def test_get_all_children(self):
c1 = generate_plate(4, 2, (5, 5), (0, 0), 5)
c2 = generate_plate(4, 2, (5, 5), (0, 0), 5)
deck = Deck()
deck.add(c1, "A1", (0, 0, 0))
deck.add(c2, "A2", (50, 50, 50))
self.assertEqual(len(deck.get_all_children()), 10)
def test_get_all_children():
c1 = generate_plate(4, 2, (5, 5), (0, 0), 5)
c2 = generate_plate(4, 2, (5, 5), (0, 0), 5)
deck = Deck()
deck.add(c1, "A1", (0, 0, 0))
deck.add(c2, "A2", (50, 50, 50))
assert len(deck.get_all_children()) == 10
def test_chain_method(self):
a = generate_plate(4, 2, (5, 5), (0, 0), 5)
b = generate_plate(4, 2, (5, 5), (0, 0), 5)
c = generate_plate(4, 2, (5, 5), (0, 0), 5)
cycle_iter = a.chain(b, c)
for i in range(4):
self.assertEqual(next(cycle_iter), a[i])
for i in range(4):
self.assertEqual(next(cycle_iter), b[i])
for i in range(4):
self.assertEqual(next(cycle_iter), c[i])
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(local_test_pipette, robot):
trash, tiprack1, tiprack2, plate, p200 = local_test_pipette
# 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
tiprack1 = generate_plate(
total_tips_per_plate, 2, (5, 5), (0, 0), 5)
tiprack2 = generate_plate(
total_tips_per_plate, 2, (5, 5), (0, 0), 5)
robot._deck['1'].add(tiprack1, 'tiprack1')
robot._deck['2'].add(tiprack2, 'tiprack2')
p200 = Pipette(
robot,
mount='right',
tip_racks=[tiprack1, tiprack2],
trash_container=tiprack1,
name='pipette-for-transfer-tests',
max_volume=200,
ul_per_mm=18.5
)
p200.move_to = mock.Mock()
for _ in range(0, total_tips_per_plate * 2):
p200.pick_up_tip()
p200.tip_attached = False # prior expectation, for test only
expected = []
for i in range(0, total_tips_per_plate):
expected.extend(build_pick_up_tip(p200, tiprack1[i]))
for i in range(0, total_tips_per_plate):
expected.extend(build_pick_up_tip(p200, tiprack2[i]))
assert p200.move_to.mock_calls == expected
# test then when we go over the total number of tips,
# Pipette raises a RuntimeWarning
robot.clear_commands()
p200.reset()
for _ in range(0, total_tips_per_plate * 2):
p200.pick_up_tip()
p200.tip_attached = False # prior expectation, for test only
with pytest.raises(RuntimeWarning):
p200.pick_up_tip()
def test_wells(self):
c = generate_plate(96, 8, (9, 9), (16, 11), 2.5, 40)
self.assertWellSeriesEqual(c.well(0), c[0])
self.assertWellSeriesEqual(c.well('A2'), c['A2'])
self.assertWellSeriesEqual(c.wells(0), c[0])
self.assertWellSeriesEqual(c.wells(), c[0:])
expected = [c[n] for n in ['A1', 'B2', 'C3']]
self.assertWellSeriesEqual(c.wells('A1', 'B2', 'C3'), expected)
self.assertWellSeriesEqual(c.get('A1', 'B2', 'C3'), expected)
self.assertWellSeriesEqual(c('A1', 'B2', 'C3'), expected)
expected = [c.rows[0][0], c.rows[0][5]]
self.assertWellSeriesEqual(c.rows['A'].wells('1', '6'), expected)
self.assertWellSeriesEqual(c.rows['A'].get('1', '6'), expected)
expected = [c.rows[0][0], c.rows[0][5]]
self.assertWellSeriesEqual(c.rows['A'].wells(['1', '6']), expected)
self.assertWellSeriesEqual(c.rows['A'].get('1', '6'), expected)
self.assertWellSeriesEqual(c.rows('A').get('1', '6'), expected)
expected = c.wells('A1', 'B1', 'C1', 'D1', 'E1', 'F1', 'G1', 'H1')
self.assertWellSeriesEqual(c.wells('A1', to='H1'), expected)
self.assertWellSeriesEqual(c.get('A1', to='H1'), expected)
expected = c.wells('A1', 'C1', 'E1', 'G1')
self.assertWellSeriesEqual(c.wells('A1', to='H1', step=2), expected)
self.assertWellSeriesEqual(c.get('A1', to='H1', step=2), expected)
expected = c.cols['1':'12':2]
self.assertWellSeriesEqual(c.cols('1', to='12', step=2), expected)
expected = c.wells('A3', 'G2', 'E2', 'C2', 'A2', 'G1', 'E1', 'C1',
'A1')
self.assertWellSeriesEqual(c.wells('A3', to='A1', step=2), expected)
