mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Daniel Blankenberg
df82f3e163
Currently this is supported in the local runner (long running set_meta() can now be canceled the same as with jobs) and in the non-staging PBS runner. There is a slight change to how new Metadata FileParameters are to be created in datatype.set_meta(), see the MAF datatype. TODO: Prevent editing of metadata on a running job when metadata is to be set externally. Have datasets which were copied before job completion use the metadata from the original output dataset; currently .set_meta() is called locally on these.
38 lines
1.9 KiB
Python
38 lines
1.9 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 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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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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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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for pickled_filenames in sys.argv[1:]:
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pickled_filename_in, pickled_filename_kwds, pickled_filename_out, pickled_filename_results_code = pickled_filenames.split( ',' )
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try:
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data = cPickle.load( open( pickled_filename_in ) )#unpickle DatasetInstance
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kwds = cPickle.load( open( pickled_filename_kwds ) )#unpickle kwds
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data.datatype.set_meta( data, **kwds )
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data.metadata.to_pickled_dict( pickled_filename_out ) # write out results of set_meta
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cPickle.dump( ( True, 'Metadata has been set successfully' ), open( pickled_filename_results_code, 'wb+' ) ) #setting metadata has suceeded
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except Exception, e:
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cPickle.dump( ( False, e ), open( pickled_filename_results_code, 'wb+' ) ) #setting metadata has failed somehow
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__main__() |