def setUp(self):
env.reset()
subprocess.call('sos remove -s', shell=True)
#self.resetDir('~/.sos')
self.temp_files = []
self.resetDir('temp')
Host.reset()
def setUp(self):
env.reset()
#self.resetDir('~/.sos')
self.temp_files = []
Host.reset()
# remove .status file left by failed workflows.
subprocess.call('sos purge', shell=True)
def testRemoteExecution(self):
subprocess.check_output('sos purge', shell=True).decode()
script = SoS_Script('''
[10]
input: for_each={'i': range(5)}
task:
run: expand=True
echo I am {i}
sleep {5+i}
''')
wf = script.workflow()
res = Base_Executor(wf, config={
'config_file': '~/docker.yml',
# do not wait for jobs
'wait_for_task': False,
'default_queue': 'docker',
'max_running_jobs': 5,
'sig_mode': 'force',
}).run()
import time
# we should be able to get status
tasks = ' '.join(res['pending_tasks'])
# wait another 15 seconds?
time.sleep(15)
out = subprocess.check_output('sos status {} -c ~/docker.yml -q docker'.format(tasks), shell=True).decode()
self.assertEqual(out.count('completed'), len(res['pending_tasks']), 'Expect all completed jobs: ' + out)
Host.reset()
# until we run the workflow again
#st = time.time()
Base_Executor(wf, config={
'config_file': '~/docker.yml',
# do not wait for jobs
'wait_for_task': True,
'default_queue': 'docker',
'resume_mode': True,
}).run()
# should finish relatively fast?
#self.assertLess(time.time() - st, 5)
out = subprocess.check_output('sos status {} -c ~/docker.yml'.format(tasks), shell=True).decode()
self.assertEqual(out.count('completed'), len(res['pending_tasks']), 'Expect all completed jobs: ' + out)
def testActiveActionOption(self):
'''Test the active option of actions'''
# disallow
self.assertRaises(
ParsingError, SoS_Script, '''
[1]
rep = range(5)
input: for_each = 'rep'
# ff should change and be usable inside run
ff = f"{_rep}.txt"
run: expand=True, active=1,2
echo {ff}
touch temp/{ff}
''')
#
for active, result in [
('0', ['temp/0.txt']),
('-1', ['temp/4.txt']),
('(1,2)', ['temp/1.txt', 'temp/2.txt']),
('[2,3]', ['temp/2.txt', 'temp/3.txt']),
('(0,2,4)', ['temp/0.txt', 'temp/2.txt', 'temp/4.txt']),
('slice(1,None)',
['temp/1.txt', 'temp/2.txt', 'temp/3.txt', 'temp/4.txt']),
('slice(1,-2)', ['temp/1.txt', 'temp/2.txt']),
('slice(None,None,2)', ['temp/0.txt', 'temp/2.txt', 'temp/4.txt']),
]:
if os.path.isdir('temp'):
shutil.rmtree('temp')
os.mkdir('temp')
# test first iteration
script = SoS_Script(('''
[1]
rep = range(5)
input: for_each = 'rep'
# ff should change and be usable inside run
ff = f"{_rep}.txt"
run: expand=True, active=%s
echo {ff}
touch temp/{ff}
''' % active).replace('/', os.sep))
wf = script.workflow()
env.config['sig_mode'] = 'force'
env.config['wait_for_task'] = True
Host.reset()
Base_Executor(wf).run()
files = list(glob.glob(os.path.join('temp', '*.txt')))
self.assertEqual(sorted(files),
sorted([x.replace('/', os.sep) for x in result]))
#
# test last iteration
shutil.rmtree('temp')
#
# test active option for task
os.mkdir('temp')
script = SoS_Script(('''
[1]
rep = range(5)
input: for_each = 'rep'
# ff should change and be usable inside run
ff = f"{_rep}.txt"
task: active=%s
run: expand=True
echo {ff}
touch temp/{ff}
''' % active).replace('/', os.sep))
wf = script.workflow()
env.config['sig_mode'] = 'force'
env.config['wait_for_task'] = True
Host.reset()
Base_Executor(wf).run()
files = list(glob.glob(os.path.join('temp', '*.txt')))
self.assertEqual(sorted(files),
sorted([x.replace('/', os.sep) for x in result]),
'With option {}'.format(active))
#
# test last iteration
shutil.rmtree('temp')