ngio 0.2.1__py3-none-any.whl → 0.2.3__py3-none-any.whl

ngio/utils/_zarr_utils.py

@@ -8,7 +8,7 @@ import fsspec
 import zarr
 from filelock import BaseFileLock, FileLock
 from zarr.errors import ContainsGroupError, GroupNotFoundError
-from zarr.storage import DirectoryStore, FSStore, Store
+from zarr.storage import DirectoryStore, FSStore, MemoryStore, Store, StoreLike
 
 from ngio.utils import NgioFileExistsError, NgioFileNotFoundError, NgioValueError
 from ngio.utils._errors import NgioError
@@ -17,7 +17,9 @@ AccessModeLiteral = Literal["r", "r+", "w", "w-", "a"]
 # StoreLike is more restrictive than it could be
 # but to make sure we can handle the store correctly
 # we need to be more restrictive
-NgioSupportedStore = str | Path | fsspec.mapping.FSMap | FSStore | DirectoryStore
+NgioSupportedStore = (
+    str | Path | fsspec.mapping.FSMap | FSStore | DirectoryStore | MemoryStore
+)
 GenericStore = Store | NgioSupportedStore
 StoreOrGroup = GenericStore | zarr.Group
 
@@ -48,9 +50,7 @@ def _check_group(group: zarr.Group, mode: AccessModeLiteral) -> zarr.Group:
     return group
 
 
-def open_group_wrapper(
-    store: StoreOrGroup, mode: AccessModeLiteral
-) -> tuple[zarr.Group, NgioSupportedStore]:
+def open_group_wrapper(store: StoreOrGroup, mode: AccessModeLiteral) -> zarr.Group:
     """Wrapper around zarr.open_group with some additional checks.
 
     Args:
@@ -62,18 +62,11 @@ def open_group_wrapper(
     """
     if isinstance(store, zarr.Group):
         group = _check_group(store, mode)
-        if hasattr(group, "store_path"):
-            _store = group.store_path
-        if isinstance(group.store, DirectoryStore):
-            _store = group.store.path
-        else:
-            _store = group.store
-
-        _store = _check_store(_store)
-        return group, _store
+        _check_store(group.store)
+        return group
 
     try:
-        store = _check_store(store)
+        _check_store(store)
         group = zarr.open_group(store=store, mode=mode)
 
     except ContainsGroupError as e:
@@ -84,7 +77,7 @@ def open_group_wrapper(
     except GroupNotFoundError as e:
         raise NgioFileNotFoundError(f"No Zarr group found at {store}") from e
 
-    return group, store
+    return group
 
 
 class ZarrGroupHandler:
@@ -119,27 +112,29 @@ class ZarrGroupHandler:
                 "If you want to use the lock mechanism, you should not use the cache."
             )
 
-        _group, _store = open_group_wrapper(store, mode)
+        group = open_group_wrapper(store, mode)
+        _store = group.store
 
         # Make sure the cache is set in the attrs
         # in the same way as the cache in the handler
-        _group.attrs.cache = cache
+        group.attrs.cache = cache
 
         if parallel_safe:
-            if not isinstance(_store, str | Path):
+            if not isinstance(_store, DirectoryStore):
                 raise NgioValueError(
-                    "The store needs to be a path to use the lock mechanism."
+                    "The store needs to be a DirectoryStore to use the lock mechanism. "
+                    f"Instead, got {_store.__class__.__name__}."
                 )
-            self._lock_path = f"{_store}.lock"
+            store_path = Path(_store.path) / group.path
+            self._lock_path = store_path.with_suffix(".lock")
             self._lock = FileLock(self._lock_path, timeout=10)
 
         else:
             self._lock_path = None
             self._lock = None
 
-        self._group = _group
+        self._group = group
         self._mode = mode
-        self._store = _store
         self.use_cache = cache
         self._parallel_safe = parallel_safe
         self._cache = {}
@@ -148,19 +143,23 @@ class ZarrGroupHandler:
     def __repr__(self) -> str:
         """Return a string representation of the handler."""
         return (
-            f"ZarrGroupHandler(full_path={self.full_path}, mode={self.mode}, "
+            f"ZarrGroupHandler(full_url={self.full_url}, mode={self.mode}, "
             f"cache={self.use_cache}"
         )
 
     @property
-    def store(self) -> NgioSupportedStore:
+    def store(self) -> StoreLike:
         """Return the store of the group."""
-        return self._store
+        return self.group.store
 
     @property
-    def full_path(self) -> str:
+    def full_url(self) -> str | None:
         """Return the store path."""
-        return f"{self._store}/{self._group.path}"
+        if isinstance(self.store, DirectoryStore | FSStore):
+            _store_path = str(self.store.path)
+            _store_path = _store_path.rstrip("/")
+            return f"{self.store.path}/{self._group.path}"
+        return None
 
     @property
     def mode(self) -> AccessModeLiteral:
@@ -275,17 +274,25 @@ class ZarrGroupHandler:
         self,
         path: str,
         create_mode: bool = False,
+        overwrite: bool = False,
     ) -> zarr.Group:
         """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.
+            overwrite (bool): If True, overwrite the group if it exists.
 
         Returns:
             zarr.Group: The Zarr group.
 
         """
+        if overwrite and not create_mode:
+            raise NgioValueError("Cannot overwrite a group without create_mode=True.")
+
+        if overwrite:
+            return self.create_group(path, overwrite=overwrite)
+
         group = self._obj_get(path)
         if isinstance(group, zarr.Group):
             return group
@@ -361,9 +368,15 @@ class ZarrGroupHandler:
     def derive_handler(
         self,
         path: str,
+        overwrite: bool = False,
     ) -> "ZarrGroupHandler":
-        """Derive a new handler from the current handler."""
-        group = self.get_group(path, create_mode=True)
+        """Derive a new handler from the current handler.
+
+        Args:
+            path (str): The path to the group.
+            overwrite (bool): If True, overwrite the group if it exists.
+        """
+        group = self.get_group(path, create_mode=True, overwrite=overwrite)
         return ZarrGroupHandler(
             store=group,
             cache=self.use_cache,
@@ -375,10 +388,11 @@ class ZarrGroupHandler:
     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)
+            return True, self.derive_handler(path, overwrite=overwrite)
         except NgioError as e:
             return False, e
 
@@ -393,7 +407,7 @@ class ZarrGroupHandler:
         )
         if n_skipped > 0:
             raise NgioValueError(
-                f"Error copying group to {handler.full_path}, "
+                f"Error copying group to {handler.full_url}, "
                 f"#{n_skipped} files where skipped."
             )
 

{ngio-0.2.1.dist-info → ngio-0.2.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ngio
-Version: 0.2.1
+Version: 0.2.3
 Summary: Next Generation file format IO
 Project-URL: homepage, https://github.com/lorenzocerrone/ngio
 Project-URL: repository, https://github.com/lorenzocerrone/ngio
@@ -23,7 +23,9 @@ Requires-Dist: filelock
 Requires-Dist: numpy
 Requires-Dist: ome-zarr-models
 Requires-Dist: pandas>=1.2.0
+Requires-Dist: polars
 Requires-Dist: pooch
+Requires-Dist: pyarrow
 Requires-Dist: pydantic
 Requires-Dist: requests
 Requires-Dist: xarray

ngio-0.2.3.dist-info/RECORD

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ngio-0.2.1.dist-info/RECORD

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