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477 lines (418 loc) · 16.5 KB
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from __future__ import annotations
import posixpath
import warnings
from contextlib import suppress
from typing import TYPE_CHECKING, Any
from packaging.version import parse as parse_version
from zarr.abc.store import (
ByteRequest,
OffsetByteRequest,
RangeByteRequest,
Store,
SuffixByteRequest,
)
from zarr.core.buffer import Buffer
from zarr.errors import ZarrUserWarning
from zarr.storage._utils import _dereference_path
if TYPE_CHECKING:
from collections.abc import AsyncIterator, Iterable
from fsspec import AbstractFileSystem
from fsspec.asyn import AsyncFileSystem
from fsspec.mapping import FSMap
from zarr.core.buffer import BufferPrototype
ALLOWED_EXCEPTIONS: tuple[type[Exception], ...] = (
FileNotFoundError,
IsADirectoryError,
NotADirectoryError,
)
def _make_async(fs: AbstractFileSystem) -> AsyncFileSystem:
"""Convert a sync FSSpec filesystem to an async FFSpec filesystem
If the filesystem class supports async operations, a new async instance is created
from the existing instance.
If the filesystem class does not support async operations, the existing instance
is wrapped with AsyncFileSystemWrapper.
"""
import fsspec
fsspec_version = parse_version(fsspec.__version__)
if fs.async_impl and fs.asynchronous:
# Already an async instance of an async filesystem, nothing to do
return fs
if fs.async_impl:
# Convert sync instance of an async fs to an async instance. Reuse the original
# constructor arguments rather than round-tripping through JSON, since storage
# options may hold objects that are not JSON-serializable (e.g. credentials).
return type(fs)(*fs.storage_args, **{**fs.storage_options, "asynchronous": True})
if fsspec_version < parse_version("2024.12.0"):
raise ImportError(
f"The filesystem '{fs}' is synchronous, and the required "
"AsyncFileSystemWrapper is not available. Upgrade fsspec to version "
"2024.12.0 or later to enable this functionality."
)
from fsspec.implementations.asyn_wrapper import AsyncFileSystemWrapper
return AsyncFileSystemWrapper(fs, asynchronous=True)
class FsspecStore(Store):
"""
Store for remote data based on FSSpec.
Parameters
----------
fs : AsyncFileSystem
The Async FSSpec filesystem to use with this store.
read_only : bool
Whether the store is read-only
path : str
The root path of the store. This should be a relative path and must not include the
filesystem scheme.
allowed_exceptions : tuple[type[Exception], ...]
When fetching data, these cases will be deemed to correspond to missing keys.
Attributes
----------
fs
allowed_exceptions
supports_writes
supports_deletes
supports_listing
Raises
------
TypeError
If the Filesystem does not support async operations.
ValueError
If the path argument includes a scheme.
Warns
-----
ZarrUserWarning
If the file system (fs) was not created with `asynchronous=True`.
Notes
-----
Closing the store does not close the underlying filesystem or its network
session. fsspec caches and shares filesystem instances across callers, so
the store cannot know whether it is the only user, and closing a shared
session would break other stores. The filesystem's lifecycle belongs to
whoever created it; use fsspec's own tools (e.g. `clear_instance_cache`)
to release it.
See Also
--------
FsspecStore.from_upath
FsspecStore.from_url
"""
# based on FSSpec
supports_writes: bool = True
supports_deletes: bool = True
supports_listing: bool = True
fs: AsyncFileSystem
allowed_exceptions: tuple[type[Exception], ...]
path: str
def __init__(
self,
fs: AsyncFileSystem,
read_only: bool = False,
path: str = "/",
allowed_exceptions: tuple[type[Exception], ...] = ALLOWED_EXCEPTIONS,
) -> None:
super().__init__(read_only=read_only)
self.fs = fs
self.path = path
self.allowed_exceptions = allowed_exceptions
if not self.fs.async_impl:
raise TypeError("Filesystem needs to support async operations.")
if not self.fs.asynchronous:
warnings.warn(
f"fs ({fs}) was not created with `asynchronous=True`, this may lead to surprising behavior",
category=ZarrUserWarning,
stacklevel=2,
)
@classmethod
def from_upath(
cls,
upath: Any,
read_only: bool = False,
allowed_exceptions: tuple[type[Exception], ...] = ALLOWED_EXCEPTIONS,
) -> FsspecStore:
"""
Create an FsspecStore from a upath object.
Parameters
----------
upath : UPath
The upath to the root of the store.
read_only : bool
Whether the store is read-only, defaults to False.
allowed_exceptions : tuple, optional
The exceptions that are allowed to be raised when accessing the
store. Defaults to ALLOWED_EXCEPTIONS.
