root/galaxy-central/lib/galaxy/tools/imp_exp/export_history.py

#!/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 galaxy import eggs
from galaxy.util.json import *
import optparse, sys, os, tempfile, tarfile

def create_archive( history_attrs_file, datasets_attrs_file, jobs_attrs_file, out_file, gzip=False ):
    """ Create archive from the given attribute/metadata files and save it to out_file. """
    tarfile_mode = "w"
    if gzip:
        tarfile_mode += ":gz"
    try:
    
        history_archive = tarfile.open( out_file, tarfile_mode )
    
        # Read datasets attributes from file.
        datasets_attr_in = open( datasets_attrs_file, 'rb' )
        datasets_attr_str = ''
        buffsize = 1048576
        try:
            while True:
                datasets_attr_str += datasets_attr_in.read( buffsize )
                if not datasets_attr_str or len( datasets_attr_str ) % buffsize != 0:
                    break
        except OverflowError:
            pass
        datasets_attr_in.close()
        datasets_attrs = from_json_string( datasets_attr_str )
    
        # Add datasets to archive and update dataset attributes.
        # TODO: security check to ensure that files added are in Galaxy dataset directory?
        for dataset_attrs in datasets_attrs:
            dataset_file_name = dataset_attrs[ 'file_name' ] # Full file name.
            dataset_archive_name = os.path.join( "datasets", os.path.split( dataset_file_name )[-1] )
            history_archive.add( dataset_file_name, arcname=dataset_archive_name )
            # Update dataset filename to be archive name.
            dataset_attrs[ 'file_name' ] = dataset_archive_name
    
        # Rewrite dataset attributes file.
        datasets_attrs_out = open( datasets_attrs_file, 'w' )
        datasets_attrs_out.write( to_json_string( datasets_attrs ) )
        datasets_attrs_out.close()
    
        # Finish archive.
        history_archive.add( history_attrs_file, arcname="history_attrs.txt" )
        history_archive.add( datasets_attrs_file, arcname="datasets_attrs.txt" )
        history_archive.add( jobs_attrs_file, arcname="jobs_attrs.txt" )
        history_archive.close()
        
        # Status.
        return 'Created history archive.'
    except Exception, e:
        return 'Error creating history archive: %s' % str( e ), sys.stderr

if __name__ == "__main__":
    # Parse command line.
    parser = optparse.OptionParser()
    parser.add_option( '-G', '--gzip', dest='gzip', action="store_true", help='Compress archive using gzip.' )
    (options, args) = parser.parse_args()    
    gzip = bool( options.gzip )
    history_attrs, dataset_attrs, job_attrs, out_file = args
    
    # Create archive.
    status = create_archive( history_attrs, dataset_attrs, job_attrs, out_file, gzip )
    print status