import hashlib
import logging
import os
import shutil
import stat
import sys
import tempfile
import uuid
from collections.abc import Iterator, Iterable
from contextlib import contextmanager
from io import BytesIO
from typing import IO, Any, Callable, Optional, Protocol, Union
from toil.lib.memoize import memoize
from toil.lib.misc import StrPath
logger = logging.getLogger(__name__)
[docs]
@memoize
def get_toil_home() -> str:
"""
Get the Toil home directory for storing configuration and global state.
Raises an error if it does not exist and cannot be created. Safe to run
simultaneously in multiple processes.
"""
# TODO: should this use an XDG config directory or ~/.config to not clutter the
# base home directory?
toil_home_dir = os.path.join(os.path.expanduser("~"), ".toil")
dir_path = try_path(toil_home_dir)
if dir_path is None:
raise RuntimeError(
f"Cannot create or access Toil configuration directory {toil_home_dir}"
)
return dir_path
TOIL_URI_SCHEME = "toilfile:"
STANDARD_SCHEMES = ["http:", "https:", "s3:", "gs:", "ftp:"]
REMOTE_SCHEMES = STANDARD_SCHEMES + [TOIL_URI_SCHEME]
ALL_SCHEMES = REMOTE_SCHEMES + ["file:"]
[docs]
def is_standard_url(filename: str) -> bool:
"""
Return True if the given URL is a non-Toil, non-file: URL.
"""
return is_url_with_scheme(filename, STANDARD_SCHEMES)
[docs]
def is_remote_url(filename: str) -> bool:
"""
Decide if a filename is a known, non-file kind of URL
"""
return is_url_with_scheme(filename, REMOTE_SCHEMES)
[docs]
def is_any_url(filename: str) -> bool:
"""
Decide if a string is a URI like http:// or file://.
Otherwise it might be a bare path.
"""
return is_url_with_scheme(filename, ALL_SCHEMES)
[docs]
def is_url_with_scheme(filename: str, schemes: list[str]) -> bool:
"""
Return True if filename is a URL with any of the given schemes and False otherwise.
"""
# TODO: "http:myfile.dat" is a valid filename and *not* a valid URL
for scheme in schemes:
if filename.startswith(scheme):
return True
return False
[docs]
def is_toil_url(filename: str) -> bool:
"""
Return True if a URL is a toilfile: URL.
"""
return is_url_with_scheme(filename, [TOIL_URI_SCHEME])
[docs]
def is_file_url(filename: str) -> bool:
"""
Return True if a URL is a file: URL.
Will return False for bare paths.
"""
return is_url_with_scheme(filename, ["file:"])
[docs]
def mkdtemp(
suffix: Optional[str] = None,
prefix: Optional[str] = None,
dir: Optional[StrPath] = 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 directory 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: StrPath) -> 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 str(final_path)
final_basename = os.path.basename(final_path)
final_ext = os.path.splitext(final_path)[1]
base_name = f"{final_basename}.{str(uuid.uuid4())}.tmp{final_ext}"
return os.path.join(final_dir, base_name)
[docs]
def atomic_install(tmp_path: StrPath, final_path: StrPath) -> 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: StrPath, 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 actual 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_path1 = os.path.join(in_directory, suggested_name)
try:
os.mkdir(generated_dir_path1)
os.chmod(generated_dir_path1, 0o777)
return generated_dir_path1
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(uuid.uuid4()).replace("-", "")[:i]
generated_dir_path2 = os.path.join(in_directory, truncated_uuid)
try:
os.mkdir(generated_dir_path2)
os.chmod(generated_dir_path2, 0o777)
return generated_dir_path2
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: list[Callable[[int], None]] = []
[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: bytes) -> None:
"""
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: Iterable[bytes]) -> None:
"""
Write each string from the given iterable, without newlines.
"""
for data in datas:
self.write(data)
[docs]
def flush(self) -> None:
"""
Flush the backing stream.
"""
self.backingStream.flush()
[docs]
def close(self) -> None:
"""
Close the backing stream.
"""
self.backingStream.close()
[docs]
class ReadableFileObj(Protocol):
"""
Protocol that is more specific than what file_digest takes as an argument.
Also guarantees a read() method.
Would extend the protocol from Typeshed for hashlib but those are only
declared for 3.11+.
"""
[docs]
def readinto(self, buf: bytearray, /) -> int: ...
[docs]
def readable(self) -> bool: ...
[docs]
def read(self, number: int) -> bytes: ...
# hashlib._Hash seems to not appear at runtime
[docs]
def file_digest(f: ReadableFileObj, alg_name: str) -> "hashlib._Hash":
"""
Polyfilled hashlib.file_digest that works on Python <3.11.
"""
if sys.version_info >= (3, 11):
return hashlib.file_digest(f, alg_name)
BUFFER_SIZE = 1024 * 1024
hasher = hashlib.new(alg_name)
buffer = f.read(BUFFER_SIZE)
while buffer:
hasher.update(buffer)
buffer = f.read(BUFFER_SIZE)
return hasher
