def test_protocol_equality(self):
# Set up a protocol.
p1 = Protocol()
p1.add_instrument('A', 'p200')
p1.add_container('C1', 'tiprack.p200')
p1.add_container('A1', 'microplate.96')
p1.calibrate('A1', x=1, y=2, z=3)
p1.calibrate_instrument('A', top=0, blowout=10)
p1.transfer('A1:A1', 'A1:A2', ul=100)
p1.transfer('A1:A2', 'A1:A3', ul=80)
# And a copy.
p2 = Protocol()
p2.add_container('A1', 'microplate.96')
p2.add_container('C1', 'tiprack.p200')
p2.add_instrument('A', 'p200')
p2.calibrate('A1', x=1, y=2, z=3)
p2.calibrate_instrument('A', top=0, blowout=10)
p2.transfer('A1:A1', 'A1:A2', ul=100)
p2.transfer('A1:A2', 'A1:A3', ul=80)
# They're identical.
self.assertEqual(p1, p2)
# Make a change.
p2.add_instrument('B', 'p10')
# No longer identical.
self.assertNotEqual(p1, p2)
class ProtocolTest(unittest.TestCase):
def setUp(self):
self.protocol = Protocol()
self.maxDiff = None
@property
def instructions(self):
return self.protocol._commands
def test_normalize_address(self):
self.protocol.add_container('A1', 'microplate.96', label="Output")
label = self.protocol._normalize_address('Output:A1')
self.assertEqual(label, ((0, 0), (0, 0)))
slot = self.protocol._normalize_address('A1:A1')
self.assertEqual(slot, ((0, 0), (0, 0)))
def test_info(self):
name = "Foo Bar"
desc = "Lorem ipsum dolor set amet."
auth = "Jane Doe"
self.protocol.set_info(name=name, description=desc, author=auth)
i = self.protocol.info
self.assertEqual(i['name'], name)
self.assertEqual(i['description'], desc)
self.assertEqual(i['author'], auth)
self.assertTrue('created' in i)
self.assertTrue('updated' in i)
def test_humanize_address(self):
self.protocol.add_container("A1", 'microplate.96', label="LaBeL")
with self.assertRaises(x.ContainerConflict):
self.protocol.add_container("A2", 'microplate.96', label="label")
self.protocol.add_container("A2", 'microplate.96', label="stuff")
lA1 = self.protocol.humanize_address(('label', 'A1'))
sA1 = self.protocol.humanize_address(('STUFF', 'A1'))
self.assertEqual(lA1, 'LaBeL:A1')
self.assertEqual(sA1, 'stuff:A1')
def test_transfer(self):
""" Basic transfer. """
self.protocol.add_container('A1', 'microplate.96')
self.protocol.add_container('B1', 'microplate.96')
self.protocol.add_instrument('A', 'p200')
self.protocol.add_instrument('B', 'p20')
self.protocol.transfer('A1:A1', 'B1:B1', ul=100, tool='p200')
expected = [{
'command': 'transfer',
'tool': 'p200',
'volume': 100,
'start': ((0, 0), (0, 0)),
'end': ((1, 0), (1, 0)),
'blowout': True,
'touchtip': True
}]
self.assertEqual(self.instructions, expected)
def test_transfer_without_pipette(self):
self.protocol.add_container('A1', 'microplate.96')
with self.assertRaises(x.InstrumentMissing):
self.protocol.transfer('A1:A1', 'A1:A2', ul=10)
def test_transfer_without_volume(self):
self.protocol.add_instrument('A', 'p200')
self.protocol.add_container('A1', 'microplate.96')
with self.assertRaises(ValueError):
self.protocol.transfer("A1:A1", "A1:A1")
def test_transfer_zero_volume(self):
with self.assertRaises(ValueError):
self.protocol.transfer("A1:A1", "A1:A1", ul=0)
with self.assertRaises(ValueError):
self.protocol.transfer("A1:A1", "A1:A1", ml=0)
