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Source code for galaxy.util.compression_utils
import bz2
import gzip
import io
import logging
import lzma
import os
import shutil
import tarfile
import tempfile
import zipfile
from typing import (
Any,
cast,
Generator,
IO,
Iterable,
List,
Optional,
overload,
Tuple,
Union,
)
from typing_extensions import Literal
from galaxy.util.path import (
safe_relpath,
StrPath,
)
from .checkers import (
is_bz2,
is_gzip,
is_xz,
)
try:
from isal import isal_zlib
except ImportError:
isal_zlib = None # type: ignore[assignment,unused-ignore]
log = logging.getLogger(__name__)
FileObjTypeStr = Union[IO[str], io.TextIOWrapper]
FileObjTypeBytes = Union[gzip.GzipFile, bz2.BZ2File, lzma.LZMAFile, IO[bytes]]
FileObjType = Union[FileObjTypeStr, FileObjTypeBytes]
@overload
def get_fileobj(
filename: str, mode: Literal["r"], compressed_formats: Optional[List[str]] = None
) -> FileObjTypeStr: ...
@overload
def get_fileobj(
filename: str, mode: Literal["rb"], compressed_formats: Optional[List[str]] = None
) -> FileObjTypeBytes: ...
@overload
def get_fileobj(filename: str) -> FileObjTypeStr: ...
@overload
def get_fileobj(filename: str, mode: str = "r", compressed_formats: Optional[List[str]] = None) -> FileObjType: ...
[docs]def get_fileobj(filename: str, mode: str = "r", compressed_formats: Optional[List[str]] = None) -> FileObjType:
"""
Returns a fileobj. If the file is compressed, return an appropriate file
reader. In text mode, always use 'utf-8' encoding.
:param filename: path to file that should be opened
:param mode: mode to pass to opener
:param compressed_formats: list of allowed compressed file formats among
'bz2', 'gzip', 'xz' and 'zip'. If left to None, all 3 formats are allowed
"""
return get_fileobj_raw(filename, mode, compressed_formats)[1]
@overload
def get_fileobj_raw(
filename: str, mode: Literal["r"], compressed_formats: Optional[List[str]] = None
) -> Tuple[Optional[str], FileObjTypeStr]: ...
@overload
def get_fileobj_raw(
filename: str, mode: Literal["rb"], compressed_formats: Optional[List[str]] = None
) -> Tuple[Optional[str], FileObjTypeBytes]: ...
@overload
def get_fileobj_raw(filename: str) -> Tuple[Optional[str], FileObjTypeStr]: ...
@overload
def get_fileobj_raw(
filename: str, mode: str = "r", compressed_formats: Optional[List[str]] = None
) -> Tuple[Optional[str], FileObjType]: ...
[docs]def get_fileobj_raw(
filename: str, mode: str = "r", compressed_formats: Optional[List[str]] = None
) -> Tuple[Optional[str], FileObjType]:
if compressed_formats is None:
compressed_formats = ["bz2", "gzip", "xz", "zip"]
# Remove 't' from mode, which may cause an error for compressed files
mode = mode.replace("t", "")
# 'U' mode is deprecated, we open in 'r'.
if mode == "U":
mode = "r"
compressed_format = None
if "gzip" in compressed_formats and is_gzip(filename):
fh: Union[gzip.GzipFile, bz2.BZ2File, lzma.LZMAFile, IO[bytes]] = gzip.GzipFile(filename, mode)
compressed_format = "gzip"
elif "bz2" in compressed_formats and is_bz2(filename):
mode = cast(Literal["a", "ab", "r", "rb", "w", "wb", "x", "xb"], mode)
fh = bz2.BZ2File(filename, mode)
compressed_format = "bz2"
elif "xz" in compressed_formats and is_xz(filename):
mode = cast(Literal["a", "ab", "r", "rb", "w", "wb", "x", "xb"], mode)
fh = lzma.LZMAFile(filename, mode)
compressed_format = "xz"
elif "zip" in compressed_formats and zipfile.is_zipfile(filename):
