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Source code for galaxy.tools.imp_exp.export_history

#!/usr/bin/env python
Export a history to an archive file using attribute files.

usage: %prog history_attrs dataset_attrs job_attrs out_file
    -G, --gzip: gzip archive file
from __future__ import print_function

import optparse
import os
import shutil
import sys

from galaxy.model.store import tar_export_directory
from galaxy.util import unicodify

[docs]def create_archive(export_directory, out_file, gzip=False): """Create archive from the given attribute/metadata files and save it to out_file.""" try: tar_export_directory(export_directory, out_file, gzip) # Status. print('Created history archive.') return 0 except Exception as e: print('Error creating history archive: %s' % unicodify(e), file=sys.stderr) return 1
[docs]def main(argv=None): # Parse command line. parser = optparse.OptionParser() parser.add_option('-G', '--gzip', dest='gzip', action="store_true", help='Compress archive using gzip.') parser.add_option('--galaxy-version', dest='galaxy_version', help='Galaxy version that initiated the command.', default=None) (options, args) = parser.parse_args(argv) galaxy_version = options.galaxy_version if galaxy_version is None: galaxy_version = "19.01" if len(args) == 4 else "19.05" gzip = bool(options.gzip) if galaxy_version == "19.01": # This job was created pre 18.0X with old argument style. out_file = args[3] temp_directory = os.path.dirname(args[0]) else: assert len(args) >= 2 # We have a 19.0X directory argument instead of individual arguments. temp_directory = args[0] out_file = args[1] if galaxy_version == "19.01": history_attrs = os.path.join(temp_directory, 'history_attrs.txt') dataset_attrs = os.path.join(temp_directory, 'datasets_attrs.txt') job_attrs = os.path.join(temp_directory, 'jobs_attrs.txt') shutil.move(args[0], history_attrs) shutil.move(args[1], dataset_attrs) provenance_path = args[1] + ".provenance" if os.path.exists(provenance_path): shutil.move(provenance_path, dataset_attrs + ".provenance") shutil.move(args[2], job_attrs) # Create archive. return create_archive(temp_directory, out_file, gzip=gzip)
if __name__ == "__main__": main()