def setUp(self):
Robot.reset_for_tests()
self.robot = Robot.get_instance()
self.robot.reset()
self.robot.connect()
self.robot.home(enqueue=False)
def setUp(self):
self.robot = Robot()
self.robot.home()
self.trash = containers_load(self.robot, 'point', '1')
self.tiprack1 = containers_load(self.robot, 'tiprack-10ul', '5')
self.tiprack2 = containers_load(self.robot, 'tiprack-10ul', '8')
self.plate = containers_load(self.robot, '96-flat', '4')
self.p200 = Pipette(
self.robot,
ul_per_mm=18.5,
trash_container=self.trash,
tip_racks=[self.tiprack1, self.tiprack2],
min_volume=10, # These are variable
mount='left',
channels=1,
name='other-pipette-for-transfer-tests'
)
self.p200.max_volume = 200
self.p200.reset()
self.p200.calibrate_plunger(top=0, bottom=10, blow_out=12, drop_tip=13)
self.robot.home()
def setUp(self):
Robot.reset_for_tests()
self.robot = Robot.get_instance()
self.robot.reset()
self.robot.connect()
self.robot.home(enqueue=False)
def setUp(self):
self.robot = Robot()
self.smoothie_version = 'edge-1c222d9NOMSD'
self.robot.reset()
self.robot.connect(options={'firmware': self.smoothie_version})
self.robot.home(enqueue=False)
def fixture(config, monkeypatch):
from opentrons.robot.robot import Robot
from opentrons.instruments.pipette import Pipette
from collections import namedtuple
from opentrons.drivers.smoothie_drivers import driver_3_0
log = []
X = (-25, 25)
Y = (-25, 25)
Z = (0, 100)
def move(self, target, *args, **kwargs):
log.append(('move', target))
self.update_position(target)
return target
def probe_axis(self, axis, probing_distance):
log.append(('probe_axis', axis, probing_distance))
mapping = {'X': X, 'Y': Y, 'Z': Z, 'A': Z}
self.update_position(
{axis.upper(): mapping[axis][0 if probing_distance > 0 else 1]})
return self._position
monkeypatch.setattr(driver_3_0.SmoothieDriver_3_0_0, 'move', move)
monkeypatch.setattr(driver_3_0.SmoothieDriver_3_0_0, 'probe_axis',
probe_axis)
robot = Robot(config=config)
pipette = Pipette(robot, mount='right')
robot.home()
return namedtuple('fixture',
'robot instrument log X Y Z')(robot=robot,
instrument=pipette,
log=log,
X=X,
Y=Y,
Z=Z)
def __init__(self, name=None, mosfet=0, container=None):
self.axis = 'M{}'.format(mosfet)
self.robot = Robot.get_instance()
self.robot.add_instrument(self.axis, self)
self.motor = self.robot.get_mosfet(mosfet)
if not name:
name = self.__class__.__name__
self.name = name
self.persisted_data = []
self.calibration_key = "{axis}:{instrument_name}".format(
axis=self.axis, instrument_name=self.name)
# a reference to the placeable set ontop the magbead module
self.container = container
self.engaged = False
persisted_key = '{axis}:{name}'.format(axis=self.axis, name=self.name)
self.init_calibrations(key=persisted_key)
self.load_persisted_data()
from opentrons.robot.robot import Robot from opentrons.robot.command import Command robot = Robot() __all__ = [Robot, Command, robot] from ._version import get_versions __version__ = get_versions()['version'] del get_versions
def reset():
global robot
robot = Robot()
return robot
class PipetteTest(unittest.TestCase):
def setUp(self):
self.robot = Robot()
self.robot.home()
self.trash = containers_load(self.robot, 'point', '1')
self.tiprack1 = containers_load(self.robot, 'tiprack-10ul', '5')
self.tiprack2 = containers_load(self.robot, 'tiprack-10ul', '8')
self.plate = containers_load(self.robot, '96-flat', '4')
self.p200 = Pipette(
self.robot,
ul_per_mm=18.5,
trash_container=self.trash,
tip_racks=[self.tiprack1, self.tiprack2],
min_volume=10, # These are variable
mount='left',
channels=1,
name='other-pipette-for-transfer-tests'
)
self.p200.max_volume = 200
self.p200.reset()
self.p200.calibrate_plunger(top=0, bottom=10, blow_out=12, drop_tip=13)
self.robot.home()
def tearDown(self):
del self.robot
def test_bad_volume_percentage(self):
self.assertRaises(RuntimeError, self.p200._volume_percentage, -1)
def test_add_instrument(self):
self.robot.reset()
Pipette(self.robot, ul_per_mm=18.5, mount='left')
self.assertRaises(RuntimeError, Pipette, self.robot, mount='left')
def test_aspirate_zero_volume(self):
assert self.robot.commands() == []
self.p200.tip_attached = True
self.p200.aspirate(0)
assert self.robot.commands() == ['Aspirating 0 uL from ? at 1.0 speed'] # noqa
def test_get_plunger_position(self):
self.assertEquals(self.p200._get_plunger_position('top'), 0)
self.assertEquals(self.p200._get_plunger_position('bottom'), 10)
