import logging
import os
import shutil
import stat
import tempfile
import uuid
from contextlib import contextmanager
from io import BytesIO
from typing import IO, Any, Callable, Iterator, Optional, Union
logger = logging.getLogger(__name__)
[docs]
def mkdtemp(suffix: Optional[str] = None, prefix: Optional[str] = None, dir: Optional[str] = None) -> str:
"""
Make a temporary directory like tempfile.mkdtemp, but with relaxed permissions.
The permissions on the directory will be 711 instead of 700, allowing the
group and all other users to traverse the directory. This is necessary if
the direcotry is on NFS and the Docker daemon would like to mount it or a
file inside it into a container, because on NFS even the Docker daemon
appears bound by the file permissions.
See <https://github.com/DataBiosphere/toil/issues/4644>, and
<https://stackoverflow.com/a/67928880> which talks about a similar problem
but in the context of user namespaces.
"""
# Make the directory
result = tempfile.mkdtemp(suffix=suffix, prefix=prefix, dir=dir)
# Grant all the permissions: full control for user, and execute for group and other
os.chmod(result, stat.S_IRUSR | stat.S_IWUSR | stat.S_IXUSR | stat.S_IXGRP | stat.S_IXOTH)
# Return the path created
return result
[docs]
def robust_rmtree(path: Union[str, bytes]) -> None:
"""
Robustly tries to delete paths.
Continues silently if the path to be removed is already gone, or if it
goes away while this function is executing.
May raise an error if a path changes between file and directory while the
function is executing, or if a permission error is encountered.
"""
# TODO: only allow str or bytes as an input
if not isinstance(path, bytes):
# Internally we must work in bytes, in case we find an undecodeable
# filename.
path = path.encode('utf-8')
if not os.path.exists(path):
# Nothing to do!
return
if not os.path.islink(path) and os.path.isdir(path):
# It is or has been a directory
try:
children = os.listdir(path)
except FileNotFoundError:
# Directory went away
return
except OSError as exc:
if exc.errno == 16:
# 'Device or resource busy'
return
raise
# We assume the directory going away while we have it open won't upset
# the listdir iterator.
for child in children:
# Get the path for each child item in the directory
child_path = os.path.join(path, child)
# Remove it if still present
robust_rmtree(child_path)
try:
# Actually remove the directory once the children are gone
shutil.rmtree(path)
except FileNotFoundError:
# Directory went away
return
except OSError as exc:
if exc.errno == 16:
# 'Device or resource busy'
return
raise
else:
# It is not or was not a directory.
try:
# Unlink it as a normal file
os.unlink(path)
except FileNotFoundError:
# File went away
return
except OSError as exc:
if exc.errno == 16:
# 'Device or resource busy'
return
raise
[docs]
def atomic_tmp_file(final_path: str) -> str:
"""Return a tmp file name to use with atomic_install. This will be in the
same directory as final_path. The temporary file will have the same extension
as finalPath. It the final path is in /dev (/dev/null, /dev/stdout), it is
returned unchanged and atomic_tmp_install will do nothing."""
final_dir = os.path.dirname(os.path.normpath(final_path)) # can be empty
if final_dir == '/dev':
return final_path
final_basename = os.path.basename(final_path)
final_ext = os.path.splitext(final_path)[1]
base_name = f"{final_basename}.{uuid.uuid4()}.tmp{final_ext}"
return os.path.join(final_dir, base_name)
[docs]
def atomic_install(tmp_path, final_path) -> None:
"""atomic install of tmp_path as final_path"""
if os.path.dirname(os.path.normpath(final_path)) != '/dev':
os.rename(tmp_path, final_path)
[docs]
@contextmanager
def AtomicFileCreate(final_path: str, keep: bool = False) -> Iterator[str]:
"""Context manager to create a temporary file. Entering returns path to
the temporary file in the same directory as finalPath. If the code in
context succeeds, the file renamed to its actually name. If an error
occurs, the file is not installed and is removed unless keep is specified.
