def test_grid_row_addresses(self):
""" Grid row groups contain the correct addresses. """
plate = Microplate()
rows = plate.row(1).human_address
self.assertEqual(
rows, ['A2', 'B2', 'C2', 'D2', 'E2', 'F2', 'G2', 'H2']
)
def test_address(self):
""" Address. """
plate = Microplate()
self.assertEqual(plate.well('A1').address, [(0, 0)])
self.assertEqual(plate.well('a1').human_address, 'A1')
deck = Deck()
deck.add_module('A1', 'microplate')
well = deck.slot('A1').well('B4')
self.assertEqual(well.human_address, 'A1:B4')
self.assertEqual(well.address, [(0, 0), (1, 3)])
def test_group_transfer(self):
plate = Microplate()
plate.col('A').transfer(10, plate.col('B'))
self.assertEqual(
plate.col('A').get_volume(), [-10 for _ in range(12)]
)
self.assertEqual(
plate.col('B').get_volume(), [10 for _ in range(12)]
)
def setUp(self):
self.plate = Microplate()
def setUp(self):
self.plate = Microplate()
self.well = self.plate.well('A1')
class MicroplateWellTest(unittest.TestCase):
def setUp(self):
self.plate = Microplate()
self.well = self.plate.well('A1')
def liquid_allocation_test(self):
"""Add volume to well."""
set_vol = 50
# Add an initial value of 100ul water to this well.
self.well.allocate(water=set_vol)
vol = self.well.get_volume()
self.assertEqual(vol, set_vol)
def liquid_capacity_test(self):
"""Reject well overflow volumes."""
set_vol = 10000
# Way too much water for a microplate!
with self.assertRaises(ValueError):
self.well.allocate(water=set_vol)
def liquid_total_capacity_test(self):
"""Reject combined well overflow."""
self.well.allocate(water=90)
self.well.add_liquid(water=10)
with self.assertRaises(ValueError):
self.well.add_liquid(water=1)
def liquid_total_mixture_test(self):
"""Reject combined well overflow from mixed liquids."""
self.well.allocate(water=90)
self.well.add_liquid(buffer=10)
with self.assertRaises(ValueError):
self.well.add_liquid(saline=1)
def mixture_transfer_test(self):
"""Mixture transfers."""
wellA = self.well
wellB = self.plate.well('A2')
wellA.allocate(water=90, buffer=9, saline=1)
wellA.transfer(20, wellB)
# Check Well A to ensure things have been removed.
wat = wellA.get_proportion('water')
buf = wellA.get_proportion('buffer')
sal = wellA.get_proportion('saline')
# We use almostEqual because it's floating-point.
self.assertAlmostEqual(wat, .9)
self.assertAlmostEqual(buf, .09)
self.assertAlmostEqual(sal, .01)
self.assertEqual(wellA.get_volume(), 80)
# Check WellB to ensure things have been added.
wat = wellB.get_proportion('water')
buf = wellB.get_proportion('buffer')
sal = wellB.get_proportion('saline')
# We use almostEqual because it's floating-point.
self.assertAlmostEqual(wat, .9)
self.assertAlmostEqual(buf, .09)
self.assertAlmostEqual(sal, .01)
self.assertEqual(wellB.get_volume(), 20)
def proportion_key_error_test(self):
"""Raises for proportion of liquid not present in mixture."""
with self.assertRaises(KeyError):
self.well.get_proportion('water')
def liquid_key_error_test(self):
"""Raises if wrong liquid named in get_volume."""
self.well.allocate(saline=10)
with self.assertRaises(KeyError):
self.well.get_volume('water')
def liquid_value_error_test(self):
"""Raises on named get_volume if multiple liquids present."""
self.well.allocate(water=10, saline=10)
with self.assertRaises(ValueError):
self.well.get_volume('water')
def ml_conversion_test(self):
"""ml to µl conversion."""
self.well.allocate(water=.1, ml=True)
self.assertEqual(self.well.get_volume(), 100)
class MicroplateTest(unittest.TestCase):
expected_margin = 9 # ANSI standard.
def setUp(self):
self.plate = Microplate()
def a2_coordinate_test(self):
"""Calibrated coordinates of A2."""
a2 = self.plate.well('A2').coordinates()
self.assertEqual(a2, (0, self.expected_margin))
def b1_coordinate_test(self):
"""Calibrated coordinates of B1."""
b1 = self.plate.well('B1').coordinates()
self.assertEqual(b1, (self.expected_margin, 0))
def b2_coordinate_test(self):
"""Calibrated coordinates of B2."""
b2 = self.plate.well('B2').coordinates()
margin = self.expected_margin
self.assertEqual(b2, (margin, margin))
def coordinate_lowercase_test(self):
"""Lowercase coordinates."""
