def test_static_coordinates(self):
"""
Containers should calculate coordinates statically.
"""
# Microplate has spacing as row: 12, col: 12.
plate = containers.load_container('microplate.example_plate')
coords = plate.calculate_offset('b12')
self.assertEqual(coords, (12*1, 12*11))
def test_static_coordinates(self):
"""
Containers should calculate coordinates statically.
"""
# Microplate has spacing as row: 12, col: 12.
plate = containers.load_container('microplate.example_plate')
coords = plate.calculate_offset('b12')
self.assertEqual(coords, (12 * 1, 12 * 11))
def test_instance_coordinates_custom_x_y_spacing(self):
"""
Custom row, col spacing should supercede spacing.
"""
# Deepwell has spacing as col: 10, row: 13
plate = containers.load_container('microplate.example_plate.deepwell')
coords = plate().get_child_coordinates('b12')
self.assertEqual(coords, (10, 13 * 11))
def test_list_example_plate(self):
"""
Custom container subset recursion.
"""
inv = containers.list_containers()
self.assertTrue('microplate.example_plate.deepwell.red' in inv)
plate = containers.load_container('microplate.example_plate.deepwell.red')
self.assertEqual(plate.depth, 25)
def test_instance_coordinates_custom_x_y_spacing(self):
"""
Custom row, col spacing should supercede spacing.
"""
# Deepwell has spacing as col: 10, row: 13
plate = containers.load_container('microplate.example_plate.deepwell')
coords = plate().get_child_coordinates('b12')
self.assertEqual(coords, (10, 13*11))
def test_list_example_plate(self):
"""
Custom container subset recursion.
"""
inv = containers.list_containers()
self.assertTrue('microplate.example_plate.deepwell.red' in inv)
plate = containers.load_container(
'microplate.example_plate.deepwell.red')
self.assertEqual(plate.depth, 25)
def test_static_coordinates_custom_x_y_spacing(self):
"""
Custom row, col spacing should supercede spacing.
"""
# Deepwell has spacing as col: 10, row: 13
plate = containers.load_container('microplate.example_plate.deepwell')
coords = plate.calculate_offset('b12')
print(plate.col_spacing, plate.row_spacing)
self.assertEqual(coords, (10, 13*11, 0))
def test_custom_container_subset(self):
"""
Custom container subsets inherit parent values.
"""
plate = containers.load_container('microplate.example_plate.deepwell')
self.assertEqual(plate.depth, 15)
self.assertEqual(plate.rows, 12)
self.assertEqual(plate.cols, 8)
self.assertEqual(plate.a1_x, 10)
self.assertEqual(plate.a1_y, 11)
def test_custom_container_subset(self):
"""
Custom container subsets inherit parent values.
"""
plate = containers.load_container('microplate.example_plate.deepwell')
self.assertEqual(plate.depth, 15)
self.assertEqual(plate.rows, 12)
self.assertEqual(plate.cols, 8)
self.assertEqual(plate.a1_x, 10)
self.assertEqual(plate.a1_y, 11)
def add_module(self, position, mod):
pos = self._normalize_position(position)
if isinstance(mod, str):
mod = load_container(mod)()
if pos not in self._children:
self._children[pos] = mod
mod.position = position
else:
raise x.ContainerConflict(
"Module already allocated to slot: {}.".format(
humanize_position(pos)))
def test_custom_container(self):
"""
Provide a custom container interface.
"""
# Example definition lives in config/containers/example.yml
plate = containers.load_container('microplate.example_plate')
self.assertIs(plate, microplates.Microplate)
self.assertEqual(plate.rows, 12)
self.assertEqual(plate.cols, 8)
self.assertEqual(plate.a1_x, 10)
self.assertEqual(plate.a1_y, 11)
self.assertEqual(plate.diameter, 7)
def test_custom_container(self):
"""
Provide a custom container interface.
"""
# Example definition lives in config/containers/example.yml
plate = containers.load_container('microplate.example_plate')
self.assertIs(plate, microplates.Microplate)
self.assertEqual(plate.rows, 12)
self.assertEqual(plate.cols, 8)
self.assertEqual(plate.a1_x, 10)
self.assertEqual(plate.a1_y, 11)
self.assertEqual(plate.diameter, 7)
def add_module(self, position, mod):
pos = self._normalize_position(position)
if isinstance(mod, str):
mod = load_container(mod)()
if pos not in self._children:
self._children[pos] = mod
mod.position = position
else:
raise x.ContainerConflict(
"Module already allocated to slot: {}."
.format(humanize_position(pos))
)
def test_custom_well_positions(self):
"""
Custom well positions.