def test_transfer_conflicting_volume(self):
with self.assertRaises(ValueError):
self.protocol.transfer("A1:A1", "A1:A1", ul=1, ml=1)
def test_transfer_group(self):
""" Transfer group. """
expected = [{
'command': 'transfer_group',
'tool': 'p20',
'transfers': [
{
'volume': 15,
'start': ((0, 0), (0, 0)), # A1:A1
'end': ((0, 0), (1, 0)), # A1:B1
'blowout': True,
'touchtip': True
},
{
'volume': 10,
'start': ((0, 0), (0, 1)), # A1:A2
'end': ((0, 0), (1, 1)), # A1:B2
'blowout': True,
'touchtip': True
},
{
'volume': 12,
'start': ((0, 0), (0, 2)), # A1:A3
'end': ((0, 0), (1, 2)), # A1:B3
'blowout': False,
'touchtip': True
},
{
'volume': 12,
'start': ((0, 0), (0, 3)), # A1:A4
'end': ((0, 0), (1, 3)), # A1:B4
'blowout': True,
'touchtip': True
},
{
'volume': 12,
'start': ((0, 0), (0, 4)), # A1:A5
'end': ((0, 0), (1, 4)), # A1:B5
'blowout': True,
'touchtip': True
}
]
}]
self.protocol.add_container('A1', 'microplate.96', label="Label")
self.protocol.add_instrument('A', 'p20')
self.protocol.transfer_group(
('A1:A1', 'A1:B1', {'ul': 15}),
('A1:A2', 'A1:B2', {'ul': 10}),
('A1:A3', 'A1:B3', {'blowout': False}),
('A1:A4', 'A1:B4'),
('A1:A5', 'A1:B5'),
ul=12,
tool='p20'
)
self.assertEqual(self.instructions, expected)
def test_transfer_group_without_pipette(self):
self.protocol.add_instrument('A', 'p200')
self.protocol.add_container('A1', 'microplate.96')
with self.assertRaises(x.InstrumentMissing):
self.protocol.transfer_group(
('A1:A1', 'A1:B1', {'ul': 15}),
('A1:A2', 'A1:B2', {'ml': 1}),
('A1:A3', 'A1:B3', {'blowout': False}),
('A1:A4', 'A1:B4'),
('A1:A5', 'A1:B5'),
ul=12,
tool='p10'
)
def test_transfer_group_without_volume(self):
self.protocol.add_container('A1', 'microplate.96')
with self.assertRaises(ValueError):
self.protocol.add_instrument('A', 'p10')
self.protocol.transfer_group(
('A1:A1', 'A1:B1'),
('A1:A2', 'A1:B2'),
('A1:A3', 'A1:B3', {'blowout': False}),
('A1:A4', 'A1:B4'),
('A1:A5', 'A1:B5'),
tool='p10'
)
def test_transfer_group_zero_volume(self):
self.protocol.add_instrument('A', 'p10')
self.protocol.add_container('A1', 'microplate.96')
with self.assertRaises(ValueError):
self.protocol.transfer_group(
('A1:A1', 'A1:B1'),
('A1:A2', 'A1:B2'),
('A1:A3', 'A1:B3', {'blowout': False}),
('A1:A4', 'A1:B4'),
('A1:A5', 'A1:B5'),
ul=0,
tool='p10'
)
with self.assertRaises(ValueError):
self.protocol.transfer_group(
('A1:A1', 'A1:B1'),
('A1:A2', 'A1:B2'),
('A1:A3', 'A1:B3', {'blowout': False}),
('A1:A4', 'A1:B4'),
('A1:A5', 'A1:B5'),
ml=0,
tool='p10'
)
def test_transfer_group_conflicting_volume(self):
self.protocol.add_instrument('A', 'p10')
self.protocol.add_container('A1', 'microplate.96')
with self.assertRaises(ValueError):
self.protocol.transfer_group(
('A1:A1', 'A1:B1'),
('A1:A2', 'A1:B2'),
('A1:A3', 'A1:B3', {'blowout': False}),
('A1:A4', 'A1:B4'),
('A1:A5', 'A1:B5'),
ul=5,
ml=4,
tool='p10'
)
def test_distribute(self):
self.protocol.add_instrument('A', 'p200')
self.protocol.add_container('A1', 'microplate.96')
self.protocol.distribute(
'A1:A1',
('A1:B1', {'ul': 50}),
('A1:C1'),
('A1:D1', {'ul': 30}),
ul=20
)
expected = [{
'command': 'distribute',
'tool': 'p200',
'start': ((0, 0), (0, 0)),
'transfers': [
