Mercurial > repos > earlhaminst > export_to_cluster

comparison export_to_cluster.py @ 0:0dbe46f58158 draft

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/ commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty
author earlhaminst
date Thu, 11 Aug 2016 15:27:30 -0400
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children a9d1991c90e3
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-1:000000000000 0:0dbe46f58158
1 #!/usr/bin/env python
2 from __future__ import print_function
3
4 import optparse
5 import os
6 import os.path
7 import re
8 import shutil
9 import sys
10
11 parser = optparse.OptionParser()
12 parser.add_option('-d', '--export_dir', help='Directory where to export the datasets')
13 parser.add_option('-p', '--dir_prefix', help='How the export dir should start')
14 (options, args) = parser.parse_args()
15 if not options.export_dir:
16 parser.error('Export directory cannot be empty')
17 if not options.dir_prefix:
18 parser.error('Directory prefix cannot be empty')
19 if len(args) < 2:
20 parser.error('Require at least two arguments')
21 if len(args) % 2 != 0:
22 parser.error('Require an even number of arguments')
23
24 real_export_dir = os.path.realpath(options.export_dir)
25 dir_prefix = options.dir_prefix.rstrip(os.sep)
26 if not real_export_dir.startswith(dir_prefix):
27 sys.exit("%s must be a subdirectory of %s" % (options.export_dir, dir_prefix))
28 if not os.path.exists(real_export_dir):
29 sys.exit("%s does not exist or it is not accessible by the Galaxy user" % options.export_dir)
30 if not os.path.isdir(real_export_dir):
31 sys.exit("%s is not a directory" % options.export_dir)
32
33 dataset_paths = args[::3]
34 dataset_names = args[1::3]
35 dataset_exts = args[2::3]
36 for dp, dn, de in zip(dataset_paths, dataset_names, dataset_exts):
37 """
38 Copied from get_valid_filename from django
39 https://github.com/django/django/blob/master/django/utils/text.py
40 """
41 dn_de = "%s.%s" % (dn, de)
42 dn_de_safe = re.sub(r'(?u)[^-\w.]', '', dn_de.strip().replace(' ', '_'))
43 dest = os.path.join(real_export_dir, dn_de_safe)
44 try:
45 shutil.copy2(dp, dest)
46 print("Dataset '%s' copied to '%s'" % (dn, dest))
47 except Exception as e:
48 msg = "Error copying dataset '%s' to '%s', %s" % (dn, dest, e)
49 print(msg)
50 sys.stderr.write(msg)