Mercurial > repos > brenninc > data_manager_for_directory_data
diff data_manager/directory_data_manager.py @ 0:43083927dfc5 draft default tip
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author | brenninc |
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date | Sat, 07 May 2016 16:59:47 -0400 |
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--- /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()