# Return fileobj for the first file in a zip file.
# 'b' is not allowed in the ZipFile mode argument
# since it always opens files in binary mode.
# For emulating text mode, we will be returning the binary fh in a
# TextIOWrapper.
zf_mode = cast(Literal["r", "w"], mode.replace("b", ""))
with zipfile.ZipFile(filename, zf_mode) as zh:
fh = zh.open(zh.namelist()[0], zf_mode)
compressed_format = "zip"
elif "b" in mode:
return compressed_format, open(filename, mode)
else:
return compressed_format, open(filename, mode, encoding="utf-8")
if "b" not in mode:
return compressed_format, io.TextIOWrapper(cast(IO[bytes], fh), encoding="utf-8")
else:
return compressed_format, fh
[docs]def file_iter(fname: str, sep: Optional[Any] = None) -> Generator[Union[List[bytes], Any, List[str]], None, None]:
"""
This generator iterates over a file and yields its lines
splitted via the C{sep} parameter. Skips empty lines and lines starting with
the C{#} character.
>>> lines = [ line for line in file_iter(__file__) ]
>>> len(lines) != 0
True
"""
with get_fileobj(fname) as fh:
for line in fh:
if line and line[0] != "#":
yield line.split(sep)
ArchiveMemberType = Union[tarfile.TarInfo, zipfile.ZipInfo]
[docs]def decompress_bytes_to_directory(content: bytes) -> str:
temp_directory = tempfile.mkdtemp()
with tempfile.NamedTemporaryFile(delete=False) as fp:
fp.write(content)
fp.close()
return CompressedFile(fp.name).extract(temp_directory)
[docs]def decompress_path_to_directory(path: str) -> str:
temp_directory = tempfile.mkdtemp()
return CompressedFile(path).extract(temp_directory)
[docs]class CompressedFile:
archive: Union[tarfile.TarFile, zipfile.ZipFile]
[docs] @staticmethod
def can_decompress(file_path: StrPath) -> bool:
return tarfile.is_tarfile(file_path) or zipfile.is_zipfile(file_path)
[docs] def __init__(self, file_path: StrPath, mode: str = "r") -> None:
file_path_str = str(file_path)
if tarfile.is_tarfile(file_path):
self.file_type = "tar"
elif zipfile.is_zipfile(file_path) and not file_path_str.endswith(".jar"):
self.file_type = "zip"
self.file_name = os.path.splitext(os.path.basename(file_path))[0]
if self.file_name.endswith(".tar"):
self.file_name = os.path.splitext(self.file_name)[0]
self.type = self.file_type
method = f"open_{self.file_type}"
if hasattr(self, method):
self.archive = getattr(self, method)(file_path, mode)
else:
raise NameError(f"File type {self.file_type} specified, no open method found.")
@property
def common_prefix_dir(self) -> str:
"""
Get the common prefix directory for all the files in the archive, if any.
Returns '' if the archive contains multiple files and/or directories at
the root of the archive.
"""
contents = self.getmembers()
common_prefix = ""
if len(contents) > 1:
common_prefix = os.path.commonprefix([self.getname(item) for item in contents])
# If the common_prefix does not end with a slash, check that is a
# directory and all other files are contained in it
common_prefix_member = self.getmember(common_prefix)
if (
len(common_prefix) >= 1
and not common_prefix.endswith(os.sep)
and common_prefix_member
and self.isdir(common_prefix_member)
and all(self.getname(item).startswith(common_prefix + os.sep) for item in contents if self.isfile(item))
):
common_prefix += os.sep
if not common_prefix.endswith(os.sep):
common_prefix = ""
return common_prefix
[docs] def extract(self, path: StrPath) -> str:
"""Determine the path to which the archive should be extracted."""