self.assertEquals(self.p200._get_plunger_position('blow_out'), 12)
self.assertEquals(self.p200._get_plunger_position('drop_tip'), 13)
self.p200.plunger_positions['drop_tip'] = None
self.assertRaises(
RuntimeError, self.p200._get_plunger_position, 'drop_tip')
self.assertRaises(
RuntimeError, self.p200._get_plunger_position, 'roll_out')
def test_deprecated_axis_call(self):
import warnings
warnings.filterwarnings('error')
# Check that user warning occurs when axis is called
self.assertRaises(
UserWarning, Pipette, self.robot, axis='a')
# Check that the warning is still valid when max_volume is also used
self.assertRaises(
UserWarning, Pipette, self.robot, axis='a', max_volume=300)
warnings.filterwarnings('default')
def test_get_instruments_by_name(self):
self.p1000 = Pipette(
self.robot,
ul_per_mm=18.5,
trash_container=self.trash,
tip_racks=[self.tiprack1],
min_volume=10, # These are variable
mount='right',
name='p1000',
channels=1,
aspirate_speed=300,
dispense_speed=500
)
result = list(self.robot.get_instruments('p1000'))
self.assertListEqual(result, [('right', self.p1000)])
def test_placeables_reference(self):
self.p200.tip_attached = True
self.p200.aspirate(100, self.plate[0])
self.p200.dispense(100, self.plate[0])
self.p200.aspirate(100, self.plate[20])
self.p200.aspirate(100, self.plate[1])
expected = [
self.plate[0],
self.plate[20],
self.plate[1]
]
self.assertEquals(self.p200.placeables, expected)
def test_unpack_location(self):
location = (self.plate[0], (1, 0, -1))
res = unpack_location(location)
self.assertEqual(res, (self.plate[0], (1, 0, -1)))
res = unpack_location(self.plate[0])
self.assertEqual(
res,
(self.plate[0], self.plate[0].from_center(x=0, y=0, z=1)))
def test_aspirate_invalid_max_volume(self):
self.p200.tip_attached = True
with self.assertRaises(RuntimeWarning):
self.p200.aspirate(500)
def test_volume_percentage(self):
self.assertRaises(RuntimeError, self.p200._volume_percentage, -1)
self.assertRaises(RuntimeError, self.p200._volume_percentage, 300)
self.assertEquals(self.p200._volume_percentage(100), 0.5)
self.assertEquals(len(self.robot.get_warnings()), 0)
self.p200._volume_percentage(self.p200.min_volume / 2)
self.assertEquals(len(self.robot.get_warnings()), 1)
def test_add_tip(self):
"""
This deals with z accrual behavior during tip add/remove, when +/- get
flipped in pose tracking logic
"""
prior_position = pose_tracker.absolute(self.robot.poses, self.p200)
self.p200._add_tip(42)
self.p200._remove_tip(42)
new_position = pose_tracker.absolute(self.robot.poses, self.p200)
assert (new_position == prior_position).all()
def test_set_speed(self):
self.p200.set_speed(aspirate=100)
self.assertEqual(self.p200.speeds['aspirate'], 100)
self.p200.set_speed(dispense=100)
self.assertEqual(self.p200.speeds['dispense'], 100)
def test_distribute(self):
self.p200.reset()
# Setting true instead of calling pick_up_tip because the test is
# currently based on an exact command list. Should make this better.
self.p200.distribute(
30,
self.plate[0],
self.plate[1:9],
new_tip='always'
)
expected = [
['Distributing', '30', 'well A1', 'wells B1...A2'],
['Transferring'],
['Picking up tip'],
['Aspirating', '190', 'well A1'],
['Dispensing', '30', 'well B1'],
['Dispensing', '30', 'well C1'],
['Dispensing', '30', 'well D1'],
['Dispensing', '30', 'well E1'],
['Dispensing', '30', 'well F1'],
['Dispensing', '30', 'well G1'],
['Blow', 'well A1'],
['Drop'],
['Pick'],
['Aspirating', '70', 'well A1'],
['Dispensing', '30', 'well H1'],
['Dispensing', '30', 'well A2'],
['Blow', 'well A1'],
['Drop']
]
fuzzy_assert(self.robot.commands(), expected=expected)
self.robot.clear_commands()
self.p200.reset()
self.p200.tip_attached = True
self.p200.distribute(
30,
self.plate[0],
self.plate[1:9],
new_tip='never'
)
expected = [
['Distributing', '30', 'well A1', 'wells B1...A2'],
['Transferring'],
['Aspirating', '190', 'well A1'],
['Dispensing', '30', 'well B1'],
['Dispensing', '30', 'well C1'],
['Dispensing', '30', 'well D1'],
['Dispensing', '30', 'well E1'],
['Dispensing', '30', 'well F1'],
['Dispensing', '30', 'well G1'],
['Blow', 'well A1'],
['Aspirating', '70', 'well A1'],
['Dispensing', '30', 'well H1'],
['Dispensing', '30', 'well A2'],
['Blow', 'well A1']
]
fuzzy_assert(self.robot.commands(), expected=expected)
self.robot.clear_commands()
self.p200.reset()
self.p200.distribute(
30,
self.plate[0],
self.plate
)
total_dispenses = 0
for c in self.robot.commands():
if 'dispensing' in c.lower():
total_dispenses += 1
