mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-01 15:37:32 +08:00
Nicola Soranzo
48 lines
1.6 KiB
Python
48 lines
1.6 KiB
Python
"""
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Reads a JSON file and uses it to call into a datatype class to extract
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a subset of a dataset for processing.
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Used by jobs that split large files into pieces to be processed concurrently
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on a gid in a scatter-gather mode. This does part of the scatter.
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"""
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import json
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import logging
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import os
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import sys
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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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# This junk is here to prevent loading errors
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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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logging.basicConfig()
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log = logging.getLogger( __name__ )
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def __main__():
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"""
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Argument: a JSON file
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"""
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file_path = sys.argv.pop( 1 )
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if not os.path.isfile(file_path):
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# Nothing to do - some splitters don't write a JSON file
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sys.exit(0)
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data = json.load(open(file_path, 'r'))
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try:
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class_name_parts = data['class_name'].split('.')
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module_name = '.'.join(class_name_parts[:-1])
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class_name = class_name_parts[-1]
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mod = __import__(module_name, globals(), locals(), [class_name])
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cls = getattr(mod, class_name)
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if not cls.process_split_file(data):
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sys.stderr.write('Writing split file failed\n')
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sys.exit(1)
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except Exception, e:
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sys.stderr.write(str(e))
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sys.exit(1)
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__main__()
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