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Source code for galaxy.tools.imp_exp.unpack_tar_gz_archive

#!/usr/bin/env python
Unpack a tar or tar.gz archive into a directory.

usage: %prog archive_source dest_dir
    --[url|file] source type, either a URL or a file.
from __future__ import print_function

import math
import optparse
import os
import tarfile
import tempfile
from base64 import b64decode

import requests

# Set max size of archive/file that will be handled to be 100 GB. This is
# arbitrary and should be adjusted as needed.
MAX_SIZE = 100 * math.pow(2, 30)

[docs]def url_to_file(url, dest_file): """ Transfer a file from a remote URL to a temporary file. """ url_reader = requests.get(url, stream=True) assert url_reader.ok, "History import failed, server returned '%s'" % url_reader.reason CHUNK = 10 * 1024 # 10k total = 0 with open(dest_file, 'wb') as fp: for chunk in url_reader.iter_content(chunk_size=CHUNK): if chunk: fp.write(chunk) total += CHUNK if total > MAX_SIZE: break return dest_file
[docs]def check_archive(archive_file, dest_dir): """ Ensure that a tar archive has no absolute paths or relative paths outside the archive. """ with tarfile.open(archive_file, mode='r') as archive_fp: for arc_path in archive_fp.getnames(): assert os.path.normpath( os.path.join( dest_dir, arc_path )).startswith(dest_dir.rstrip(os.sep) + os.sep), \ "Archive member would extract outside target directory: %s" % arc_path return True
[docs]def unpack_archive(archive_file, dest_dir): """ Unpack a tar and/or gzipped archive into a destination directory. """ archive_fp = tarfile.open(archive_file, mode='r') archive_fp.extractall(path=dest_dir) archive_fp.close()
[docs]def main(options, args): is_url = bool(options.is_url) is_file = bool(options.is_file) archive_source, dest_dir = args if options.is_b64encoded: archive_source = b64decode(archive_source).decode('utf-8') dest_dir = b64decode(dest_dir).decode('utf-8') # Get archive from URL. if is_url: archive_file = url_to_file(archive_source, tempfile.NamedTemporaryFile(dir=dest_dir).name) elif is_file: archive_file = archive_source # Unpack archive. check_archive(archive_file, dest_dir) unpack_archive(archive_file, dest_dir)
if __name__ == "__main__": # Parse command line. parser = optparse.OptionParser() parser.add_option('-U', '--url', dest='is_url', action="store_true", help='Source is a URL.') parser.add_option('-F', '--file', dest='is_file', action="store_true", help='Source is a file.') parser.add_option('-e', '--encoded', dest='is_b64encoded', action="store_true", default=False, help='Source and destination dir values are base64 encoded.') (options, args) = parser.parse_args() main(options, args)