# Copyright (c) 2018 The Pooch Developers.
# Distributed under the terms of the BSD 3-Clause License.
# SPDX-License-Identifier: BSD-3-Clause
#
# This code is part of the Fatiando a Terra project (https://www.fatiando.org)
#
# pylint: disable=line-too-long
"""
Post-processing hooks
"""
import abc
import os
import bz2
import gzip
import lzma
import shutil
from zipfile import ZipFile
from tarfile import TarFile
from .utils import get_logger
class ExtractorProcessor(abc.ABC): # pylint: disable=too-few-public-methods
"""
Abstract base class for extractions from compressed archives.
Subclasses can be used with :meth:`pooch.Pooch.fetch` and
:func:`pooch.retrieve` to unzip a downloaded data file into a folder in the
local data store. :meth:`~pooch.Pooch.fetch` will return a list with the
names of the extracted files instead of the archive.
Parameters
----------
members : list or None
If None, will unpack all files in the archive. Otherwise, *members*
must be a list of file names to unpack from the archive. Only these
files will be unpacked.
extract_dir : str or None
If None, files will be unpacked to the default location (a folder in
the same location as the downloaded zip file, with a suffix added).
Otherwise, files will be unpacked to ``extract_dir``, which is
interpreted as a *relative path* (relative to the cache location
provided by :func:`pooch.retrieve` or :meth:`pooch.Pooch.fetch`).
"""
def __init__(self, members=None, extract_dir=None):
self.members = members
self.extract_dir = extract_dir
@property
@abc.abstractmethod
def suffix(self):
"""
String appended to unpacked archive folder name.
Only used if extract_dir is None.
MUST BE IMPLEMENTED BY CHILD CLASSES.
"""
@abc.abstractmethod
def _all_members(self, fname):
"""
Return all the members in the archive.
MUST BE IMPLEMENTED BY CHILD CLASSES.
"""
@abc.abstractmethod
def _extract_file(self, fname, extract_dir):
"""
This method receives an argument for the archive to extract and the
destination path.
MUST BE IMPLEMENTED BY CHILD CLASSES.
"""
def __call__(self, fname, action, pooch):
"""
Extract all files from the given archive.
Parameters
----------
fname : str
Full path of the zipped file in local storage.
action : str
Indicates what action was taken by :meth:`pooch.Pooch.fetch` or
:func:`pooch.retrieve`:
* ``"download"``: File didn't exist locally and was downloaded
* ``"update"``: Local file was outdated and was re-download
* ``"fetch"``: File exists and is updated so it wasn't downloaded
pooch : :class:`pooch.Pooch`
The instance of :class:`pooch.Pooch` that is calling this.
Returns
-------
fnames : list of str
A list of the full path to all files in the extracted archive.
"""
if self.extract_dir is None:
self.extract_dir = fname + self.suffix
else:
archive_dir = fname.rsplit(os.path.sep, maxsplit=1)[0]
self.extract_dir = os.path.join(archive_dir, self.extract_dir)
# Get a list of everyone who is supposed to be in the unpacked folder
# so we can check if they are all there or if we need to extract new
# files.
if self.members is None or not self.members:
members = self._all_members(fname)
else:
members = self.members
if (
(action in ("update", "download"))
or (not os.path.exists(self.extract_dir))
or not all(
os.path.exists(os.path.join(self.extract_dir, m)) for m in members
)
):
# Make sure that the folder with the extracted files exists
os.makedirs(self.extract_dir, exist_ok=True)
self._extract_file(fname, self.extract_dir)
# Get a list of all file names (including subdirectories) in our folder
# of unzipped files, filtered by the given members list
fnames = []
for path, _, files in os.walk(self.extract_dir):
for filename in files:
relpath = os.path.normpath(
os.path.join(os.path.relpath(path, self.extract_dir), filename)
)
if self.members is None or any(
relpath.startswith(os.path.normpath(m)) for m in self.members
):
fnames.append(os.path.join(path, filename))
return fnames
[docs]
class Unzip(ExtractorProcessor): # pylint: disable=too-few-public-methods
"""
Processor that unpacks a zip archive and returns a list of all files.