self.assertWellSeriesEqual(c.get('A3', to='A1', step=2), expected)
expected = c.wells('A1', 'B1', 'C1', 'D1', 'E1', 'F1', 'G1', 'H1')
self.assertWellSeriesEqual(c.wells('A1', length=8), expected)
expected = c.wells('A1', 'C1', 'E1', 'G1', 'A2', 'C2', 'E2', 'G2')
self.assertWellSeriesEqual(c.wells('A1', length=8, step=2), expected)
expected = c.wells('A1', 'H12', 'G12', 'F12')
self.assertWellSeriesEqual(c.wells('A1', length=4, step=-1), expected)
expected = c.wells('A1', 'H12', 'G12', 'F12')
self.assertWellSeriesEqual(c.wells('A1', length=-4, step=-1), expected)
expected = c.wells('A1', 'H12', 'G12', 'F12')
self.assertWellSeriesEqual(c.wells('A1', length=-4, step=1), expected)
expected = c.wells('A1', 'B1', 'C1', 'D1')
self.assertWellSeriesEqual(c.wells(length=4), expected)
self.assertWellSeriesEqual(c.wells(43), c.wells(x=3, y=5))
self.assertWellSeriesEqual(c.rows(3), c.wells(y=3))
self.assertWellSeriesEqual(c.cols(4), c.wells(x=4))
self.assertRaises(ValueError, c.wells, **{'x': '1', 'y': '2'})
def test_slice_with_strings(self):
c = generate_plate(96, 8, (9, 9), (16, 11), 2.5, 40)
self.assertWellSeriesEqual(c['A1':'A2'], c[0:8])
self.assertWellSeriesEqual(c['A12':], c.cols[-1][0:])
self.assertWellSeriesEqual(c.cols['4':'8'], c.cols[3:7])
self.assertWellSeriesEqual(c.rows['B':'E'], c.rows[1:4])
self.assertWellSeriesEqual(c.rows['B']['1':'7'], c.rows[1][0:6])
def test_top_bottom(self):
deck = Deck()
slot = Slot()
plate = generate_plate(wells=4,
cols=2,
spacing=(10, 10),
offset=(0, 0),
radius=5,
height=10)
deck.add(slot, 'A1', (0, 0, 0))
slot.add(plate)
self.assertEqual(plate['A1'].bottom(10),
(plate['A1'], Vector(5, 5, 10)))
self.assertEqual(plate['A1'].top(10), (plate['A1'], Vector(5, 5, 20)))
self.assertEqual(plate['A1'].bottom(10, radius=1.0, degrees=90),
(plate['A1'], Vector(5, 10, 10)))
self.assertEqual(plate['A1'].top(10, radius=1.0, degrees=90),
(plate['A1'], Vector(5, 10, 20)))
self.assertEqual(plate['A1'].bottom(10, radius=0.5, degrees=270),
(plate['A1'], Vector(5, 2.5, 10.00)))
self.assertEqual(plate['A1'].top(10, radius=0.5, degrees=270),
(plate['A1'], Vector(5, 2.5, 20.00)))
def test_add_placeables(self):
a = generate_plate(4, 2, (5, 5), (0, 0), 5)
b = generate_plate(4, 2, (5, 5), (0, 0), 5)
result = a + b
self.assertEqual(len(result), 8)
for i in range(len(a)):
self.assertEqual(a[i], result[i])
for i in range(len(b)):
self.assertEqual(b[i], result[i + len(a)])
result = a.cols(0) + b.rows(0)
self.assertEqual(len(result), 4)
self.assertEqual(a[0], result[0])
self.assertEqual(a[1], result[1])
self.assertEqual(b[0], result[2])
self.assertEqual(b[2], result[3])
def test_add_placeables():
a = generate_plate(4, 2, (5, 5), (0, 0), 5)
b = generate_plate(4, 2, (5, 5), (0, 0), 5)
result = a + b
assert len(result) == 8
for i in range(len(a)):
assert a[i] == result[i]
for i in range(len(b)):
assert b[i] == result[i + len(a)]
result = a.cols(0) + b.rows(0)
assert len(result) == 4
assert a[0] == result[0]
assert a[1] == result[1]
assert b[0] == result[2]
assert b[2] == result[3]
def test_generate_plate(self):
c = generate_plate(wells=96,
cols=8,
spacing=(10, 15),
offset=(5, 15),
radius=5)
self.assertEqual(c['A1'].coordinates(), (5, 15, 0))
self.assertEqual(c['B2'].coordinates(), (15, 30, 0))
def test_generate_plate(robot):
c = generate_plate(wells=96,
cols=8,
spacing=(10, 15),
offset=(5, 15),
radius=5)
assert c['A1'].coordinates() == (5, 15, 0)
assert c['B2'].coordinates() == (15, 30, 0)
def test_coordinates(robot):
deck = Deck()
slot = Slot()
plate = generate_plate(wells=96,
cols=8,
spacing=(10, 15),
offset=(5, 15),
radius=5)
deck.add(slot, 'B2', (100, 200, 0))
slot.add(plate)