"""
tmp_path = atomic_tmp_file(final_path)
try:
yield tmp_path
atomic_install(tmp_path, final_path)
except Exception:
if not keep:
try:
os.unlink(tmp_path)
except Exception:
pass
raise
[docs]
def atomic_copy(src_path: str, dest_path: str, executable: Optional[bool] = None) -> None:
"""Copy a file using posix atomic creations semantics."""
if executable is None:
executable = os.stat(src_path).st_mode & stat.S_IXUSR != 0
with AtomicFileCreate(dest_path) as dest_path_tmp:
shutil.copyfile(src_path, dest_path_tmp)
if executable:
os.chmod(dest_path_tmp, os.stat(dest_path_tmp).st_mode | stat.S_IXUSR)
[docs]
def atomic_copyobj(src_fh: BytesIO, dest_path: str, length: int = 16384, executable: bool = False) -> None:
"""Copy an open file using posix atomic creations semantics."""
with AtomicFileCreate(dest_path) as dest_path_tmp:
with open(dest_path_tmp, 'wb') as dest_path_fh:
shutil.copyfileobj(src_fh, dest_path_fh, length=length)
if executable:
os.chmod(dest_path_tmp, os.stat(dest_path_tmp).st_mode | stat.S_IXUSR)
[docs]
def make_public_dir(in_directory: str, suggested_name: Optional[str] = None) -> str:
"""
Make a publicly-accessible directory in the given directory.
:param suggested_name: Use this directory name first if possible.
Try to make a random directory name with length 4 that doesn't exist, with the given prefix.
Otherwise, try length 5, length 6, etc, up to a max of 32 (len of uuid4 with dashes replaced).
This function's purpose is mostly to avoid having long file names when generating directories.
If somehow this fails, which should be incredibly unlikely, default to a normal uuid4, which was
our old default.
"""
if suggested_name is not None:
generated_dir_path: str = os.path.join(in_directory, suggested_name)
try:
os.mkdir(generated_dir_path)
os.chmod(generated_dir_path, 0o777)
return generated_dir_path
except FileExistsError:
pass
for i in range(4, 32 + 1): # make random uuids and truncate to lengths starting at 4 and working up to max 32
for _ in range(10): # make 10 attempts for each length
truncated_uuid: str = str(uuid.uuid4()).replace('-', '')[:i]
generated_dir_path: str = os.path.join(in_directory, truncated_uuid)
try:
os.mkdir(generated_dir_path)
os.chmod(generated_dir_path, 0o777)
return generated_dir_path
except FileExistsError:
pass
this_should_never_happen: str = os.path.join(in_directory, str(uuid.uuid4()))
os.mkdir(this_should_never_happen)
os.chmod(this_should_never_happen, 0o777)
return this_should_never_happen
[docs]
def try_path(path: str, min_size: int = 100 * 1024 * 1024) -> Optional[str]:
"""
Try to use the given path. Return it if it exists or can be made,
and we can make things within it, or None otherwise.
:param min_size: Reject paths on filesystems smaller than this many bytes.
"""
try:
os.makedirs(path, exist_ok=True)
except OSError:
# Maybe we lack permissions
return None
if not os.path.exists(path):
# We didn't manage to make it
return None
if not os.access(path, os.W_OK):
# It doesn't look writable
return None
try:
stats = os.statvfs(path)
except OSError:
# Maybe we lack permissions
return None
# Is the filesystem big enough?
# We need to look at the FS size and not the free space so we don't change
# over to a different filesystem when this one fills up.
fs_size = stats.f_frsize * stats.f_blocks
if fs_size < min_size:
# Too small
return None
return path
[docs]
class WriteWatchingStream:
"""
A stream wrapping class that calls any functions passed to onWrite() with the number of bytes written for every write.
Not seekable.
"""
def __init__(self, backingStream: IO[Any]) -> None:
"""
Wrap the given backing stream.
"""
self.backingStream = backingStream
# We have no write listeners yet
self.writeListeners = []
[docs]
def onWrite(self, listener: Callable[[int], None]) -> None:
"""
Call the given listener with the number of bytes written on every write.
"""
self.writeListeners.append(listener)
# Implement the file API from https://docs.python.org/2.4/lib/bltin-file-objects.html
[docs]
def write(self, data):
"""
Write the given data to the file.
"""
# Do the write
self.backingStream.write(data)
for listener in self.writeListeners:
# Send out notifications
listener(len(data))
[docs]
def writelines(self, datas):
"""
Write each string from the given iterable, without newlines.
"""
for data in datas:
self.write(data)
[docs]
def flush(self):
"""
Flush the backing stream.
"""
self.backingStream.flush()
[docs]
def close(self):
"""
Close the backing stream.
"""
self.backingStream.close()
