peacock-data-public-datasets-idc-cronscript
/
venv
/lib
/python3.10
/site-packages
/joblib
/_store_backends.py
"""Storage providers backends for Memory caching.""" | |
from pickle import PicklingError | |
import re | |
import os | |
import os.path | |
import datetime | |
import json | |
import shutil | |
import time | |
import warnings | |
import collections | |
import operator | |
import threading | |
from abc import ABCMeta, abstractmethod | |
from .backports import concurrency_safe_rename | |
from .disk import mkdirp, memstr_to_bytes, rm_subdirs | |
from .logger import format_time | |
from . import numpy_pickle | |
CacheItemInfo = collections.namedtuple('CacheItemInfo', | |
'path size last_access') | |
class CacheWarning(Warning): | |
"""Warning to capture dump failures except for PicklingError.""" | |
pass | |
def concurrency_safe_write(object_to_write, filename, write_func): | |
"""Writes an object into a unique file in a concurrency-safe way.""" | |
thread_id = id(threading.current_thread()) | |
temporary_filename = '{}.thread-{}-pid-{}'.format( | |
filename, thread_id, os.getpid()) | |
write_func(object_to_write, temporary_filename) | |
return temporary_filename | |
class StoreBackendBase(metaclass=ABCMeta): | |
"""Helper Abstract Base Class which defines all methods that | |
a StorageBackend must implement.""" | |
location = None | |
def _open_item(self, f, mode): | |
"""Opens an item on the store and return a file-like object. | |
This method is private and only used by the StoreBackendMixin object. | |
Parameters | |
---------- | |
f: a file-like object | |
The file-like object where an item is stored and retrieved | |
mode: string, optional | |
the mode in which the file-like object is opened allowed valued are | |
'rb', 'wb' | |
Returns | |
------- | |
a file-like object | |
""" | |
def _item_exists(self, location): | |
"""Checks if an item location exists in the store. | |
This method is private and only used by the StoreBackendMixin object. | |
Parameters | |
---------- | |
location: string | |
The location of an item. On a filesystem, this corresponds to the | |
absolute path, including the filename, of a file. | |
Returns | |
------- | |
True if the item exists, False otherwise | |
""" | |
def _move_item(self, src, dst): | |
"""Moves an item from src to dst in the store. | |
This method is private and only used by the StoreBackendMixin object. | |
Parameters | |
---------- | |
src: string | |
The source location of an item | |
dst: string | |
The destination location of an item | |
""" | |
def create_location(self, location): | |
"""Creates a location on the store. | |
Parameters | |
---------- | |
location: string | |
The location in the store. On a filesystem, this corresponds to a | |
directory. | |
""" | |
def clear_location(self, location): | |
"""Clears a location on the store. | |
Parameters | |
---------- | |
location: string | |
The location in the store. On a filesystem, this corresponds to a | |
directory or a filename absolute path | |
""" | |
def get_items(self): | |
"""Returns the whole list of items available in the store. | |
Returns | |
------- | |
The list of items identified by their ids (e.g filename in a | |
filesystem). | |
""" | |
def configure(self, location, verbose=0, backend_options=dict()): | |
"""Configures the store. | |
Parameters | |
---------- | |
location: string | |
The base location used by the store. On a filesystem, this | |
corresponds to a directory. | |
verbose: int | |
The level of verbosity of the store | |
backend_options: dict | |
Contains a dictionary of named parameters used to configure the | |
store backend. | |
""" | |
class StoreBackendMixin(object): | |
"""Class providing all logic for managing the store in a generic way. | |
The StoreBackend subclass has to implement 3 methods: create_location, | |
clear_location and configure. The StoreBackend also has to provide | |
a private _open_item, _item_exists and _move_item methods. The _open_item | |
method has to have the same signature as the builtin open and return a | |
file-like object. | |
""" | |
def load_item(self, call_id, verbose=1, timestamp=None, metadata=None): | |
"""Load an item from the store given its id as a list of str.""" | |
full_path = os.path.join(self.location, *call_id) | |
if verbose > 1: | |
ts_string = ('{: <16}'.format(format_time(time.time() - timestamp)) | |
if timestamp is not None else '') | |
signature = os.path.basename(call_id[0]) | |
if metadata is not None and 'input_args' in metadata: | |
kwargs = ', '.join('{}={}'.format(*item) | |
for item in metadata['input_args'].items()) | |
signature += '({})'.format(kwargs) | |
msg = '[Memory]{}: Loading {}'.format(ts_string, signature) | |
if verbose < 10: | |
