""" Reads a JSON file and uses it to call into a datatype class to extract a subset of a dataset for processing. Used by jobs that split large files into pieces to be processed concurrently on a gid in a scatter-gather mode. This does part of the scatter. """ import json import logging import os import sys sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, "lib"))) # This junk is here to prevent loading errors 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 logging.basicConfig() log = logging.getLogger(__name__) def __main__(): """ Argument: a JSON file """ file_path = sys.argv.pop(1) if not os.path.isfile(file_path): # Nothing to do - some splitters don't write a JSON file sys.exit(0) data = json.load(open(file_path)) try: class_name_parts = data["class_name"].split(".") module_name = ".".join(class_name_parts[:-1]) class_name = class_name_parts[-1] mod = __import__(module_name, globals(), locals(), [class_name]) cls = getattr(mod, class_name) if not cls.process_split_file(data): sys.stderr.write("Writing split file failed\n") sys.exit(1) except Exception as e: sys.stderr.write(str(e)) sys.exit(1) __main__()