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703 lines (582 loc) · 23.9 KB
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from __future__ import annotations
import os
import threading
import weakref
from logging import getLogger
from typing import TYPE_CHECKING, Any, Self
from zarr.abc.store import ByteRequest, Store
from zarr.core.buffer import Buffer, gpu
from zarr.core.buffer.core import default_buffer_prototype
from zarr.core.common import concurrent_map
from zarr.storage._utils import (
_join_paths,
_normalize_byte_range_index,
normalize_path,
parse_store_url,
)
if TYPE_CHECKING:
from collections.abc import AsyncIterator, Iterable, MutableMapping
from zarr.core.buffer import BufferPrototype
logger = getLogger(__name__)
def _copy_buffer(value: Buffer) -> Buffer:
"""Copy `value` so the store does not retain the caller's memory.
Encoding a chunk can hand the store a zero-copy view of the user's array
(an uncompressed write is the common case), and unlike stores that
serialize on write, this one keeps whatever it is given alive in a dict.
Without this copy a later mutation of the user's array would rewrite
chunks already committed to the store.
"""
return type(value).from_array_like(value.as_array_like().copy())
class MemoryStore(Store):
"""
Store for local memory.
Parameters
----------
store_dict : dict
Initial data
read_only : bool
Whether the store is read-only
Attributes
----------
supports_writes
supports_deletes
supports_listing
Notes
-----
Writes copy the buffer they are given, so the store never aliases the
caller's memory. Buffers passed via `store_dict` are the caller's
responsibility and are stored as-is.
"""
supports_writes: bool = True
supports_deletes: bool = True
supports_listing: bool = True
_store_dict: MutableMapping[str, Buffer]
def __init__(
self,
store_dict: MutableMapping[str, Buffer] | None = None,
*,
read_only: bool = False,
) -> None:
super().__init__(read_only=read_only)
if store_dict is None:
store_dict = {}
self._store_dict = store_dict
def with_read_only(self, read_only: bool = False) -> MemoryStore:
# docstring inherited
return type(self)(
store_dict=self._store_dict,
read_only=read_only,
)
async def clear(self) -> None:
# docstring inherited
self._store_dict.clear()
def __str__(self) -> str:
return f"memory://{id(self._store_dict)}"
def __repr__(self) -> str:
return f"MemoryStore('{self}')"
def __eq__(self, other: object) -> bool:
return (
isinstance(other, type(self))
and self._store_dict == other._store_dict
and self.read_only == other.read_only
)
# -------------------------------------------------------------------
# Synchronous store methods
# -------------------------------------------------------------------
def get_sync(
self,
key: str,
*,
prototype: BufferPrototype | None = None,
byte_range: ByteRequest | None = None,
) -> Buffer | None:
if prototype is None:
prototype = default_buffer_prototype()
if not self._is_open:
self._is_open = True
try:
value = self._store_dict[key]
start, stop = _normalize_byte_range_index(value, byte_range)
return prototype.buffer.from_buffer(value[start:stop])
except KeyError:
return None
def set_sync(self, key: str, value: Buffer) -> None:
self._check_writable()
if not self._is_open:
self._is_open = True
if not isinstance(value, Buffer):
raise TypeError(
f"MemoryStore.set(): `value` must be a Buffer instance. Got an instance of {type(value)} instead."
