Add test for bad .zarr file with missing OME info

.gitignore

@@ -1,5 +1,6 @@
 .pytest_cache
 coverage.xml
+.coverage*
 htmlcov
 pytools/_version.py
 __pycache__

pytools/HedwigZarrImage.py

@@ -196,7 +196,7 @@ def shader_type(
         """
         Produces the shader type one of: RGB, Grayscale, or MultiChannel.
         """
-        if self.ome_info.maybe_rgb(self.ome_idx):
+        if self.ome_info and self.ome_info.maybe_rgb(self.ome_idx):
             return "RGB"
         if self._ome_ngff_multiscale_dims()[1] == "C" and self.shape[1] == 1:
             return "Grayscale"
@@ -207,6 +207,9 @@ def neuroglancer_shader_parameters(self, mad_scale=3) -> dict:
         Produces the "shaderParameters" portion of the metadata for Neuroglancer
         returns JSON serializable object
         """
+        if self.ome_info is None:
+            return {}
+
         _shader_type = self.shader_type
         if _shader_type == "RGB":
             return {}

pytools/HedwigZarrImages.py

@@ -48,8 +48,6 @@ def ome_xml_path(self) -> Optional[Path]:
             _xml_path = Path(self.zarr_store.path) / self.zarr_root["OME"].path / "METADATA.ome.xml"
             if _xml_path.exists():
                 return _xml_path
-            else:
-                return None
 
     @property
     def ome_info(self) -> Optional[AnyStr]:
@@ -79,12 +77,12 @@ def get_series_keys(self) -> Iterable[str]:
 
     def __getitem__(self, item) -> HedwigZarrImage:
         for k_idx, k in enumerate(self.get_series_keys()):
-            if item == k:
+            if item == k and "OME" in self.zarr_root.group_keys():
                 ome_index_to_zarr_group = self.zarr_root["OME"].attrs["series"]
                 zarr_idx = ome_index_to_zarr_group[k_idx]
                 return HedwigZarrImage(self.zarr_root[zarr_idx], self.ome_info, k_idx)
 
-        return HedwigZarrImage(self.zarr_root[item])
+        return HedwigZarrImage(self.zarr_root[item], None, 404)
 
     def series(self) -> Iterable[Tuple[str, HedwigZarrImage]]:
         """An Iterable of key and HedwigZarrImages stored in the ZARR structure."""

requirements-dev.txt

@@ -6,4 +6,5 @@ flake8
 black
 wheel
 packaging
+pytest-cov
 -r requirements.txt

test/test_HedwigZarrImage.py

@@ -0,0 +1,41 @@
+#
+#  Licensed under the Apache License, Version 2.0 (the "License");
+#  you may not use this file except in compliance with the License.
+#  You may obtain a copy of the License at
+#
+#         http://www.apache.org/licenses/LICENSE-2.0.txt
+#
+#  Unless required by applicable law or agreed to in writing, software
+#  distributed under the License is distributed on an "AS IS" BASIS,
+#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#  See the License for the specific language governing permissions and
+#  limitations under the License.
+#
+
+import pytest
+import shutil
+from pytools.HedwigZarrImages import HedwigZarrImages
+
+
+@pytest.mark.parametrize(
+    "zarr_name, image_ext, array_shape, dims, shader_type, ngff_dims, shader_params",
+    [("OM_P1_S1_ScanOnly_1k.zarr", "png", (1, 3, 1, 1024, 521), "XYC", "MultiChannel", "TCZYX", {})],
+)
+def test_HedwigZarrImage_info(
+    data_path, zarr_name, image_ext, array_shape, dims, shader_type, ngff_dims, shader_params, tmp_path
+):
+    # Remove OME directory from the .zarr file
+    shutil.copytree(data_path / zarr_name, tmp_path / zarr_name)
+    shutil.rmtree(tmp_path / zarr_name / "OME")
+
+    zi = HedwigZarrImages(tmp_path / zarr_name)
+    assert zi.ome_xml_path is None
+    assert zi.ome_info is None
+    # keys = list(zi.get_series_keys())
+
+    for k, z_img in zi.series():
+        assert array_shape == z_img.shape
+        assert dims == z_img.dims
+        assert shader_type == z_img.shader_type
+        assert ngff_dims == z_img._ome_ngff_multiscale_dims()
+        assert shader_params == z_img.neuroglancer_shader_parameters()

test/test_HedwigZarrImages.py

@@ -28,7 +28,6 @@ def temp_zarr_path(request, tmp_path_factory, data_path):
     tmp_zarr = tmp_path_factory.mktemp("Z") / zarr_name
     shutil.copytree(data_path / zarr_name, tmp_zarr)
 
-    print(f"temp_zarr_path: {tmp_zarr}")
     return tmp_zarr
 
 
@@ -52,15 +51,10 @@ def test_HedwigZarrImage_info(
     data_path, zarr_name, image_ext, array_shape, dims, shader_type, ngff_dims, shader_params
 ):
     zi = HedwigZarrImages(data_path / zarr_name)
-    keys = list(zi.get_series_keys())
-    print(f"zarr groups: {keys}")
-
-    print(zi.ome_xml_path)
 
     for k, z_img in zi.series():
         assert image_ext in k
         assert array_shape == z_img.shape
-        print(f"{z_img.path=}")
         assert dims == z_img.dims
         assert shader_type == z_img.shader_type
         assert ngff_dims == z_img._ome_ngff_multiscale_dims()