Merge pull request #349 from berombau/master

Support init of ome_zarr_py.io.ZarrLocation with zarr.storage.FSStore

.isort.cfg

@@ -1,5 +1,5 @@
 [settings]
-known_third_party = dask,numcodecs,numpy,pytest,scipy,setuptools,skimage,zarr
+known_third_party = dask,fsspec,numcodecs,numpy,pytest,scipy,setuptools,skimage,zarr
 multi_line_output = 3
 include_trailing_comma = True
 force_grid_wrap = 0

ome_zarr/io.py

@@ -28,7 +28,10 @@ class ZarrLocation:
     """
 
     def __init__(
-        self, path: Union[Path, str], mode: str = "r", fmt: Format = CurrentFormat()
+        self,
+        path: Union[Path, str, FSStore],
+        mode: str = "r",
+        fmt: Format = CurrentFormat(),
     ) -> None:
         LOGGER.debug("ZarrLocation.__init__ path: %s, fmt: %s", path, fmt.version)
         self.__fmt = fmt
@@ -37,13 +40,17 @@ def __init__(
             self.__path = str(path.resolve())
         elif isinstance(path, str):
             self.__path = path
+        elif isinstance(path, FSStore):
+            self.__path = path.path
         else:
             raise TypeError(f"not expecting: {type(path)}")
 
         loader = fmt
         if loader is None:
             loader = CurrentFormat()
-        self.__store = loader.init_store(self.__path, mode)
+        self.__store: FSStore = (
+            path if isinstance(path, FSStore) else loader.init_store(self.__path, mode)
+        )
 
         self.__init_metadata()
         detected = detect_format(self.__metadata, loader)

tests/test_io.py

@@ -0,0 +1,38 @@
+from pathlib import Path
+
+import fsspec
+import pytest
+import zarr
+
+from ome_zarr.data import create_zarr
+from ome_zarr.io import ZarrLocation, parse_url
+
+
+class TestIO:
+    @pytest.fixture(autouse=True)
+    def initdir(self, tmpdir):
+        self.path = tmpdir.mkdir("data")
+        create_zarr(str(self.path))
+        self.store = parse_url(str(self.path), mode="w").store
+        self.root = zarr.group(store=self.store)
+
+    def test_parse_url(self):
+        assert parse_url(str(self.path))
+
+    def test_parse_nonexistent_url(self):
+        assert parse_url(self.path + "/does-not-exist") is None
+
+    def test_loc_str(self):
+        assert ZarrLocation(str(self.path))
+
+    def test_loc_path(self):
+        assert ZarrLocation(Path(self.path))
+
+    def test_loc_store(self):
+        assert ZarrLocation(self.store)
+
+    def test_loc_fs(self):
+        fs = fsspec.filesystem("memory")
+        fsstore = zarr.storage.FSStore(url="/", fs=fs)
+        loc = ZarrLocation(fsstore)
+        assert loc