Mercurial > repos > brenninc > data_manager_for_directory_data
view data_manager/directory_data_manager.py @ 0:43083927dfc5 draft default tip
Uploaded
author | brenninc |
---|---|
date | Sat, 07 May 2016 16:59:47 -0400 |
parents | |
children |
line wrap: on
line source
#!/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()