b2 = self.plate.well('b2').coordinates()
margin = self.expected_margin
self.assertEqual(b2, (margin, margin))
def col_sanity_test(self):
"""Don't return out-of-range columns."""
col = chr(ord('a') + self.plate.cols + 1)
with self.assertRaises(KeyError):
self.plate.well('{}1'.format(col))
def unicode_coord_test(self):
"""Unicode coordinates."""
self.plate.well(u'A1')
def row_sanity_test(self):
"""Don't return out-of-range rows."""
row = self.plate.rows + 1
with self.assertRaises(KeyError):
self.plate.well('A{}'.format(row))
def col_type_sanity_test(self):
"""Sanity check on well coordinates."""
with self.assertRaises(ValueError):
self.plate.well('ABC')
class MicroplateTest(unittest.TestCase):
expected_margin = 9 # ANSI standard.
def setUp(self):
self.plate = Microplate()
def a2_coordinate_test(self):
"""Calibrated coordinates of A2."""
a2 = self.plate.well('A2').coordinates()
self.assertEqual(a2, (0, self.expected_margin))
def b1_coordinate_test(self):
"""Calibrated coordinates of B1."""
b1 = self.plate.well('B1').coordinates()
self.assertEqual(b1, (self.expected_margin, 0))
def b2_coordinate_test(self):
"""Calibrated coordinates of B2."""
b2 = self.plate.well('B2').coordinates()
margin = self.expected_margin
self.assertEqual(b2, (margin, margin))
def coordinate_lowercase_test(self):
"""Lowercase coordinates."""
b2 = self.plate.well('b2').coordinates()
margin = self.expected_margin
self.assertEqual(b2, (margin, margin))
def col_sanity_test(self):
"""Don't return out-of-range columns."""
col = chr(ord('a') + self.plate.cols + 1)
with self.assertRaises(x.SlotMissing):
self.plate.well('{}1'.format(col))
def unicode_coord_test(self):
"""Unicode coordinates."""
self.plate.well(u'A1')
def row_sanity_test(self):
"""Don't return out-of-range rows."""
row = self.plate.rows + 1
with self.assertRaises(x.SlotMissing):
self.plate.well('A{}'.format(row))
def col_type_sanity_test(self):
"""Sanity check on well coordinates."""
with self.assertRaises(ValueError):
self.plate.well('ABC')
def setUp(self):
self.plate = Microplate()
self.well = self.plate.well('A1')
def setUp(self):
self.plate = Microplate()
self.plate.calibrate(x=10, y=11, z=12)
def setUp(self):
self.plate = Microplate()
def test_grid_col_addresses(self):
""" Grid row groups contain the correct addresses. """
plate = Microplate()
rows = plate.col('A').human_address
self.assertEqual(rows, ['A{}'.format(i + 1) for i in range(12)])
def test_grid_row_group(self):
""" Grid row acts as group. """
plate = Microplate()
plate.col('A').allocate(water=10)
vols = [plate.well((0, r)).get_volume('water') for r in range(12)]
self.assertEqual([10 for _ in range(12)], vols)
self.assertEqual(plate.col('A').get_volume('water'), vols)
vols = [plate.well((0, r)).get_volume('water') for r in range(12)]
expected_vols = [15 for _ in range(8)]
expected_vols[0] += 10 # Remember, we added to the column.
plate.row(0).allocate(water=15)
rvols = [plate.well((c, 0)).get_volume('water') for c in range(8)]
self.assertEqual(plate.row(0).get_volume('water'), expected_vols)
self.assertEqual(rvols, plate.row(0).get_volume('water'))
self.assertEqual(plate.row(0).get_volume('water'), rvols)
def test_module_add(self):
"""Add a module to the deck."""
self.deck.add_modules(a1=Microplate())
plate = self.deck.slot('a1')
self.assertTrue(isinstance(plate, Microplate))
class MicroplateWellTest(unittest.TestCase):
def setUp(self):
self.plate = Microplate()
self.well = self.plate.well('A1')
def liquid_allocation_test(self):
"""Add volume to well."""
set_vol = 50
# Add an initial value of 100ul water to this well.
self.well.allocate(water=set_vol)
vol = self.well.get_volume()
self.assertEqual(vol, set_vol)
def liquid_capacity_test(self):
"""Reject well overflow volumes."""
set_vol = 10000
# Way too much water for a microplate!
with self.assertRaises(x.LiquidOverflow):
self.well.allocate(water=set_vol)
def liquid_total_capacity_test(self):
"""Reject combined well overflow."""
self.well.allocate(water=90)
self.well.add_liquid(water=10)
with self.assertRaises(x.LiquidOverflow):
self.well.add_liquid(water=1)
def liquid_total_mixture_test(self):
"""Reject combined well overflow from mixed liquids."""