Returns
-------
FsspecStore
"""
# A UPath hands back a filesystem in whatever mode it was constructed with, which is
# synchronous unless the caller passed asynchronous=True. Route it through _make_async so
# that sync-mode instances of async filesystems are re-created in async mode, and
# genuinely synchronous filesystems are wrapped.
return cls(
fs=_make_async(upath.fs),
path=upath.path.rstrip("/"),
read_only=read_only,
allowed_exceptions=allowed_exceptions,
)
@classmethod
def from_mapper(
cls,
fs_map: FSMap,
read_only: bool = False,
allowed_exceptions: tuple[type[Exception], ...] = ALLOWED_EXCEPTIONS,
) -> FsspecStore:
"""
Create an FsspecStore from an FSMap object.
Parameters
----------
fs_map : FSMap
Fsspec mutable mapping object.
read_only : bool
Whether the store is read-only, defaults to False.
allowed_exceptions : tuple, optional
The exceptions that are allowed to be raised when accessing the
store. Defaults to ALLOWED_EXCEPTIONS.
Returns
-------
FsspecStore
"""
fs = _make_async(fs_map.fs)
return cls(
fs=fs,
path=fs_map.root,
read_only=read_only,
allowed_exceptions=allowed_exceptions,
)
@classmethod
def from_url(
cls,
url: str,
storage_options: dict[str, Any] | None = None,
read_only: bool = False,
allowed_exceptions: tuple[type[Exception], ...] = ALLOWED_EXCEPTIONS,
) -> FsspecStore:
"""
Create an FsspecStore from a URL. The type of store is determined from the URL scheme.
Parameters
----------
url : str
The URL to the root of the store.
storage_options : dict, optional
The options to pass to fsspec when creating the filesystem.
read_only : bool
Whether the store is read-only, defaults to False.
allowed_exceptions : tuple, optional
The exceptions that are allowed to be raised when accessing the
store. Defaults to ALLOWED_EXCEPTIONS.
Returns
-------
FsspecStore
"""
try:
from fsspec import url_to_fs
except ImportError:
# before fsspec==2024.3.1
from fsspec.core import url_to_fs
opts = storage_options or {}
opts = {"asynchronous": True, **opts}
fs, path = url_to_fs(url, **opts)
if not fs.async_impl:
fs = _make_async(fs)
return cls(fs=fs, path=path, read_only=read_only, allowed_exceptions=allowed_exceptions)
def with_read_only(self, read_only: bool = False) -> FsspecStore:
# docstring inherited
return type(self)(
fs=self.fs,
path=self.path,
allowed_exceptions=self.allowed_exceptions,
read_only=read_only,
)
async def clear(self) -> None:
# docstring inherited
try:
for subpath in await self.fs._find(self.path, withdirs=True):
if subpath != self.path:
await self.fs._rm(subpath, recursive=True)
except FileNotFoundError:
pass
def __repr__(self) -> str:
return f"<FsspecStore({type(self.fs).__name__}, {self.path})>"
def __eq__(self, other: object) -> bool:
return (
isinstance(other, type(self))
and self.path == other.path
and self.read_only == other.read_only
and self.fs == other.fs
)
async def get(
self,
key: str,
prototype: BufferPrototype,
byte_range: ByteRequest | None = None,
) -> Buffer | None:
# docstring inherited
if not self._is_open:
await self._open()
path = _dereference_path(self.path, key)
try:
if byte_range is None:
value = prototype.buffer.from_bytes(await self.fs._cat_file(path))
elif isinstance(byte_range, RangeByteRequest):
value = prototype.buffer.from_bytes(
await self.fs._cat_file(
path,
start=byte_range.start,
end=byte_range.end,
)
)
elif isinstance(byte_range, OffsetByteRequest):
value = prototype.buffer.from_bytes(
await self.fs._cat_file(path, start=byte_range.offset, end=None)
)
elif isinstance(byte_range, SuffixByteRequest):
value = prototype.buffer.from_bytes(
await self.fs._cat_file(path, start=-byte_range.suffix, end=None)
)
else:
raise ValueError(f"Unexpected byte_range, got {byte_range}.")
except self.allowed_exceptions:
return None
except OSError as e:
if "not satisfiable" in str(e):
# this is an s3-specific condition we probably don't want to leak
return prototype.buffer.from_bytes(b"")
raise
else:
return value
async def set(
self,
key: str,
value: Buffer,
byte_range: tuple[int, int] | None = None,
) -> None:
# docstring inherited
if not self._is_open:
await self._open()
self._check_writable()
if not isinstance(value, Buffer):
raise TypeError(
f"FsspecStore.set(): `value` must be a Buffer instance. Got an instance of {type(value)} instead."
