def test_run_02(error, info):
"""It handles a timeout error."""
args = {'assembler': 'my_assembler', 'timeout': 10}
asm = BaseAssembler(args, 'cxn')
asm.assemble = MagicMock(side_effect=TimeoutError())
with pytest.raises(TimeoutError) as timeout_error:
asm.run()
error_msg = str(timeout_error.value)
if error_msg[-1] != '.':
error_msg += '.'
assert error_msg == (
'Time ran out for the assembler after 0:00:10 (HH:MM:SS).')
expect = 'Assembling shards with {}: iteration {}'.format(
args['assembler'], asm.state['iteration'])
info.assert_called_once_with(expect)
# Python 3.6 formats exceptions differently so we need to do this
assert error.call_count == 1
regex = re.compile(
r'Time ran out for the assembler after 0:00:10 \(HH:MM:SS\)')
assert regex.match(error.call_args[0][0])
def test_run_02(error, info):
"""It handles a timeout error."""
args = {'assembler': 'my_assembler', 'timeout': 10}
asm = BaseAssembler(args, 'cxn')
asm.assemble = MagicMock(side_effect=TimeoutError())
with pytest.raises(TimeoutError) as timeout_error:
asm.run()
error_msg = str(timeout_error.value)
if error_msg[-1] != '.':
error_msg += '.'
assert error_msg == (
'Time ran out for the assembler after 0:00:10 (HH:MM:SS).')
expect = 'Assembling shards with {}: iteration {}'.format(
args['assembler'], asm.state['iteration'])
info.assert_called_once_with(expect)
# Python 3.6 formats exceptions differently so we need to do this
assert error.call_count == 1
regex = re.compile(
r'Time ran out for the assembler after 0:00:10 \(HH:MM:SS\)')
assert regex.match(error.call_args[0][0])
def test_run_ok(self, info):
args = {'assembler': 'my_assembler', 'timeout': 10}
assembler = BaseAssembler(args, 'db_conn')
assembler.set_state('blast_db', 'query_file', 99)
assembler.assemble = MagicMock()
assembler.run()
info.assert_called_once_with('Assembling shards with {}: '
'iteration {}'.format(
args['assembler'],
assembler.state['iteration']))
def test_run_called_process_error(self, error, info):
args = {'assembler': 'my_assembler', 'timeout': 10}
error_code = 88
cmd = 'my command'
error = subprocess.CalledProcessError(error_code, cmd)
assembler = BaseAssembler(args, 'db_conn')
assembler.set_state('blast_db', 'query_file', 99)
assembler.assemble = MagicMock(side_effect=error)
with pytest.raises(RuntimeError) as runtime_error:
assembler.run()
error_msg = str(runtime_error.value)
if error_msg[-1] != '.':
error_msg += '.'
assert error_msg == (
"The assembler failed with error: Command 'my command' "
"returned non-zero exit status 88.")
expect = 'Assembling shards with {}: iteration {}'.format(
args['assembler'], assembler.state['iteration'])
info.assert_called_once_with(expect)