self.well.allocate(water=90)
self.well.add_liquid(buffer=10)
with self.assertRaises(x.LiquidOverflow):
self.well.add_liquid(saline=1)
def mixture_transfer_test(self):
"""Mixture transfers."""
wellA = self.well
wellB = self.plate.well('A2')
wellA.allocate(water=90, buffer=9, saline=1)
wellA.transfer(20, wellB)
# Check Well A to ensure things have been removed.
wat = wellA.get_proportion('water')
buf = wellA.get_proportion('buffer')
sal = wellA.get_proportion('saline')
# We use almostEqual because it's floating-point.
self.assertAlmostEqual(wat, .9)
self.assertAlmostEqual(buf, .09)
self.assertAlmostEqual(sal, .01)
self.assertEqual(wellA.get_volume(), 80)
# Check WellB to ensure things have been added.
wat = wellB.get_proportion('water')
buf = wellB.get_proportion('buffer')
sal = wellB.get_proportion('saline')
# We use almostEqual because it's floating-point.
self.assertAlmostEqual(wat, .9)
self.assertAlmostEqual(buf, .09)
self.assertAlmostEqual(sal, .01)
self.assertEqual(wellB.get_volume(), 20)
def proportion_key_error_test(self):
"""Raises for proportion of liquid not present in mixture."""
with self.assertRaises(x.LiquidMismatch):
self.well.get_proportion('water')
def liquid_key_error_test(self):
"""Raises if wrong liquid named in get_volume."""
self.well.allocate(saline=10)
with self.assertRaises(x.LiquidMismatch):
self.well.get_volume('water')
def liquid_value_error_test(self):
"""Raises on named get_volume if multiple liquids present."""
self.well.allocate(water=10, saline=10)
with self.assertRaises(x.LiquidMismatch):
self.well.get_volume('water')
def ml_conversion_test(self):
"""ml to µl conversion."""
self.well.allocate(water=.1, ml=True)
self.assertEqual(self.well.get_volume(), 100)
def test_module_add_to_filled_slot(self):
"""Raise when adding module to filled deck slot."""
self.deck.add_modules(a1=Microplate())
with self.assertRaises(x.ContainerConflict):
self.deck.add_modules(a1=Microplate())
class MicroplateTest(unittest.TestCase):
expected_margin = 9 # ANSI standard.
def setUp(self):
self.plate = Microplate()
self.plate.calibrate(x=10, y=11, z=12)
def a1_calibration_test(self):
"""Basic calibration."""
a1 = self.plate.well('A1').coordinates()
print(self.plate._calibration)
self.assertEqual(a1, (10, 11, 12))
def a2_coordinate_test(self):
"""Calibrated coordinates of A2."""
a2 = self.plate.well('A2').coordinates()
self.assertEqual(a2, (10, 11 + self.expected_margin, 12))
def b1_coordinate_test(self):
"""Calibrated coordinates of B1."""
b1 = self.plate.well('B1').coordinates()
self.assertEqual(b1, (10 + self.expected_margin, 11, 12))
def b2_coordinate_test(self):
"""Calibrated coordinates of B2."""
b2 = self.plate.well('B2').coordinates()
margin = self.expected_margin
self.assertEqual(b2, (10 + margin, 11 + margin, 12))
def coordinate_lowercase_test(self):
"""Lowercase coordinates."""
b2 = self.plate.well('b2').coordinates()
margin = self.expected_margin
self.assertEqual(b2, (10 + margin, 11 + margin, 12))
def col_sanity_test(self):
"""Don't return out-of-range columns."""
col = chr(ord('a') + self.plate.cols + 1)
with self.assertRaises(KeyError):
self.plate.well('{}1'.format(col))
def unicode_coord_test(self):
"""Unicode coordinates."""
self.plate.well(u'A1')
def row_sanity_test(self):
"""Don't return out-of-range rows."""
row = self.plate.rows + 1
with self.assertRaises(KeyError):
self.plate.well('A{}'.format(row))
def col_type_sanity_test(self):
"""Sanity check on well coordinates."""
with self.assertRaises(ValueError):
self.plate.well('ABC')
def deck_calibration_test(self):
"""Calibrates through deck."""
config = {
'calibration': {
'a1': {
'type': 'microplate_96',
'x': 10,
'y': 11,
'z': 12
}
}
}
deck = Deck(a1=Microplate())
deck.configure(config)
margin = self.expected_margin
plate = deck.slot('a1')
a1 = plate.well('a1').coordinates()
b2 = plate.well('b2').coordinates()
self.assertEqual(a1, (10, 11, 12))
self.assertEqual(b2, (10 + margin, 11 + margin, 12))