print('{0}...'.format(msg)) | |
else: | |
print('{0} from {1}'.format(msg, full_path)) | |
mmap_mode = (None if not hasattr(self, 'mmap_mode') | |
else self.mmap_mode) | |
filename = os.path.join(full_path, 'output.pkl') | |
if not self._item_exists(filename): | |
raise KeyError("Non-existing item (may have been " | |
"cleared).\nFile %s does not exist" % filename) | |
# file-like object cannot be used when mmap_mode is set | |
if mmap_mode is None: | |
with self._open_item(filename, "rb") as f: | |
item = numpy_pickle.load(f) | |
else: | |
item = numpy_pickle.load(filename, mmap_mode=mmap_mode) | |
return item | |
def dump_item(self, call_id, item, verbose=1): | |
"""Dump an item in the store at the id given as a list of str.""" | |
try: | |
item_path = os.path.join(self.location, *call_id) | |
if not self._item_exists(item_path): | |
self.create_location(item_path) | |
filename = os.path.join(item_path, 'output.pkl') | |
if verbose > 10: | |
print('Persisting in %s' % item_path) | |
def write_func(to_write, dest_filename): | |
with self._open_item(dest_filename, "wb") as f: | |
try: | |
numpy_pickle.dump(to_write, f, compress=self.compress) | |
except PicklingError as e: | |
# TODO(1.5) turn into error | |
warnings.warn( | |
"Unable to cache to disk: failed to pickle " | |
"output. In version 1.5 this will raise an " | |
f"exception. Exception: {e}.", | |
FutureWarning | |
) | |
self._concurrency_safe_write(item, filename, write_func) | |
except Exception as e: # noqa: E722 | |
warnings.warn( | |
"Unable to cache to disk. Possibly a race condition in the " | |
f"creation of the directory. Exception: {e}.", | |
CacheWarning | |
) | |
def clear_item(self, call_id): | |
"""Clear the item at the id, given as a list of str.""" | |
item_path = os.path.join(self.location, *call_id) | |
if self._item_exists(item_path): | |
self.clear_location(item_path) | |
def contains_item(self, call_id): | |
"""Check if there is an item at the id, given as a list of str.""" | |
item_path = os.path.join(self.location, *call_id) | |
filename = os.path.join(item_path, 'output.pkl') | |
return self._item_exists(filename) | |
def get_item_info(self, call_id): | |
"""Return information about item.""" | |
return {'location': os.path.join(self.location, *call_id)} | |
def get_metadata(self, call_id): | |
"""Return actual metadata of an item.""" | |
try: | |
item_path = os.path.join(self.location, *call_id) | |
filename = os.path.join(item_path, 'metadata.json') | |
with self._open_item(filename, 'rb') as f: | |
return json.loads(f.read().decode('utf-8')) | |
except: # noqa: E722 | |
return {} | |
def store_metadata(self, call_id, metadata): | |
"""Store metadata of a computation.""" | |
try: | |
item_path = os.path.join(self.location, *call_id) | |
self.create_location(item_path) | |
filename = os.path.join(item_path, 'metadata.json') | |
def write_func(to_write, dest_filename): | |
with self._open_item(dest_filename, "wb") as f: | |
f.write(json.dumps(to_write).encode('utf-8')) | |
self._concurrency_safe_write(metadata, filename, write_func) | |
except: # noqa: E722 | |
pass | |
def contains_path(self, call_id): | |
"""Check cached function is available in store.""" | |
func_path = os.path.join(self.location, *call_id) | |
return self.object_exists(func_path) | |
def clear_path(self, call_id): | |
"""Clear all items with a common path in the store.""" | |
func_path = os.path.join(self.location, *call_id) | |
if self._item_exists(func_path): | |
self.clear_location(func_path) | |
def store_cached_func_code(self, call_id, func_code=None): | |
"""Store the code of the cached function.""" | |
func_path = os.path.join(self.location, *call_id) | |
if not self._item_exists(func_path): | |
self.create_location(func_path) | |
if func_code is not None: | |
filename = os.path.join(func_path, "func_code.py") | |
with self._open_item(filename, 'wb') as f: | |
f.write(func_code.encode('utf-8')) | |
def get_cached_func_code(self, call_id): | |
"""Store the code of the cached function.""" | |
filename = os.path.join(self.location, *call_id, 'func_code.py') | |
try: | |
with self._open_item(filename, 'rb') as f: | |
return f.read().decode('utf-8') | |
except: # noqa: E722 | |
raise | |
def get_cached_func_info(self, call_id): | |
"""Return information related to the cached function if it exists.""" | |
return {'location': os.path.join(self.location, *call_id)} | |
def clear(self): | |
"""Clear the whole store content.""" | |
self.clear_location(self.location) | |
def enforce_store_limits( | |
self, bytes_limit, items_limit=None, age_limit=None | |
): | |
""" | |
Remove the store's oldest files to enforce item, byte, and age limits. | |
""" | |
items_to_delete = self._get_items_to_delete( | |
