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#!/usr/bin/env python
# File created on 09 Feb 2010
from __future__ import division
__author__ = "Greg Caporaso"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Greg Caporaso", "Jai Ram Rideout"]
__license__ = "GPL"
__version__ = "1.8.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
from qiime.util import make_option
from qiime.parallel.poller import poller, get_function_handle
from qiime.util import parse_command_line_parameters
script_info={}
script_info['brief_description']="""Poller for parallel QIIME scripts."""
script_info['script_description'] = """Script for polling parallel runs to check completion."""
script_info['script_usage'] = [(
"Poller example",
"Runs the poller, which checks for the existence of two input files "
"(file1.txt and file2.txt) and merges their contents. A cleanup file is "
"provided that instructs the poller to remove the newly merged file.",
"%prog -f run_complete.txt -m poller_test_completed.txt -d clean_up.txt"
)]
script_info['version'] = __version__
script_info['output_description']= "No output created."
script_info['required_options'] = [
make_option('-f','--check_run_complete_file',
help='path to file containing a list of files that must exist to '
'declare a run complete [REQUIRED]')
]
script_info['optional_options'] = [
make_option('-r','--check_run_complete_f',
help='function which returns True when run is completed '
'[default: %default]',
default='qiime.parallel.poller.basic_check_run_complete_f'),
make_option('-p','--process_run_results_f',
help='function to be called when runs complete [default: %default]',
default='qiime.parallel.poller.basic_process_run_results_f'),
make_option('-m','--process_run_results_file',
help='path to file containing a map of tmp filepaths which should'
' be written to final output filepaths [default: %default]'),
make_option('-c','--clean_up_f',
help='function called after processing result [default: %default]',
default='qiime.parallel.poller.basic_clean_up_f'),
make_option('-d','--clean_up_file',
help='List of files and directories to remove after run'
' [default: %default]'),
make_option('-t','--time_to_sleep',type='int',
help='time to wait between calls to status_callback_f'
' (in seconds) [default: %default]',default=3)
]
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
poller(get_function_handle(opts.check_run_complete_f),
get_function_handle(opts.process_run_results_f),
get_function_handle(opts.clean_up_f),
list(open(opts.check_run_complete_file)),
list(open(opts.process_run_results_file)),
list(open(opts.clean_up_file)),
seconds_to_sleep=opts.time_to_sleep)
if __name__ == "__main__":
main()
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