self.assertEqual(total_dispenses, 96)
self.robot.clear_commands()
self.p200.reset()
self.p200.transfer(
30,
self.plate[0],
self.plate[1:9],
trash=False
)
expected = [
['Transferring', '30', 'well A1'],
['Pick'],
['Aspirating', '30', 'well A1'],
['Dispensing', '30', 'well B1'],
['Aspirating', '30', 'well A1'],
['Dispensing', '30', 'well C1'],
['Aspirating', '30', 'well A1'],
['Dispensing', '30', 'well D1'],
['Aspirating', '30', 'well A1'],
['Dispensing', '30', 'well E1'],
['Aspirating', '30', 'well A1'],
['Dispensing', '30', 'well F1'],
['Aspirating', '30', 'well A1'],
['Dispensing', '30', 'well G1'],
['Aspirating', '30', 'well A1'],
['Dispensing', '30', 'well H1'],
['Aspirating', '30', 'well A1'],
['Dispensing', '30', 'well A2'],
['Return'],
['Drop']
]
fuzzy_assert(self.robot.commands(), expected=expected)
self.robot.clear_commands()
def test_consolidate(self):
self.p200.reset()
self.p200.consolidate(
30,
self.plate[0:8],
self.plate['A2'],
new_tip='always'
)
expected = [
['Consolidating', '30'],
['Transferring', '30'],
['Pick'],
['Aspirating', '30', 'Well A1'],
['Aspirating', '30', 'Well B1'],
['Aspirating', '30', 'Well C1'],
['Aspirating', '30', 'Well D1'],
['Aspirating', '30', 'Well E1'],
['Aspirating', '30', 'Well F1'],
['Dispensing', '180', 'Well A2'],
['Drop'],
['Pick'],
['Aspirating', '30', 'Well G1'],
['Aspirating', '30', 'Well H1'],
['Dispensing', '60', 'Well A2'],
['Drop']
]
fuzzy_assert(self.robot.commands(),
expected=expected)
self.robot.clear_commands()
self.p200.reset()
self.p200.tip_attached = True
self.p200.consolidate(
30,
self.plate[0:8],
self.plate['A2'],
new_tip='never'
)
expected = [
['Consolidating', '30'],
['Transferring', '30'],
['Aspirating', '30', 'Well A1'],
['Aspirating', '30', 'Well B1'],
['Aspirating', '30', 'Well C1'],
['Aspirating', '30', 'Well D1'],
['Aspirating', '30', 'Well E1'],
['Aspirating', '30', 'Well F1'],
['Dispensing', '180', 'Well A2'],
['Aspirating', '30', 'Well G1'],
['Aspirating', '30', 'Well H1'],
['Dispensing', '60', 'Well A2'],
]
fuzzy_assert(self.robot.commands(), expected=expected)
self.robot.clear_commands()
self.p200.reset()
self.p200.consolidate(
30,
self.plate,
self.plate[0]
)
total_aspirates = 0
for c in self.robot.commands():
if 'aspirating' in c.lower():
total_aspirates += 1
self.assertEqual(total_aspirates, 96)
self.robot.clear_commands()
self.p200.reset()
self.p200.transfer(
30,
self.plate[0:8],
self.plate['A2']
)
expected = [
['Transferring', '30'],
['Pick'],
['Aspirating', '30', 'Well A1'],
['Dispensing', '30', 'Well A2'],
['Aspirating', '30', 'Well B1'],
['Dispensing', '30', 'Well A2'],
['Aspirating', '30', 'Well C1'],
['Dispensing', '30', 'Well A2'],
['Aspirating', '30', 'Well D1'],
['Dispensing', '30', 'Well A2'],
['Aspirating', '30', 'Well E1'],
['Dispensing', '30', 'Well A2'],
['Aspirating', '30', 'Well F1'],
['Dispensing', '30', 'Well A2'],
['Aspirating', '30', 'Well G1'],
['Dispensing', '30', 'Well A2'],
['Aspirating', '30', 'Well H1'],
['Dispensing', '30', 'Well A2'],
['Drop']
]
fuzzy_assert(self.robot.commands(), expected=expected)
self.robot.clear_commands()
def test_transfer(self):
self.p200.reset()
self.p200.transfer(
30,
self.plate[0:8],
self.plate[1:9],
new_tip='always',
air_gap=10,
disposal_vol=20, # ignored by transfer
touch_tip=True,
blow_out=True,
trash=True
)
expected = [
['Transferring', '30'],
['pick'],
['aspirating', '30', 'Well A1'],
['air'],
['aspirating', '10'],
['touch'],
['dispensing', '10', 'Well B1'],
['dispensing', '30', 'Well B1'],
['blow'],
['touch'],
['drop'],
['pick'],
['aspirating', '30', 'Well B1'],
['air'],
['aspirating', '10'],
['touch'],
['dispensing', '10', 'Well C1'],
['dispensing', '30', 'Well C1'],
['blow'],
['touch'],
['drop'],
['pick'],
['aspirating', '30', 'Well C1'],
['air'],
['aspirating', '10'],
['touch'],
['dispensing', '10', 'Well D1'],
['dispensing', '30', 'Well D1'],
['blow'],
['touch'],
['drop'],
['pick'],
['aspirating', '30', 'Well D1'],
['air'],
['aspirating', '10'],
['touch'],
['dispensing', '10', 'Well E1'],
['dispensing', '30', 'Well E1'],
['blow'],
['touch'],
['drop'],
['pick'],
['aspirating', '30', 'Well E1'],
['air'],
['aspirating', '10'],
['touch'],
['dispensing', '10', 'Well F1'],
['dispensing', '30', 'Well F1'],
['blow'],
['touch'],
['drop'],
['pick'],
['aspirating', '30', 'Well F1'],
['air'],
['aspirating', '10'],
['touch'],
['dispensing', '10', 'Well G1'],
['dispensing', '30', 'Well G1'],
['blow'],
['touch'],
['drop'],
['pick'],