)
self._store_dict[key] = _copy_buffer(value)
def delete_sync(self, key: str) -> None:
self._check_writable()
if not self._is_open:
self._is_open = True
try:
del self._store_dict[key]
except KeyError:
logger.debug("Key %s does not exist.", key)
async def get(
self,
key: str,
prototype: BufferPrototype | None = None,
byte_range: ByteRequest | None = None,
) -> Buffer | None:
# docstring inherited
if prototype is None:
prototype = default_buffer_prototype()
if not self._is_open:
await self._open()
try:
value = self._store_dict[key]
start, stop = _normalize_byte_range_index(value, byte_range)
return prototype.buffer.from_buffer(value[start:stop])
except KeyError:
return None
async def get_partial_values(
self,
prototype: BufferPrototype,
key_ranges: Iterable[tuple[str, ByteRequest | None]],
) -> list[Buffer | None]:
# docstring inherited
# All the key-ranges arguments goes with the same prototype
async def _get(key: str, byte_range: ByteRequest | None) -> Buffer | None:
return await self.get(key, prototype=prototype, byte_range=byte_range)
return await concurrent_map(key_ranges, _get, limit=None)
async def exists(self, key: str) -> bool:
# docstring inherited
return key in self._store_dict
async def set(self, key: str, value: Buffer, byte_range: tuple[int, int] | None = None) -> None:
# docstring inherited
self._check_writable()
await self._ensure_open()
if not isinstance(value, Buffer):
raise TypeError(
f"MemoryStore.set(): `value` must be a Buffer instance. Got an instance of {type(value)} instead."
)
if byte_range is not None:
buf = self._store_dict[key]
buf[byte_range[0] : byte_range[1]] = value
self._store_dict[key] = buf
else:
self._store_dict[key] = _copy_buffer(value)
async def set_if_not_exists(self, key: str, value: Buffer) -> None:
# docstring inherited
self._check_writable()
await self._ensure_open()
self._store_dict.setdefault(key, _copy_buffer(value))
async def delete(self, key: str) -> None:
# docstring inherited
self._check_writable()
try:
del self._store_dict[key]
except KeyError:
logger.debug("Key %s does not exist.", key)
async def list(self) -> AsyncIterator[str]:
# docstring inherited
for key in self._store_dict:
yield key
async def list_prefix(self, prefix: str) -> AsyncIterator[str]:
# docstring inherited
# note: we materialize all dict keys into a list here so we can mutate the dict in-place (e.g. in delete_prefix)
for key in list(self._store_dict):
if key.startswith(prefix):
yield key
async def list_dir(self, prefix: str) -> AsyncIterator[str]:
# docstring inherited
prefix = prefix.rstrip("/")
if prefix == "":
keys_unique = {k.split("/")[0] for k in self._store_dict}
else:
# Our dictionary doesn't contain directory markers, but we want to include
# a pseudo directory when there's a nested item and we're listing an
# intermediate level.
keys_unique = {
key.removeprefix(f"{prefix}/").split("/")[0]
for key in self._store_dict
if key.startswith(f"{prefix}/") and key not in {prefix, f"{prefix}/"}
}
for key in keys_unique:
yield key
class GpuMemoryStore(MemoryStore):
"""
Store for GPU memory.
Stores every chunk in GPU memory irrespective of the original location.
The dictionary of buffers to initialize this memory store with *must* be
GPU Buffers.
Writing data to this store through ``.set`` will move the buffer to the GPU
if necessary.
Parameters
----------
store_dict : MutableMapping, optional
A mutable mapping with string keys and [zarr.core.buffer.gpu.Buffer][]
values.
read_only : bool
Whether to open the store in read-only mode.
"""
_store_dict: MutableMapping[str, gpu.Buffer] # type: ignore[assignment]
def __init__(
self,
store_dict: MutableMapping[str, gpu.Buffer] | None = None,
*,
read_only: bool = False,
) -> None:
super().__init__(store_dict=store_dict, read_only=read_only) # type: ignore[arg-type]
def __str__(self) -> str:
return f"gpumemory://{id(self._store_dict)}"
def __repr__(self) -> str:
return f"GpuMemoryStore('{self}')"
@classmethod
def from_dict(cls, store_dict: MutableMapping[str, Buffer]) -> Self:
"""
Create a GpuMemoryStore from a dictionary of buffers at any location.
The dictionary backing the newly created ``GpuMemoryStore`` will not be
the same as ``store_dict``.
Parameters
----------
store_dict : mapping
A mapping of strings keys to arbitrary Buffers. The buffer data
will be moved into a [`gpu.Buffer`][zarr.core.buffer.gpu.Buffer].
