diff export_to_cluster.py @ 0:0dbe46f58158 draft

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/export_to_cluster/ commit e80af91bced56efdb4fbf62ac03232655a22f25d-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/export_to_cluster.py	Thu Aug 11 15:27:30 2016 -0400
@@ -0,0 +1,50 @@
+#!/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) < 2:
+    parser.error('Require at least two arguments')
+if len(args) % 2 != 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):
+    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
+    """
+    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)
+        sys.stderr.write(msg)