['aspirating', '30', 'Well G1'],
['air'],
['aspirating', '10'],
['touch'],
['dispensing', '10', 'Well H1'],
['dispensing', '30', 'Well H1'],
['blow'],
['touch'],
['drop'],
['pick'],
['aspirating', '30', 'Well H1'],
['air'],
['aspirating', '10'],
['touch'],
['dispensing', '10', 'Well A2'],
['dispensing', '30', 'Well A2'],
['blow'],
['touch'],
['drop']
]
fuzzy_assert(self.robot.commands(),
expected=expected)
self.robot.clear_commands()
def test_bad_transfer(self):
self.p200.reset()
self.assertRaises(
ValueError,
self.p200.transfer,
30,
self.plate[0:2],
self.plate[0:3]
)
self.assertRaises(
ValueError,
self.p200.transfer,
30,
self.plate[0:3],
self.plate[0:2]
)
self.assertRaises(
RuntimeError,
self.p200.transfer,
[30, 30, 30],
self.plate[0:2],
self.plate[0:2]
)
self.assertRaises(
ValueError,
self.p200.transfer,
30,
self.plate[0],
self.plate[1],
new_tip='sometimes'
)
self.assertRaises(
ValueError,
self.p200.transfer,
[20, 20, 20, 20],
self.plate[0:3],
self.plate[1:4],
new_tip='sometimes'
)
def test_divisible_locations(self):
self.p200.reset()
self.p200.transfer(
100,
self.plate[0:4],
self.plate[0:2]
)
expected = [
['transferring', '100'],
['pick'],
['aspirating', '100', 'Well A1'],
['dispensing', '100', 'Well A1'],
['aspirating', '100', 'Well B1'],
['dispensing', '100', 'Well A1'],
['aspirating', '100', 'Well C1'],
['dispensing', '100', 'Well B1'],
['aspirating', '100', 'Well D1'],
['dispensing', '100', 'Well B1'],
['drop']
]
fuzzy_assert(self.robot.commands(),
expected=expected)
self.robot.clear_commands()
self.p200.reset()
self.p200.consolidate(
100,
self.plate[0:4],
self.plate[0:2]
)
expected = [
['consolidating', '100'],
['transferring', '100'],
['pick'],
['aspirating', '100', 'Well A1'],
['aspirating', '100', 'Well B1'],
['dispensing', '200', 'Well A1'],
['aspirating', '100', 'Well C1'],
['aspirating', '100', 'Well D1'],
['dispensing', '200', 'Well B1'],
['drop']
]
fuzzy_assert(self.robot.commands(),
expected=expected
)
self.robot.clear_commands()
self.p200.reset()
self.p200.distribute(
100,
self.plate[0:2],
self.plate[0:4],
disposal_vol=0
)
expected = [
['distributing', '100'],
['transferring', '100'],
['pick'],
['aspirating', '200', 'Well A1'],
['dispensing', '100', 'Well A1'],
['dispensing', '100', 'Well B1'],
['aspirating', '200', 'Well B1'],
['dispensing', '100', 'Well C1'],
['dispensing', '100', 'Well D1'],
['drop']
]
fuzzy_assert(self.robot.commands(),
expected=expected
)
self.robot.clear_commands()
def test_transfer_mix(self):
self.p200.reset()
self.p200.transfer(
200,
self.plate[0],
self.plate[1],
mix_before=(1, 10),
mix_after=(1, 10)
)
expected = [
['Transferring', '200'],
['pick'],
['mix', '10'],
['aspirating', 'Well A1'],
['dispensing'],
['aspirating', '200', 'Well A1'],
['dispensing', '200', 'Well B1'],
['mix', '10'],
['aspirating', 'Well B1'],
['dispensing'],
['drop']
]
fuzzy_assert(self.robot.commands(),
expected=expected)
self.robot.clear_commands()
def test_transfer_air_gap(self):
self.p200.reset()
self.p200.transfer(
120,
self.plate[0],
self.plate[1],
air_gap=20
)
expected = [
['Transferring', '120'],
['pick'],
['aspirating', '120', 'Well A1'],
['air gap'],
['aspirating', '20'],
['dispensing', '20', 'Well B1'],
['dispensing', '120', 'Well B1'],
['drop']
]
fuzzy_assert(self.robot.commands(),
expected=expected)
self.robot.clear_commands()
def test_consolidate_air_gap(self):
self.p200.reset()
self.p200.consolidate(
60,
self.plate[0:2],
self.plate[2],
air_gap=20
)
expected = [
['consolidating', '60'],
['transferring', '60'],
['pick'],
['aspirating', '60', 'Well A1'],
['aspirating', '60', 'Well B1'],
['dispensing', '120', 'Well C1'],
['drop']
]
fuzzy_assert(self.robot.commands(),
expected=expected)
self.robot.clear_commands()
def test_distribute_air_gap(self):
self.p200.reset()
self.p200.distribute(
60,
self.plate[2],
self.plate[0:2],
air_gap=20
)
expected = [
['distributing', '60'],
['transferring', '60'],
['pick'],
['aspirating', '130', 'Well C1'],
['air gap'],
['aspirating', '20'],
['dispensing', '20'],
['dispensing', '60', 'Well A1'],
['air gap'],
['aspirating', '20'],
['dispensing', '20'],
['dispensing', '60', 'Well B1'],
['blow', 'Well A1'],
['drop']
]
fuzzy_assert(self.robot.commands(), expected=expected)
self.robot.clear_commands()
def test_distribute_air_gap_and_disposal_vol(self):
self.p200.reset()
self.p200.distribute(
60,
self.plate[2],
self.plate[0:2],
air_gap=20,
disposal_vol=20
)
expected = [
['distributing', '60'],
['transferring', '60'],
