Merge pull request #266 from will-moore/remote_exception_handling

Don't handle exception in Multiscales init()

Author: joshmoore

ome_zarr/data.py

@@ -104,7 +104,7 @@ def create_zarr(
     label_name: str = "coins",
     fmt: Format = CurrentFormat(),
     chunks: Union[Tuple, List] = None,
-) -> None:
+) -> zarr.Group:
     """Generate a synthetic image pyramid with labels."""
     pyramid, labels = method()
 
@@ -192,3 +192,5 @@ def create_zarr(
             "properties": properties,
             "source": {"image": "../../"},
         }
+
+    return grp

ome_zarr/reader.py

@@ -277,28 +277,24 @@ def matches(zarr: ZarrLocation) -> bool:
     def __init__(self, node: Node) -> None:
         super().__init__(node)
 
-        try:
-            multiscales = self.lookup("multiscales", [])
-            version = multiscales[0].get(
-                "version", "0.1"
-            )  # should this be matched with Format.version?
-            datasets = multiscales[0]["datasets"]
-            axes = multiscales[0].get("axes")
-            fmt = format_from_version(version)
-            # Raises ValueError if not valid
-            axes_obj = Axes(axes, fmt)
-            node.metadata["axes"] = axes_obj.to_list()
-            # This will get overwritten by 'omero' metadata if present
-            node.metadata["name"] = multiscales[0].get("name")
-            paths = [d["path"] for d in datasets]
-            self.datasets: List[str] = paths
-            transformations = [d.get("coordinateTransformations") for d in datasets]
-            if any(trans is not None for trans in transformations):
-                node.metadata["coordinateTransformations"] = transformations
-            LOGGER.info("datasets %s", datasets)
-        except Exception:
-            LOGGER.exception("Failed to parse multiscale metadata")
-            return  # EARLY EXIT
+        multiscales = self.lookup("multiscales", [])
+        version = multiscales[0].get(
+            "version", "0.1"
+        )  # should this be matched with Format.version?
+        datasets = multiscales[0]["datasets"]
+        axes = multiscales[0].get("axes")
+        fmt = format_from_version(version)
+        # Raises ValueError if not valid
+        axes_obj = Axes(axes, fmt)
+        node.metadata["axes"] = axes_obj.to_list()
+        # This will get overwritten by 'omero' metadata if present
+        node.metadata["name"] = multiscales[0].get("name")
+        paths = [d["path"] for d in datasets]
+        self.datasets: List[str] = paths
+        transformations = [d.get("coordinateTransformations") for d in datasets]
+        if any(trans is not None for trans in transformations):
+            node.metadata["coordinateTransformations"] = transformations
+        LOGGER.info("datasets %s", datasets)
 
         for resolution in self.datasets:
             data: da.core.Array = self.array(resolution, version)

tests/test_reader.py

@@ -33,6 +33,24 @@ def test_label(self):
         assert len(list(reader())) == 3
 
 
+class TestInvalid:
+    @pytest.fixture(autouse=True)
+    def initdir(self, tmpdir):
+        self.path = tmpdir.mkdir("data")
+
+    def test_invalid_version(self):
+        grp = create_zarr(str(self.path))
+        # update version to something invalid
+        attrs = grp.attrs.asdict()
+        attrs["multiscales"][0]["version"] = "invalid"
+        grp.attrs.put(attrs)
+        # should raise exception
+        with pytest.raises(ValueError) as exe:
+            reader = Reader(parse_url(str(self.path)))
+            assert len(list(reader())) == 2
+        assert str(exe.value) == "Version invalid not recognized"
+
+
 class TestHCSReader:
     @pytest.fixture(autouse=True)
     def initdir(self, tmpdir):