Mercurial > repos > earlhaminst > export_to_cluster

comparison export_to_cluster.py @ 2:b97775e9fe06 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/ commit f5c5f3d6ce676937f5c673ec7fc0631a9f490dc2
author earlhaminst
date Fri, 24 Mar 2017 12:20:48 -0400
parents a9d1991c90e3
children 9838eed606ad
comparison
equal deleted inserted replaced
1:a9d1991c90e3 2:b97775e9fe06
22 parser.error('Require an even number of arguments') 22 parser.error('Require an even number of arguments')
23 23
24 real_export_dir = os.path.realpath(options.export_dir) 24 real_export_dir = os.path.realpath(options.export_dir)
25 dir_prefix = options.dir_prefix.rstrip(os.sep) 25 dir_prefix = options.dir_prefix.rstrip(os.sep)
26 if not real_export_dir.startswith(dir_prefix): 26 if not real_export_dir.startswith(dir_prefix):
27 sys.exit("%s must be a subdirectory of %s" % (options.export_dir, dir_prefix)) 27 raise Exception("%s must be a subdirectory of %s" % (options.export_dir, dir_prefix))
28 if not os.path.exists(real_export_dir): 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) 29 raise Exception("%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): 30 if not os.path.isdir(real_export_dir):
31 sys.exit("%s is not a directory" % options.export_dir) 31 raise Exception("%s is not a directory" % options.export_dir)
32 32
33 dataset_paths = args[::3] 33 dataset_paths = args[::3]
34 dataset_names = args[1::3] 34 dataset_names = args[1::3]
35 dataset_exts = args[2::3] 35 dataset_exts = args[2::3]
36 exit_code = 0
36 for dp, dn, de in zip(dataset_paths, dataset_names, dataset_exts): 37 for dp, dn, de in zip(dataset_paths, dataset_names, dataset_exts):
37 """ 38 """
38 Copied from get_valid_filename from django 39 Copied from get_valid_filename from django
39 https://github.com/django/django/blob/master/django/utils/text.py 40 https://github.com/django/django/blob/master/django/utils/text.py
40 """ 41 """
44 try: 45 try:
45 shutil.copy2(dp, dest) 46 shutil.copy2(dp, dest)
46 print("Dataset '%s' copied to '%s'" % (dn, dest)) 47 print("Dataset '%s' copied to '%s'" % (dn, dest))
47 except Exception as e: 48 except Exception as e:
48 msg = "Error copying dataset '%s' to '%s', %s" % (dn, dest, e) 49 msg = "Error copying dataset '%s' to '%s', %s" % (dn, dest, e)
49 print(msg) 50 print(msg, file=sys.stderr)
50 sys.stderr.write(msg) 51 exit_code = 1
52 sys.exit(exit_code)