Returns
-------
GpuMemoryStore
"""
gpu_store_dict = {k: gpu.Buffer.from_buffer(v) for k, v in store_dict.items()}
return cls(gpu_store_dict)
async def set(self, key: str, value: Buffer, byte_range: tuple[int, int] | None = None) -> None:
# docstring inherited
self._check_writable()
if not isinstance(value, Buffer):
raise TypeError(
f"GpuMemoryStore.set(): `value` must be a Buffer instance. Got an instance of {type(value)} instead."
)
# Convert to gpu.Buffer
gpu_value = value if isinstance(value, gpu.Buffer) else gpu.Buffer.from_buffer(value)
await super().set(key, gpu_value, byte_range=byte_range)
def set_sync(self, key: str, value: Buffer) -> None:
# docstring inherited
self._check_writable()
if not isinstance(value, Buffer):
raise TypeError(
f"GpuMemoryStore.set(): `value` must be a Buffer instance. Got an instance of {type(value)} instead."
)
# Convert to gpu.Buffer, mirroring `set` above: every value in this store's
# backing dict must be a gpu.Buffer, regardless of which API wrote it.
gpu_value = value if isinstance(value, gpu.Buffer) else gpu.Buffer.from_buffer(value)
super().set_sync(key, gpu_value)
# -----------------------------------------------------------------------------
# ManagedMemoryStore and its registry
# -----------------------------------------------------------------------------
# ManagedMemoryStore owns the lifecycle of its backing dict, enabling proper
# weakref-based tracking. This allows memory:// URLs to be resolved back to
# the store's dict within the same process.
class _ManagedStoreDict(dict[str, Buffer]):
"""
A dict subclass that supports weak references.
Regular dicts don't support weakrefs, but we need to track managed store dicts
in a WeakValueDictionary so they can be garbage collected when no longer
referenced. This subclass adds the necessary __weakref__ slot.
"""
__slots__ = ("__weakref__",)
class _ManagedStoreDictRegistry:
"""
Registry for managed store dicts.
This registry is the source of truth for managed store dicts. It creates
new dicts, tracks them via weak references, and looks them up by name.
"""
def __init__(self) -> None:
self._registry: weakref.WeakValueDictionary[str, _ManagedStoreDict] = (
weakref.WeakValueDictionary()
)
self._counter = 0
self._lock = threading.Lock()
def _generate_name(self) -> str:
"""Generate a unique name for a store.
Must be called while holding `self._lock`.
"""
name = str(self._counter)
self._counter += 1
return name
def get_or_create(self, name: str | None = None) -> tuple[_ManagedStoreDict, str]:
"""
Get an existing managed dict by name, or create a new one.
Thread-safe: uses a lock to prevent TOCTOU races between
checking for an existing entry and inserting a new one.
Parameters
----------
name : str | None
The name for the store. If None, a unique name is auto-generated.
If a store with this name already exists, returns the existing store.
Names cannot contain '/' characters.
Returns
-------
tuple[_ManagedStoreDict, str]
The store dict and its name.
Raises
------
ValueError
If the name contains '/' characters.
"""
with self._lock:
if name is None:
name = self._generate_name()
elif "/" in name:
raise ValueError(
f"Store name cannot contain '/': {name!r}. "
"Use the 'path' parameter to specify a path within the store."
)
existing = self._registry.get(name)
if existing is not None:
return existing, name
store_dict = _ManagedStoreDict()
self._registry[name] = store_dict
return store_dict, name
def get(self, name: str) -> _ManagedStoreDict | None:
"""
Look up a managed store dict by name.
Parameters
----------
name : str
The name of the store.
Returns
-------
_ManagedStoreDict | None
The store dict if found, None otherwise.
"""
return self._registry.get(name)
_managed_store_dict_registry = _ManagedStoreDictRegistry()
class ManagedMemoryStore(MemoryStore):
"""
A memory store that owns and manages the lifecycle of its backing dict.
Unlike ``MemoryStore`` which accepts any ``MutableMapping``, this store
creates and owns its backing dict internally. This enables proper lifecycle
management and allows the store to be looked up by its ``memory://`` URL
within the same process.
