def test_token_lifetime(self, mock_req, mock_auth, mock_njs):
# Test get token lifetime
config = NJS_JOB_PARAMS[1]
resp = AUTH_V2_TOKEN
mock_req.get.return_value = MockAuth(resp)
jr = JobRunner(self.config, self.njs_url, self.jobid, self.token,
self.admin_token)
mlog = MockLogger()
jr.logger = mlog
exp = jr._get_token_lifetime(config)
self.assertGreater(exp, 0)
mock_req.get.side_effect = OSError("bad request")
with self.assertRaises(OSError):
jr._get_token_lifetime(config)
def test_run_volume(self, mock_njs, mock_auth):
self._cleanup(self.jobid)
params = deepcopy(NJS_JOB_PARAMS)
params[0]['method'] = 'mock_app.voltest'
params[0]['params'] = {'param1': 'value1'}
jr = JobRunner(self.config, self.njs_url, self.jobid, self.token,
self.admin_token)
rv = deepcopy(CATALOG_GET_MODULE_VERSION)
rv['docker_img_name'] = 'mock_app:latest'
vols = deepcopy(CATALOG_LIST_VOLUME_MOUNTS)
jr.cc.catalog.get_module_version = MagicMock(return_value=rv)
jr.cc.catalog.list_volume_mounts = MagicMock(return_value=vols)
jr.cc.catalog.get_secure_config_params = MagicMock(return_value=None)
jr.logger.njs.add_job_logs = MagicMock(return_value=rv)
jr.njs.get_job_params.return_value = params
jr.njs.check_job_canceled.return_value = {'finished': False}
jr.auth.get_user.return_value = "bogus"
jr._get_token_lifetime = MagicMock(return_value=self.future)
if not os.path.exists('/tmp/bogus'):
os.mkdir('/tmp/bogus')
with open('/tmp/bogus/input.fa', 'w') as f:
f.write('>contig-50_0 length_64486 read_count_327041\n')
f.write('GTCGTGCTGCTGCCGATCGACCGCGCCTATGCGATGTTGCCGGACGGCATCC\n')
out = jr.run()
self.assertIn('result', out)
self.assertNotIn('error', out)
def test_run_online(self, mock_njs):
self._cleanup(self.jobid)
params = deepcopy(NJS_JOB_PARAMS)
jr = JobRunner(self.config, self.njs_url, self.jobid, self.token,
self.admin_token)
rv = deepcopy(CATALOG_GET_MODULE_VERSION)
rv['docker_img_name'] = 'mock_app:latest'
jr.logger.njs.add_job_logs = MagicMock(return_value=rv)
jr.njs.check_job_canceled.return_value = {'finished': False}
jr.njs.get_job_params.return_value = params
jr._get_token_lifetime = MagicMock(return_value=self.future)
out = jr.run()
self.assertIn('result', out)
self.assertNotIn('error', out)
def test_run(self, mock_njs, mock_auth):
self._cleanup(self.jobid)
params = deepcopy(NJS_JOB_PARAMS)
params[0]['method'] = 'mock_app.bogus'
params[0]['params'] = {'param1': 'value1'}
jr = JobRunner(self.config, self.njs_url, self.jobid, self.token,
self.admin_token)
rv = deepcopy(CATALOG_GET_MODULE_VERSION)
rv['docker_img_name'] = 'mock_app:latest'
jr.cc.catalog.get_module_version = MagicMock(return_value=rv)
jr.cc.catalog.list_volume_mounts = MagicMock(return_value=[])
jr.cc.catalog.get_secure_config_params = MagicMock(return_value=None)
jr.logger.njs.add_job_logs = MagicMock(return_value=rv)
jr.njs.get_job_params.return_value = params
jr.njs.check_job_canceled.return_value = {'finished': False}
jr.auth.get_user.return_value = "bogus"
jr._get_token_lifetime = MagicMock(return_value=self.future)
out = jr.run()
self.assertIn('result', out)
self.assertNotIn('error', out)
def test_run_slurm(self, mock_njs, mock_auth):
self._cleanup(self.jobid)
params = deepcopy(NJS_JOB_PARAMS)
params[0]['method'] = 'RunTester.run_RunTester'
params[0]['params'] = [{'do_slurm': 1}]
params[1]['auth-service-url'] = self.config['auth-service-url']
params[1]['auth.service.url.v2'] = self.config['auth2-url']
jr = JobRunner(self.config, self.njs_url, self.jobid, self.token,
self.admin_token)
rv = deepcopy(CATALOG_GET_MODULE_VERSION)
rv['docker_img_name'] = 'test/runtester:latest'
jr.cc.catalog.get_module_version = MagicMock(return_value=rv)
jr.cc.catalog.list_volume_mounts = MagicMock(return_value=[])
jr.cc.catalog.get_secure_config_params = MagicMock(return_value=None)
jr.logger.njs.add_job_logs = MagicMock(return_value=rv)
jr.njs.get_job_params.return_value = params
jr.njs.check_job_canceled.return_value = {'finished': False}
jr.auth.get_user.return_value = "bogus"
jr._get_token_lifetime = MagicMock(return_value=self.future)
out = jr.run()
self.assertNotIn('error', out)
def test_max_jobs(self, mock_njs, mock_auth):
self._cleanup(self.jobid)
params = deepcopy(NJS_JOB_PARAMS)
params[0]['method'] = 'RunTester.run_RunTester'
params[0]['params'] = [{'depth': 2, 'size': 1000, 'parallel': 5}]
config = deepcopy(self.config)
config['max_tasks'] = 2
jr = JobRunner(config, self.njs_url, self.jobid, self.token,
self.admin_token)
rv = deepcopy(CATALOG_GET_MODULE_VERSION)
rv['docker_img_name'] = 'test/runtester:latest'
jr.cc.catalog.get_module_version = MagicMock(return_value=rv)
jr.cc.catalog.list_volume_mounts = MagicMock(return_value=[])
jr.cc.catalog.get_secure_config_params = MagicMock(return_value=None)
jr.logger.njs.add_job_logs = MagicMock(return_value=rv)
jr._get_token_lifetime = MagicMock(return_value=self.future)
jr.njs.get_job_params.return_value = params
jr.njs.check_job_canceled.return_value = {'finished': False}
jr.auth.get_user.return_value = "bogus"
out = jr.run()
self.assertIn('error', out)