{
'volume': 50,
'end': ((0, 0), (1, 0)), # A1:B1
'blowout': True,
'touchtip': True
},
{
'volume': 20, # Default
'end': ((0, 0), (2, 0)), # A1:C1
'blowout': True,
'touchtip': True
},
{
'volume': 30,
'end': ((0, 0), (3, 0)), # A1:D1
'blowout': True,
'touchtip': True
}
]
}]
self.assertEqual(self.instructions, expected)
def test_distribute_without_pipette(self):
self.protocol.add_container('A1', 'microplate.96')
with self.assertRaises(x.InstrumentMissing):
self.protocol.distribute(
'A1:A1',
('A1:B1', {'ul': 50}),
('A1:C1', {'ul': 5}),
('A1:D1', {'ul': 10})
)
def test_distribute_zero_volume(self):
self.protocol.add_instrument('A', 'p10')
self.protocol.add_container('A1', 'microplate.96')
with self.assertRaises(ValueError):
self.protocol.distribute(
'A1:A1',
('A1:B1', {'ul': 4}),
('A1:C1', {'ul': 5}),
('A1:D1', {'ul': 0})
)
def test_distribute_conflicting_volume(self):
self.protocol.add_instrument('A', 'p10')
self.protocol.add_container('A1', 'microplate.96')
with self.assertRaises(ValueError):
self.protocol.distribute(
'A1:A1',
('A1:B1'),
('A1:C1'),
('A1:D1', {'ul': 10, 'ml': 5}),
ul=5
)
def test_consolidate(self):
""" Consolidate. """
self.protocol.add_container('A1', 'microplate.96')
self.protocol.add_instrument('A', 'p200')
self.protocol.consolidate(
'A1:A1',
('A1:B1', {'ul': 50}),
('A1:C1', {'ul': 25}),
('A1:D1'),
ul=30
)
expected = [{
'command': 'consolidate',
'tool': 'p200',
'end': ((0, 0), (0, 0)),
'transfers': [
{
'volume': 50,
'start': ((0, 0), (1, 0)), # A1:B1
'blowout': True,
'touchtip': True
},
{
'volume': 25,
'start': ((0, 0), (2, 0)), # A1:C1
'blowout': True,
'touchtip': True
},
{
'volume': 30,
'start': ((0, 0), (3, 0)), # A1:D1
'blowout': True,
'touchtip': True
}
]
}]
self.assertEqual(self.instructions, expected)
def test_consolidate_without_pipette(self):
self.protocol.add_container('A1', 'microplate.96')
with self.assertRaises(x.InstrumentMissing):
self.protocol.consolidate(
'A1:A1',
('A1:B1', {'ul': 50}),
('A1:C1', {'ul': 5}),
('A1:D1', {'ul': 10})
)
def test_consolidate_zero_volume(self):
self.protocol.add_instrument('A', 'p10')
self.protocol.add_container('A1', 'microplate.96')
with self.assertRaises(ValueError):
self.protocol.consolidate(
'A1:A1',
('A1:B1', {'ul': 4}),
('A1:C1', {'ul': 5}),
('A1:D1', {'ul': 0})
)
def test_consolidate_conflicting_volume(self):
self.protocol.add_instrument('A', 'p10')
self.protocol.add_container('A1', 'microplate.96')
with self.assertRaises(ValueError):
self.protocol.consolidate(
'A1:A1',
('A1:B1', {'ul': 5}),
('A1:C1', {'ul': 5}),
('A1:D1', {'ul': 10, 'ml': 5})
)
def test_mix(self):
""" Mix. """
self.protocol.add_container('A1', 'microplate.96')
self.protocol.add_instrument('A', 'p200')
self.protocol.mix('A1:A1', ul=50, repetitions=10)
expected = [{
'command': 'mix',
'tool': 'p200',
'start': ((0, 0), (0, 0)), # A1:A1
'blowout': True,
'touchtip': True,
'volume': 50,
'reps': 10
}]
self.assertEqual(self.instructions, expected)
def test_mix_without_pipette(self):
self.protocol.add_container('A1', 'microplate.96')
with self.assertRaises(x.InstrumentMissing):
self.protocol.mix('A1:A1', ul=50, repetitions=10, tool='p200')
