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53 lines
2.4 KiB
Python
53 lines
2.4 KiB
Python
"""
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Execute an external process to set_meta() on a provided list of pickled datasets.
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This should not be called directly! Use the set_metadata.sh script in Galaxy's
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top level directly.
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"""
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import logging
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logging.basicConfig()
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import os, sys, cPickle
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assert sys.version_info[:2] >= ( 2, 4 )
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new_path = [ os.path.join( os.getcwd(), "lib" ) ]
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new_path.extend( sys.path[1:] ) # remove scripts/ from the path
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sys.path = new_path
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from galaxy import eggs
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import pkg_resources
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pkg_resources.require("simplejson")
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import simplejson
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import galaxy.model.mapping #need to load this before we unpickle, in order to setup properties assigned by the mappers
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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
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galaxy.datatypes.metadata.DATABASE_CONNECTION_AVAILABLE = False #Let metadata know that there is no database connection, and to just assume object ids are valid
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from galaxy.util import stringify_dictionary_keys
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def __main__():
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file_path = sys.argv.pop( 1 )
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tmp_dir = sys.argv.pop( 1 )
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galaxy.model.Dataset.file_path = file_path
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galaxy.datatypes.metadata.MetadataTempFile.tmp_dir = tmp_dir
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# Set up datatypes registry
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config_root = sys.argv.pop( 1 )
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datatypes_config = sys.argv.pop( 1 )
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galaxy.model.set_datatypes_registry( galaxy.datatypes.registry.Registry( config_root, datatypes_config ) )
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for filenames in sys.argv[1:]:
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filename_in, filename_kwds, filename_out, filename_results_code, dataset_filename_override = filenames.split( ',' )
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try:
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dataset = cPickle.load( open( filename_in ) ) #load DatasetInstance
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if dataset_filename_override:
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dataset.dataset.external_filename = dataset_filename_override
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kwds = stringify_dictionary_keys( simplejson.load( open( filename_kwds ) ) )#load kwds; need to ensure our keywords are not unicode
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dataset.datatype.set_meta( dataset, **kwds )
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dataset.metadata.to_JSON_dict( filename_out ) # write out results of set_meta
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simplejson.dump( ( True, 'Metadata has been set successfully' ), open( filename_results_code, 'wb+' ) ) #setting metadata has suceeded
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except Exception, e:
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simplejson.dump( ( False, str( e ) ), open( filename_results_code, 'wb+' ) ) #setting metadata has failed somehow
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__main__()
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