Use FsspecStore.from_url() for creation

ome_zarr/format.py

@@ -5,7 +5,7 @@
 from collections.abc import Iterator
 from typing import Any, Optional
 
-from zarr.storage import FSStore
+from zarr.storage import FsspecStore
 
 LOGGER = logging.getLogger("ome_zarr.format")
 
@@ -60,7 +60,7 @@ def matches(self, metadata: dict) -> bool:  # pragma: no cover
         raise NotImplementedError()
 
     @abstractmethod
-    def init_store(self, path: str, mode: str = "r") -> FSStore:
+    def init_store(self, path: str, mode: str = "r") -> FsspecStore:
         raise NotImplementedError()
 
     # @abstractmethod
@@ -134,9 +134,13 @@ def matches(self, metadata: dict) -> bool:
         LOGGER.debug("%s matches %s?", self.version, version)
         return version == self.version
 
-    def init_store(self, path: str, mode: str = "r") -> FSStore:
-        store = FSStore(path, mode=mode, dimension_separator=".")
-        LOGGER.debug("Created legacy flat FSStore(%s, %s)", path, mode)
+    def init_store(self, path: str, mode: str = "r") -> FsspecStore:
+        storage_options: dict[str, Any] = {}
+        # TODO: dimension_separator: "."
+        store = FsspecStore.from_url(
+            path, read_only=(mode == "r"), storage_options=storage_options
+        )
+        LOGGER.debug("Created legacy flat FsspecStore(%s, %s)", path, mode)
         return store
 
     def generate_well_dict(
@@ -180,30 +184,22 @@ class FormatV02(FormatV01):
     def version(self) -> str:
         return "0.2"
 
-    def init_store(self, path: str, mode: str = "r") -> FSStore:
+    def init_store(self, path: str, mode: str = "r") -> FsspecStore:
         """
         Not ideal. Stores should remain hidden
         TODO: could also check dimension_separator
         """
 
-        kwargs = {
-            "dimension_separator": "/",
-            "normalize_keys": False,
-        }
-
-        mkdir = True
+        print("format.init_store...", path, mode)
+        read_only = False
         if "r" in mode or path.startswith(("http", "s3")):
-            # Could be simplified on the fsspec side
-            mkdir = False
-        if mkdir:
-            kwargs["auto_mkdir"] = True
-
-        store = FSStore(
-            path,
-            mode=mode,
-            **kwargs,
+            read_only = True
+
+        store = FsspecStore.from_url(
+            path, read_only=read_only
         )  # TODO: open issue for using Path
-        LOGGER.debug("Created nested FSStore(%s, %s, %s)", path, mode, kwargs)
+        LOGGER.debug("Created nested FsspecStore(%s, %s, %s)", path, mode)
+        print("...format.init_store: store:", store)
         return store
 
 

ome_zarr/io.py

@@ -10,7 +10,7 @@
 from urllib.parse import urljoin
 
 import dask.array as da
-from zarr.storage import FSStore
+from zarr.storage import FsspecStore
 
 from .format import CurrentFormat, Format, detect_format
 from .types import JSONDict
@@ -20,7 +20,7 @@
 
 class ZarrLocation:
     """
-    IO primitive for reading and writing Zarr data. Uses FSStore for all
+    IO primitive for reading and writing Zarr data. Uses FsspecStore for all
     data access.
 
     No assumptions about the existence of the given path string are made.
@@ -29,7 +29,7 @@ class ZarrLocation:
 
     def __init__(
         self,
-        path: Union[Path, str, FSStore],
+        path: Union[Path, str, FsspecStore],
         mode: str = "r",
         fmt: Format = CurrentFormat(),
     ) -> None:
@@ -40,16 +40,18 @@ def __init__(
             self.__path = str(path.resolve())
         elif isinstance(path, str):
             self.__path = path
-        elif isinstance(path, FSStore):
+        elif isinstance(path, FsspecStore):
             self.__path = path.path
         else:
             raise TypeError(f"not expecting: {type(path)}")
 
         loader = fmt
         if loader is None:
             loader = CurrentFormat()
-        self.__store: FSStore = (
-            path if isinstance(path, FSStore) else loader.init_store(self.__path, mode)
+        self.__store: FsspecStore = (
+            path
+            if isinstance(path, FsspecStore)
+            else loader.init_store(self.__path, mode)
         )
 
         self.__init_metadata()
@@ -104,7 +106,7 @@ def path(self) -> str:
         return self.__path
 
