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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.

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

from galaxy.datatypes import sniff

# 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 get_file_sources(file_sources_path): assert os.path.exists(file_sources_path), f"file sources path [{file_sources_path}] does not exist" from galaxy.files import ConfiguredFileSources with open(file_sources_path) as f: file_sources_as_dict = json.load(f) file_sources = ConfiguredFileSources.from_dict(file_sources_as_dict) return file_sources
[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 ), f"Archive member would extract outside target directory: {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 = sniff.stream_url_to_file(archive_source, file_sources=get_file_sources(options.file_sources)) 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.", ) parser.add_option("--file-sources", type=str, help="file sources json") (options, args) = parser.parse_args() main(options, args)