def test_mix_without_volume(self):
self.protocol.add_container('A1', 'microplate.96')
self.protocol.add_instrument('A', 'p10')
with self.assertRaises(ValueError):
self.protocol.mix('A1:A1', repetitions=10, tool='p10')
def test_mix_zero_volume(self):
self.protocol.add_instrument('A', 'p10')
self.protocol.add_container('A1', 'microplate.96')
with self.assertRaises(ValueError):
self.protocol.mix('A1:A1', ul=0, repetitions=10, tool='p10')
with self.assertRaises(ValueError):
self.protocol.mix('A1:A1', ml=0, repetitions=10, tool='p10')
def test_mix_conflicting_volume(self):
self.protocol.add_instrument('A', 'p10')
self.protocol.add_container('A1', 'microplate.96')
with self.assertRaises(ValueError):
self.protocol.mix('A1:A1', ul=1, ml=1, repetitions=10, tool='p10')
def test_protocol_run_twice(self):
""" Run a protocol twice without error. """
self.protocol.add_instrument('A', 'p200')
self.protocol.add_container('C1', 'tiprack.p200')
self.protocol.add_container('A1', 'microplate.96')
self.protocol.calibrate('A1', x=1, y=2, z=3)
self.protocol.calibrate_instrument('A', top=0, blowout=10)
self.protocol.transfer('A1:A1', 'A1:A2', ul=100)
self.protocol.transfer('A1:A2', 'A1:A3', ul=80)
self.protocol.run_all()
self.protocol.run_all()
def test_protocol_equality(self):
# Set up a protocol.
p1 = Protocol()
p1.add_instrument('A', 'p200')
p1.add_container('C1', 'tiprack.p200')
p1.add_container('A1', 'microplate.96')
p1.calibrate('A1', x=1, y=2, z=3)
p1.calibrate_instrument('A', top=0, blowout=10)
p1.transfer('A1:A1', 'A1:A2', ul=100)
p1.transfer('A1:A2', 'A1:A3', ul=80)
# And a copy.
p2 = Protocol()
p2.add_container('A1', 'microplate.96')
p2.add_container('C1', 'tiprack.p200')
p2.add_instrument('A', 'p200')
p2.calibrate('A1', x=1, y=2, z=3)
p2.calibrate_instrument('A', top=0, blowout=10)
p2.transfer('A1:A1', 'A1:A2', ul=100)
p2.transfer('A1:A2', 'A1:A3', ul=80)
# They're identical.
self.assertEqual(p1, p2)
# Make a change.
p2.add_instrument('B', 'p10')
# No longer identical.
self.assertNotEqual(p1, p2)
def test_protocol_version(self):
# Set up a protocol.
self.protocol.add_instrument('A', 'p200')
self.protocol.add_container('C1', 'tiprack.p200')
self.protocol.add_container('A1', 'microplate.96')
self.protocol.calibrate('A1', x=1, y=2, z=3)
self.protocol.calibrate_instrument('A', top=0, blowout=10)
self.protocol.transfer('A1:A1', 'A1:A2', ul=100)
self.protocol.transfer('A1:A2', 'A1:A3', ul=80)
# First version bump.
v1 = self.protocol.bump_version()
self.assertEqual(v1, '0.0.1')
# No changes, version will stay the same.
v2 = self.protocol.bump_version()
self.assertEqual(v1, v2)
# Make a change, bump the version.
self.protocol.transfer('A1:A2', 'A1:A3', ul=80)
v3 = self.protocol.bump_version()
self.assertEqual(v3, '0.0.2')
# Make a change, bump the version.
self.protocol.transfer('A1:A1', 'A1:A1', ul=20)
v4 = self.protocol.bump_version('feature')
self.assertEqual(v4, '0.1.0')
# Make a change, bump the version.
self.protocol.transfer('A1:A1', 'A1:A1', ul=20)
v5 = self.protocol.bump_version('major')
self.assertEqual(v5, '1.0.0')
def test_partial_protocol(self):
p = Protocol.partial()
p.transfer('A1:A1', 'A1:A3', ul=1)
