def _run_subprocess(cls, args_list):
proc = subprocess.run(args_list,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
universal_newlines=True)
utils.log_error(args_list, proc.stderr, proc.returncode)
if proc.stderr or proc.returncode != 0:
raise RuntimeError(
"ERROR running process: %s, error = %s and exit code = %s" %
(args_list, proc.stderr, proc.returncode))
return proc.stdout
def test_logging_4(self):
with mock.patch('checks.utils.logging.error') as mock_logging:
utils.log_error('samtools quickcheck', "error", 0)
mock_logging.assert_called_once_with('samtools quickcheck had exit status 0, but threw an error: error ')
def test_logging_3(self):
with mock.patch('checks.utils.logging.error') as mock_logging:
utils.log_error('samtools quickcheck', "error", 1)
mock_logging.assert_called_once_with('samtools quickcheck exited with code: 1 and threw an error: error ')
def test_logging_2(self):
with mock.patch('checks.utils.logging.error') as mock_logging:
utils.log_error('samtools quickcheck', None, 1)
mock_logging.assert_called_once_with('samtools quickcheck had no error, but exit code is non zero: 1')
def test_logging_1(self):
with mock.patch('checks.utils.logging.info') as mock_logging:
utils.log_error('samtools quickcheck', None, 0)
mock_logging.assert_called_once_with('Ran successfully samtools quickcheck')
def _run_subprocess(cls, args_list):
proc = subprocess.run(args_list, stdout=subprocess.PIPE, stderr=subprocess.PIPE, universal_newlines=True)
utils.log_error(args_list, proc.stderr, proc.returncode)
if proc.stderr or proc.returncode != 0:
raise RuntimeError("ERROR running process: %s, error = %s and exit code = %s" % (args_list, proc.stderr, proc.returncode))
return proc.stdout
def test_logging_4(self):
with mock.patch('checks.utils.logging.error') as mock_logging:
utils.log_error('samtools quickcheck', "error", 0)
mock_logging.assert_called_once_with(
'samtools quickcheck had exit status 0, but threw an error: error '
)
def test_logging_3(self):
with mock.patch('checks.utils.logging.error') as mock_logging:
utils.log_error('samtools quickcheck', "error", 1)
mock_logging.assert_called_once_with(
'samtools quickcheck exited with code: 1 and threw an error: error '
)
def test_logging_2(self):
with mock.patch('checks.utils.logging.error') as mock_logging:
utils.log_error('samtools quickcheck', None, 1)
mock_logging.assert_called_once_with(
'samtools quickcheck had no error, but exit code is non zero: 1'
)
def test_logging_1(self):
with mock.patch('checks.utils.logging.info') as mock_logging:
utils.log_error('samtools quickcheck', None, 0)
mock_logging.assert_called_once_with(
'Ran successfully samtools quickcheck')
