Mercurial > repos > earlhaminst > export_to_cluster
view 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
author | earlhaminst |
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date | Fri, 24 Mar 2017 12:20:48 -0400 |
parents | a9d1991c90e3 |
children | 9838eed606ad |
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#!/usr/bin/env python from __future__ import print_function import optparse import os import os.path import re import shutil import sys parser = optparse.OptionParser() parser.add_option('-d', '--export_dir', help='Directory where to export the datasets') parser.add_option('-p', '--dir_prefix', help='How the export dir should start') (options, args) = parser.parse_args() if not options.export_dir: parser.error('Export directory cannot be empty') if not options.dir_prefix: parser.error('Directory prefix cannot be empty') if len(args) < 3: parser.error('Require at least two arguments') if len(args) % 3 != 0: 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 """ dn_de = "%s.%s" % (dn, de) dn_de_safe = re.sub(r'(?u)[^-\w.]', '', dn_de.strip().replace(' ', '_')) dest = os.path.join(real_export_dir, dn_de_safe) 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)