--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/directory_data_manager.py	Sat May 07 16:59:47 2016 -0400
@@ -0,0 +1,92 @@
+#!/usr/bin/env python
+
+import gzip
+import json
+import optparse  # using optparse as hydra still python 2.6
+import os.path
+import shutil
+
+def _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry ):
+    data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
+    data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] )
+    data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry )
+    return data_manager_dict
+
+
+def get_param(name, params, default=None,  check_tab=True):
+    value = params.get(name)
+    print name, value
+    return check_param(name, value, default=default, check_tab=check_tab)
+
+
+def check_param(name, value, default=None,  check_tab=True):
+    if value in [ None, '', '?' ]:
+        if default:
+            print "Using {0} for {1} as no value provided".format( default, name )
+            value = default
+        else:
+            raise Exception( '{0} is not a valid {1}. You must specify a valid {1}.'.format( value, name ) )
+    if check_tab and "\t" in value:
+        raise Exception( '{0} is not a valid {1}. It may not contain a tab because these are used as seperators by galaxy .'.format( value, name ) )
+    return value
+
+def check_extension(extension):
+    extension = extension.strip()
+    if extension[0] == ".":
+        extension = extension[1:]
+    return extension
+
+
+def check_path(path, original_extension):
+    files = os.listdir(path)
+    check = "." + original_extension
+    for a_file in files:
+        if a_file.endswith(check):
+            return True
+    raise Exception( 'path {0} does not contain any files ending with {1}'.format( path, check ) )
+
+
+def main():
+
+    #Parse Command Line
+    parser = optparse.OptionParser()
+    parser.add_option( '--data_table_name', action='store', type="string", default=None, help='path' )
+    parser.add_option( '--json_output_file', action='store', type="string", default=None, help='path' )
+    (options, args) = parser.parse_args()
+
+    data_table_name = check_param("data_table_name", options.data_table_name)
+    json_output_file = check_param("json_output_file", options.json_output_file, check_tab=False)
+
+    param_dict = json.loads( open( json_output_file ).read() )
+    params = param_dict.get("param_dict")
+    print "input params:"
+    print params
+
+    data_table_entry = {}
+    data_table_entry["original_extension"] = check_extension(get_param("original_extension", params))
+    data_table_entry["galaxy_extension"] = check_extension(get_param("galaxy_extension", params))
+    data_table_entry["decompress"] = get_param("decompress", params)
+    if not (data_table_entry["decompress"] in ["No","Yes"]):
+        raise Exception( "Only legal values for dcompress are No and Yes." )
+    data_table_entry["path"] = get_param("path", params)
+    check_path(data_table_entry["path"], data_table_entry["original_extension"])
+ 
+    basename = os.path.basename(data_table_entry["path"])
+    filename = os.path.splitext(basename)[0]
+    data_table_entry["name"] = get_param("name", params, default=filename)
+    data_table_entry["value"] = get_param("value", params, default=data_table_entry["name"])
+    data_table_entry["dbkey"] = get_param("dbkey", params, default=data_table_entry["value"])
+
+    data_manager_dict = {}
+    _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )
+
+    print "output:"
+    print data_manager_dict
+    # save info to json file
+    with open( json_output_file, 'wb' ) as output_file:
+        output_file.write( json.dumps( data_manager_dict ) )
+        output_file.write( "\n" )
+
+
+if __name__ == "__main__": 
+    main()