Parameters
----------
name : str | None
The name for this store, used in the ``memory://`` URL. If None, a unique
name is auto-generated. If a store with this name already exists, the
new store will share the same backing dict.
path : str
The root path for this store. All keys will be prefixed with this path.
read_only : bool
Whether the store is read-only.
Attributes
----------
name : str
The name of this store.
path : str
The root path of this store.
Notes
-----
The backing dict is tracked via weak references and will be garbage collected
when no ``ManagedMemoryStore`` instances reference it. URLs pointing to a
garbage-collected store will fail to resolve.
See Also
--------
MemoryStore : A memory store that accepts any MutableMapping.
Examples
--------
>>> store = ManagedMemoryStore(name="my-data")
>>> str(store)
'memory://my-data'
>>> # Later, resolve the URL back to the store's dict
>>> store2 = ManagedMemoryStore.from_url("memory://my-data")
>>> store2._store_dict is store._store_dict
True
>>> # Create a store with a path prefix
>>> store3 = ManagedMemoryStore.from_url("memory://my-data/subdir")
>>> store3.path
'subdir'
"""
_store_dict: _ManagedStoreDict
_name: str
path: str
def __init__(self, name: str | None = None, *, path: str = "", read_only: bool = False) -> None:
# Skip MemoryStore.__init__ and call Store.__init__ directly
# because we manage _store_dict via the registry, not via a user-supplied
# MutableMapping. If MemoryStore.__init__ ever adds logic beyond setting
# _store_dict, that logic must be replicated here.
Store.__init__(self, read_only=read_only)
# Get or create a managed dict from the registry
self._store_dict, self._name = _managed_store_dict_registry.get_or_create(name)
self.path = normalize_path(path)
def __str__(self) -> str:
return _join_paths([f"memory://{self._name}", self.path])
def __repr__(self) -> str:
return f"ManagedMemoryStore('{self}')"
def __eq__(self, other: object) -> bool:
return (
isinstance(other, type(self))
and self._store_dict is other._store_dict
and self.path == other.path
and self.read_only == other.read_only
)
@property
def name(self) -> str:
"""The name of this store, used in the memory:// URL."""
return self._name
@classmethod
def _from_managed_dict(
cls,
managed_dict: _ManagedStoreDict,
name: str,
*,
path: str = "",
read_only: bool = False,
) -> ManagedMemoryStore:
"""Internal: create a store from an existing managed dict."""
store = object.__new__(cls)
Store.__init__(store, read_only=read_only)
store._store_dict = managed_dict
store._name = name
store.path = normalize_path(path)
return store
def with_read_only(self, read_only: bool = False) -> ManagedMemoryStore:
# docstring inherited
return type(self)._from_managed_dict(
self._store_dict, self._name, path=self.path, read_only=read_only
)
@classmethod
def from_url(cls, url: str, *, read_only: bool = False) -> ManagedMemoryStore:
"""
Create a ManagedMemoryStore from a memory:// URL.
This looks up the backing dict in the process-wide registry and creates
a new store instance that shares the same dict.
Parameters
----------
url : str
A URL like "memory://my-store" or "memory://my-store/path/to/data"
identifying the store and optional path prefix.
read_only : bool
Whether the new store should be read-only.
Returns
-------
ManagedMemoryStore
A store sharing the same backing dict as the original.
Raises
------
ValueError
If the URL is not a valid memory:// URL or the store has been
garbage collected.
"""
parsed = parse_store_url(url)
if parsed.scheme != "memory":
raise ValueError(
f"Expected a 'memory://' URL, got scheme {parsed.scheme!r} in '{url}'."
)
name = parsed.name or ""
managed_dict = _managed_store_dict_registry.get(name)
if managed_dict is None:
raise ValueError(
f"Memory store not found for URL '{url}'. "
"The store may have been garbage collected."