['pick'],
['aspirating', '140', 'Well C1'],
['air gap'],
['aspirating', '20'],
['dispensing', '20', 'Well A1'],
['dispensing', '60', 'Well A1'],
['air gap'],
['aspirating', '20'],
['dispensing', '20', 'Well B1'],
['dispensing', '60', 'Well B1'],
['blow', 'Well A1'],
['drop']
]
fuzzy_assert(self.robot.commands(),
expected=expected
)
self.robot.clear_commands()
def test_consolidate_mix(self):
self.p200.reset()
self.p200.consolidate(
200,
self.plate[0:2],
self.plate[2],
mix_before=(1, 10),
mix_after=(1, 10)
)
expected = [
['consolidating', '200'],
['transferring', '200'],
['pick'],
['aspirating', '200', 'Well A1'],
['dispensing', '200', 'Well C1'],
['mix', '10'],
['aspirating', 'Well C1'],
['dispensing'],
['aspirating', '200', 'Well B1'],
['dispensing', '200', 'Well C1'],
['mix', '10'],
['aspirating', 'Well C1'],
['dispensing'],
['drop']
]
fuzzy_assert(self.robot.commands(),
expected=expected
)
self.robot.clear_commands()
def test_distribute_mix(self):
self.p200.reset()
self.p200.distribute(
200,
self.plate[0],
self.plate[1:3],
mix_before=(1, 10),
mix_after=(1, 10)
)
expected = [
['distributing', '200'],
['transferring', '200'],
['pick'],
['mix', '10'],
['aspirating', 'Well A1'],
['dispensing'],
['aspirating', '200', 'Well A1'],
['dispensing', '200', 'Well B1'],
['mix', '10'],
['aspirating', 'Well A1'],
['dispensing'],
['aspirating', '200', 'Well A1'],
['dispensing', '200', 'Well C1'],
['drop']
]
fuzzy_assert(self.robot.commands(),
expected=expected
)
self.robot.clear_commands()
def test_transfer_multichannel(self):
self.p200.reset()
self.p200.channels = 8
self.p200.transfer(
200,
self.plate.cols[0],
self.plate.cols[1],
touch_tip=False,
blow_out=False,
trash=False
)
expected = [
['Transferring', '200'],
['pick'],
['aspirating', '200', 'wells A1...H1'],
['dispensing', '200', 'wells A2...H2'],
['return'],
['drop']
]
fuzzy_assert(self.robot.commands(),
expected=expected
)
self.robot.clear_commands()
def test_transfer_single_channel(self):
self.p200.reset()
self.p200.channels = 1
self.p200.transfer(
200,
self.plate.cols('1', '2'),
self.plate.cols('3'),
touch_tip=False,
blow_out=False,
trash=False
)
expected = [
['Transferring', '200'],
['pick'],
['aspirating', '200', 'Well A1'],
['dispensing', '200', 'Well A3'],
['aspirating', '200', 'Well B1'],
['dispensing', '200', 'Well A3'],
['aspirating', '200', 'Well C1'],
['dispensing', '200', 'Well B3'],
['aspirating', '200', 'Well D1'],
['dispensing', '200', 'Well B3'],
['aspirating', '200', 'Well E1'],
['dispensing', '200', 'Well C3'],
['aspirating', '200', 'Well F1'],
['dispensing', '200', 'Well C3'],
['aspirating', '200', 'Well G1'],
['dispensing', '200', 'Well D3'],
['aspirating', '200', 'Well H1'],
['dispensing', '200', 'Well D3'],
['aspirating', '200', 'Well A2'],
['dispensing', '200', 'Well E3'],
['aspirating', '200', 'Well B2'],
['dispensing', '200', 'Well E3'],
['aspirating', '200', 'Well C2'],
['dispensing', '200', 'Well F3'],
['aspirating', '200', 'Well D2'],
['dispensing', '200', 'Well F3'],
['aspirating', '200', 'Well E2'],
['dispensing', '200', 'Well G3'],
['aspirating', '200', 'Well F2'],
['dispensing', '200', 'Well G3'],
['aspirating', '200', 'Well G2'],
['dispensing', '200', 'Well H3'],
['aspirating', '200', 'Well H2'],
['dispensing', '200', 'Well H3'],
['return'],
['drop']
]
fuzzy_assert(
self.robot.commands(),
expected=expected
)
self.robot.clear_commands()
def test_touch_tip(self):
self.p200.pick_up_tip()
self.p200.robot.move_to = mock.Mock()
self.p200.touch_tip(self.plate[0])
self.p200.touch_tip(v_offset=-3)
self.p200.touch_tip(self.plate[1], radius=0.5)
expected = [
mock.call(self.plate[0],
instrument=self.p200,
strategy='arc'),
mock.call(
(self.plate[0], (6.40, 3.20, 9.50)),
instrument=self.p200,
strategy='direct'),
mock.call(
(self.plate[0], (0.00, 3.20, 9.50)),
instrument=self.p200,
strategy='direct'),
mock.call(
(self.plate[0], (3.20, 6.40, 9.50)),
instrument=self.p200,
strategy='direct'),
mock.call(
(self.plate[0], (3.20, 0.00, 9.50)),
instrument=self.p200,
strategy='direct'),
mock.call(
(self.plate[0], (6.40, 3.20, 7.50)),
instrument=self.p200,
strategy='direct'),
mock.call(
(self.plate[0], (0.00, 3.20, 7.50)),
instrument=self.p200,
strategy='direct'),
mock.call(
(self.plate[0], (3.20, 6.40, 7.50)),
instrument=self.p200,
strategy='direct'),
mock.call(
(self.plate[0], (3.20, 0.00, 7.50)),
instrument=self.p200,
strategy='direct'),
mock.call(self.plate[1],
instrument=self.p200,
strategy='arc'),