Use with :meth:`pooch.Pooch.fetch` or :func:`pooch.retrieve` to unzip a
downloaded data file into a folder in the local data store. The
method/function will return a list with the names of the unzipped files
instead of the zip archive.
The output folder is ``{fname}.unzip``.
Parameters
----------
members : list or None
If None, will unpack all files in the zip archive. Otherwise, *members*
must be a list of file names to unpack from the archive. Only these
files will be unpacked.
extract_dir : str or None
If None, files will be unpacked to the default location (a folder in
the same location as the downloaded zip file, with the suffix
``.unzip`` added). Otherwise, files will be unpacked to
``extract_dir``, which is interpreted as a *relative path* (relative to
the cache location provided by :func:`pooch.retrieve` or
:meth:`pooch.Pooch.fetch`).
"""
@property
def suffix(self):
"""
String appended to unpacked archive folder name.
Only used if extract_dir is None.
"""
return ".unzip"
def _all_members(self, fname):
"""Return all members from a given archive."""
with ZipFile(fname, "r") as zip_file:
return zip_file.namelist()
def _extract_file(self, fname, extract_dir):
"""
This method receives an argument for the archive to extract and the
destination path.
"""
with ZipFile(fname, "r") as zip_file:
if self.members is None:
get_logger().info(
"Unzipping contents of '%s' to '%s'", fname, extract_dir
)
# Unpack all files from the archive into our new folder
zip_file.extractall(path=extract_dir)
else:
for member in self.members:
get_logger().info(
"Extracting '%s' from '%s' to '%s'", member, fname, extract_dir
)
# If the member is a dir, we need to get the names of the
# elements it contains for extraction (ZipFile does not
# support dirs on .extract). If it's not a dir, this will
# only include the member itself.
# Based on:
# https://stackoverflow.com/questions/8008829/extract-only-a-single-directory-from-tar
subdir_members = [
name
for name in zip_file.namelist()
if os.path.normpath(name).startswith(os.path.normpath(member))
]
# Extract the data file from within the archive
zip_file.extractall(members=subdir_members, path=extract_dir)
[docs]
class Untar(ExtractorProcessor): # pylint: disable=too-few-public-methods
"""
Processor that unpacks a tar archive and returns a list of all files.
Use with :meth:`pooch.Pooch.fetch` or :func:`pooch.retrieve` to untar a
downloaded data file into a folder in the local data store. The
method/function will return a list with the names of the extracted files
instead of the archive.
The output folder is ``{fname}.untar``.
Parameters
----------
members : list or None
If None, will unpack all files in the archive. Otherwise, *members*
must be a list of file names to unpack from the archive. Only these
files will be unpacked.
extract_dir : str or None
If None, files will be unpacked to the default location (a folder in
the same location as the downloaded tar file, with the suffix
``.untar`` added). Otherwise, files will be unpacked to
``extract_dir``, which is interpreted as a *relative path* (relative to
the cache location provided by :func:`pooch.retrieve` or
:meth:`pooch.Pooch.fetch`).
"""
@property
def suffix(self):
"""
String appended to unpacked archive folder name.
Only used if extract_dir is None.
"""
return ".untar"
def _all_members(self, fname):
"""Return all members from a given archive."""
with TarFile.open(fname, "r") as tar_file:
return [info.name for info in tar_file.getmembers()]
def _extract_file(self, fname, extract_dir):
"""
This method receives an argument for the archive to extract and the
destination path.
"""
with TarFile.open(fname, "r") as tar_file:
if self.members is None:
get_logger().info(
"Untarring contents of '%s' to '%s'", fname, extract_dir
)
# Unpack all files from the archive into our new folder
tar_file.extractall(path=extract_dir)
else:
for member in self.members:
get_logger().info(
"Extracting '%s' from '%s' to '%s'", member, fname, extract_dir
)
# If the member is a dir, we need to get the names of the
# elements it contains for extraction (TarFile does not
# support dirs on .extract). If it's not a dir, this will
# only include the member itself.
# Based on:
# https://stackoverflow.com/questions/8008829/extract-only-a-single-directory-from-tar
# Can't use .getnames because extractall expects TarInfo
# objects.
subdir_members = [
info
for info in tar_file.getmembers()
if os.path.normpath(info.name).startswith(
os.path.normpath(member)
)
]
# Extract the data file from within the archive
tar_file.extractall(members=subdir_members, path=extract_dir)
[docs]
class Decompress: # pylint: disable=too-few-public-methods
"""
Processor that decompress a file and returns the decompressed version.
