def load_json(json_byte_stream):
json_str = convert_byte_stream_to_str(json_byte_stream)
api_response = {'errors': None, 'warnings': []}
robot = Robot.get_instance()
robot.reset()
jpp = None
errors, warnings = [], []
try:
jpp = JSONProtocolProcessor(json_str)
jpp.process()
robot.simulate()
except JSON_ERROR:
errors.append('Cannot parse invalid JSON')
except Exception as e:
errors.append(str(e))
if jpp:
errors.extend(jpp.errors)
warnings.extend(jpp.warnings)
if robot.get_warnings():
warnings.extend(robot.get_warnings())
api_response['errors'] = errors
api_response['warnings'] = warnings
return api_response
def test_process_head(self):
protocol = self.get_protocol()
jpp = JSONProtocolProcessor(protocol)
jpp.process_deck()
jpp.process_head()
expected_settings = {
"tip-racks": [
self.robot._deck.containers()['p200-rack']
],
"trash-container": self.robot._deck.containers()['trash'],
"down-plunger-speed": 200,
"up-plunger-speed": 500,
"tip-plunge": 6,
"extra-pull-volume": 0,
"extra-pull-delay": 200,
"distribute-percentage": 0.1,
"points": [
{
"f1": 1,
"f2": 1
},
{
"f1": 5,
"f2": 5
},
{
"f1": 7,
"f2": 7
},
{
"f1": 10,
"f2": 10
}
]
}
instrument = self.robot._instruments["B"]
head_expected = {
'p200': {
'instance': instrument,
'settings': expected_settings
}
}
self.assertDictEqual(head_expected, jpp.head)
self.assertEqual(1, instrument.channels)
self.assertEqual(0, instrument.min_volume)
self.assertEqual(200, instrument.max_volume)
self.assertEqual('p200', instrument.name)
def test_process_instructions(self):
protocol = self.get_protocol()
jpp = JSONProtocolProcessor(protocol)
jpp.process_deck()
jpp.process_head()
jpp.process_instructions()
api_calls = [
get_name_from_closure(cmd.do) for cmd in self.robot._commands
]
api_calls_expected = [
'pick_up_tip', 'aspirate', 'dispense', 'delay', 'aspirate',
'dispense', 'delay', 'drop_tip'
]
self.assertEqual(api_calls, api_calls_expected)
# self.robot.run()
instrument = self.robot._instruments["B"]
wells_referenced = [(i.get_parent().get_name(), i.get_name())
for i in instrument.placeables]
wells_referenced_expected = [
('p200-rack', 'A1'), # Location of first tip in tiprack
('.75 mL Tube Rack', 'A1'), # 1st transfer
('.75 mL Tube Rack', 'C1'), # 1st transfer
('.75 mL Tube Rack', 'A1'), # 2nd transfer
('.75 mL Tube Rack', 'C1'), # 2nd transfer
('trash', 'A1') # Location of tiprack in trash
]
self.assertEqual(wells_referenced, wells_referenced_expected)
def test_all(self):
failures = []
for protocol_path, protocol_dict in self.get_protocols():
Robot.reset_for_tests()
try:
jpp = JSONProtocolProcessor(protocol_dict)
jpp.process()
except Exception as e:
failures.append((protocol_path, e, jpp.errors))
if failures:
print('The following protocols failed to parse')
for path, exc, reason in failures:
print("[{}]. Reason: {}".format(path, exc))
assert False
def test_process_command(self):
jpp = JSONProtocolProcessor(self.get_protocol())
jpp.handle_consolidate = mock.Mock()
jpp.handle_distribute = mock.Mock()
jpp.handle_transfer = mock.Mock()
jpp.handle_mix = mock.Mock()
for cmd in ['consolidate', 'distribute', 'mix', 'transfer']:
jpp.process_command(None, cmd, None)
for cmd in ['consolidate', 'distribute', 'mix', 'transfer']:
getattr(jpp, "handle_{}".format(cmd), mock.Mock()).called
with self.assertRaises(JSONProcessorRuntimeError):
jpp.process_command(None, 'foo', None)
def test_deck(self):
protocol = self.get_protocol()
deck_dict = protocol['deck']
jpp = JSONProtocolProcessor(protocol)
jpp.process_deck()
robot_deck = self.robot._deck
robot_containers = robot_deck.containers()
deck_expected = {k: {'instance': v}
for k, v in robot_containers.items()}
self.assertDictEqual(jpp.deck, deck_expected)
for name, container_instance in robot_containers.items():
self.assertEqual(
robot_deck[deck_dict[name]['slot']][0], container_instance)
def test_all(self):
failures = []
for protocol_path, protocol_dict in self.get_protocols():
Robot.reset_for_tests()
try:
jpp = JSONProtocolProcessor(protocol_dict)
jpp.process()
except Exception as e:
failures.append(
(protocol_path, e, jpp.errors)
)
if failures:
print('The following protocols failed to parse')
for path, exc, reason in failures:
print("[{}]. Reason: {}".format(path, exc))
assert False