assert plate['A1'].coordinates(deck) == (105, 215, 0)
def test_well_from_center(robot):
deck = Deck()
slot = Slot()
plate = generate_plate(wells=4,
cols=2,
spacing=(10, 10),
offset=(0, 0),
radius=5)
deck.add(slot, 'A1', (0, 0, 0))
slot.add(plate)
assert plate['B2'].center() == (5, 5, 0)
assert plate['B2'].from_center(x=0.0, y=0.0, z=0.0) == (5, 5, 0)
assert plate['B2'].from_center(r=1.0, theta=math.pi / 2, h=0.0)\
== (5.0, 10.0, 0.0)
def test_well_from_center():
deck = Deck()
slot = Slot()
plate = generate_plate(wells=4,
cols=2,
spacing=(10, 10),
offset=(0, 0),
radius=5,
height=20)
deck.add(slot, 'A1', (0, 0, 0))
slot.add(plate)
assert plate['B2'].center() == (5, 5, 10)
assert plate['B2'].from_center(x=0.0, y=0.0, z=2.0) == (5, 5, 30)
assert plate['B2'].from_center(r=1.0, theta=pi / 2, h=5.0) == (5, 10, 60)
assert plate['B2'].top()[1] == (5, 5, 20)
assert plate['B2'].bottom()[1] == (5, 5, 0)
def test_well_from_center_new(split_labware_def):
print("Split labware definitions? {}".format(
ff.split_labware_definitions()))
deck = Deck()
slot = Slot()
plate = generate_plate(wells=4,
cols=2,
spacing=(10, 10),
offset=(0, 0),
radius=5,
height=20)
deck.add(slot, 'A1', (0, 0, 0))
slot.add(plate)
assert plate['B2'].center() == (5, 5, 10)
assert plate['B2'].from_center(x=0.0, y=0.0, z=2.0) == (5, 5, 30)
assert plate['B2'].from_center(r=1.0, theta=pi / 2, h=5.0) == (5, 10, 60)
assert plate['B2'].top()[1] == (5, 5, 20)
assert plate['B2'].bottom()[1] == (5, 5, 0)
def test_next(self):
c = generate_plate(4, 2, (5, 5), (0, 0), 5)
well = c['A1']
expected = c.get_child_by_name('B1')
self.assertEqual(next(well), expected)
def test_iterate_without_parent(self):
c = generate_plate(4, 2, (5, 5), (0, 0), 5)
self.assertRaises(Exception, next, c)
def test_int_index(robot):
c = generate_plate(4, 2, (5, 5), (0, 0), 5)
assert c[3] == c.get_child_by_name('B2')
assert c[1] == c.get_child_by_name('B1')
def test_next(robot):
c = generate_plate(4, 2, (5, 5), (0, 0), 5)
well = c['A1']
expected = c.get_child_by_name('B1')
assert next(well) == expected
def test_iterator(robot):
c = generate_plate(4, 2, (5, 5), (0, 0), 5)
res = [well.coordinates() for well in c]
expected = [(0, 0, 0), (5, 0, 0), (0, 5, 0), (5, 5, 0)]
assert res == expected
def test_back_container_getitem(robot):
c = generate_plate(4, 2, (5, 5), (0, 0), 5)
with pytest.raises(TypeError):
c.__getitem__((1, 1))
def test_iterate_without_parent(robot):
c = generate_plate(4, 2, (5, 5), (0, 0), 5)
with pytest.raises(Exception):
next(c)
def test_int_index(self):
c = generate_plate(4, 2, (5, 5), (0, 0), 5)
self.assertEqual(c[3], c.get_child_by_name('B2'))
self.assertEqual(c[1], c.get_child_by_name('B1'))
def test_back_container_getitem(self):
c = generate_plate(4, 2, (5, 5), (0, 0), 5)
self.assertRaises(TypeError, c.__getitem__, (1, 1))
def test_get_name(self):
c = generate_plate(4, 2, (5, 5), (0, 0), 5)
expected = '<Well A1>'
self.assertEqual(str(c['A1']), expected)
expected = '<Container>'
self.assertEqual(str(c), expected)
def test_iter_method(self):
c = generate_plate(4, 2, (5, 5), (0, 0), 5)
cycle_iter = c.iter()
for i in range(4):
self.assertEqual(next(cycle_iter), c[i])
def test_cycle(self):
c = generate_plate(4, 2, (5, 5), (0, 0), 5)
cycle_iter = c.cycle()
for n in range(3):
for i in range(4):
self.assertEqual(next(cycle_iter), c[i])
def test_iter_method():
c = generate_plate(4, 2, (5, 5), (0, 0), 5)
cycle_iter = c.iter()
for i in range(4):
assert next(cycle_iter) == c[i]
def test_iterator(self):
c = generate_plate(4, 2, (5, 5), (0, 0), 5)
res = [well.coordinates() for well in c]
expected = [(0, 0, 0), (5, 0, 0), (0, 5, 0), (5, 5, 0)]
self.assertListEqual(res, expected)