"""
rack = containers.load_container('tuberack.15-50ml')
# Values taken from legacy containers.json file.
self.assertEqual(rack.coordinates('A1'), (0, 0))
self.assertEqual(rack.coordinates('A3'), (10, 50))
self.assertEqual(rack.coordinates('B1'), (32, 0))
self.assertEqual(rack.coordinates('B2'), (32, 24))
self.assertEqual(rack.coordinates('B3'), (55, 50))
self.assertEqual(rack.coordinates('C1'), (64, 0))
self.assertEqual(rack.coordinates('C2'), (64, 24))
def test_custom_well_positions(self):
"""
Custom well positions.
"""
rack = containers.load_container('tuberack.15-50ml')
# Values taken from legacy containers.json file.
self.assertEqual(rack.coordinates('A1'), (0, 0))
self.assertEqual(rack.coordinates('A3'), (10, 50))
self.assertEqual(rack.coordinates('B1'), (32, 0))
self.assertEqual(rack.coordinates('B2'), (32, 24))
self.assertEqual(rack.coordinates('B3'), (55, 50))
self.assertEqual(rack.coordinates('C1'), (64, 0))
self.assertEqual(rack.coordinates('C2'), (64, 24))
def test_custom_well_properties(self):
"""
Custom well properties.
"""
rack = containers.load_container('tuberack.15-50ml')()
self.assertEqual(rack.volume, 15000) # Default volume.
self.assertEqual(rack.tube('A1').max_volume, 15000)
self.assertEqual(rack.tube('B3').max_volume, 50000)
self.assertEqual(rack.tube('A1').depth, 76)
self.assertEqual(rack.tube('A3').depth, 76)
self.assertEqual(rack.tube('A1').diameter, 16)
self.assertEqual(rack.tube('A3').diameter, 26)
def test_custom_well_properties(self):
"""
Custom well properties.
"""
rack = containers.load_container('tuberack.15-50ml')()
self.assertEqual(rack.volume, 15000) # Default volume.
self.assertEqual(rack.tube('A1').max_volume, 15000)
self.assertEqual(rack.tube('B3').max_volume, 50000)
self.assertEqual(rack.tube('A1').depth, 76)
self.assertEqual(rack.tube('A3').depth, 76)
self.assertEqual(rack.tube('A1').diameter, 16)
self.assertEqual(rack.tube('A3').diameter, 26)
def test_tiprack_next_tip(self):
"""
Tip offset.
"""
rack = containers.load_container('tiprack.1000ul')()
a1 = rack.tip_offset(0)
a2 = rack.tip_offset(1)
a3 = rack.tip_offset(2)
a4 = rack.tip_offset(3)
b1 = rack.tip_offset(12)
b3 = rack.tip_offset(14)
self.assertEqual(a1, rack.coordinates('a1'))
self.assertEqual(a2, rack.coordinates('a2'))
self.assertEqual(a3, rack.coordinates('a3'))
self.assertEqual(a4, rack.coordinates('a4'))
self.assertEqual(b1, rack.coordinates('b1'))
self.assertEqual(b3, rack.coordinates('b3'))
def test_tiprack_next_tip(self):
"""
Tip offset.
"""
rack = containers.load_container('tiprack.1000ul')()
a1 = rack.tip_offset(0)
a2 = rack.tip_offset(1)
a3 = rack.tip_offset(2)
a4 = rack.tip_offset(3)
b1 = rack.tip_offset(12)
b3 = rack.tip_offset(14)
self.assertEqual(a1, rack.coordinates('a1'))
self.assertEqual(a2, rack.coordinates('a2'))
self.assertEqual(a3, rack.coordinates('a3'))
self.assertEqual(a4, rack.coordinates('a4'))
self.assertEqual(b1, rack.coordinates('b1'))
self.assertEqual(b3, rack.coordinates('b3'))
def test_tiprack_tag(self):
"""
Tips on specific racks can be tagged for reuse.
"""
rack = containers.load_container('tiprack.1000ul')()
a1 = rack.get_next_tip().coordinates()
a2 = rack.get_next_tip().coordinates()
a3 = rack.get_next_tip().coordinates()
a4 = rack.get_next_tip(tag='water').coordinates()
a5 = rack.get_next_tip(tag='saline').coordinates()
also_a4 = rack.get_next_tip(tag='water').coordinates()
also_a5 = rack.get_next_tip('saline').coordinates()
self.assertEqual(a1, rack.coordinates('a1'))
self.assertEqual(a2, rack.coordinates('a2'))
self.assertEqual(a3, rack.coordinates('a3'))
self.assertEqual(a4, rack.coordinates('a4'))
self.assertEqual(a5, rack.coordinates('a5'))
self.assertEqual(also_a4, rack.coordinates('a4'))
self.assertEqual(also_a5, rack.coordinates('a5'))
def test_tiprack_tag(self):
"""
Tips on specific racks can be tagged for reuse.
