Source code for fsspec.implementations.cached

import hashlib
import inspect
import logging
import os
import pickle
import tempfile
import time
from shutil import move, rmtree

from fsspec import AbstractFileSystem, filesystem
from fsspec.callbacks import _DEFAULT_CALLBACK
from fsspec.compression import compr
from fsspec.core import BaseCache, MMapCache
from fsspec.spec import AbstractBufferedFile
from fsspec.utils import infer_compression

logger = logging.getLogger("fsspec")


[docs]class CachingFileSystem(AbstractFileSystem): """Locally caching filesystem, layer over any other FS This class implements chunk-wise local storage of remote files, for quick access after the initial download. The files are stored in a given directory with random hashes for the filenames. If no directory is given, a temporary one is used, which should be cleaned up by the OS after the process ends. The files themselves as sparse (as implemented in MMapCache), so only the data which is accessed takes up space. Restrictions: - the block-size must be the same for each access of a given file, unless all blocks of the file have already been read - caching can only be applied to file-systems which produce files derived from fsspec.spec.AbstractBufferedFile ; LocalFileSystem is also allowed, for testing """ protocol = ("blockcache", "cached")
[docs] def __init__( self, target_protocol=None, cache_storage="TMP", cache_check=10, check_files=False, expiry_time=604800, target_options=None, fs=None, same_names=False, compression=None, **kwargs, ): """ Parameters ---------- target_protocol: str (optional) Target filesystem protocol. Provide either this or ``fs``. cache_storage: str or list(str) Location to store files. If "TMP", this is a temporary directory, and will be cleaned up by the OS when this process ends (or later). If a list, each location will be tried in the order given, but only the last will be considered writable. cache_check: int Number of seconds between reload of cache metadata check_files: bool Whether to explicitly see if the UID of the remote file matches the stored one before using. Warning: some file systems such as HTTP cannot reliably give a unique hash of the contents of some path, so be sure to set this option to False. expiry_time: int The time in seconds after which a local copy is considered useless. Set to falsy to prevent expiry. The default is equivalent to one week. target_options: dict or None Passed to the instantiation of the FS, if fs is None. fs: filesystem instance The target filesystem to run against. Provide this or ``protocol``. same_names: bool (optional) By default, target URLs are hashed, so that files from different backends with the same basename do not conflict. If this is true, the original basename is used. compression: str (optional) To decompress on download. Can be 'infer' (guess from the URL name), one of the entries in ``fsspec.compression.compr``, or None for no decompression. """ super().__init__(**kwargs) if not (fs is None) ^ (target_protocol is None): raise ValueError( "Please provide one of filesystem instance (fs) or" " remote_protocol, not both" ) if cache_storage == "TMP": storage = [tempfile.mkdtemp()] else: if isinstance(cache_storage, str): storage = [cache_storage] else: storage = cache_storage os.makedirs(storage[-1], exist_ok=True) self.storage = storage self.kwargs = target_options or {} self.cache_check = cache_check self.check_files = check_files self.expiry = expiry_time self.compression = compression # TODO: same_names should allow for variable prefix, not only # to keep the basename self.same_names = same_names self.target_protocol = ( target_protocol if isinstance(target_protocol, str) else (fs.protocol if isinstance(fs.protocol, str) else fs.protocol[0]) ) self.load_cache() self.fs = fs if fs is not None else filesystem(target_protocol, **self.kwargs) def _strip_protocol(path): # acts as a method, since each instance has a difference target return self.fs._strip_protocol(type(self)._strip_protocol(path)) self._strip_protocol = _strip_protocol
def _mkcache(self): os.makedirs(self.storage[-1], exist_ok=True) def load_cache(self): """Read set of stored blocks from file""" cached_files = [] for storage in self.storage: fn = os.path.join(storage, "cache") if os.path.exists(fn): with open(fn, "rb") as f: # TODO: consolidate blocks here loaded_cached_files = pickle.load(f) for c in loaded_cached_files.values(): if isinstance(c["blocks"], list): c["blocks"] = set(c["blocks"]) cached_files.append(loaded_cached_files) else: cached_files.append({}) self._mkcache() self.cached_files = cached_files or [{}] self.last_cache = time.time() def save_cache(self): """Save set of stored blocks from file""" fn = os.path.join(self.storage[-1], "cache") # TODO: a file lock could be used to ensure file does not change # between re-read and write; but occasional duplicated reads ok. cache = self.cached_files[-1] if os.path.exists(fn): with open(fn, "rb") as f: cached_files = pickle.load(f) for