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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
"""
#sub-1s resolution in system?
one_second_per_job = None
throw_exception = False
import os
tempdir = os.path.relpath(os.path.abspath(os.path.splitext(__file__)[0])) + "/"
import sys
# add grandparent to search path for testing
grandparent_dir = os.path.abspath(os.path.join(os.path.dirname(__file__), "..", ".."))
sys.path.insert(0, grandparent_dir)
# module name = script name without extension
module_name = os.path.splitext(os.path.basename(__file__))[0]
import ruffus
from ruffus import pipeline_run, pipeline_printout, Pipeline, collate, mkdir, regex, suffix, formatter, originate, transform
from ruffus.ruffus_exceptions import RethrownJobError
from ruffus.ruffus_utility import CHECKSUM_FILE_TIMESTAMPS, RUFFUS_HISTORY_FILE, get_default_history_file_name
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
#
# imports
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
import unittest
import shutil
try:
from StringIO import StringIO
except:
from io import StringIO
import re
#___________________________________________________________________________
#
# generate_initial_files1
#___________________________________________________________________________
@originate([tempdir + prefix + "_name.tmp1" for prefix in "abcd"])
def generate_initial_files1(on):
with open(on, 'w') as outfile:
pass
#___________________________________________________________________________
#
# generate_initial_files2
#___________________________________________________________________________
@originate([tempdir + "e_name.tmp1", tempdir + "f_name.tmp1"])
def generate_initial_files2(on):
with open(on, 'w') as outfile:
pass
#___________________________________________________________________________
#
# generate_initial_files3
#___________________________________________________________________________
@originate([tempdir + "/g_name.tmp1", tempdir + "/h_name.tmp1"])
def generate_initial_files3(on):
with open(on, 'w') as outfile:
pass
#___________________________________________________________________________
#
# generate_initial_files1
#___________________________________________________________________________
@originate(tempdir + "i_name.tmp1")
def generate_initial_files4(on):
with open(on, 'w') as outfile:
pass
#___________________________________________________________________________
#
# test_task2
#___________________________________________________________________________
@collate([generate_initial_files1, generate_initial_files2, generate_initial_files3,
generate_initial_files4],
formatter(),
"{path[0]}/all.tmp2")
#@transform([generate_initial_files1, generate_initial_files2, generate_initial_files3,
# generate_initial_files4],
# formatter( ),
# "{path[0]}/{basename[0]}.tmp2")
def test_task2( infiles, outfile):
with open(outfile, "w") as p:
pass
#print >>sys.stderr, "8" * 80, "\n", " task2 :%s %s " % (infiles, outfile)
#___________________________________________________________________________
#
# test_task3
#___________________________________________________________________________
@transform(test_task2, suffix(".tmp2"), ".tmp3")
def test_task3( infile, outfile):
global throw_exception
if throw_exception != None:
throw_exception = not throw_exception
if throw_exception:
#print >>sys.stderr, "Throw exception for ", infile, outfile
raise Exception("oops")
else:
#print >>sys.stderr, "No throw exception for ", infile, outfile
pass
with open(outfile, "w") as p: pass
#print >>sys.stderr, "8" * 80, "\n", " task3 :%s %s " % (infile, outfile)
#___________________________________________________________________________
#
# test_task4
#___________________________________________________________________________
@transform(test_task3, suffix(".tmp3"), ".tmp4")
def test_task4( infile, outfile):
with open(outfile, "w") as p: pass
#print >>sys.stderr, "8" * 80, "\n", " task4 :%s %s " % (infile, outfile)
def cleanup_tmpdir():
os.system('rm -f %s %s' % (os.path.join(tempdir, '*'), RUFFUS_HISTORY_FILE))
VERBOSITY = 5
VERBOSITY = 11
cnt_pipelines = 0
class Test_job_history_with_exceptions(unittest.TestCase):
def setUp(self):
try:
os.mkdir(tempdir)
except OSError:
pass
#___________________________________________________________________________
#
# test product() pipeline_printout and pipeline_run
#___________________________________________________________________________
def test_job_history_with_exceptions(self):
cleanup_tmpdir()
s = StringIO()
pipeline_printout(s, [test_task4], verbose=VERBOSITY, wrap_width = 10000, pipeline= "main")
#print s.getvalue()
def create_pipeline (self):
#each pipeline has a different name
global cnt_pipelines
cnt_pipelines = cnt_pipelines + 1
test_pipeline = Pipeline("test %d" % cnt_pipelines)
test_pipeline.originate(task_func = generate_initial_files1,
output = [tempdir + prefix + "_name.tmp1" for prefix in "abcd"])
test_pipeline.originate(task_func = generate_initial_files2,
output = [tempdir + "e_name.tmp1", tempdir + "f_name.tmp1"])
test_pipeline.originate(task_func = generate_initial_files3,
output = [tempdir + "g_name.tmp1", tempdir + "h_name.tmp1"])
test_pipeline.originate(task_func = generate_initial_files4,
output = tempdir + "i_name.tmp1")
test_pipeline.collate( task_func = test_task2,
input = [generate_initial_files1,
generate_initial_files2,
generate_initial_files3,
generate_initial_files4],
filter = formatter(),
output = "{path[0]}/all.tmp2")
test_pipeline.transform(task_func = test_task3,
input = test_task2,
filter = suffix(".tmp2"),
output = ".tmp3")
test_pipeline.transform(task_func = test_task4,
input = test_task3,
filter = suffix(".tmp3"),
output = ".tmp4")
return test_pipeline
def test_job_history_with_exceptions_run(self):
"""Run"""
for i in range(1):
cleanup_tmpdir()
try:
pipeline_run([test_task4], verbose = 0,
#multithread = 2,
one_second_per_job = one_second_per_job, pipeline= "main")
except:
pass
s = StringIO()
pipeline_printout(s, [test_task4], verbose=VERBOSITY, wrap_width = 10000, pipeline= "main")
#
# task 2 should be up to date because exception was throw in task 3
#
pipeline_printout_str = s.getvalue()
correct_order = not re.search('Tasks which will be run:.*\n(.*\n)*Task = test_task2', pipeline_printout_str)
if not correct_order:
print(pipeline_printout_str)
self.assertTrue(correct_order)
sys.stderr.write(".")