     @property
-    def store(self) -> FSStore:
+    def store(self) -> FsspecStore:
         """Return the initialized store for this location"""
         assert self.__store is not None
         return self.__store

ome_zarr/scale.py

@@ -138,7 +138,7 @@ def __assert_values(self, pyramid: list[np.ndarray]) -> None:
 
     def __create_group(
         self, store: MutableMapping, base: np.ndarray, pyramid: list[np.ndarray]
-    ) -> zarr.hierarchy.Group:
+    ) -> zarr.Group:
         """Create group and datasets."""
         grp = zarr.group(store)
         grp.create_dataset("base", data=base)

ome_zarr/writer.py

@@ -190,7 +190,7 @@ def write_multiscale(
     :param pyramid:
         The image data to save. Largest level first. All image arrays MUST be up to
         5-dimensional with dimensions ordered (t, c, z, y, x)
-    :type group: :class:`zarr.hierarchy.Group`
+    :type group: :class:`zarr.Group`
     :param group: The group within the zarr store to store the data in
     :type chunks: int or tuple of ints, optional
     :param chunks:
@@ -305,7 +305,7 @@ def write_multiscales_metadata(
     """
     Write the multiscales metadata in the group.
 
-    :type group: :class:`zarr.hierarchy.Group`
+    :type group: :class:`zarr.Group`
     :param group: The group within the zarr store to write the metadata in.
     :type datasets: list of dicts
     :param datasets:
@@ -385,7 +385,7 @@ def write_plate_metadata(
     """
     Write the plate metadata in the group.
 
-    :type group: :class:`zarr.hierarchy.Group`
+    :type group: :class:`zarr.Group`
     :param group: The group within the zarr store to write the metadata in.
     :type rows: list of str
     :param rows: The list of names for the plate rows.
@@ -428,7 +428,7 @@ def write_well_metadata(
     """
     Write the well metadata in the group.
 
-    :type group: :class:`zarr.hierarchy.Group`
+    :type group: :class:`zarr.Group`
     :param group: The group within the zarr store to write the metadata in.
     :type images: list of dict
     :param images: The list of dictionaries for all fields of views.
@@ -465,7 +465,7 @@ def write_image(
       if the scaler argument is non-None.
       Image array MUST be up to 5-dimensional with dimensions
       ordered (t, c, z, y, x).  Image can be a numpy or dask Array.
-    :type group: :class:`zarr.hierarchy.Group`
+    :type group: :class:`zarr.Group`
     :param group: The group within the zarr store to write the metadata in.
     :type scaler: :class:`ome_zarr.scale.Scaler`
     :param scaler:
@@ -664,7 +664,7 @@ def write_label_metadata(
     The label data must have been written to a sub-group,
     with the same name as the second argument.
 
-    :type group: :class:`zarr.hierarchy.Group`
+    :type group: :class:`zarr.Group`
     :param group: The group within the zarr store to write the metadata in.
     :type name: str
     :param name: The name of the label sub-group.
@@ -722,7 +722,7 @@ def write_multiscale_labels(
       the image label data to save. Largest level first
       All image arrays MUST be up to 5-dimensional with dimensions
       ordered (t, c, z, y, x)
-    :type group: :class:`zarr.hierarchy.Group`
+    :type group: :class:`zarr.Group`
     :param group: The group within the zarr store to write the metadata in.
     :type name: str, optional
     :param name: The name of this labels data.
@@ -811,7 +811,7 @@ def write_labels(
       if the scaler argument is non-None.
       Label array MUST be up to 5-dimensional with dimensions
       ordered (t, c, z, y, x)
-    :type group: :class:`zarr.hierarchy.Group`
+    :type group: :class:`zarr.Group`
     :param group: The group within the zarr store to write the metadata in.
     :type name: str, optional
     :param name: The name of this labels data.