From 82787696ef154fa62a0588a724de849ad89961de Mon Sep 17 00:00:00 2001 From: John Chilton Date: Thu, 2 Jan 2014 17:50:14 -0600 Subject: [PATCH] PEP-8 fixes for set_metadata.py. --- scripts/set_metadata.py | 31 +++++++++++++++++-------------- 1 file changed, 17 insertions(+), 14 deletions(-) diff --git a/scripts/set_metadata.py b/scripts/set_metadata.py index 3921729b5e4..fdeb2b0da09 100644 --- a/scripts/set_metadata.py +++ b/scripts/set_metadata.py @@ -10,7 +10,9 @@ import logging logging.basicConfig() log = logging.getLogger( __name__ ) -import os, sys, cPickle +import os +import sys +import cPickle # ensure supported version from check_python import check_python try: @@ -19,15 +21,15 @@ except: sys.exit(1) new_path = [ os.path.join( os.getcwd(), "lib" ) ] -new_path.extend( sys.path[1:] ) # remove scripts/ from the path +new_path.extend( sys.path[ 1: ] ) # remove scripts/ from the path sys.path = new_path from galaxy import eggs import pkg_resources pkg_resources.require("simplejson") import simplejson -import galaxy.model.mapping #need to load this before we unpickle, in order to setup properties assigned by the mappers -galaxy.model.Job() #this looks REAL stupid, but it is REQUIRED in order for SA to insert parameters into the classes defined by the mappers --> it appears that instantiating ANY mapper'ed class would suffice here +import galaxy.model.mapping # need to load this before we unpickle, in order to setup properties assigned by the mappers +galaxy.model.Job() # this looks REAL stupid, but it is REQUIRED in order for SA to insert parameters into the classes defined by the mappers --> it appears that instantiating ANY mapper'ed class would suffice here from galaxy.util import stringify_dictionary_keys from galaxy.util.json import from_json_string from sqlalchemy.orm import clear_mappers @@ -35,6 +37,7 @@ from galaxy.objectstore import build_object_store_from_config from galaxy import config import ConfigParser + def __main__(): file_path = sys.argv.pop( 1 ) tmp_dir = sys.argv.pop( 1 ) @@ -45,7 +48,7 @@ def __main__(): config_file_name = sys.argv.pop( 1 ) if not os.path.isabs( config_file_name ): config_file_name = os.path.join( config_root, config_file_name ) - + # Set up reference to object store # First, read in the main config file for Galaxy; this is required because # the object store configuration is stored there @@ -65,7 +68,7 @@ def __main__(): universe_config = config.Configuration(**conf_dict) object_store = build_object_store_from_config(universe_config) galaxy.model.Dataset.object_store = object_store - + # Set up datatypes registry datatypes_config = sys.argv.pop( 1 ) datatypes_registry = galaxy.datatypes.registry.Registry() @@ -89,32 +92,32 @@ def __main__(): filename_out = fields.pop( 0 ) filename_results_code = fields.pop( 0 ) dataset_filename_override = fields.pop( 0 ) - #Need to be careful with the way that these parameters are populated from the filename splitting, - #because if a job is running when the server is updated, any existing external metadata command-lines + # Need to be careful with the way that these parameters are populated from the filename splitting, + # because if a job is running when the server is updated, any existing external metadata command-lines #will not have info about the newly added override_metadata file if fields: override_metadata = fields.pop( 0 ) else: override_metadata = None try: - dataset = cPickle.load( open( filename_in ) ) #load DatasetInstance + dataset = cPickle.load( open( filename_in ) ) # load DatasetInstance if dataset_filename_override: dataset.dataset.external_filename = dataset_filename_override if ext_override.get( dataset.dataset.id, None ): dataset.extension = ext_override[ dataset.dataset.id ] - #Metadata FileParameter types may not be writable on a cluster node, and are therefore temporarily substituted with MetadataTempFiles + # Metadata FileParameter types may not be writable on a cluster node, and are therefore temporarily substituted with MetadataTempFiles if override_metadata: override_metadata = simplejson.load( open( override_metadata ) ) for metadata_name, metadata_file_override in override_metadata: if galaxy.datatypes.metadata.MetadataTempFile.is_JSONified_value( metadata_file_override ): metadata_file_override = galaxy.datatypes.metadata.MetadataTempFile.from_JSON( metadata_file_override ) setattr( dataset.metadata, metadata_name, metadata_file_override ) - kwds = stringify_dictionary_keys( simplejson.load( open( filename_kwds ) ) )#load kwds; need to ensure our keywords are not unicode + kwds = stringify_dictionary_keys( simplejson.load( open( filename_kwds ) ) ) # load kwds; need to ensure our keywords are not unicode dataset.datatype.set_meta( dataset, **kwds ) - dataset.metadata.to_JSON_dict( filename_out ) # write out results of set_meta - simplejson.dump( ( True, 'Metadata has been set successfully' ), open( filename_results_code, 'wb+' ) ) #setting metadata has succeeded + dataset.metadata.to_JSON_dict( filename_out ) # write out results of set_meta + simplejson.dump( ( True, 'Metadata has been set successfully' ), open( filename_results_code, 'wb+' ) ) # setting metadata has succeeded except Exception, e: - simplejson.dump( ( False, str( e ) ), open( filename_results_code, 'wb+' ) ) #setting metadata has failed somehow + simplejson.dump( ( False, str( e ) ), open( filename_results_code, 'wb+' ) ) # setting metadata has failed somehow clear_mappers() # Shut down any additional threads that might have been created via the ObjectStore object_store.shutdown()