bytes_limit, items_limit, age_limit | |
) | |
for item in items_to_delete: | |
if self.verbose > 10: | |
print('Deleting item {0}'.format(item)) | |
try: | |
self.clear_location(item.path) | |
except OSError: | |
# Even with ignore_errors=True shutil.rmtree can raise OSError | |
# with: | |
# [Errno 116] Stale file handle if another process has deleted | |
# the folder already. | |
pass | |
def _get_items_to_delete( | |
self, bytes_limit, items_limit=None, age_limit=None | |
): | |
""" | |
Get items to delete to keep the store under size, file, & age limits. | |
""" | |
if isinstance(bytes_limit, str): | |
bytes_limit = memstr_to_bytes(bytes_limit) | |
items = self.get_items() | |
if not items: | |
return [] | |
size = sum(item.size for item in items) | |
if bytes_limit is not None: | |
to_delete_size = size - bytes_limit | |
else: | |
to_delete_size = 0 | |
if items_limit is not None: | |
to_delete_items = len(items) - items_limit | |
else: | |
to_delete_items = 0 | |
if age_limit is not None: | |
older_item = min(item.last_access for item in items) | |
deadline = datetime.datetime.now() - age_limit | |
else: | |
deadline = None | |
if ( | |
to_delete_size <= 0 and to_delete_items <= 0 | |
and (deadline is None or older_item > deadline) | |
): | |
return [] | |
# We want to delete first the cache items that were accessed a | |
# long time ago | |
items.sort(key=operator.attrgetter('last_access')) | |
items_to_delete = [] | |
size_so_far = 0 | |
items_so_far = 0 | |
for item in items: | |
if ( | |
(size_so_far >= to_delete_size) | |
and items_so_far >= to_delete_items | |
and (deadline is None or deadline < item.last_access) | |
): | |
break | |
items_to_delete.append(item) | |
size_so_far += item.size | |
items_so_far += 1 | |
return items_to_delete | |
def _concurrency_safe_write(self, to_write, filename, write_func): | |
"""Writes an object into a file in a concurrency-safe way.""" | |
temporary_filename = concurrency_safe_write(to_write, | |
filename, write_func) | |
self._move_item(temporary_filename, filename) | |
def __repr__(self): | |
"""Printable representation of the store location.""" | |
return '{class_name}(location="{location}")'.format( | |
class_name=self.__class__.__name__, location=self.location) | |
class FileSystemStoreBackend(StoreBackendBase, StoreBackendMixin): | |
"""A StoreBackend used with local or network file systems.""" | |
_open_item = staticmethod(open) | |
_item_exists = staticmethod(os.path.exists) | |
_move_item = staticmethod(concurrency_safe_rename) | |
def clear_location(self, location): | |
"""Delete location on store.""" | |
if (location == self.location): | |
rm_subdirs(location) | |
else: | |
shutil.rmtree(location, ignore_errors=True) | |
def create_location(self, location): | |
"""Create object location on store""" | |
mkdirp(location) | |
def get_items(self): | |
"""Returns the whole list of items available in the store.""" | |
items = [] | |
for dirpath, _, filenames in os.walk(self.location): | |
is_cache_hash_dir = re.match('[a-f0-9]{32}', | |
os.path.basename(dirpath)) | |
if is_cache_hash_dir: | |
output_filename = os.path.join(dirpath, 'output.pkl') | |
try: | |
last_access = os.path.getatime(output_filename) | |
except OSError: | |
try: | |
last_access = os.path.getatime(dirpath) | |
except OSError: | |
# The directory has already been deleted | |
continue | |
last_access = datetime.datetime.fromtimestamp(last_access) | |
try: | |
full_filenames = [os.path.join(dirpath, fn) | |
for fn in filenames] | |
dirsize = sum(os.path.getsize(fn) | |
for fn in full_filenames) | |
except OSError: | |
# Either output_filename or one of the files in | |
# dirpath does not exist any more. We assume this | |
# directory is being cleaned by another process already | |
continue | |
items.append(CacheItemInfo(dirpath, dirsize, | |
last_access)) | |
return items | |
def configure(self, location, verbose=1, backend_options=None): | |
"""Configure the store backend. | |
For this backend, valid store options are 'compress' and 'mmap_mode' | |
""" | |
if backend_options is None: | |
backend_options = {} | |
# setup location directory | |
self.location = location | |
if not os.path.exists(self.location): | |
mkdirp(self.location) | |
# item can be stored compressed for faster I/O | |
self.compress = backend_options.get('compress', False) | |
# FileSystemStoreBackend can be used with mmap_mode options under | |
# certain conditions. | |
mmap_mode = backend_options.get('mmap_mode') | |
if self.compress and mmap_mode is not None: | |
warnings.warn('Compressed items cannot be memmapped in a ' | |
'filesystem store. Option will be ignored.', | |
stacklevel=2) | |
self.mmap_mode = mmap_mode | |
self.verbose = verbose | |