contents = self.getmembers()
extraction_path = path
common_prefix_dir = self.common_prefix_dir
if len(contents) == 1:
# The archive contains a single file, return the extraction path.
if self.isfile(contents[0]):
extraction_path = os.path.join(path, self.file_name)
if not os.path.exists(extraction_path):
os.makedirs(extraction_path)
if isinstance(self.archive, tarfile.TarFile):
members_t = cast(Iterable[tarfile.TarInfo], self.safemembers())
self.archive.extractall(extraction_path, members=members_t)
else:
members_z = cast(Iterable[str], self.safemembers())
self.archive.extractall(extraction_path, members=members_z)
else:
if not common_prefix_dir:
extraction_path = os.path.join(path, self.file_name)
if not os.path.exists(extraction_path):
os.makedirs(extraction_path)
if isinstance(self.archive, tarfile.TarFile):
members_t = cast(Iterable[tarfile.TarInfo], self.safemembers())
self.archive.extractall(extraction_path, members=members_t)
else:
members_z = cast(Iterable[str], self.safemembers())
self.archive.extractall(extraction_path, members=members_z)
# Since .zip files store unix permissions separately, we need to iterate through the zip file
# and set permissions on extracted members.
if self.file_type == "zip":
assert isinstance(self.archive, zipfile.ZipFile)
for zipped_file in contents:
filename = self.getname(zipped_file)
absolute_filepath = os.path.join(extraction_path, filename)
external_attributes = self.archive.getinfo(filename).external_attr
# The 2 least significant bytes are irrelevant, the next two contain unix permissions.
unix_permissions = external_attributes >> 16
if unix_permissions != 0:
if os.path.exists(absolute_filepath):
os.chmod(absolute_filepath, unix_permissions)
else:
log.warning(
f"Unable to change permission on extracted file '{absolute_filepath}' as it does not exist"
)
return os.path.abspath(os.path.join(extraction_path, common_prefix_dir))
[docs] def safemembers(self) -> Union[Iterable[tarfile.TarInfo], Iterable[str]]:
members = self.archive
common_prefix_dir = self.common_prefix_dir
if self.file_type == "tar":
assert isinstance(members, tarfile.TarFile)
for finfo in members:
if not safe_relpath(finfo.name):
raise Exception(f"Path '{finfo.name}' is blocked (illegal path).")
if finfo.issym() or finfo.islnk():
link_target = os.path.join(os.path.dirname(finfo.name), finfo.linkname)
if not safe_relpath(link_target) or not os.path.normpath(link_target).startswith(common_prefix_dir):
raise Exception(f"Link '{finfo.name}' to '{finfo.linkname}' is blocked.")
yield finfo
elif self.file_type == "zip":
assert isinstance(members, zipfile.ZipFile)
for name in members.namelist():
if not safe_relpath(name):
raise Exception(f"{name} is blocked (illegal path).")
yield name
[docs] def getmembers_tar(self) -> List[tarfile.TarInfo]:
assert isinstance(self.archive, tarfile.TarFile)
return self.archive.getmembers()
[docs] def getmembers_zip(self) -> List[zipfile.ZipInfo]:
assert isinstance(self.archive, zipfile.ZipFile)
return self.archive.infolist()
[docs] def getmember(self, name: str) -> Optional[ArchiveMemberType]:
for member in self.getmembers():
if self.getname(member) == name:
return member
return None
[docs] def getmembers(self) -> List[ArchiveMemberType]:
return cast(List[ArchiveMemberType], getattr(self, f"getmembers_{self.type}")())
[docs] def getname(self, member: ArchiveMemberType) -> str:
return cast(str, getattr(self, f"getname_{self.type}")(member))
[docs] def isdir(self, member: ArchiveMemberType) -> bool:
return cast(bool, getattr(self, f"isdir_{self.type}")(member))
[docs] def isdir_zip(self, member: zipfile.ZipInfo) -> bool:
if member.filename.endswith(os.sep):
return True
return False
[docs] def isfile(self, member: ArchiveMemberType) -> bool:
if not self.isdir(member):
return True
return False
[docs] def open_tar(self, filepath: StrPath, mode: str) -> tarfile.TarFile:
return tarfile.open(filepath, mode, errorlevel=0)
[docs] def open_zip(self, filepath: StrPath, mode: str) -> zipfile.ZipFile:
mode = cast(Literal["a", "r", "w", "x"], mode)
return zipfile.ZipFile(filepath, mode)
[docs] def zipfile_ok(self, path_to_archive: StrPath) -> bool:
"""
This function is a bit pedantic and not functionally necessary. It checks whether there is
no file pointing outside of the extraction, because ZipFile.extractall() has some potential
security holes. See python zipfile documentation for more details.
