--- a/data_manager/data_manager_plant_tribes_scaffolds_download.py	Wed Nov 23 13:29:01 2016 -0500
+++ b/data_manager/data_manager_plant_tribes_scaffolds_download.py	Wed Nov 23 17:02:25 2016 -0500
@@ -31,7 +31,7 @@
         shutil.rmtree(dir)
 
 
-def url_download(data_manager_dict, target_directory, url, description, data_table_names=DEFAULT_DATA_TABLE_NAMES):
+def url_download(target_directory, url, description, data_table_names=DEFAULT_DATA_TABLE_NAMES):
     work_directory = os.path.abspath(os.path.join(os.getcwd(), 'scaffolds'))
     make_directory(work_directory)
     file_path = os.path.join(work_directory, os.path.basename(url))
@@ -66,10 +66,11 @@
     for filename in os.listdir(work_directory):
         shutil.move(os.path.join(work_directory, filename), target_directory)
     remove_directory(work_directory)
+    data_manager_dict = {}
     # Populate the data table, there should be a single entry in target_directory.
     for file_path in os.listdir(target_directory):
         entry_name = "%s" % os.path.basename(file_path)
-        data_table_entry = dict(value=entry_name, name=entry_name, path=file_path, description=description)
+        data_table_entry = dict(value=entry_name.lower(), name=entry_name, path=file_path, description=description)
         for data_table_name in data_table_names:
             data_manager_dict = add_data_table_entry(data_manager_dict, data_table_name, data_table_entry)
     return data_manager_dict
@@ -77,30 +78,28 @@
 
 parser = argparse.ArgumentParser()
 parser.add_argument('--description', dest='description', default=None, help='Description')
-parser.add_argument('--create_symlink', dest='create_symlink', default=None, help='Link files instead of copying')
-parser.add_argument('--file_system_paths', dest='file_system_paths', default=None, help='File system paths')
 parser.add_argument('--name', dest='name', help='Data table entry unique ID')
 parser.add_argument('--out_file', dest='out_file', help='JSON output file')
-parser.add_argument('--web_url', dest='web_url', default=None, help='Web URL')
+parser.add_argument('--web_url', dest='web_url', help='Web URL')
 
 args = parser.parse_args()
 
 # Some magic happens with tools of type "manage_data" in that the output
-# file magically contains some JSON data that wllos us to define the target
+# file magically contains some JSON data that allows us to define the target
 # directory.
 params = json.loads(open(args.out_file).read())
 target_directory = params['output_data'][0]['extra_files_path']
 make_directory(target_directory)
 
-data_table_names = DEFAULT_DATA_TABLE_NAMES
 if args.description is None:
     description = ''
 else:
     description = args.description.strip()
 
-# Initialize the data table.
-data_manager_dict = {}
 # Get the scaffolds data.
-data_manager_dict = url_download(data_manager_dict, target_directory, args.web_url, description, data_table_names=DEFAULT_DATA_TABLE_NAMES)
+data_manager_dict = url_download(target_directory, args.web_url, description)
 # Write the JSON output dataset.
-file(args.out_file, 'w').write(json.dumps(data_manager_dict))
+fh = open(args.out_file, 'wb')
+fh.write(json.dumps(data_manager_dict))
+fh.close()
+