def test_ok_run(self):
argv = ['run', '-d', '/path/to/dir']
args = utils.get_args(argv)
self.assertEqual(args.directory, '/path/to/dir')
self.assertEqual(args.force_qc, False)
self.assertEqual(args.email_list, None)
def test_ok_step(self):
argv = ['step', '-d', '/path/to/dir', '-s', '001']
args = utils.get_args(argv)
self.assertEqual(args.directory, '/path/to/dir')
self.assertEqual(args.step, 1)
self.assertEqual(args.force_qc, False)
def test_sub_array_for_cmdfile(self):
sched = Local()
cmdfile = self.datadir + "/cmdfiles/sleeper.sh"
argv = ['sub', '-P', 'project', '-q', 'normal', '-K',
'-M', '500', '-o', 'tmp/out.%J.%I.txt', '-e',
'tmp/err.%J.%I.txt', '-i', cmdfile]
args = utils.get_args(argv)
array_ids = sched.sub_array_for_cmdfile(args)
self.assertTrue(isinstance(array_ids, list))
self.assertEqual(len(array_ids), 1)
def test_jobs_from_arrays(self):
lsf = LSF()
cmdfile = self.datadir + "/cmdfiles/sleeper.sh"
argv = [
'sub', '-P', 'project', '-q', 'normal', '-K', '-M', '500', '-o',
'tmp/out.%J.%I.txt', '-e', 'tmp/err.%J.%I.txt', '-S', '3', '-i',
cmdfile
]
args = utils.get_args(argv)
array_ids = lsf.sub_array_for_cmdfile(args)
jobs = lsf.jobs_from_arrays(array_ids)
self.assertEqual(len(jobs), 4)
def test_sub_array_for_cmdfile_split(self):
lsf = LSF()
cmdfile = self.datadir + "/cmdfiles/sleeper.sh"
argv = [
'sub', '-P', 'project', '-q', 'normal', '-K', '-M', '500', '-o',
'tmp/out.%J.%I.txt', '-e', 'tmp/err.%J.%I.txt', '-S', '3', '-i',
cmdfile
]
args = utils.get_args(argv)
array_ids = lsf.sub_array_for_cmdfile(args)
self.assertTrue(isinstance(array_ids, list))
self.assertEqual(len(array_ids), 2)
for array_id in array_ids:
self.assertTrue(utils.isint(array_id))
def test_ok_sub(self):
argv = [
'sub', '-P', 'project', '-q', 'normal', '-n', '5', '-K', '-s',
'LSF', '-M', '500', '-o', 'out.%J.%I.txt', '-e', 'err.%J.%I.txt',
'-i', 'cmds.sh'
]
args = utils.get_args(argv)
self.assertEqual(args.project, 'project')
self.assertEqual(args.queue, 'normal')
self.assertEqual(args.ncores, 5)
self.assertTrue(args.hang)
self.assertEqual(args.system, 'LSF')
self.assertEqual(args.stdout, 'out.%J.%I.txt')
self.assertEqual(args.stderr, 'err.%J.%I.txt')
self.assertEqual(args.cmdfile, 'cmds.sh')
def main():
""" Main routine """
args = utils.get_args(sys.argv[1:])
action = sys.argv[1]
if action == "sub":
if not args.system:
args.system = detect_scheduler()
if not args.jobname:
args.jobname = os.path.basename(args.cmdfile)
core.phoenix_sub(args)
elif action == "step":
core.phoenix_step(args.directory, args.step, args.force_qc)
elif action == "run":
core.phoenix_run(args.directory, args.step, args.email_list)
else:
sys.exit("ERROR: Unknown action '{}'".format(action))