"""
basename = os.path.realpath(os.path.dirname(path_to_archive))
zip_archive = zipfile.ZipFile(path_to_archive)
for member in zip_archive.namelist():
member_path = os.path.realpath(os.path.join(basename, member))
if not member_path.startswith(basename):
return False
return True
[docs]class FastZipFile(zipfile.ZipFile):
"""
Simple wrapper around ZipFile that uses the default compression strategy of ISA-L
to write zip files. Ignores compresslevel and compresstype arguments, and is
3 to 4 times faster than the zlib implementation at the default compression level.
"""
def _open_to_write(self, *args, **kwargs): # type: ignore[no-untyped-def]
zwf = super()._open_to_write(*args, **kwargs) # type: ignore[misc]
if isal_zlib and self.compression == zipfile.ZIP_DEFLATED:
zwf._compressor = isal_zlib.compressobj(isal_zlib.ISAL_DEFAULT_COMPRESSION, isal_zlib.DEFLATED, -15, 9)
return zwf
# modified from shutil._make_zipfile
[docs]def make_fast_zipfile(
base_name: str,
base_dir: str,
verbose: int = 0,
dry_run: int = 0,
logger: Optional[logging.Logger] = None,
owner: Optional[str] = None,
group: Optional[str] = None,
root_dir: Optional[str] = None,
) -> str:
"""Create a zip file from all the files under 'base_dir'.
The output zip file will be named 'base_name' + ".zip". Returns the
name of the output zip file.
"""
zip_filename = base_name + ".zip"
archive_dir = os.path.dirname(base_name)
if archive_dir and not os.path.exists(archive_dir):
if logger is not None:
logger.info("creating %s", archive_dir)
if not dry_run:
os.makedirs(archive_dir)
if logger is not None:
logger.info("creating '%s' and adding '%s' to it", zip_filename, base_dir)
if not dry_run:
with FastZipFile(zip_filename, mode="w", compression=zipfile.ZIP_DEFLATED) as zf:
arcname = os.path.normpath(base_dir)
if root_dir is not None:
base_dir = os.path.join(root_dir, base_dir)
base_dir = os.path.normpath(base_dir)
if arcname != os.curdir:
zf.write(base_dir, arcname)
if logger is not None:
logger.info("adding '%s'", base_dir)
for dirpath, dirnames, filenames in os.walk(base_dir):
arcdirpath = dirpath
if root_dir is not None:
arcdirpath = os.path.relpath(arcdirpath, root_dir)
arcdirpath = os.path.normpath(arcdirpath)
for name in sorted(dirnames):
path = os.path.join(dirpath, name)
arcname = os.path.join(arcdirpath, name)
zf.write(path, arcname)
if logger is not None:
logger.info("adding '%s'", path)
for name in filenames:
path = os.path.join(dirpath, name)
path = os.path.normpath(path)
if os.path.isfile(path):
arcname = os.path.join(arcdirpath, name)
zf.write(path, arcname)
if logger is not None:
logger.info("adding '%s'", path)
if root_dir is not None:
zip_filename = os.path.abspath(zip_filename)
return zip_filename
shutil.register_archive_format("fastzip", make_fast_zipfile)