1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
|
#!/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"]
__license__ = "GPL"
__version__ = "1.4.0"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
__status__ = "Release"
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. See Qiime/scripts/poller_example.py for example usage."""
script_info['script_usage'] = []
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()
|
