def test2_lsf_job(self, subprocess_patch):
laimsapp = LaimsApp()
config = laimsapp.lsf_job_options()
config.pop("queue", None)
config.pop("stdout", None)
print(config)
job = LsfJob(config)
self.assertTrue(isinstance(job, LsfJob))
available_opts = LsfJob.available_options
self.assertEqual(len(available_opts), 9,
"available options count is 9")
expected_cmd = [
'bsub', '-a', 'docker(registry.gsc.wustl.edu/mgi/laims:latest)',
'-N', '-u', '*****@*****.**', 'echo', 'hello', 'world'
]
self.assertEqual(job.bsub_cmd(['echo', 'hello', 'world']),
expected_cmd)
job.created_options["stdout"] = "/var/log/out"
expected_cmd = [
'bsub', '-M', '10000000', '-R',
'"select[mem>10000] rusage[mem=10000]"', '-a',
'docker(hello-world)', "-oo", "/var/log/out", '-N', '-u',
'*****@*****.**', 'echo', 'hello', 'world'
]
self.assertEqual(
job.bsub_cmd(['echo', 'hello', 'world'], {
"docker": "hello-world",
"memory_in_gb": 10
}), expected_cmd)
job.created_options["stdout"] = "/var/log"
expected_cmd = [
'bsub', '-M', '10000000', '-R',
'"select[mem>10000] rusage[mem=10000]"', '-a',
'docker(hello-world)', "-oo", "/var/log/log1.out", '-N', '-u',
'*****@*****.**', 'echo', 'hello', 'world'
]
self.assertEqual(
job.bsub_cmd(
['echo', 'hello', 'world'], {
"docker": "hello-world",
"memory_in_gb": 10,
"stdout_bn": "log1.out"
}), expected_cmd)
subprocess_patch.return_value = 1
self.assertFalse(
job.launch(['echo', 'hello', 'world'], {"docker": "hello-world"}),
expected_cmd)
def test4_job_options(self):
laimsapp = LaimsApp(config_file=self.config_fn)
laimsapp.queue = "ccdg"
laimsapp.stdout = "/var/log/out"
self.assertTrue(laimsapp)
opts = laimsapp.lsf_job_options()
expected_opts = {
"email": "*****@*****.**",
"queue": "ccdg",
"docker": "registry.gsc.wustl.edu/mgi/laims:latest",
"stdout": "/var/log/out",
}
self.assertDictEqual(opts, expected_opts,
"LSF job options fetched from config")