comparison export_to_cluster.py @ 2:b97775e9fe06 draft

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/ commit f5c5f3d6ce676937f5c673ec7fc0631a9f490dc2

1:a9d1991c90e3

    parser.error('Require an even number of arguments')

real_export_dir = os.path.realpath(options.export_dir)
dir_prefix = options.dir_prefix.rstrip(os.sep)
if not real_export_dir.startswith(dir_prefix):
    sys.exit("%s must be a subdirectory of %s" % (options.export_dir, dir_prefix))
if not os.path.exists(real_export_dir):
    sys.exit("%s does not exist or it is not accessible by the Galaxy user" % options.export_dir)
if not os.path.isdir(real_export_dir):
    sys.exit("%s is not a directory" % options.export_dir)

dataset_paths = args[::3]
dataset_names = args[1::3]
dataset_exts = args[2::3]
for dp, dn, de in zip(dataset_paths, dataset_names, dataset_exts):
    """
    Copied from get_valid_filename from django
    https://github.com/django/django/blob/master/django/utils/text.py
    """

    try:
        shutil.copy2(dp, dest)
        print("Dataset '%s' copied to '%s'" % (dn, dest))
    except Exception as e:
        msg = "Error copying dataset '%s' to '%s', %s" % (dn, dest, e)
        print(msg)
        sys.stderr.write(msg)

2:b97775e9fe06

    parser.error('Require an even number of arguments')

real_export_dir = os.path.realpath(options.export_dir)
dir_prefix = options.dir_prefix.rstrip(os.sep)
if not real_export_dir.startswith(dir_prefix):
    raise Exception("%s must be a subdirectory of %s" % (options.export_dir, dir_prefix))
if not os.path.exists(real_export_dir):
    raise Exception("%s does not exist or it is not accessible by the Galaxy user" % options.export_dir)
if not os.path.isdir(real_export_dir):
    raise Exception("%s is not a directory" % options.export_dir)

dataset_paths = args[::3]
dataset_names = args[1::3]
dataset_exts = args[2::3]
exit_code = 0
for dp, dn, de in zip(dataset_paths, dataset_names, dataset_exts):
    """
    Copied from get_valid_filename from django
    https://github.com/django/django/blob/master/django/utils/text.py
    """

    try:
        shutil.copy2(dp, dest)
        print("Dataset '%s' copied to '%s'" % (dn, dest))
    except Exception as e:
        msg = "Error copying dataset '%s' to '%s', %s" % (dn, dest, e)
        print(msg, file=sys.stderr)
        exit_code = 1
sys.exit(exit_code)