# As long as it doesn't throw an Exception, we're good.
def test_partial_protocol_run(self):
p = Protocol.partial()
p.transfer('A1:A1', 'A1:A3', ul=1)
with self.assertRaises(x.PartialProtocolException):
# This shouldn't run because it's not valid.
p.run_all()
def test_valid_partial_protocol_run(self):
p = Protocol.partial()
p.add_instrument('A', 'p10')
p.add_container("A1", "microplate.96")
p.transfer('A1:A1', 'A1:A3', ul=1)
# This should run because there are no Partial problems.
p.run_all()
def test_partial_protocol_export(self):
p = Protocol.partial()
p.transfer('A1:A1', 'A1:A3', ul=1)
with self.assertRaises(x.PartialProtocolException):
# This shouldn't export because it's not valid.
p.export(JSONFormatter)
def test_valid_partial_protocol_export(self):
p = Protocol.partial()
p.add_instrument('A', 'p10')
p.add_container("A1", "microplate.96")
p.transfer('A1:A1', 'A1:A3', ul=1)
# This should export because there are no Partial problems.
p.export(JSONFormatter)
def test_protocol_addition_of_partial(self):
p1 = Protocol()
p1.add_instrument('A', 'p20')
p1.add_container('A1', 'microplate.96')
p1.transfer('A1:A1', 'A1:A2', ul=10)
p2 = Protocol.partial()
p2.add_container('A2', 'microplate.96')
p2.transfer('A1:A1', 'A1:A3', ul=20)
p2.transfer('A2:A1', 'A2:A4', ul=15)
p3 = Protocol()
p3.add_instrument('A', 'p20')
p3.add_container('A1', 'microplate.96')
p3.add_container('A2', 'microplate.96')
p3.transfer('A1:A1', 'A1:A2', ul=10)
p3.transfer('A1:A1', 'A1:A3', ul=20)
p3.transfer('A2:A1', 'A2:A4', ul=15)
self.assertEqual(p3, p1 + p2)
def test_protocol_addition_of_partials(self):
p1 = Protocol()
p1.add_instrument('A', 'p20')
p1.add_container('A1', 'microplate.96')
p1.transfer('A1:A1', 'A1:A2', ul=10)
p2 = Protocol.partial()
p2.add_container('A2', 'microplate.96')
p2.transfer('A1:A1', 'A1:A3', ul=20)
p2.transfer('A2:A1', 'A2:A4', ul=15)
p3 = Protocol.partial()
p3.add_container('A3', 'microplate.96')
p3.transfer('A1:A1', 'A1:A3', ul=20)
p3.transfer('A1:A1', 'A3:A4', ul=15)
p4 = Protocol()
p4.add_instrument('A', 'p20')
p4.add_container('A1', 'microplate.96')
p4.add_container('A2', 'microplate.96')
p4.add_container('A3', 'microplate.96')
p4.transfer('A1:A1', 'A1:A2', ul=10)
p4.transfer('A1:A1', 'A1:A3', ul=20)
p4.transfer('A2:A1', 'A2:A4', ul=15)
p4.transfer('A1:A1', 'A1:A3', ul=20)
p4.transfer('A1:A1', 'A3:A4', ul=15)
self.assertEqual(p4, p1 + p2 + p3)
def test_protocol_added_to_partial(self):
p1 = Protocol()
p1.add_instrument('A', 'p20')
p1.add_container('A1', 'microplate.96')
p1.transfer('A1:A1', 'A1:A2', ul=10)
p2 = Protocol.partial()
p2.add_container('A2', 'microplate.96')
p2.transfer('A1:A1', 'A1:A3', ul=20)
p2.transfer('A2:A1', 'A2:A4', ul=15)
with self.assertRaises(TypeError):
p2 + p1
def test_protocol_addition(self):
p1 = Protocol()
p1.add_instrument('A', 'p10')
p1.add_container('A1', 'microplate.96')
p1.transfer('A1:A1', 'A1:A1', ul=10)
p2 = Protocol()
p2.add_instrument('A', 'p10') # Same definition; no conflict.
p2.add_instrument('B', 'p20') # New instrument.
