def setUp(self):
Robot.reset()
self.robot = Robot.get_instance()
# self.robot.connect(port='/dev/tty.usbmodem1421')
# self.robot.home()
self.trash = containers.load('point', 'A1', 'trash')
self.tiprack = containers.load('tiprack-200ul', 'B2', 'p200-rack')
self.trough = containers.load('trough-12row', 'B2', 'trough')
self.plate = containers.load('96-flat', 'A2', 'magbead')
self.p200 = instruments.Pipette(
name="p200",
trash_container=self.trash,
tip_racks=[self.tiprack],
min_volume=10, # These are variable
axis="b",
channels=1)
self.p1000 = instruments.Pipette(
name="p1000",
trash_container=self.trash,
tip_racks=[self.tiprack],
min_volume=100, # These are variable
axis="a",
channels=1)
def setUp(self):
self.robot = Robot.reset()
options = {
'limit_switches': True,
'firmware': 'v1.0.5',
'config': {
'ot_version': 'one_pro',
'version': 'v1.0.3', # config version
'alpha_steps_per_mm': 80.0,
'beta_steps_per_mm': 80.0
}
}
self.robot.connect(options=options)
self.robot.home()
self.trash = containers.load('point', 'A1')
self.tiprack = containers.load('tiprack-10ul', 'B2')
self.plate = containers.load('96-flat', 'A2')
self.p200 = instruments.Pipette(
trash_container=self.trash,
tip_racks=[self.tiprack],
min_volume=10, # These are variable
axis="b",
channels=1
)
self.p200.calibrate_plunger(top=0, bottom=10, blow_out=12, drop_tip=13)
self.p200.set_max_volume(200)
def test_serial_dilution(self):
plate = containers.load('96-flat', 'B1', 'plate')
tiprack = containers.load(
'tiprack-200ul', # container type from library
'A1', # slot on deck
'tiprack' # calibration reference for 1.2 compatibility
)
trough = containers.load('trough-12row', 'B1', 'trough')
trash = containers.load('point', 'A2', 'trash')
p200 = instruments.Pipette(
trash_container=trash,
tip_racks=[tiprack],
min_volume=10, # These are variable
axis="b",
channels=1)
p200.set_max_volume(200)
p200.calibrate_plunger(top=0, bottom=10, blow_out=12, drop_tip=13)
for t, col in enumerate(plate.cols):
p200.pick_up_tip(tiprack[t])
p200.aspirate(10, trough[t])
p200.dispense(10, col[0])
for well, next_well in zip(col[:-1], col[1:]):
p200.aspirate(10, well)
p200.dispense(10, next_well).mix(3)
p200.drop_tip(trash)
def test_get_instruments_by_name(self):
self.p1000 = instruments.Pipette(
trash_container=self.trash,
tip_racks=[self.tiprack],
min_volume=10, # These are variable
axis="a",
name="p1000",
channels=1,
aspirate_speed=300,
dispense_speed=500
)
result = list(self.robot.get_instruments('p1000'))
self.assertListEqual(result, [('A', self.p1000)])
def test_protocol_head(self):
trash = containers.load('point', 'A1', 'myTrash')
tiprack = containers.load('tiprack-10ul', 'B2')
p200 = instruments.Pipette(
name='myPipette',
trash_container=trash,
tip_racks=[tiprack],
min_volume=10, # These are variable
axis="b",
channels=1
)
instruments_list = self.robot.get_instruments()
self.assertEqual(instruments_list[0], ('B', p200))
instruments_list = self.robot.get_instruments('myPipette')
self.assertEqual(instruments_list[0], ('B', p200))
def protocol(self):
robot = Robot.get_instance()
robot.get_serial_ports_list()
options = {
'limit_switches': True,
'firmware': 'v1.0.5',
'config': {
'ot_version': 'one_pro',