mock.call(
(self.plate[1], (4.80, 3.20, 9.50)),
instrument=self.p200,
strategy='direct'),
mock.call(
(self.plate[1], (1.60, 3.20, 9.50)),
instrument=self.p200,
strategy='direct'),
mock.call(
(self.plate[1], (3.20, 4.80, 9.50)),
instrument=self.p200,
strategy='direct'),
mock.call(
(self.plate[1], (3.20, 1.60, 9.50)),
instrument=self.p200,
strategy='direct')
]
self.assertEquals(expected, self.p200.robot.move_to.mock_calls)
def test_mix(self):
# It is necessary to aspirate before it is mocked out
# so that you have liquid
self.p200.pick_up_tip()
self.p200.aspirate = mock.Mock()
self.p200.dispense = mock.Mock()
self.p200.mix(3, 100, self.plate[1])
dispense_expected = [
mock.call.dispense(100, rate=1.0),
mock.call.dispense(100, rate=1.0),
mock.call.dispense(100, rate=1.0)
]
self.assertEqual(self.p200.dispense.mock_calls, dispense_expected)
aspirate_expected = [
mock.call.aspirate(volume=100, location=self.plate[1], rate=1.0),
mock.call.aspirate(100, rate=1.0),
mock.call.aspirate(100, rate=1.0)
]
self.assertEqual(self.p200.aspirate.mock_calls, aspirate_expected)
def test_air_gap(self):
self.p200.pick_up_tip()
self.p200.aspirate(50, self.plate[0])
self.p200.air_gap()
self.assertEquals(self.p200.current_volume, 200)
self.p200.dispense()
self.p200.aspirate(50, self.plate[1])
self.p200.air_gap(10)
self.assertEquals(self.p200.current_volume, 60)
self.p200.dispense()
self.p200.aspirate(50, self.plate[2])
self.p200.air_gap(10, 10)
self.assertEquals(self.p200.current_volume, 60)
self.p200.dispense()
self.p200.aspirate(50, self.plate[2])
self.p200.air_gap(0)
self.assertEquals(self.p200.current_volume, 50)
def test_pipette_home(self):
self.p200.home()
self.assertEquals(len(self.robot.commands()), 1)
def test_mix_with_named_args(self):
self.p200.current_volume = 100
self.p200.pick_up_tip()
self.p200.aspirate = mock.Mock()
self.p200.dispense = mock.Mock()
self.p200.mix(volume=50, repetitions=2)
self.assertEqual(
self.p200.dispense.mock_calls,
[
mock.call.dispense(50, rate=1.0),
mock.call.dispense(50, rate=1.0)
]
)
self.assertEqual(
self.p200.aspirate.mock_calls,
[
mock.call.aspirate(volume=50,
location=None,
rate=1.0),
mock.call.aspirate(50, rate=1.0)
]
)
def test_tip_tracking_simple(self):
self.p200.move_to = mock.Mock()
self.p200.pick_up_tip()
self.p200.tip_attached = False # prior expectation, for test only
self.p200.pick_up_tip()
assert self.p200.move_to.mock_calls == \
self.build_pick_up_tip(self.tiprack1[0]) + \
self.build_pick_up_tip(self.tiprack1[1])
def test_simulate_plunger_while_enqueing(self):
self.p200.pick_up_tip()
self.assertEquals(self.p200.current_volume, 0)
self.p200.aspirate(200)
self.assertEquals(self.p200.current_volume, 200)
self.p200.dispense(20)
self.assertEquals(self.p200.current_volume, 180)
self.p200.dispense(20)
self.assertEquals(self.p200.current_volume, 160)
self.p200.dispense(60)
self.assertEquals(self.p200.current_volume, 100)
self.p200.dispense(100)
self.assertEquals(self.p200.current_volume, 0)
self.p200.drop_tip()
def test_tip_tracking_chain(self):
# TODO (ben 20171130): revise this test to make more sense in the
# context of required tip pick_up/drop sequencing, etc.
total_tips_per_plate = 4
self.tiprack1 = generate_plate(
total_tips_per_plate, 2, (5, 5), (0, 0), 5)
self.tiprack2 = generate_plate(
total_tips_per_plate, 2, (5, 5), (0, 0), 5)
self.robot._deck['1'].add(self.tiprack1, 'tiprack1')
self.robot._deck['2'].add(self.tiprack2, 'tiprack2')
self.p200 = Pipette(
self.robot,
mount='right',
tip_racks=[self.tiprack1, self.tiprack2],
trash_container=self.tiprack1,
name='pipette-for-transfer-tests',
ul_per_mm=18.5
)
self.p200.max_volume = 200
self.p200.move_to = mock.Mock()
for _ in range(0, total_tips_per_plate * 2):
self.p200.pick_up_tip()
self.p200.tip_attached = False # prior expectation, for test only
expected = []
for i in range(0, total_tips_per_plate):
expected.extend(self.build_pick_up_tip(self.tiprack1[i]))
for i in range(0, total_tips_per_plate):
expected.extend(self.build_pick_up_tip(self.tiprack2[i]))
self.assertEqual(
self.p200.move_to.mock_calls,
expected
)
# test then when we go over the total number of tips,
# Pipette raises a RuntimeWarning
self.robot.clear_commands()
self.p200.reset()
for _ in range(0, total_tips_per_plate * 2):
self.p200.pick_up_tip()
self.p200.tip_attached = False # prior expectation, for test only
self.assertRaises(RuntimeWarning, self.p200.pick_up_tip)
def test_tip_tracking_chain_multi_channel(self):