Use with :meth:`pooch.Pooch.fetch` or :func:`pooch.retrieve` to decompress
a downloaded data file so that it can be easily opened. Useful for data
files that take a long time to decompress (exchanging disk space for
speed).
Supported decompression methods are LZMA (``.xz``), bzip2 (``.bz2``), and
gzip (``.gz``).
File names with the standard extensions (see above) can use
``method="auto"`` to automatically determine the compression method. This
can be overwritten by setting the *method* argument.
.. note::
To unpack zip and tar archives with one or more files, use
:class:`pooch.Unzip` and :class:`pooch.Untar` instead.
The output file is ``{fname}.decomp`` by default but it can be changed by
setting the ``name`` parameter.
.. warning::
Passing in ``name`` can cause existing data to be lost! For example, if
a file already exists with the specified name it will be overwritten
with the new decompressed file content. **Use this option with
caution.**
Parameters
----------
method : str
Name of the compression method. Can be "auto", "lzma", "xz", "bzip2",
or "gzip".
name : None or str
Defines the decompressed file name. The file name will be
``{fname}.decomp`` if ``None`` (default) or the given name otherwise.
Note that the name should **not** include the full (or relative) path,
it should be just the file name itself.
"""
modules = {"auto": None, "lzma": lzma, "xz": lzma, "gzip": gzip, "bzip2": bz2}
extensions = {".xz": "lzma", ".gz": "gzip", ".bz2": "bzip2"}
def __init__(self, method="auto", name=None):
self.method = method
self.name = name
[docs]
def __call__(self, fname, action, pooch):
"""
Decompress the given file.
The output file will be either ``{fname}.decomp`` or the given *name*
class attribute.
Parameters
----------
fname : str
Full path of the compressed file in local storage.
action : str
Indicates what action was taken by :meth:`pooch.Pooch.fetch` or
:func:`pooch.retrieve`:
- ``"download"``: File didn't exist locally and was downloaded
- ``"update"``: Local file was outdated and was re-download
- ``"fetch"``: File exists and is updated so it wasn't downloaded
pooch : :class:`pooch.Pooch`
The instance of :class:`pooch.Pooch` that is calling this.
Returns
-------
fname : str
The full path to the decompressed file.
"""
if self.name is None:
decompressed = fname + ".decomp"
else:
decompressed = os.path.join(os.path.dirname(fname), self.name)
if action in ("update", "download") or not os.path.exists(decompressed):
get_logger().info(
"Decompressing '%s' to '%s' using method '%s'.",
fname,
decompressed,
self.method,
)
module = self._compression_module(fname)
with open(decompressed, "w+b") as output:
with module.open(fname) as compressed:
shutil.copyfileobj(compressed, output)
return decompressed
def _compression_module(self, fname):
"""
Get the Python module compatible with fname and the chosen method.
If the *method* attribute is "auto", will select a method based on the
extension. If no recognized extension is in the file name, will raise a
ValueError.
"""
error_archives = "To unpack zip/tar archives, use pooch.Unzip/Untar instead."
if self.method not in self.modules:
message = (
f"Invalid compression method '{self.method}'. "
f"Must be one of '{list(self.modules.keys())}'."
)
if self.method in {"zip", "tar"}:
message = " ".join([message, error_archives])
raise ValueError(message)
if self.method == "auto":
ext = os.path.splitext(fname)[-1]
if ext not in self.extensions:
message = (
f"Unrecognized file extension '{ext}'. "
f"Must be one of '{list(self.extensions.keys())}'."
)
if ext in {".zip", ".tar"}:
message = " ".join([message, error_archives])
raise ValueError(message)
return self.modules[self.extensions[ext]]
return self.modules[self.method]