_list_group_arrays(self, store_fixture):
+        from ngio.io.zarr_group_utils import list_group_arrays
+
+        store, zarr_format = store_fixture
+
+        arrays = list_group_arrays(store=store, zarr_format=zarr_format)
+        assert len(arrays) == 3, "Arrays were not listed correctly."
+
+    def test_list_group_groups(self, store_fixture):
+        from ngio.io.zarr_group_utils import list_group_groups
+
+        store, zarr_format = store_fixture
+
+        groups = list_group_groups(store=store, zarr_format=zarr_format)
+        assert len(groups) == 3, "Groups were not listed correctly."