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Description: Remove code from Stack Overflow
Stack Overflow content is CC-BY-SA licensed,
which this package is not supposed to be. These snippets may be
too small to be copyrightable, but removing them to be safe.
Author: Rebecca N. Palmer <rebecca_palmer@zoho.com>
Forwarded: no - one part needs Python 3.6+
--- a/snakemake/remote/S3Mocked.py
+++ b/snakemake/remote/S3Mocked.py
@@ -9,6 +9,7 @@ from contextlib import contextmanager
import pickle
import time
import functools
+import pathlib
# intra-module
from snakemake.remote.S3 import (
@@ -120,26 +121,19 @@ class RemoteObject(S3RemoteObject):
# ====== Helpers =====
-def touch(fname, mode=0o666, dir_fd=None, **kwargs):
- # create lock file faster
- # https://stackoverflow.com/a/1160227
- flags = os.O_CREAT | os.O_APPEND
- with os.fdopen(os.open(fname, flags=flags, mode=mode, dir_fd=dir_fd)) as f:
- os.utime(
- f.fileno() if os.utime in os.supports_fd else fname,
- dir_fd=None if os.supports_fd else dir_fd,
- **kwargs
- )
-
+def touch(fname, mode=0o666):
+ pathlib.Path(fname).touch(mode=mode, exist_ok=True)
@contextmanager
def file_lock(filepath):
lock_file = filepath + ".lock"
- while os.path.isfile(lock_file):
- time.sleep(2)
-
- touch(lock_file)
+ while True:
+ try:
+ pathlib.Path(lock_file).touch(exist_ok=False)
+ break
+ except FileExistsError:
+ time.sleep(2)
try:
yield
--- a/snakemake/utils.py
+++ b/snakemake/utils.py
@@ -481,32 +481,21 @@ def min_version(version):
def update_config(config, overwrite_config):
"""Recursively update dictionary config with overwrite_config in-place.
- See
- https://stackoverflow.com/questions/3232943/update-value-of-a-nested-dictionary-of-varying-depth
- for details.
-
Args:
config (dict): dictionary to update
overwrite_config (dict): dictionary whose items will overwrite those in config
"""
- def _update_config(config, overwrite_config):
- """Necessary as recursive calls require a return value,
- but `update_config()` has no return value.
- """
- for key, value in overwrite_config.items():
- if not isinstance(config, collections.abc.Mapping):
- # the config cannot be updated as it is no dict
- # -> just overwrite it with the new value
- config = {}
- if isinstance(value, collections.abc.Mapping):
- sub_config = config.get(key, {})
- config[key] = _update_config(sub_config, value)
+ def nestedupdate(old_d, new_d):
+ for k, v in new_d.items():
+ if isinstance(v, collections.abc.Mapping):
+ if k not in old_d or old_d[k] is None:
+ old_d[k] = {}
+ nestedupdate(old_d[k], v)
else:
- config[key] = value
- return config
+ old_d[k] = v
- _update_config(config, overwrite_config)
+ nestedupdate(config, overwrite_config)
def available_cpu_count():
--- a/tests/test_static_remote/S3MockedForStaticTest.py
+++ b/tests/test_static_remote/S3MockedForStaticTest.py
@@ -10,6 +10,7 @@ import pickle
import time
import threading
import functools
+import pathlib
# intra-module
from snakemake.remote.S3 import (
@@ -133,26 +134,20 @@ class RemoteObject(S3RemoteObject):
# ====== Helpers =====
-def touch(fname, mode=0o666, dir_fd=None, **kwargs):
- # create lock file faster
- # https://stackoverflow.com/a/1160227
- flags = os.O_CREAT | os.O_APPEND
- with os.fdopen(os.open(fname, flags=flags, mode=mode, dir_fd=dir_fd)) as f:
- os.utime(
- f.fileno() if os.utime in os.supports_fd else fname,
- dir_fd=None if os.supports_fd else dir_fd,
- **kwargs
- )
+def touch(fname, mode=0o666):
+ pathlib.Path(fname).touch(mode=mode, exist_ok=True)
@contextmanager
def file_lock(filepath):
lock_file = filepath + ".lock"
- while os.path.isfile(lock_file):
- time.sleep(2)
-
- touch(lock_file)
+ while True:
+ try:
+ pathlib.Path(lock_file).touch(exist_ok=False)
+ break
+ except FileExistsError:
+ time.sleep(2)
try:
yield
|
