ngio 0.5.0a2__py3-none-any.whl → 0.5.0b1__py3-none-any.whl

ngio/utils/_zarr_utils.py

@@ -1,19 +1,22 @@
 """Common utilities for working with Zarr groups in consistent ways."""
 
+import json
 import warnings
 from pathlib import Path
 from typing import Literal
 
+import dask.array as da
 import fsspec
 import zarr
 from filelock import BaseFileLock, FileLock
+from pydantic_zarr.v2 import ArraySpec as AnyArraySpecV2
+from pydantic_zarr.v3 import ArraySpec as AnyArraySpecV3
 from zarr.abc.store import Store
 from zarr.errors import ContainsGroupError
-from zarr.storage import FsspecStore, LocalStore, MemoryStore
+from zarr.storage import FsspecStore, LocalStore, MemoryStore, ZipStore
 
 from ngio.utils._cache import NgioCache
 from ngio.utils._errors import (
-    NgioError,
     NgioFileExistsError,
     NgioFileNotFoundError,
     NgioValueError,
@@ -24,7 +27,13 @@ AccessModeLiteral = Literal["r", "r+", "w", "w-", "a"]
 # but to make sure we can handle the store correctly
 # we need to be more restrictive
 NgioSupportedStore = (
-    str | Path | fsspec.mapping.FSMap | FsspecStore | MemoryStore | LocalStore
+    str
+    | Path
+    | fsspec.mapping.FSMap
+    | FsspecStore
+    | MemoryStore
+    | LocalStore
+    | ZipStore
 )
 GenericStore = Store | NgioSupportedStore
 StoreOrGroup = GenericStore | zarr.Group
@@ -125,6 +134,7 @@ class ZarrGroupHandler:
 
         self._group_cache: NgioCache[zarr.Group] = NgioCache(use_cache=cache)
         self._array_cache: NgioCache[zarr.Array] = NgioCache(use_cache=cache)
+        self._handlers_cache: NgioCache[ZarrGroupHandler] = NgioCache(use_cache=cache)
         self._lock: tuple[Path, BaseFileLock] | None = None
 
     def __repr__(self) -> str:
@@ -144,8 +154,17 @@ class ZarrGroupHandler:
         """Return the store path."""
         if isinstance(self.store, LocalStore):
             return (self.store.root / self.group.path).as_posix()
-        if isinstance(self.store, FsspecStore):
-            return self.store.fs.map.root_path
+        elif isinstance(self.store, FsspecStore):
+            return f"{self.store.path}/{self.group.path}"
+        elif isinstance(self.store, ZipStore):
+            return (self.store.path / self.group.path).as_posix()
+        elif isinstance(self.store, MemoryStore):
+            return None
+        warnings.warn(
+            f"Cannot determine full URL for store type {type(self.store)}. ",
+            UserWarning,
+            stacklevel=2,
+        )
         return None
 
     @property
@@ -325,25 +344,6 @@ class ZarrGroupHandler:
         self._group_cache.set(path, group, overwrite=overwrite)
         return group
 
-    def safe_get_group(
-        self, path: str, create_mode: bool = False
-    ) -> tuple[bool, zarr.Group | NgioError]:
-        """Get a group from the group.
-
-        Args:
-            path (str): The path to the group.
-            create_mode (bool): If True, create the group if it does not exist.
-
-        Returns:
-            zarr.Group | None: The Zarr group or None if it does not exist
-                or an error occurs.
-
-        """
-        try:
-            return True, self.get_group(path, create_mode)
-        except NgioError as e:
-            return False, e
-
     def get_array(self, path: str) -> zarr.Array:
         """Get an array from the group."""
         array = self._array_cache.get(path)
@@ -358,47 +358,49 @@ class ZarrGroupHandler:
             raise NgioValueError(f"The object at {path} is not an array, but a group.")
         raise NgioFileNotFoundError(f"No array found at {path}")
 
-    def derive_handler(
+    def get_handler(
         self,
         path: str,
+        create_mode: bool = True,
         overwrite: bool = False,
     ) -> "ZarrGroupHandler":
-        """Derive a new handler from the current handler.
+        """Get a new handler for a group in the current handler group.
 
         Args:
             path (str): The path to the group.
+            create_mode (bool): If True, create the group if it does not exist.
             overwrite (bool): If True, overwrite the group if it exists.
         """
-        group = self.get_group(path, create_mode=True, overwrite=overwrite)
-        return ZarrGroupHandler(
-            store=group, zarr_format=self.zarr_format, cache=self.use_cache, mode="r+"
+        handler = self._handlers_cache.get(path)
+        if handler is not None:
+            return handler
+        group = self.get_group(path, create_mode=create_mode, overwrite=overwrite)
+        mode = "r" if group.read_only else "r+"
+        handler = ZarrGroupHandler(
+            store=group, zarr_format=self.zarr_format, cache=self.use_cache, mode=mode
         )
+        self._handlers_cache.set(path, handler)
+        return handler
 