# TODO (ben 20171130): revise this test to make more sense in the
# context of required tip pick_up/drop sequencing, etc.
p200_multi = Pipette(
self.robot,
trash_container=self.trash,
tip_racks=[self.tiprack1, self.tiprack2],
min_volume=10, # These are variable
mount='right',
channels=8,
ul_per_mm=18.5
)
p200_multi.calibrate_plunger(
top=0, bottom=10, blow_out=12, drop_tip=13)
p200_multi.move_to = mock.Mock()
for _ in range(0, 12 * 2):
p200_multi.pick_up_tip()
p200_multi.tip_attached = False # prior expectation, for test only
expected = []
for i in range(0, 12):
expected.extend(self.build_pick_up_tip(self.tiprack1.cols[i]))
for i in range(0, 12):
expected.extend(self.build_pick_up_tip(self.tiprack2.cols[i]))
self.assertEqual(
p200_multi.move_to.mock_calls,
expected
)
def test_tip_tracking_start_at_tip(self):
self.p200.start_at_tip(self.tiprack1['B2'])
self.p200.pick_up_tip()
self.assertEquals(self.tiprack1['B2'], self.p200.current_tip())
def test_tip_tracking_return(self):
# Note: because this test mocks out `drop_tip`, as a side-effect
# `tip_attached` must be manually set as it would be under the
# `return_tip` callstack, making this tesk somewhat fragile
self.p200.drop_tip = mock.Mock()
self.p200.pick_up_tip()
self.p200.return_tip()
self.p200.tip_attached = False
self.p200.pick_up_tip()
self.p200.return_tip()
expected = [
mock.call(self.tiprack1[0], home_after=True),
mock.call(self.tiprack1[1], home_after=True)
]
self.assertEqual(self.p200.drop_tip.mock_calls, expected)
def test_direct_movement_within_well(self):
self.robot.move_to = mock.Mock()
self.p200.move_to(self.plate[0])
self.p200.move_to(self.plate[0].top())
self.p200.move_to(self.plate[0].bottom())
self.p200.move_to(self.plate[1])
self.p200.move_to(self.plate[2])
self.p200.move_to(self.plate[2].bottom())
expected = [
mock.call(
self.plate[0], instrument=self.p200, strategy='arc'),
mock.call(
self.plate[0].top(), instrument=self.p200, strategy='direct'),
mock.call(
self.plate[0].bottom(), instrument=self.p200, strategy='direct'),
mock.call(
self.plate[1], instrument=self.p200, strategy='arc'),
mock.call(
self.plate[2], instrument=self.p200, strategy='arc'),
mock.call(
self.plate[2].bottom(), instrument=self.p200, strategy='direct')
]
self.assertEqual(self.robot.move_to.mock_calls, expected)
def build_pick_up_tip(self, well):
plunge = -10
return [
mock.call(well.top()),
mock.call(well.top(plunge), strategy='direct'),
mock.call(well.top(), strategy='direct'),
mock.call(well.top(plunge - 1), strategy='direct'),
mock.call(well.top(), strategy='direct'),
mock.call(well.top(plunge - 2), strategy='direct'),
mock.call(well.top(), strategy='direct')
]
def __init__(self,
axis,
name=None,
channels=1,
min_volume=0,
max_volume=None,
trash_container=None,
tip_racks=[],
aspirate_speed=300,
dispense_speed=500):
self.axis = axis
self.channels = channels
if not name:
name = self.__class__.__name__
self.name = name
self.trash_container = trash_container
self.tip_racks = tip_racks
# default mm above tip to execute drop-tip
# this gives room for the drop-tip mechanism to work
self._drop_tip_offset = 15
self.reset_tip_tracking()
self.robot = Robot.get_instance()
self.robot.add_instrument(self.axis, self)
self.motor = self.robot.get_motor(self.axis)
self.placeables = []
self.previous_placeable = None
self.current_volume = 0
self.speeds = {'aspirate': aspirate_speed, 'dispense': dispense_speed}
self.min_volume = min_volume
self.max_volume = max_volume or (min_volume + 1)
self.positions = {
'top': None,
'bottom': None,
'blow_out': None,
'drop_tip': None
}
self.calibrated_positions = copy.deepcopy(self.positions)
self.calibration_data = {}
# Pipette properties to persist between sessions
persisted_attributes = ['calibration_data', 'positions', 'max_volume']
persisted_key = '{axis}:{name}'.format(axis=self.axis, name=self.name)
self.init_calibrations(key=persisted_key,
attributes=persisted_attributes)
self.load_persisted_data()
self.calibrator = Calibrator(self.robot._deck, self.calibration_data)
# if the user passed an initialization value,
# overwrite the loaded persisted data with it
if isinstance(max_volume, (int, float, complex)) and max_volume > 0:
self.max_volume = max_volume
self.update_calibrations()
class RobotTest(unittest.TestCase):
def setUp(self):
self.robot = Robot()
self.smoothie_version = 'edge-1c222d9NOMSD'
self.robot.reset()
self.robot.connect(options={'firmware': self.smoothie_version})
self.robot.home(enqueue=False)
def test_firmware_verson(self):
self.assertEquals(self.smoothie_version,
self.robot._driver.firmware_version)
def test_add_container(self):
c1 = self.robot.add_container('96-flat', 'A1')
res = self.robot.containers()
expected = {'96-flat': c1}
self.assertEquals(res, expected)
c2 = self.robot.add_container('96-flat', 'A2', 'my-special-plate')
res = self.robot.containers()
expected = {'96-flat': c1, 'my-special-plate': c2}
self.assertEquals(res, expected)
def test_comment(self):
self.robot.clear_commands()
self.robot.comment('hello')
self.assertEquals(len(self.robot.commands()), 1)
self.assertEquals(self.robot._commands[0], 'hello')
def test_home_after_disconnect(self):
self.robot._driver.connection = None
self.assertRaises(RuntimeError, self.robot.home)
