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PEP-8 fixes for set_metadata.py.

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This commit is contained in:
John Chilton
2014-01-02 17:50:14 -06:00
parent 3122393fb7
commit 82787696ef
1 changed files with 17 additions and 14 deletions
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scripts/set_metadata.py
+17 -14
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@@ -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()