mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-21 13:50:20 +08:00
Daniel Blankenberg
3fdac6ca6b
e.g:
Exception exceptions.TypeError: TypeError('<galaxy.datatypes.metadata.MetadataTempFile object at 0x40d9a10> is not JSON serializable',) in <bound method MutableAttrInstanceState._cleanup of <sqlalchemy.orm.state.MutableAttrInstanceState object at 0x40d99d0>> ignored
56 lines
2.5 KiB
Python
56 lines
2.5 KiB
Python
"""
|
|
Execute an external process to set_meta() on a provided list of pickled datasets.
|
|
|
|
This should not be called directly! Use the set_metadata.sh script in Galaxy's
|
|
top level directly.
|
|
|
|
"""
|
|
|
|
import logging
|
|
logging.basicConfig()
|
|
log = logging.getLogger( __name__ )
|
|
|
|
import os, sys, cPickle
|
|
assert sys.version_info[:2] >= ( 2, 4 )
|
|
|
|
new_path = [ os.path.join( os.getcwd(), "lib" ) ]
|
|
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
|
|
galaxy.datatypes.metadata.DATABASE_CONNECTION_AVAILABLE = False #Let metadata know that there is no database connection, and to just assume object ids are valid
|
|
from galaxy.util import stringify_dictionary_keys
|
|
from sqlalchemy.orm import clear_mappers
|
|
|
|
def __main__():
|
|
file_path = sys.argv.pop( 1 )
|
|
tmp_dir = sys.argv.pop( 1 )
|
|
galaxy.model.Dataset.file_path = file_path
|
|
galaxy.datatypes.metadata.MetadataTempFile.tmp_dir = tmp_dir
|
|
|
|
# Set up datatypes registry
|
|
config_root = sys.argv.pop( 1 )
|
|
datatypes_config = sys.argv.pop( 1 )
|
|
galaxy.model.set_datatypes_registry( galaxy.datatypes.registry.Registry( config_root, datatypes_config ) )
|
|
|
|
for filenames in sys.argv[1:]:
|
|
filename_in, filename_kwds, filename_out, filename_results_code, dataset_filename_override = filenames.split( ',' )
|
|
try:
|
|
dataset = cPickle.load( open( filename_in ) ) #load DatasetInstance
|
|
if dataset_filename_override:
|
|
dataset.dataset.external_filename = dataset_filename_override
|
|
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 suceeded
|
|
except Exception, e:
|
|
simplejson.dump( ( False, str( e ) ), open( filename_results_code, 'wb+' ) ) #setting metadata has failed somehow
|
|
clear_mappers()
|
|
|
|
__main__()
|