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

リビジョン 2, 2.8 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1#!/usr/bin/env python
2"""
3Export a history to an archive file using attribute files.
4
5usage: %prog history_attrs dataset_attrs job_attrs out_file
6    -G, --gzip: gzip archive file
7"""
8
9from galaxy import eggs
10from galaxy.util.json import *
11import optparse, sys, os, tempfile, tarfile
12
13def create_archive( history_attrs_file, datasets_attrs_file, jobs_attrs_file, out_file, gzip=False ):
14    """ Create archive from the given attribute/metadata files and save it to out_file. """
15    tarfile_mode = "w"
16    if gzip:
17        tarfile_mode += ":gz"
18    try:
19   
20        history_archive = tarfile.open( out_file, tarfile_mode )
21   
22        # Read datasets attributes from file.
23        datasets_attr_in = open( datasets_attrs_file, 'rb' )
24        datasets_attr_str = ''
25        buffsize = 1048576
26        try:
27            while True:
28                datasets_attr_str += datasets_attr_in.read( buffsize )
29                if not datasets_attr_str or len( datasets_attr_str ) % buffsize != 0:
30                    break
31        except OverflowError:
32            pass
33        datasets_attr_in.close()
34        datasets_attrs = from_json_string( datasets_attr_str )
35   
36        # Add datasets to archive and update dataset attributes.
37        # TODO: security check to ensure that files added are in Galaxy dataset directory?
38        for dataset_attrs in datasets_attrs:
39            dataset_file_name = dataset_attrs[ 'file_name' ] # Full file name.
40            dataset_archive_name = os.path.join( "datasets", os.path.split( dataset_file_name )[-1] )
41            history_archive.add( dataset_file_name, arcname=dataset_archive_name )
42            # Update dataset filename to be archive name.
43            dataset_attrs[ 'file_name' ] = dataset_archive_name
44   
45        # Rewrite dataset attributes file.
46        datasets_attrs_out = open( datasets_attrs_file, 'w' )
47        datasets_attrs_out.write( to_json_string( datasets_attrs ) )
48        datasets_attrs_out.close()
49   
50        # Finish archive.
51        history_archive.add( history_attrs_file, arcname="history_attrs.txt" )
52        history_archive.add( datasets_attrs_file, arcname="datasets_attrs.txt" )
53        history_archive.add( jobs_attrs_file, arcname="jobs_attrs.txt" )
54        history_archive.close()
55       
56        # Status.
57        return 'Created history archive.'
58    except Exception, e:
59        return 'Error creating history archive: %s' % str( e ), sys.stderr
60
61if __name__ == "__main__":
62    # Parse command line.
63    parser = optparse.OptionParser()
64    parser.add_option( '-G', '--gzip', dest='gzip', action="store_true", help='Compress archive using gzip.' )
65    (options, args) = parser.parse_args()   
66    gzip = bool( options.gzip )
67    history_attrs, dataset_attrs, job_attrs, out_file = args
68   
69    # Create archive.
70    status = create_archive( history_attrs, dataset_attrs, job_attrs, out_file, gzip )
71    print status
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