"""
rack = containers.load_container('tiprack.1000ul')()
a1 = rack.get_next_tip().coordinates()
a2 = rack.get_next_tip().coordinates()
a3 = rack.get_next_tip().coordinates()
a4 = rack.get_next_tip(tag='water').coordinates()
a5 = rack.get_next_tip(tag='saline').coordinates()
also_a4 = rack.get_next_tip(tag='water').coordinates()
also_a5 = rack.get_next_tip('saline').coordinates()
self.assertEqual(a1, rack.coordinates('a1'))
self.assertEqual(a2, rack.coordinates('a2'))
self.assertEqual(a3, rack.coordinates('a3'))
self.assertEqual(a4, rack.coordinates('a4'))
self.assertEqual(a5, rack.coordinates('a5'))
self.assertEqual(also_a4, rack.coordinates('a4'))
self.assertEqual(also_a5, rack.coordinates('a5'))
def test_legacy_container_load(self):
"""
All legacy containers load.
"""
containers.load_legacy_containers_file()
containers.load_container('legacy.tube-rack-2ml_PCR')
def test_custom_container_volume(self):
"""
Custom containers can specify custom volume.
"""
rack = containers.load_container('tuberack.750ul')
self.assertEqual(rack.volume, 750)
def test_microplate_subsubset(self):
"""
Provide access to subchild microplates.
"""
plate = containers.load_container('microplate.96.deepwell')
self.assertIs(plate, microplates.Microplate_96_Deepwell)
def test_microplate_subset(self):
"""
Provide access to child microplates.
"""
plate = containers.load_container('microplate.96')
self.assertIs(plate, microplates.Microplate)
def test_tiprack(self):
"""
Provide access to tipracks.
"""
rack = containers.load_container('tiprack')
self.assertIs(rack, tipracks.Tiprack)
def test_custom_container_volume(self):
"""
Custom containers can specify custom volume.
"""
rack = containers.load_container('tuberack.750ul')
self.assertEqual(rack.volume, 750)
def load_calibration(self, data):
for pos in data:
Container = load_container(data[pos]['name'])
self.add_module(pos, Container())
self.calibrate(**data)
def test_custom_tiprack(self):
"""
Custom container should inherit from Tiprack type.
"""
rack = containers.load_container('tiprack.example_rack')
self.assertIs(rack, tipracks.Tiprack)
def test_microplate_subset(self):
"""
Provide access to child microplates.
"""
plate = containers.load_container('microplate.96')
self.assertIs(plate, microplates.Microplate)
def test_microplate(self):
"""
Provide access to microplates.
"""
plate = containers.load_container('microplate')
self.assertIs(plate, microplates.Microplate)
def test_invaid_container_name(self):
"""
Enforce valid container name.
"""
with self.assertRaises(KeyError):
containers.load_container('fake_container')
def test_microplate_subsubset(self):
"""
Provide access to subchild microplates.
"""
plate = containers.load_container('microplate.96.deepwell')
self.assertIs(plate, microplates.Microplate_96_Deepwell)
def test_tiprack(self):
"""
Provide access to tipracks.
"""
rack = containers.load_container('tiprack')
self.assertIs(rack, tipracks.Tiprack)
def test_24_well_microplate(self):
"""
24 well microplate should exist.
"""
plate = containers.load_container('microplate.24')
self.assertEqual(plate.rows * plate.cols, 24)
def test_microplate(self):
"""
Provide access to microplates.
"""
plate = containers.load_container('microplate')
self.assertIs(plate, microplates.Microplate)
def test_custom_tiprack(self):
"""
Custom container should inherit from Tiprack type.
"""
rack = containers.load_container('tiprack.example_rack')
self.assertIs(rack, tipracks.Tiprack)
def test_invaid_container_name(self):
"""
Enforce valid container name.
"""
with self.assertRaises(KeyError):
containers.load_container('fake_container')
def test_24_well_microplate(self):
"""
24 well microplate should exist.
"""
plate = containers.load_container('microplate.24')
self.assertEqual(plate.rows*plate.cols, 24)
def test_legacy_container_load(self):
"""
All legacy containers load.
"""
containers.load_legacy_containers_file()
containers.load_container('legacy.tube-rack-2ml_PCR')