p2.add_container('A1', 'microplate.96') # No conflict.
p2.add_container('A2', 'microplate.96') # New container.
p2.transfer('A1:A1', 'A1:A1', ul=12)
p2.transfer('A1:A1', 'A2:A2', ul=20)
p3 = Protocol()
p3.add_instrument('A', 'p10')
p3.add_instrument('B', 'p20')
p3.add_container('A1', 'microplate.96')
p3.add_container('A2', 'microplate.96')
p3.transfer('A1:A1', 'A1:A1', ul=10)
p3.transfer('A1:A1', 'A1:A1', ul=12)
p3.transfer('A1:A1', 'A2:A2', ul=20)
self.assertEqual(p3, p1 + p2)
def test_protocol_label_addition(self):
p1 = Protocol()
p1.add_instrument('A', 'p10')
p1.add_container('A1', 'microplate.96', label="Input")
p1.transfer('A1:A1', 'A1:A1', ul=10)
p2 = Protocol()
p2.add_instrument('A', 'p10') # Same definition; no conflict.
p2.add_instrument('B', 'p20') # New instrument.
p2.add_container('A1', 'microplate.96', label="Input") # No conflict.
p2.add_container('A2', 'microplate.96') # New container.
p2.transfer('A1:A1', 'A1:A1', ul=9)
p2.transfer('Input:A1', 'A2:A2', ul=20)
p3 = Protocol()
p3.add_instrument('A', 'p10')
p3.add_instrument('B', 'p20')
p3.add_container('A1', 'microplate.96', label="Input")
p3.add_container('A2', 'microplate.96')
p3.transfer('A1:A1', 'A1:A1', ul=10)
p3.transfer('A1:A1', 'A1:A1', ul=9)
p3.transfer('A1:A1', 'A2:A2', ul=20)
self.assertEqual(p3, p1 + p2)
def test_protocol_addition_label_conflict(self):
p1 = Protocol()
p1.add_instrument('A', 'p10')
p1.add_container('A1', 'microplate.96', label="Input")
p1.transfer('A1:A1', 'A1:A1', ul=10)
p2 = Protocol()
p2.add_instrument('A', 'p10') # Same definition; no conflict.
p2.add_instrument('B', 'p20') # New instrument.
p2.add_container('A1', 'microplate.96', label="Output") # Conflict.
p2.add_container('A2', 'microplate.96') # New container.
p2.transfer('A1:A1', 'A1:A1', ul=12)
p2.transfer('Output:A1', 'A2:A2', ul=20)
with self.assertRaises(x.ContainerConflict):
p1 + p2
def test_protocol_addition_label_case(self):
p1 = Protocol()
p1.add_instrument('A', 'p10')
p1.add_container('A1', 'microplate.96', label="Input")
p2 = Protocol()
p2.add_instrument('A', 'p10')
p2.add_container('A1', 'microplate.96', label="INPUT")
p3 = Protocol()
p3.add_instrument('A', 'p10')
p3.add_container('A1', 'microplate.96', label="INPUT")
self.assertEqual((p1 + p2), p3)
def test_protocol_addition_info(self):
p1 = Protocol()
p1.set_info(author="John Doe", name="Lorem Ipsum")
p2 = Protocol()
p2.set_info(author="Jane Doe")
p3 = p1 + p2
self.assertEqual('Jane Doe', p3.info['author'])
self.assertEqual('Lorem Ipsum', p3.info['name'])
def test_protocol_addition_container_conflict(self):
p1 = Protocol()
p1.add_instrument('A', 'p10')
p1.add_container('A1', 'microplate.96')
p1.transfer('A1:A1', 'A1:A2', ul=10)
p2 = Protocol()
p2.add_container('A1', 'tiprack.p20')
with self.assertRaises(x.ContainerConflict):
p1 + p2
class ProtocolRequirementsTest(unittest.TestCase):
def setUp(self):
self.protocol = Protocol()
def assertRequirements(self, expected, reqs=None):
reqs = reqs or self.protocol.run_requirements
ouch = []
extra = deepcopy(reqs)
missing = deepcopy(expected)
for ei, e in enumerate(expected):
for ri, r in enumerate(reqs):
try:
self.assertEqual(e, r)
except AssertionError:
continue
extra[ri] = None
missing[ei] = None
extra = [x for x in extra if x is not None]
missing = [x for x in missing if x is not None]
if len(extra) > 0:
ouch.append("Found {} extra items: {}".format(len(extra), extra))
if len(missing) > 0:
ouch.append("Missing items: {}".format(missing))
if len(ouch) > 0:
assert False, "\n".join(ouch)
def test_requirements_assertion(self):
self.assertRequirements([{
'foo': 'bar'
}, {
'bizz': 'buzz'
}], [{
'foo': 'bar'
}, {
'bizz': 'buzz'
}])
with self.assertRaises(AssertionError):
self.assertRequirements([{
'foo': 'bar'
}], [{
'foo': 'bar'
}, {
'bizz': 'buzz'
}])
with self.assertRaises(AssertionError):
self.assertRequirements([{
'foo': 'bar'
}, {
'bizz': 'buzz'
}], [{
'foo': 'bar'
}])
def test_require_instrument_calibration(self):
self.protocol.add_instrument('A', 'p20')
self.protocol.add_container('A1', 'microplate')
self.protocol.add_container('A2', 'tiprack.p20')
self.protocol.transfer('A1:A1', 'A1:A2', ul=10)
reqs = [{
'type': 'calibrate_instrument',
'axis': 'A',
'instrument_name': 'p20'
}, {
'type': 'calibrate_container',
'axis': 'A',
'address': (0, 0),
'container_name': 'microplate',
'instrument_name': 'p20'
}, {
'type': 'calibrate_container',
'axis': 'A',
'address': (0, 1),
'container_name': 'tiprack.p20',
'instrument_name': 'p20'
}]
self.assertRequirements(reqs)
self.protocol.calibrate_instrument(axis='A',
top=10,
bottom=10,
blowout=10)
reqs.pop(0)
self.assertRequirements(reqs)
self.protocol.calibrate('A1', axis='A')
reqs.pop(0)
self.assertRequirements(reqs)
self.protocol.calibrate('A2', axis='A')
reqs.pop(0)
self.assertRequirements(reqs)
def test_requirements_calibration_multiple_racks(self):
self.protocol.add_instrument('A', 'p20')
self.protocol.add_container('A1', 'microplate')
self.protocol.add_container('A2', 'tiprack.p20')
self.protocol.add_container('A3', 'tiprack.p20')
for _ in range(50):
self.protocol.transfer('A1:A1', 'A1:A2', ul=10)
self.protocol.transfer('A1:A2', 'A1:A1', ul=10)
reqs = [{
'type': 'calibrate_instrument',
'axis': 'A',
'instrument_name': 'p20'
}, {
'type': 'calibrate_container',
'axis': 'A',
'address': (0, 0),
'container_name': 'microplate',
'instrument_name': 'p20'
}, {
'type': 'calibrate_container',
'axis': 'A',
'address': (0, 1),
'container_name': 'tiprack.p20',
'instrument_name': 'p20'
}, {
'type': 'calibrate_container',
'axis': 'A',
'address': (0, 2),
'container_name': 'tiprack.p20',
'instrument_name': 'p20'
}]
self.assertRequirements(reqs)
def test_no_errors_from_commands(self):
self.protocol.add_instrument('B', 'p200')
self.protocol.add_container('A1', 'microplate.96')
self.protocol.add_container('B1', 'tiprack.p200')
self.protocol.add_container('C1', 'point.trash')
self.protocol.calibrate('A1')
self.protocol.calibrate('B1')
self.protocol.calibrate('C1')
self.protocol.calibrate('A1', x=1, y=2, top=3, bottom=13)
self.protocol.calibrate_instrument('B', top=0, blowout=10, droptip=25)
self.protocol.transfer('A1:A1', 'A1:A2', ul=100)
self.protocol.transfer_group(('A1:A1', 'A1:A2', {'ul': 100}))
self.protocol.consolidate('A1:A1', ('A1:A2', {