# TODO: reevaluate/implement this test...
# def test_stop_run(self):
# p200 = pipette.Pipette(
# self.robot, axis='b', name='my-fancy-pancy-pipette'
# )
# p200.calibrate_plunger(top=0, bottom=5, blow_out=6, drop_tip=7)
#
# for i in range(1000):
# p200.aspirate().dispense()
#
# res = None
#
# def _run():
# nonlocal res
# self.assertRaises(RuntimeError, self.robot.run)
#
# thread = threading.Thread(target=_run)
# thread.start()
#
# self.robot.stop()
#
# thread.join()
def test_calibrated_max_dimension(self):
expected = self.robot._deck.max_dimensions(self.robot._deck)
res = self.robot._calibrated_max_dimension()
self.assertEquals(res, expected)
p200 = pipette.Pipette(self.robot,
axis='b',
name='my-fancy-pancy-pipette')
plate = containers_load(self.robot, '96-flat', 'A1')
self.robot.move_head(x=10, y=10, z=10)
p200.calibrate_position((plate, Vector(0, 0, 0)))
res = self.robot._calibrated_max_dimension()
expected = Vector(plate.max_dimensions(plate)) + Vector(10, 10, 10)
self.assertEquals(res, expected)
def test_create_arc(self):
p200 = pipette.Pipette(self.robot,
axis='b',
name='my-fancy-pancy-pipette')
plate = containers_load(self.robot, '96-flat', 'A1')
plate2 = containers_load(self.robot, '96-flat', 'B1')
self.robot.move_head(x=10, y=10, z=10)
p200.calibrate_position((plate, Vector(0, 0, 0)))
self.robot.move_head(x=10, y=10, z=100)
p200.calibrate_position((plate2, Vector(0, 0, 0)))
res = self.robot._create_arc((0, 0, 0), plate[0])
expected = [{'z': 100}, {'x': 0, 'y': 0}, {'z': 0}]
self.assertEquals(res, expected)
res = self.robot._create_arc((0, 0, 0), plate[0])
expected = [{'z': 20.5 + 5}, {'x': 0, 'y': 0}, {'z': 0}]
self.assertEquals(res, expected)
def test_disconnect(self):
self.robot.disconnect()
res = self.robot.is_connected()
self.assertEquals(bool(res), False)
def test_get_connected_port(self):
res = self.robot.get_connected_port()
self.assertEquals(res, drivers.VIRTUAL_SMOOTHIE_PORT)
def test_robot_move_to(self):
self.robot.move_to((Deck(), (100, 0, 0)))
position = self.robot._driver.get_head_position()['current']
self.assertEqual(position, (100, 0, 0))
def test_move_head(self):
self.robot.move_head(x=100, y=0, z=20)
current = self.robot._driver.get_head_position()['current']
self.assertEquals(current, (100, 0, 20))
def test_home(self):
self.robot.disconnect()
self.robot.connect()
# Check that all axes are marked as not homed
self.assertDictEqual(self.robot.axis_homed, {
'x': False,
'y': False,
'z': False,
'a': False,
'b': False
})
# self.robot.clear_commands()
# Home X & Y axes
self.robot.home('xa')
# self.assertDictEqual(self.robot.axis_homed, {
# 'x': False, 'y': False, 'z': False, 'a': False, 'b': False
# })
# Verify X & Y axes are marked as homed
self.assertDictEqual(self.robot.axis_homed, {
'x': True,
'y': False,
'z': False,
'a': True,
'b': False
})
# Home all axes
self.robot.home()
# Verify all axes are marked as homed
self.assertDictEqual(self.robot.axis_homed, {
'x': True,
'y': True,
'z': True,
'a': True,
'b': True
})
def test_robot_pause_and_resume(self):
self.robot.move_to((Deck(), (100, 0, 0)))
self.robot.move_to((Deck(), (101, 0, 0)))
self.assertEqual(len(self.robot._commands), 0)
#
# FIXME: pause and resume can't be measured based on whether commands
# in the command queue are executed since all robot actions will be
# called immediately
#
# self.robot.pause()
#
# def _run():
# self.robot.run()
#
# thread = threading.Thread(target=_run)
# thread.start()
# self.robot.resume()
# thread.join(0.5)
#
# self.assertEquals(thread.is_alive(), False)
# self.assertEqual(len(self.robot._commands), 2)
#
# self.robot.clear_commands()
# self.assertEqual(len(self.robot._commands), 0)
#
# self.robot.move_to((Deck(), (100, 0, 0)), enqueue=True)
# self.robot.move_to((Deck(), (101, 0, 0)), enqueue=True)
#
# def _run():
# self.robot.run()
#
# self.robot.pause()
#
# thread = threading.Thread(target=_run)
# thread.start()
# thread.join(0.01)
#
# self.assertEquals(thread.is_alive(), True)
# self.assertEqual(len(self.robot._commands) > 0, True)
#
# self.robot.resume()
#
# thread.join(1)
# self.assertEqual(len(self.robot._commands), 2)
def test_versions(self):
res = self.robot.versions()
expected = {
'config': {
'version': 'v2.0.0',
'compatible': True
},
'firmware': {
'version': self.smoothie_version,
'compatible': True
},
'ot_version': {
'version': 'one_pro_plus',
'compatible': True
}
}
self.assertDictEqual(res, expected)
def test_diagnostics(self):
res = self.robot.diagnostics()
expected = {
'axis_homed': {
'x': True,
'y': True,
'z': True,
'a': True,
'b': True
},
'switches': {
'x': False,
'y': False,
'z': False,
'a': False,
'b': False
},
'steps_per_mm': {
'x': 80.0,
'y': 80.0
}
}
self.assertDictEqual(res, expected)
self.robot.disconnect()
self.robot.connect()
self.assertRaises(RuntimeWarning, self.robot.move_head, x=-199)
res = self.robot.diagnostics()
expected = {
'axis_homed': {
'x': False,
'y': False,
'z': False,
'a': False,
'b': False
},
'switches': {
'x': True,
'y': False,
'z': False,
'a': False,
'b': False
},
'steps_per_mm': {
'x': 80.0,
'y': 80.0
}
}
self.assertDictEqual(res, expected)
self.robot.home('x', enqueue=False)
res = self.robot.diagnostics()
expected = {
'axis_homed': {
'x': True,
'y': False,
'z': False,
'a': False,
'b': False
},
'switches': {
'x': False,
'y': False,
'z': False,
'a': False,
'b': False
},
'steps_per_mm': {
'x': 80.0,
'y': 80.0
}
}
self.assertDictEqual(res, expected)
def test_get_motor_caching(self):
a_motor = self.robot.get_motor('a')
self.assertEqual(a_motor, self.robot.get_motor('a'))
b_motor = self.robot.get_motor('b')
self.assertEqual(b_motor, self.robot.get_motor('b'))
def test_get_mosfet_caching(self):
m0 = self.robot.get_mosfet(0)
self.assertEqual(m0, self.robot.get_mosfet(0))
m1 = self.robot.get_mosfet(1)
self.assertEqual(m1, self.robot.get_mosfet(1))