print()
def test_newstyle_recreate_job_history(self):
"""Run"""
test_pipeline = self.create_pipeline()
global throw_exception
throw_exception = None
cleanup_tmpdir()
#
# print "Initial run without creating sqlite file"
#
test_pipeline.run([test_task4], verbose = 0,
checksum_level = CHECKSUM_FILE_TIMESTAMPS,
multithread = 10,
one_second_per_job = one_second_per_job)
#
# print "printout without sqlite"
#
s = StringIO()
test_pipeline.printout(s, [test_task4], checksum_level = CHECKSUM_FILE_TIMESTAMPS)
self.assertTrue(not re.search('Tasks which will be run:.*\n(.*\n)*Task = ', s.getvalue()))
#
# print "printout expecting sqlite file"
#
s = StringIO()
test_pipeline.printout(s, [test_task4])
self.assertTrue(re.search('Tasks which will be run:.*\n(.*\n)*Task = ', s.getvalue()))
#
# print "Regenerate sqlite file"
#
test_pipeline.run([test_task4],
checksum_level = CHECKSUM_FILE_TIMESTAMPS,
history_file = get_default_history_file_name (),
multithread = 1,
verbose = 0,
touch_files_only = 2,
one_second_per_job = one_second_per_job)
#
# print "printout expecting sqlite file"
#
s = StringIO()
test_pipeline.printout(s, [test_task4], verbose = VERBOSITY)
succeed = not re.search('Tasks which will be run:.*\n(.*\n)*Task = ', s.getvalue())
if not succeed:
print(s.getvalue(), file=sys.stderr)
self.assertTrue(succeed)
throw_exception = False
#
def test_newstyle_job_history_with_exceptions_run(self):
"""Run"""
test_pipeline = self.create_pipeline()
for i in range(1):
cleanup_tmpdir()
try:
test_pipeline.run([test_task4], verbose = 0,
#multithread = 2,
one_second_per_job = one_second_per_job)
except:
pass
s = StringIO()
test_pipeline.printout(s, [test_task4], verbose=VERBOSITY, wrap_width = 10000)
#
# task 2 should be up to date because exception was throw in task 3
#
pipeline_printout_str = s.getvalue()
correct_order = not re.search('Tasks which will be run:.*\n(.*\n)*Task = test_task2', pipeline_printout_str)
if not correct_order:
print(pipeline_printout_str)
self.assertTrue(correct_order)
sys.stderr.write(".")
print()
def test_recreate_job_history(self):
"""Run"""
global throw_exception
throw_exception = None
cleanup_tmpdir()
#
# print "Initial run without creating sqlite file"
#
pipeline_run([test_task4], verbose = 0,
checksum_level = CHECKSUM_FILE_TIMESTAMPS,
multithread = 10,
one_second_per_job = one_second_per_job, pipeline= "main")
#
# print "printout without sqlite"
#
s = StringIO()
pipeline_printout(s, [test_task4], checksum_level = CHECKSUM_FILE_TIMESTAMPS, pipeline= "main")
self.assertTrue(not re.search('Tasks which will be run:.*\n(.*\n)*Task = ', s.getvalue()))
#
# print "printout expecting sqlite file"
#
s = StringIO()
pipeline_printout(s, [test_task4], pipeline= "main")
self.assertTrue(re.search('Tasks which will be run:.*\n(.*\n)*Task = ', s.getvalue()))
#
# print "Regenerate sqlite file"
#
pipeline_run([test_task4],
checksum_level = CHECKSUM_FILE_TIMESTAMPS,
history_file = get_default_history_file_name (),
multithread = 1,
verbose = 0,
touch_files_only = 2,
one_second_per_job = one_second_per_job, pipeline= "main")
#
# print "printout expecting sqlite file"
#
s = StringIO()
pipeline_printout(s, [test_task4], verbose = VERBOSITY, pipeline= "main")
succeed = not re.search('Tasks which will be run:.*\n(.*\n)*Task = ', s.getvalue())
if not succeed:
print(s.getvalue(), file=sys.stderr)
self.assertTrue(succeed)
throw_exception = False
#___________________________________________________________________________
#
# cleanup
#___________________________________________________________________________
def tearDown(self):
shutil.rmtree(tempdir)
pass
#
# Necessary to protect the "entry point" of the program under windows.
# see: http://docs.python.org/library/multiprocessing.html#multiprocessing-programming
#
if __name__ == '__main__':
#pipeline_printout(sys.stdout, [test_product_task], verbose = VERBOSITY, pipeline= "main")
unittest.main()
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