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#!/usr/bin/env python
from __future__ import print_function
"""
test_job_history_with_exceptions.py
Make sure that when an exception is thrown only the current and following tasks fail
"""
import unittest
import os
import sys
import shutil
try:
from StringIO import StringIO
except:
from io import StringIO
import time
import re
import subprocess
exe_path = os.path.split(os.path.abspath(sys.argv[0]))[0]
sys.path.insert(0, os.path.abspath(os.path.join(exe_path,"..", "..")))
from ruffus import *
from ruffus import (pipeline_run, pipeline_printout, suffix, transform, split,
merge, dbdict, follows)
#from ruffus.combinatorics import *
from ruffus.ruffus_exceptions import RethrownJobError
from ruffus.drmaa_wrapper import run_job
from ruffus.ruffus_utility import (RUFFUS_HISTORY_FILE,
CHECKSUM_FILE_TIMESTAMPS,
get_default_history_file_name)
workdir = 'tmp_test_job_history_with_exceptions'
#sub-1s resolution in system?
one_second_per_job = None
throw_exception = False
#___________________________________________________________________________
#
# generate_initial_files1
#___________________________________________________________________________
@mkdir(workdir)
@originate([workdir + "/" + prefix + "_name.tmp1" for prefix in "abcdefghijk"])
def generate_initial_files1(on):
with open(on, 'w') as outfile:
pass
#___________________________________________________________________________
#
# test_task2
#___________________________________________________________________________
@transform(generate_initial_files1,
suffix(".tmp1"), ".tmp2")
def test_task2( infile, outfile):
print ("%s start to run " % infile)
run_job("./five_second.py", run_locally = True)
print ("%s wake up " % infile)
with open(outfile, "w") as p:
pass
#___________________________________________________________________________
#
# test_task3
#___________________________________________________________________________
@transform(test_task2, suffix(".tmp2"), ".tmp3")
def test_task3( infile, outfile):
print ("%s start to run " % infile)
#subprocess.check_call("./five_second.py")
run_job("./five_second.py", run_locally = True)
print ("%s wake up " % infile)
with open(outfile, "w") as p:
pass
def cleanup_tmpdir():
os.system('rm -f %s %s' % (os.path.join(workdir, '*'), RUFFUS_HISTORY_FILE))
def do_main ():
print("Press Ctrl-C Now!!", file=sys.stdout)
sys.stdout.flush()
time.sleep(2)
print("Start....", file=sys.stdout)
sys.stdout.flush()
pipeline_run(verbose = 11,
multiprocess = 5, pipeline= "main")
print("too late!!", file=sys.stdout)
sys.stdout.flush()
cleanup_tmpdir()
do_main()
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