k, c in cached_files.items(): if k in cache: if c["blocks"] is True or cache[k]["blocks"] is True: c["blocks"] = True else: c["blocks"] = set(c["blocks"]).union(cache[k]["blocks"]) c["time"] = max(c["time"], cache[k]["time"]) c["uid"] = cache[k]["uid"] # Files can be added to cache after it was written once for k, c in cache.items(): if k not in cached_files: cached_files[k] = c else: cached_files = cache cache = {k: v.copy() for k, v in cached_files.items()} for c in cache.values(): if isinstance(c["blocks"], set): c["blocks"] = list(c["blocks"]) fn2 = tempfile.mktemp() with open(fn2, "wb") as f: pickle.dump(cache, f) self._mkcache() move(fn2, fn) self.cached_files[-1] = cached_files self.last_cache = time.time() def _check_cache(self): """Reload caches if time elapsed or any disappeared""" self._mkcache() if not self.cache_check: # explicitly told not to bother checking return timecond = time.time() - self.last_cache > self.cache_check existcond = all(os.path.exists(storage) for storage in self.storage) if timecond or not existcond: self.load_cache() def _check_file(self, path): """Is path in cache and still valid""" path = self._strip_protocol(path) self._check_cache() for storage, cache in zip(self.storage, self.cached_files): if path not in cache: continue detail = cache[path].copy() if self.check_files: if detail["uid"] != self.fs.ukey(path): continue if self.expiry: if time.time() - detail["time"] > self.expiry: continue fn = os.path.join(storage, detail["fn"]) if os.path.exists(fn): return detail, fn return False def clear_cache(self): """Remove all files and metadat from the cache In the case of multiple cache locations, this clears only the last one, which is assumed to be the read/write one. """ rmtree(self.storage[-1]) self.load_cache() def pop_from_cache(self, path): """Remove cached version of given file Deletes local copy of the given (remote) path. If it is found in a cache location which is not the last, it is assumed to be read-only, and raises PermissionError """ path = self._strip_protocol(path) _, fn = self._check_file(path) if fn is None: return if fn.startswith(self.storage[-1]): # is in in writable cache os.remove(fn) self.cached_files[-1].pop(path) self.save_cache() else: raise PermissionError( "Can only delete cached file in last, writable cache location" ) def _open( self, path, mode="rb", block_size=None, autocommit=True, cache_options=None, **kwargs, ): """Wrap the target _open If the whole file exists in the cache, just open it locally and return that. Otherwise, open the file on the target FS, and make it have a mmap cache pointing to the location which we determine, in our cache. The ``blocks`` instance is shared, so as the mmap cache instance updates, so does the entry in our ``cached_files`` attribute. We monkey-patch this file, so that when it closes, we call ``close_and_update`` to save the state of the blocks. """ path = self._strip_protocol(path) path = self.fs._strip_protocol(path) if "r" not in mode: return self.fs._open( path, mode=mode, block_size=block_size, autocommit=autocommit, cache_options=cache_options, **kwargs, ) detail = self._check_file(path) if detail: # file is in cache detail, fn = detail hash, blocks = detail["fn"], detail["blocks"] if blocks is True: # stored file is complete logger.debug("Opening local copy of %s" % path) return open(fn, mode) # TODO: action where partial file exists in read-only cache logger.debug("Opening partially cached copy of %s" % path) else: hash = self.hash_name(path, self.same_names) fn = os.path.join(self.storage[-1], hash) blocks = set() detail = { "original": path, "fn": hash, "blocks": blocks, "time": time.time(), "uid": self.fs.ukey(path), } self.cached_files[-1][path] = detail logger.debug("Creating local sparse file for %s" % path) # call target filesystems open self._mkcache() f = self.fs._open( path, mode=mode, block_size=block_size, autocommit=autocommit, cache_options=cache_options, cache_type=None, **kwargs, ) if self.compression: comp = ( infer_compression(path) if self.compression == "infer" else self.compression ) f = compr[comp](f, mode="rb") if "blocksize" in detail: if detail["blocksize"] != f.blocksize: raise ValueError( "Cached file must be reopened with same block" "size as original (old: %i, new %i)" "" % (detail["blocksize"], f.blocksize) ) else: detail["blocksize"] = f.blocksize f.cache = MMapCache(f.blocksize, f._fetch_range, f.size, fn, blocks) close = f.close f.close = lambda: self.close_and_update(f, close) self.save_cache() return f def hash_name(self, path, same_name): return hash_name(path, same_name=same_name) def close_and_update(self, f, close): """Called when a file is closing, so store the set of blocks""" if f.closed: return path = self._strip_protocol(f.path) c = self.cached_files[-1][path] if c["blocks"] is not True and len(c["blocks"]) * f.blocksize >= f.size: c["blocks"] = True try: logger.debug("going to save") self.save_cache() logger.debug("saved") except (IOError, OSError): logger.debug("Cache