'version': 'v1.0.3', # config version
'alpha_steps_per_mm': 80.0,
'beta_steps_per_mm': 80.0
}
}
robot.connect(options=options)
robot.home()
tiprack = containers.load(
'tiprack-200ul', # container type
'A1', # slot
'tiprack' # user-defined name
)
plate = containers.load('96-flat', 'B1', 'plate')
trash = containers.load('point', 'C2', 'trash')
trough = containers.load('trough-12row', 'B2', 'trough')
p200 = instruments.Pipette(name="p200",
trash_container=trash,
tip_racks=[tiprack],
min_volume=0.5,
axis="b",
channels=1)
p200.set_max_volume(200)
calibration_data = """
{
"b": {
"blowout": 28.0,
"bottom": 26.0,
"droptip": 32.0,
"resting": 0,
"theContainers": {
"plate": {
"rel_x": 181.696,
"rel_y": 0.700999999999965,
"rel_z": 9.600999999999999,
"x": 202.195,
"y": 370.304,
"z": 125.7
},
"tiprack": {
"rel_x": 0.0,
"rel_y": 0.0,
"rel_z": 0.0,
"x": 20.499,
"y": 369.603,
"z": 116.099
},
"trough": {
"rel_x": 0.0,
"rel_y": 0.0,
"rel_z": 0.0,
"x": 20.499,
"y": 269.603,
"z": 116.099
},
"trash": {
"rel_x": 212.701,
"rel_y": -200.801,
"rel_z": -58.399,
"x": 233.2,
"y": 171.305,
"z": 57.7
}
},
"tip_rack_origin": "tiprack",
"tip_racks": [
{
"container": "tiprack"
}
],
"top": 13.0,
"trash_container": {
"container": "trash"
},
"volume": 200
}
}
"""
import_calibration_json(calibration_data, robot, True)
robot.clear()
# distribute
p200.pick_up_tip(tiprack[0])
p200.aspirate(96 * 2, trough[0])
for i in range(96):
p200.dispense(2, plate[i]).touch_tip()
p200.drop_tip(tiprack[0])
p200.pick_up_tip(tiprack[1])
for i in range(96):
p200.aspirate(2, plate[95 - i])
p200.dispense(trough[0])
p200.drop_tip(tiprack[1])
def process_head(self):
"""
res example:
{ name: {
'instance': ..,
'settings': {'down-plunger-speed', '
}
}
:return:
"""
head_dict = self.protocol['head']
SUPPORTED_TOOL_OPTIONS = {
'tool', 'tip-racks', 'trash-container', 'multi-channel', 'axis',
'volume', 'down-plunger-speed', 'up-plunger-speed', 'tip-plunge',
'extra-pull-volume', 'extra-pull-delay', 'distribute-percentage',
'points'
}
head_obj = {}
for tool_name, tool_config in head_dict.items():
# Validate tool_config keys
# Create a warning if unknown keys are detected
user_provided_tool_options = set(tool_config.keys())
if not (SUPPORTED_TOOL_OPTIONS >= user_provided_tool_options):
invalid_options = (user_provided_tool_options -
SUPPORTED_TOOL_OPTIONS)
self.warnings.append(
'Encountered unsupported tool options for "{}": {}'.format(
tool_name, ', '.join(invalid_options)))
tool_config.pop('tool')
tool_instance = instruments.Pipette(
name=tool_name,
axis=tool_config.pop('axis'),
min_volume=0,
channels=(8 if tool_config.pop('multi-channel') else 1),
)
tool_instance.set_max_volume(tool_config.pop('volume'))
# robot_containers = robot._deck.containers()
tip_rack_objs = [
self.deck[item['container']]['instance']
for item in tool_config.pop('tip-racks')
]
tool_config['tip-racks'] = tip_rack_objs
trash_obj = self.deck[tool_config.pop('trash-container')
['container']]['instance']
tool_config['trash-container'] = trash_obj
tool_config['points'] = [
dict(i) for i in tool_config.pop('points')
]
head_obj[tool_name] = {
'instance': tool_instance,
'settings': dict(tool_config)
}
self.head = head_obj