-    def safe_derive_handler(
-        self,
-        path: str,
-        overwrite: bool = False,
-    ) -> tuple[bool, "ZarrGroupHandler | NgioError"]:
-        """Derive a new handler from the current handler."""
-        try:
-            return True, self.derive_handler(path, overwrite=overwrite)
-        except NgioError as e:
-            return False, e
+    @property
+    def is_listable(self) -> bool:
+        return is_group_listable(self.group)
 
-    def copy_handler(self, handler: "ZarrGroupHandler") -> None:
+    def delete_group(self, path: str) -> None:
+        """Delete a group from the current group.
+
+        Args:
+            path (str): The path to the group to delete.
+        """
+        if self.group.read_only:
+            raise NgioValueError("Cannot delete a group in read only mode.")
+        self.group.__delitem__(path)
+        self._group_cache._cache.pop(path, None)
+        self._handlers_cache._cache.pop(path, None)
+
+    def copy_group(self, dest_group: zarr.Group):
         """Copy the group to a new store."""
-        _, n_skipped, _ = zarr.copy_store(
-            source=self.group.store,
-            dest=handler.group.store,
-            source_path=self.group.path,
-            dest_path=handler.group.path,
-            if_exists="replace",
-        )
-        if n_skipped > 0:
-            raise NgioValueError(
-                f"Error copying group to {handler.full_url}, "
-                f"#{n_skipped} files where skipped."
-            )
+        copy_group(self.group, dest_group)
 
 
 def find_dimension_separator(array: zarr.Array) -> Literal[".", "/"]:
@@ -417,8 +419,116 @@ def find_dimension_separator(array: zarr.Array) -> Literal[".", "/"]:
     else:
         separator = array.metadata.chunk_key_encoding
         if not isinstance(separator, DefaultChunkKeyEncoding):
-            raise ValueError(
+            raise NgioValueError(
                 "Only DefaultChunkKeyEncoding is supported in this example."
             )
         separator = separator.separator
     return separator
+
+
+def is_group_listable(group: zarr.Group) -> bool:
+    """Check if a Zarr group is listable.
+
+    A group is considered listable if it contains at least one array or subgroup.
+
+    Args:
+        group (zarr.Group): The Zarr group to check.
+
+    Returns:
+        bool: True if the group is listable, False otherwise.
+    """
+    if not group.store.supports_listing:
+        # If the store does not support listing
+        # then for sure it is not listable
+        return False
+    try:
+        next(group.keys())
+        return True
+    except StopIteration:
+        # Group is listable but empty
+        return True
+    except Exception as _:
+        # Some stores may raise errors when listing
+        # consider those not listable
+        return False
+
+
+def _make_sync_fs(fs: fsspec.AbstractFileSystem) -> fsspec.AbstractFileSystem:
+    fs_dict = json.loads(fs.to_json())
+    fs_dict["asynchronous"] = False
+    return fsspec.AbstractFileSystem.from_json(json.dumps(fs_dict))
+
+
+def _get_mapper(store: LocalStore | FsspecStore, path: str):
+    if isinstance(store, LocalStore):
+        fs = fsspec.filesystem("file")
+        full_path = (store.root / path).as_posix()
+    else:
+        fs = _make_sync_fs(store.fs)
+        full_path = f"{store.path}/{path}"
+    return fs.get_mapper(full_path)
+
+
+def _fsspec_copy(
+    src_fs: LocalStore | FsspecStore,
+    src_path: str,
+    dest_fs: LocalStore | FsspecStore,
+    dest_path: str,
+):
+    src_mapper = _get_mapper(src_fs, src_path)
+    dest_mapper = _get_mapper(dest_fs, dest_path)
+    for key in src_mapper.keys():
+        dest_mapper[key] = src_mapper[key]
+
+
+def _zarr_python_copy(src_group: zarr.Group, dest_group: zarr.Group):
+    # Copy attributes
+    dest_group.attrs.put(src_group.attrs.asdict())
+    # Copy arrays
+    for name, array in src_group.arrays():
+        if array.metadata.zarr_format == 2:
+            spec = AnyArraySpecV2.from_zarr(array)
+        else:
+            spec = AnyArraySpecV3.from_zarr(array)
+        dst = spec.to_zarr(
+            store=dest_group.store,
+            path=f"{dest_group.path}/{name}",
+            overwrite=True,
+        )
+        if array.ndim > 0:
+            dask_array = da.from_zarr(array)
+            da.to_zarr(dask_array, dst, overwrite=False)
+    # Copy subgroups
+    for name, subgroup in src_group.groups():
+        dest_subgroup = dest_group.create_group(name, overwrite=True)
+        _zarr_python_copy(subgroup, dest_subgroup)
+
+
+def copy_group(
+    src_group: zarr.Group, dest_group: zarr.Group, suppress_warnings: bool = False
+):
+    if src_group.metadata.zarr_format != dest_group.metadata.zarr_format:
+        raise NgioValueError(
+            "Different Zarr format versions between source and destination, "
+            "cannot copy."
+        )
+
+    if not is_group_listable(src_group):
+        raise NgioValueError("Source group is not listable, cannot copy.")
+
+    if dest_group.read_only:
+        raise NgioValueError("Destination group is read only, cannot copy.")
+    if isinstance(src_group.store, LocalStore | FsspecStore) and isinstance(
+        dest_group.store, LocalStore | FsspecStore
+    ):
+        _fsspec_copy(src_group.store, src_group.path, dest_group.store, dest_group.path)
+        return
+    if not suppress_warnings:
+        warnings.warn(
+            "Fsspec copy not possible, falling back to Zarr Python API for the copy. "
+            "This will preserve some tabular data non-zarr native (parquet, and csv), "
+            "and it will be slower for large datasets.",
+            UserWarning,
+            stacklevel=2,
+        )
+    _zarr_python_copy(src_group, dest_group)