saving failed while closing file") except NameError: logger.debug("Cache save failed due to interpreter shutdown") close() f.closed = True def __getattribute__(self, item): if item in [ "load_cache", "_open", "save_cache", "close_and_update", "__init__", "__getattribute__", "__reduce__", "_make_local_details", "open", "cat", "cat_file", "get", "read_block", "tail", "head", "_check_file", "_check_cache", "_mkcache", "clear_cache", "pop_from_cache", "_mkcache", "local_file", "_paths_from_path", "get_mapper", "open_many", "commit_many", "hash_name", "__hash__", "__eq__", "to_json", ]: # all the methods defined in this class. Note `open` here, since # it calls `_open`, but is actually in superclass return lambda *args, **kw: getattr(type(self), item).__get__(self)( *args, **kw ) if item in ["__reduce_ex__"]: raise AttributeError if item in ["_cache"]: # class attributes return getattr(type(self), item) if item == "__class__": return type(self) d = object.__getattribute__(self, "__dict__") fs = d.get("fs", None) # fs is not immediately defined if item in d: return d[item] elif fs is not None: if item in fs.__dict__: # attribute of instance return fs.__dict__[item] # attributed belonging to the target filesystem cls = type(fs) m = getattr(cls, item) if (inspect.isfunction(m) or inspect.isdatadescriptor(m)) and ( not hasattr(m, "__self__") or m.__self__ is None ): # instance method return m.__get__(fs, cls) return m # class method or attribute else: # attributes of the superclass, while target is being set up return super().__getattribute__(item) def __eq__(self, other): """Test for equality.""" if self is other: return True if not isinstance(other, type(self)): return False return ( self.storage == other.storage and self.kwargs == other.kwargs and self.cache_check == other.cache_check and self.check_files == other.check_files and self.expiry == other.expiry and self.compression == other.compression and self.same_names == other.same_names and self.target_protocol == other.target_protocol ) def __hash__(self): """Calculate hash.""" return ( hash(tuple(self.storage)) ^ hash(str(self.kwargs)) ^ hash(self.cache_check) ^ hash(self.check_files) ^ hash(self.expiry) ^ hash(self.compression) ^ hash(self.same_names) ^ hash(self.target_protocol) ) def to_json(self): """Calculate JSON representation. Not implemented yet for CachingFileSystem. """ raise NotImplementedError( "CachingFileSystem JSON representation not implemented" )
[docs]class WholeFileCacheFileSystem(CachingFileSystem): """Caches whole remote files on first access This class is intended as a layer over any other file system, and will make a local copy of each file accessed, so that all subsequent reads are local. This is similar to ``CachingFileSystem``, but without the block-wise functionality and so can work even when sparse files are not allowed. See its docstring for definition of the init arguments. The class still needs access to the remote store for listing files, and may refresh cached files. """ protocol = "filecache" local_file = True def open_many(self, open_files): paths = [of.path for of in open_files] if "r" in open_files.mode: self._mkcache() else: return [ LocalTempFile(self.fs, path, mode=open_files.mode, autocommit=False) for path in paths ] if self.compression: raise NotImplementedError details = [self._check_file(sp) for sp in paths] downpath = [p for p, d in zip(paths, details) if not d] downfn0 = [ os.path.join(self.storage[-1], self.hash_name(p, self.same_names)) for p, d in zip(paths, details) ] # keep these path names for opening later downfn = [fn for fn, d in zip(downfn0, details) if not d] if downpath: # skip if all files are already cached and up to date self.fs.get(downpath, downfn) # update metadata - only happens when downloads are successful newdetail = [ { "original": path, "fn": self.hash_name(path, self.same_names), "blocks": True, "time": time.time(), "uid": self.fs.ukey(path), } for path in downpath ] self.cached_files[-1].update( {path: detail for path, detail in zip(downpath, newdetail)} ) self.save_cache() def firstpart(fn): # helper to adapt both whole-file and simple-cache return fn[1] if isinstance(fn, tuple) else fn return [ open(firstpart(fn0) if fn0 else fn1, mode=open_files.mode) for fn0, fn1 in zip(details, downfn0) ] def commit_many(self, open_files): self.fs.put([f.fn for f in open_files], [f.path for f in open_files]) def _make_local_details(self, path): hash = self.hash_name(path, self.same_names) fn = os.path.join(self.storage[-1], hash) detail = { "original": path, "fn": hash, "blocks": True, "time": time.time(), "uid": self.fs.ukey(path), } self.cached_files[-1][path] = detail logger.debug("Copying %s to local cache" % path) return fn def cat( self, path, recursive=False, on_error="raise", callback=_DEFAULT_CALLBACK, **kwargs, ): paths = self.expand_path( path, recursive=recursive, maxdepth=kwargs.get("maxdepth", None) ) getpaths = [] storepaths = [] fns = [] for p in paths: detail = self._check_file(p) if not detail: fn = self._make_local_details(p) getpaths.append(p) storepaths.append(fn) else: detail, fn = detail if isinstance(detail, tuple) else (None, detail) fns.append(fn) if getpaths: self.fs.get(getpaths, storepaths) self.save_cache() out = {} callback.set_size(len(paths)) for p, fn in zip(paths, fns): out[p] = open(fn, "rb").read() callback.relative_update(1) if isinstance(path, str) and len(paths) == 1 and recursive is False: out = out[paths[0]] return out def _open(self, path, mode="rb", **kwargs): path = self._strip_protocol(path) if "r" not in mode: return self.fs._open(path, mode=mode, **kwargs) detail = self._check_file(path) if detail: detail, fn = detail _, blocks = detail["fn"], detail["blocks"] if blocks is True: logger.debug("Opening local copy of %s" % path) # In order to support downstream filesystems to be able to # infer the compression from the original filename, like # the `TarFileSystem`, let's extend the `io.BufferedReader` # fileobject protocol by adding a dedicated attribute # `original`. f = open(fn, mode) f.original = detail.get("original") return f else: raise ValueError( "Attempt to open partially cached file %s" "as a wholly cached file" % path ) else: fn = self._make_local_details(path) kwargs["mode"] = mode # call target filesystems open self._mkcache() if self.compression: with self.fs._open(path, **kwargs) as f, open(fn, "wb") as f2: if isinstance(f, AbstractBufferedFile): # want no type of caching if just downloading whole thing f.cache = BaseCache(0, f.cache.fetcher, f.size) comp = ( infer_compression(path) if self.compression == "infer" else self.compression ) f = compr[comp](f, mode="rb") data = True while data: block = getattr(f, "blocksize", 5 * 2 ** 20) data = f.read(block) f2.write(data) else: self.fs.get(path, fn) self.save_cache() return self._open(path, mode)
[docs]class SimpleCacheFileSystem(WholeFileCacheFileSystem): """Caches whole remote files on first access This class is intended as a layer over any other file system, and will make a local copy of each file accessed, so that all subsequent reads are local. This implementation only copies whole files, and does not keep any metadata about the download time or file details. It is therefore safer to use in multi-threaded/concurrent situations. This is the only of the caching filesystems that supports write: you will be given a real local open file, and upon close and commit, it will be uploaded to the target filesystem; the writability or the target URL is not checked until that time. """ protocol = "simplecache" local_file = True
[docs] def __init__(self, **kwargs): kw = kwargs.copy() for key in ["cache_check", "expiry_time", "check_files"]: kw[key] = False super().__init__(**kw) for storage in self.storage: if not os.path.exists(storage): os.makedirs(storage, exist_ok=True) self.cached_files = [{}]
def _check_file(self, path): self._check_cache() sha = self.hash_name(path, self.same_names) for storage in self.storage: fn = os.path.join(storage, sha) if os.path.exists(fn): return fn def save_cache(self): pass def load_cache(self): pass def _open(self, path, mode="rb", **kwargs): path = self._strip_protocol(path) if "r" not in mode: return LocalTempFile(self, path, mode=mode) fn = self._check_file(path) if fn: return open(fn, mode) sha = self.hash_name(path, self.same_names) fn = os.path.join(self.storage[-1], sha) logger.debug("Copying %s to local cache" % path) kwargs["mode"] = mode self._mkcache() if self.compression: with self.fs._open(path, **kwargs) as f, open(fn, "wb") as f2: if isinstance(f, AbstractBufferedFile): # want no type of caching if just downloading whole thing f.cache = BaseCache(0, f.cache.fetcher, f.size) comp = ( infer_compression(path) if self.compression == "infer" else self.compression ) f = compr[comp](f, mode="rb") data = True while data: block = getattr(f, "blocksize", 5 * 2 ** 20) data = f.read(block) f2.write(data) else: self.fs.get(path, fn) return self._open(path, mode)
class LocalTempFile: """A temporary local file, which will be uploaded on commit""" def __init__(self, fs, path, fn=None, mode="wb", autocommit=True, seek=0): fn = fn or tempfile.mktemp() self.mode = mode self.fn = fn self.fh = open(fn, mode) if seek: self.fh.seek(seek) self.path = path self.fs = fs self.closed = False self.autocommit = autocommit def __reduce__(self): # always open in rb+ to allow continuing writing at a location return ( LocalTempFile, (self.fs, self.path, self.fn, "rb+", self.autocommit, self.tell()), ) def __enter__(self): return self.fh def __exit__(self, exc_type, exc_val, exc_tb): self.close() def close(self): self.fh.close() self.closed = True if self.autocommit: self.commit() def discard(self): self.fh.close() os.remove(self.fn) def commit(self): self.fs.put(self.fn, self.path) def __getattr__(self, item): return getattr(self.fh, item) def hash_name(path, same_name): if same_name: hash = os.path.basename(path) else: hash = hashlib.sha256(path.encode()).hexdigest() return hash