def test_process_command(self):
jpp = JSONProtocolProcessor(self.get_protocol())
jpp.handle_consolidate = mock.Mock()
jpp.handle_distribute = mock.Mock()
jpp.handle_transfer = mock.Mock()
jpp.handle_mix = mock.Mock()
for cmd in ['consolidate', 'distribute', 'mix', 'transfer']:
jpp.process_command(None, cmd, None)
for cmd in ['consolidate', 'distribute', 'mix', 'transfer']:
getattr(jpp, "handle_{}".format(cmd), mock.Mock()).called
with self.assertRaises(JSONProcessorRuntimeError):
jpp.process_command(None, 'foo', None)
def test_deck(self):
protocol = self.get_protocol()
deck_dict = protocol['deck']
jpp = JSONProtocolProcessor(protocol)
jpp.process_deck()
robot_deck = self.robot._deck
robot_containers = robot_deck.containers()
deck_expected = {
k: {
'instance': v
}
for k, v in robot_containers.items()
}
self.assertDictEqual(jpp.deck, deck_expected)
for name, container_instance in robot_containers.items():
self.assertEqual(robot_deck[deck_dict[name]['slot']][0],
container_instance)
def test_validate_protocol(self):
protocol = self.get_protocol()
jpp = JSONProtocolProcessor(protocol)
jpp.validate()
self.assertEqual(jpp.errors, [])
self.assertEqual(
jpp.warnings,
['JSON Protocol section "Ingredients" will not be used'])
protocol = self.get_protocol()
jpp = JSONProtocolProcessor(protocol)
del jpp.protocol['head']
self.assertRaises(JSONProcessorValidationError, jpp.validate)
protocol = self.get_protocol()
jpp = JSONProtocolProcessor(protocol)
del jpp.protocol['deck']
self.assertRaises(JSONProcessorValidationError, jpp.validate)
protocol = self.get_protocol()
jpp = JSONProtocolProcessor(protocol)
del jpp.protocol['instructions']
self.assertRaises(JSONProcessorValidationError, jpp.validate)
def test_process_head(self):
protocol = self.get_protocol()
jpp = JSONProtocolProcessor(protocol)
jpp.process_deck()
jpp.process_head()
expected_settings = {
"tip-racks": [self.robot._deck.containers()['p200-rack']],
"trash-container":
self.robot._deck.containers()['trash'],
"down-plunger-speed":
200,
"up-plunger-speed":
500,
"tip-plunge":
6,
"extra-pull-volume":
0,
"extra-pull-delay":
200,
"distribute-percentage":
0.1,
"points": [{
"f1": 1,
"f2": 1
}, {
"f1": 5,
"f2": 5
}, {
"f1": 7,
"f2": 7
}, {
"f1": 10,
"f2": 10
}]
}
instrument = self.robot._instruments["B"]
head_expected = {
'p200': {
'instance': instrument,
'settings': expected_settings
}
}
self.assertDictEqual(head_expected, jpp.head)
self.assertEqual(1, instrument.channels)
self.assertEqual(0, instrument.min_volume)
self.assertEqual(200, instrument.max_volume)
self.assertEqual('p200', instrument.name)
def test_process_instructions(self):
protocol = self.get_protocol()
jpp = JSONProtocolProcessor(protocol)
jpp.process_deck()
jpp.process_head()
jpp.process_instructions()
api_calls = [
get_name_from_closure(cmd.do)
for cmd in self.robot._commands
]
api_calls_expected = [
'pick_up_tip',
'aspirate',
'dispense',
'delay',
'aspirate',
'dispense',
'delay',
'drop_tip'
]
self.assertEqual(api_calls, api_calls_expected)
# self.robot.run()
instrument = self.robot._instruments["B"]
wells_referenced = [
(i.get_parent().get_name(), i.get_name())
for i in instrument.placeables
]
wells_referenced_expected = [
('p200-rack', 'A1'), # Location of first tip in tiprack
('.75 mL Tube Rack', 'A1'), # 1st transfer
('.75 mL Tube Rack', 'C1'), # 1st transfer
('.75 mL Tube Rack', 'A1'), # 2nd transfer
('.75 mL Tube Rack', 'C1'), # 2nd transfer
('B2', 'trash') # Location of tiprack in trash
]
self.assertEqual(wells_referenced, wells_referenced_expected)
def test_validate_protocol(self):
protocol = self.get_protocol()
jpp = JSONProtocolProcessor(protocol)
jpp.validate()
self.assertEqual(jpp.errors, [])
self.assertEqual(
jpp.warnings,
['JSON Protocol section "Ingredients" will not be used']
)
protocol = self.get_protocol()
jpp = JSONProtocolProcessor(protocol)
del jpp.protocol['head']
self.assertRaises(JSONProcessorValidationError, jpp.validate)
protocol = self.get_protocol()
jpp = JSONProtocolProcessor(protocol)
del jpp.protocol['deck']
self.assertRaises(JSONProcessorValidationError, jpp.validate)
protocol = self.get_protocol()
jpp = JSONProtocolProcessor(protocol)
del jpp.protocol['instructions']
self.assertRaises(JSONProcessorValidationError, jpp.validate)