)
return cls._from_managed_dict(managed_dict, name, path=parsed.path, read_only=read_only)
# Override MemoryStore methods to use path prefix and check process
def get_sync(
self,
key: str,
*,
prototype: BufferPrototype | None = None,
byte_range: ByteRequest | None = None,
) -> Buffer | None:
# docstring inherited
return super().get_sync(
_join_paths([self.path, key]), prototype=prototype, byte_range=byte_range
)
def set_sync(self, key: str, value: Buffer) -> None:
# docstring inherited
super().set_sync(_join_paths([self.path, key]), value)
def delete_sync(self, key: str) -> None:
# docstring inherited
super().delete_sync(_join_paths([self.path, key]))
async def get(
self,
key: str,
prototype: BufferPrototype | None = None,
byte_range: ByteRequest | None = None,
) -> Buffer | None:
# docstring inherited
return await super().get(
_join_paths([self.path, key]), prototype=prototype, byte_range=byte_range
)
# get_partial_values is intentionally NOT overridden here: MemoryStore.get_partial_values
# dispatches per-key through `self.get`, which already resolves to the override above.
# Re-prefixing the keys here as well would apply `self.path` twice.
async def exists(self, key: str) -> bool:
# docstring inherited
return await super().exists(_join_paths([self.path, key]))
async def set(self, key: str, value: Buffer, byte_range: tuple[int, int] | None = None) -> None:
# docstring inherited
return await super().set(_join_paths([self.path, key]), value, byte_range=byte_range)
async def set_if_not_exists(self, key: str, value: Buffer) -> None:
# docstring inherited
return await super().set_if_not_exists(_join_paths([self.path, key]), value)
async def delete(self, key: str) -> None:
# docstring inherited
return await super().delete(_join_paths([self.path, key]))
async def list(self) -> AsyncIterator[str]:
# docstring inherited
prefix = f"{self.path}/" if self.path else ""
async for key in super().list():
if key.startswith(prefix):
yield key.removeprefix(prefix)
async def list_prefix(self, prefix: str) -> AsyncIterator[str]:
# docstring inherited
# Manual concatenation instead of _join_paths because we need "path/"
# as the prefix when prefix is empty (to list all keys under self.path)
full_prefix = f"{self.path}/{prefix}" if self.path else prefix
path_prefix = f"{self.path}/" if self.path else ""
async for key in super().list_prefix(full_prefix):
yield key.removeprefix(path_prefix)
async def list_dir(self, prefix: str) -> AsyncIterator[str]:
# docstring inherited
full_prefix = _join_paths([self.path, prefix])
async for key in super().list_dir(full_prefix):
yield key
def __reduce__(
self,
) -> tuple[type[ManagedMemoryStore], tuple[str | None], dict[str, Any]]:
"""
Support pickling of ManagedMemoryStore.
On unpickle, the store will reconnect to an existing store with the same
name if one exists in the registry, or create a new empty store otherwise.
Note that the backing dict data is NOT serialized - only the store's
identity (name, path, read_only) is preserved. If the original store has
been garbage collected, the unpickled store will have an empty dict.
The current process ID is preserved so that cross-process unpickling can be
detected and will raise an error at unpickle time.
"""
return (
self.__class__,
(self._name,),
{
"path": self.path,
"read_only": self.read_only,
"created_pid": os.getpid(),
},
)
def __setstate__(self, state: dict[str, Any]) -> None:
"""Restore state after unpickling.
The pickle protocol calls ``cls(name)`` (via ``__reduce__``'s args)
then ``__setstate__(state)``. ``__init__`` already set up
``_store_dict`` and ``_name`` from the registry — we just restore
path and read_only here.
"""
# Check for cross-process usage first, before mutating state
created_pid = state.get("created_pid")
if created_pid is not None and created_pid != os.getpid():
raise RuntimeError(
f"ManagedMemoryStore '{self._name}' was created in process {created_pid} "
f"but is being unpickled in process {os.getpid()}. "
"ManagedMemoryStore instances cannot be shared across processes because "
"their backing dict is not serialized. Use a persistent store (e.g., "
"LocalStore, ZipStore) for cross-process data sharing."
)
self.path = normalize_path(state.get("path", ""))
# Use the Store-level _read_only attribute directly because
# Store.__init__ was already called by __init__ during unpickling
self._read_only = state.get("read_only", False)