# HG changeset patch
# User greg
# Date 1479913914 18000
# Node ID 83834587ba933764bf8054f4ec266544f0033e45
# Parent  e87b66359c13b5a72b6de2515d73fb6c7e499bd9
Uploaded

diff -r e87b66359c13 -r 83834587ba93 data_manager/data_manager_plant_tribes_scaffolds_download.py
--- a/data_manager/data_manager_plant_tribes_scaffolds_download.py	Wed Nov 23 10:06:02 2016 -0500
+++ b/data_manager/data_manager_plant_tribes_scaffolds_download.py	Wed Nov 23 10:11:54 2016 -0500
@@ -41,7 +41,7 @@
     return files
 
 
-def import_from_server(data_manager_dict, target_directory, file_system_paths, description, link_to_data=False, data_table_names=DEFAULT_DATA_TABLE_NAMES):
+def import_from_server(data_manager_dict, target_directory, file_system_paths, description, create_symlink, data_table_names=DEFAULT_DATA_TABLE_NAMES):
     """
     Creates references to the specified file(s) on the Galaxy
     server in the data table.
@@ -53,7 +53,7 @@
         source_file = os.path.basename(f)
         target_file = os.path.join(target_directory, source_file)
         entry_name = source_file
-        if link_to_data:
+        if create_symlink == 'create_symlink':
             os.symlink(f, target_file)
         else:
             shutil.copyfile(f, target_file)
@@ -150,7 +150,7 @@
 if args.data_source == 'web_url':
     data_manager_dict = url_download(data_manager_dict, target_directory, args.web_url, description, data_table_names=DEFAULT_DATA_TABLE_NAMES)
 else:
-    data_manager_dict = import_from_server(data_manager_dict, target_directory, args.file_system_paths, description, create_symlink=args.create_symlink, data_table_names=DEFAULT_DATA_TABLE_NAMES)
+    data_manager_dict = import_from_server(data_manager_dict, target_directory, args.file_system_paths, description, args.create_symlink, data_table_names=DEFAULT_DATA_TABLE_NAMES)
 
 # Write the JSON output dataset.
 file(args.out_file, 'w').write(json.dumps(data_manager_dict))