)
path = _dereference_path(self.path, key)
# write data
if byte_range:
raise NotImplementedError
await self.fs._pipe_file(path, value.to_bytes())
async def delete(self, key: str) -> None:
# docstring inherited
self._check_writable()
path = _dereference_path(self.path, key)
try:
await self.fs._rm(path)
except FileNotFoundError:
pass
except self.allowed_exceptions:
pass
async def delete_dir(self, prefix: str) -> None:
# docstring inherited
if not self.supports_deletes:
raise NotImplementedError(
"This method is only available for stores that support deletes."
)
self._check_writable()
path_to_delete = _dereference_path(self.path, prefix)
with suppress(*self.allowed_exceptions):
await self.fs._rm(path_to_delete, recursive=True)
async def exists(self, key: str) -> bool:
# docstring inherited
path = _dereference_path(self.path, key)
exists: bool = await self.fs._exists(path)
return exists
async def get_partial_values(
self,
prototype: BufferPrototype,
key_ranges: Iterable[tuple[str, ByteRequest | None]],
) -> list[Buffer | None]:
# docstring inherited
# Materialise first: key_ranges may be a one-shot iterable, so a bare
# truthiness check (e.g. `if key_ranges`) would be unreliable for an
# empty generator. _cat_ranges also expects lists of paths/starts/stops.
key_ranges = list(key_ranges)
if not key_ranges:
return []
paths: list[str] = []
starts: list[int | None] = []
stops: list[int | None] = []
for key, byte_range in key_ranges:
paths.append(_dereference_path(self.path, key))
if byte_range is None:
starts.append(None)
stops.append(None)
elif isinstance(byte_range, RangeByteRequest):
starts.append(byte_range.start)
stops.append(byte_range.end)
elif isinstance(byte_range, OffsetByteRequest):
starts.append(byte_range.offset)
stops.append(None)
elif isinstance(byte_range, SuffixByteRequest):
starts.append(-byte_range.suffix)
stops.append(None)
else:
raise ValueError(f"Unexpected byte_range, got {byte_range}.")
# TODO: expectations for exceptions or missing keys?
res = await self.fs._cat_ranges(paths, starts, stops, on_error="return")
# the following is an s3-specific condition we probably don't want to leak
res = [b"" if (isinstance(r, OSError) and "not satisfiable" in str(r)) else r for r in res]
for r in res:
if isinstance(r, Exception) and not isinstance(r, self.allowed_exceptions):
raise r
return [None if isinstance(r, Exception) else prototype.buffer.from_bytes(r) for r in res]
async def list(self) -> AsyncIterator[str]:
# docstring inherited
allfiles = await self.fs._find(self.path, detail=False, withdirs=False)
for onefile in (a.removeprefix(f"{self.path}/") for a in allfiles):
yield onefile
async def list_dir(self, prefix: str) -> AsyncIterator[str]:
# docstring inherited
# A store path of "" or "/" is the root of the filesystem. Joining it with a
# leading "/" gives "/a" or "//a", which ReferenceFileSystem does not find,
# since it keys entries by bare names like "a/zarr.json".
root = self.path.rstrip("/")
prefix = f"{root}/{prefix.rstrip('/')}" if root else prefix.rstrip("/")
try:
allfiles = await self.fs._ls(prefix, detail=False)
except FileNotFoundError:
return
seen: set[str] = set()
for onefile in allfiles:
name = onefile.replace(f"{prefix}/", "").removeprefix(self.path).removeprefix("/")
if onefile.startswith(("http://", "https://")):
# An HTTP listing is scraped from the links on an HTML page. In-page anchors
# and queries name the page itself, not an object, and relative links such
# as "./a" need normalizing.
if "#" in name or "?" in name:
continue
name = posixpath.normpath(name)
# Only direct children, each once: an HTTP listing marks directories with a
# trailing "/", and a link back to the listed directory reduces to "" or ".".
name = name.rstrip("/")
if name in ("", ".", "..") or "/" in name or name in seen:
continue
seen.add(name)
yield name
async def list_prefix(self, prefix: str) -> AsyncIterator[str]:
# docstring inherited
# Same root handling as list_dir.
root = self.path.rstrip("/")
for onefile in await self.fs._find(
f"{root}/{prefix}" if root else prefix, detail=False, maxdepth=None, withdirs=False
):
yield onefile.removeprefix(f"{root}/") if root else onefile.removeprefix("/")
async def getsize(self, key: str) -> int:
path = _dereference_path(self.path, key)
info = await self.fs._info(path)
size = info.get("size")
if size is None:
# Not all filesystems support size. Fall back to reading the entire object
return await super().getsize(key)
else:
# fsspec doesn't have typing. We'll need to assume or verify this is true
return int(size)