{ngio-0.5.0a2.dist-info → ngio-0.5.0b1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.5.0a2
+Version: 0.5.0b1
 Summary: Next Generation file format IO
 Project-URL: homepage, https://github.com/BioVisionCenter/ngio
 Project-URL: repository, https://github.com/BioVisionCenter/ngio
@@ -31,7 +31,6 @@ Requires-Dist: pydantic
 Requires-Dist: requests
 Requires-Dist: zarr>3
 Provides-Extra: dev
-Requires-Dist: devtools; extra == 'dev'
 Requires-Dist: matplotlib; extra == 'dev'
 Requires-Dist: mypy; extra == 'dev'
 Requires-Dist: napari; extra == 'dev'
@@ -60,8 +59,13 @@ Requires-Dist: rich; extra == 'docs'
 Requires-Dist: scikit-image; extra == 'docs'
 Requires-Dist: tabulate; extra == 'docs'
 Provides-Extra: test
+Requires-Dist: boto; extra == 'test'
+Requires-Dist: devtools; extra == 'test'
+Requires-Dist: moto[server]; extra == 'test'
 Requires-Dist: pytest; extra == 'test'
 Requires-Dist: pytest-cov; extra == 'test'
+Requires-Dist: pytest-httpserver; extra == 'test'
+Requires-Dist: s3fs; extra == 'test'
 Requires-Dist: scikit-image; extra == 'test'
 Description-Content-Type: text/markdown
 

ngio-0.5.0b1.dist-info/RECORD

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+ngio/tables/v1/_condition_table.py,sha256=T0Uq5BKkmMoEspt_Rx0U99Ow6S9GAMZDHqvUO5obCAM,1780
+ngio/tables/v1/_feature_table.py,sha256=n9uMHwoBh-_dlOhUXCFbmAjXFVXncNCR3SjE2qzXI68,3821
+ngio/tables/v1/_generic_table.py,sha256=1ktJHeuv7U1g5Z8PFUuTkCjOzcYMQd8xegKHKUedJB8,1240
+ngio/tables/v1/_roi_table.py,sha256=DuKJlDmtQtLOfL0g4CSdncfm4hBsKWG6F6fkMUpt4Nk,17821
+ngio/transforms/__init__.py,sha256=JA0-Ui7skbXkm9ofN-AEhU1FTLutkMkwTdVD-310frQ,113
+ngio/transforms/_zoom.py,sha256=otyE-vxFnywUJ8U4mHjat-bNG_7_jv62ckTpqDMxyVQ,550
+ngio/utils/__init__.py,sha256=1eIInpFEEWQtMeGaRhAyVjqSKWUCuksMkx2cqg9D9nI,987
+ngio/utils/_cache.py,sha256=Ey9fgc_BTdMyqg6c80C0CuGDhOafln8-3e_1MQ0MFzw,1283
+ngio/utils/_datasets.py,sha256=6GtxfPkjutNaeg5BHuJDBP0GudvQXHLU6mmHp_o0bGA,5650
+ngio/utils/_errors.py,sha256=pKQ12LUjQLYE1nUawemA5h7HsgznjaSvV1n2PQU33N0,759
+ngio/utils/_fractal_fsspec_store.py,sha256=RdcCFOgHexRKX9zZvJV5RI-5OPc7VOPS6q_IeRxm24I,1548
+ngio/utils/_zarr_utils.py,sha256=nvSsdKDS9EGVFdk2mZl4TO1aSPVPbz5z3UzSLkkgw5o,17914
+ngio-0.5.0b1.dist-info/METADATA,sha256=_OgT6FBzjh1aFFXqlbPRXNivN8nMQC9boocEPIZ8vRs,6294
+ngio-0.5.0b1.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+ngio-0.5.0b1.dist-info/licenses/LICENSE,sha256=UgN_a1QCeNh9rZWfz-wORQFxE3elQzLWPQaoK6N6fxQ,1502
+ngio-0.5.0b1.dist-info/RECORD,,

{ngio-0.5.0a2.dist-info → ngio-0.5.0b1.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: hatchling 1.27.0
+Generator: hatchling 1.28.0
 Root-Is-Purelib: true
 Tag: py3-none-any