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#!/usr/bin/env python2.5
"""
test_tasks.py
"""
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
# options
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from optparse import OptionParser
import sys, os
import os.path
import StringIO
# add self to search path for testing
exe_path = os.path.split(os.path.abspath(sys.argv[0]))[0]
if __name__ == '__main__':
module_name = os.path.split(sys.argv[0])[1]
module_name = os.path.splitext(module_name)[0];
else:
module_name = __name__
parser = OptionParser(version="%prog 1.0")
parser.add_option("-t", "--target_tasks", dest="target_tasks",
action="append",
default = list(),
metavar="JOBNAME",
type="string",
help="Target task(s) of pipeline.")
parser.add_option("-f", "--forced_tasks", dest="forced_tasks",
action="append",
default = list(),
metavar="JOBNAME",
type="string",
help="Pipeline task(s) which will be included even if they are up to date.")
parser.add_option("-j", "--jobs", dest="jobs",
default=5,
metavar="jobs",
type="int",
help="Specifies the number of jobs (commands) to run simultaneously.")
parser.add_option("-v", "--verbose", dest = "verbose",
action="store_true", default=False,
help="Do not echo to shell but only print to log.")
parser.add_option("-d", "--dependency", dest="dependency_file",
default="simple.svg",
metavar="FILE",
type="string",
help="Print a dependency graph of the pipeline that would be executed "
"to FILE, but do not execute it.")
parser.add_option("-F", "--dependency_graph_format", dest="dependency_graph_format",
metavar="FORMAT",
type="string",
default = 'svg',
help="format of dependency graph file. Can be 'ps' (PostScript), "+
"'svg' 'svgz' (Structured Vector Graphics), " +
"'png' 'gif' (bitmap graphics) etc ")
parser.add_option("-n", "--just_print", dest="just_print",
action="store_true", default=False,
help="Print a description of the jobs that would be executed, "
"but do not execute them.")
parser.add_option("-M", "--minimal_rebuild_mode", dest="minimal_rebuild_mode",
action="store_true", default=False,
help="Rebuild a minimum of tasks necessary for the target. "
"Ignore upstream out of date tasks if intervening tasks are fine.")
parser.add_option("-K", "--no_key_legend_in_graph", dest="no_key_legend_in_graph",
action="store_true", default=False,
help="Do not print out legend and key for dependency graph.")
parser.add_option("-H", "--draw_graph_horizontally", dest="draw_horizontally",
action="store_true", default=False,
help="Draw horizontal dependency graph.")
parameters = [
]
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
# imports
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import StringIO
import re
import operator
import sys
from collections import defaultdict
sys.path.append(os.path.abspath(os.path.join(exe_path,"..", "..")))
from ruffus import *
import json
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
# Functions
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def create_custom_file_func(params):
"""
creates function which can be used as input to @files_func
"""
def cust_func ():
for job_param in params:
yield job_param
return cust_func
def is_job_uptodate (infiles, outfiles, *extra_params):
"""
assumes first two parameters are files, checks if they are up to date
"""
return task.needs_update_check_modify_time (infiles, outfiles, *extra_params)
def test_post_task_function ():
print "Hooray"
import time
def test_job_io(infiles, outfiles, extra_params):
"""
cat input files content to output files
after writing out job parameters
"""
# dump parameters
params = (infiles, outfiles) + extra_params
sys.stdout.write(' job = %s\n' % json.dumps(params))
if isinstance(infiles, str):
infiles = [infiles]
elif infiles is None:
infiles = []
if isinstance(outfiles, str):
outfiles = [outfiles]
output_text = list()
for f in infiles:
output_text.append(open(f).read())
output_text = "".join(sorted(output_text))
output_text += json.dumps(infiles) + " -> " + json.dumps(outfiles) + "\n"
for f in outfiles:
open(f, "w").write(output_text)
time.sleep(1)
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
# Main logic
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
# get help string
f =StringIO.StringIO()
parser.print_help(f)
helpstr = f.getvalue()
(options, remaining_args) = parser.parse_args()
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
# Tasks
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
#
# task1
#
@files(None, 'a.1')
def task1(infiles, outfiles, *extra_params):
"""
First task
"""
test_job_io(infiles, outfiles, extra_params)
#
# task2
#
@files_re('*.1', '(.*).1', r'\1.1', r'\1.2')
@follows(task1)
def task2(infiles, outfiles, *extra_params):
"""
Second task
"""
test_job_io(infiles, outfiles, extra_params)
#
# task3
#
@files_re('*.1', '(.*).1', r'\1.2', r'\1.3')
@follows(task2)
def task3(infiles, outfiles, *extra_params):
"""
Third task
"""
test_job_io(infiles, outfiles, extra_params)
#
# task4
#
@files_re('*.1', '(.*).1', r'\1.3', r'\1.4')
@follows(task3)
def task4(infiles, outfiles, *extra_params):
"""
Fourth task
"""
test_job_io(infiles, outfiles, extra_params)
if options.just_print:
pipeline_printout(sys.stdout, options.target_tasks, options.forced_tasks,
long_winded=True,
gnu_make_maximal_rebuild_mode = not options.minimal_rebuild_mode)
elif options.dependency_file:
pipeline_printout_graph ( open(options.dependency_file, "w"),
options.dependency_graph_format,
options.target_tasks,
options.forced_tasks,
draw_vertically = not options.draw_horizontally,
gnu_make_maximal_rebuild_mode = not options.minimal_rebuild_mode,
no_key_legend = options.no_key_legend_in_graph)
else:
pipeline_run(options.target_tasks, options.forced_tasks, multiprocess = options.jobs,
gnu_make_maximal_rebuild_mode = not options.minimal_rebuild_mode)
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