'ul': 100
}), ('A1:A2', {
'ul': 150
}))
self.protocol.distribute('A1:A1', ('A1:A2', {
'ul': 100
}), ('A1:A2', {
'ul': 150
}))
self.protocol.mix('A1:A2', ul=100, repetitions=5)
self.protocol.run_requirements
class ProtocolTest(unittest.TestCase):
def setUp(self):
self.protocol = Protocol()
@property
def instructions(self):
return self.protocol._commands
def test_normalize_address(self):
self.protocol.add_container('A1', 'microplate.96', label="Output")
label = self.protocol._normalize_address('Output:A1')
self.assertEqual(label, ('output', (0, 0)))
slot = self.protocol._normalize_address('A1:A1')
self.assertEqual(slot, ((0, 0), (0, 0)))
def test_transfer(self):
""" Basic transfer. """
self.protocol.add_container('A1', 'microplate.96')
self.protocol.add_container('B1', 'microplate.96')
self.protocol.add_instrument('A', 'p200')
self.protocol.add_instrument('B', 'p20')
self.protocol.transfer('A1:A1', 'B1:B1', ul=100, tool='p20')
expected = [{
'transfer': {
'tool': 'p20',
'volume': 100,
'start': ((0, 0), (0, 0)),
'end': ((1, 0), (1, 0)),
'blowout': True,
'touchtip': True
}
}]
self.assertEqual(self.instructions, expected)
def test_transfer_group(self):
""" Transfer group. """
expected = [{
'transfer_group': {
'tool': 'p10',
'transfers': [
{
'volume': 15,
'start': ((0, 0), (0, 0)), # A1:A1
'end': ((1, 0), (1, 0)), # B1:B1
'blowout': True,
'touchtip': True
},
{
'volume': 1000,
'start': ((0, 1), (0, 1)), # A2:A2
'end': ((1, 1), (1, 1)), # B2:B2
'blowout': True,
'touchtip': True
},
{
'volume': 12,
'start': ((0, 2), (0, 2)), # A3:A3
'end': ((1, 2), (1, 2)), # B3:B3
'blowout': False,
'touchtip': True
},
{
'volume': 12,
'start': ((0, 3), (0, 3)), # A4:A4
'end': ((1, 3), (1, 3)), # B4:B4
'blowout': True,
'touchtip': True
},
{
'volume': 12,
'start': ('label', (0, 4)), # label:A5
'end': ((1, 4), (2, 0)), # B5:C1
'blowout': True,
'touchtip': True
}
]
}
}]
self.protocol.add_container('A1', 'microplate.96', label="Label")
self.protocol.transfer_group(
('A1:A1', 'B1:B1', {'ul': 15}),
('A2:A2', 'B2:B2', {'ml': 1}),
('A3:A3', 'B3:B3', {'blowout': False}),
('A4:A4', 'B4:B4'),
('Label:A5', 'B5:C1'),
ul=12,
tool='p10'
)
self.assertEqual(self.instructions, expected)
def test_distribute(self):
self.protocol.distribute(
'A1:A1',
('B1:B1', 50),
('C1:C1', 5),
('D1:D1', 10)
)
expected = [{
'distribute': {
'tool': 'p10',
'blowout': True,
'start': ((0, 0), (0, 0)),
'transfers': [
{
'volume': 50,
'end': ((1, 0), (1, 0)), # B1:B1
},
{
'volume': 5,
'end': ((2, 0), (2, 0)), # C1:C1
},
{
'volume': 10,
'end': ((3, 0), (3, 0)) # D1:D1
}
]
}
}]
self.assertEqual(self.instructions, expected)
def test_consolidate(self):
""" Consolidate. """
self.protocol.consolidate(
'A1:A1',
('B1:B1', 50),
('C1:C1', 5),
('D1:D1', 10)
)
expected = [{
'consolidate': {
'tool': 'p10',
'blowout': True,
'end': ((0, 0), (0, 0)),
'transfers': [
{
'volume': 50,
'start': ((1, 0), (1, 0)), # B1:B1
},
{
'volume': 5,
'start': ((2, 0), (2, 0)), # C1:C1
},
{
'volume': 10,
'start': ((3, 0), (3, 0)) # D1:D1
}
]
}
}]
self.assertEqual(self.instructions, expected)
def test_mix(self):
""" Mix. """
self.protocol.mix(
'A1:A1',
volume=50,
repetitions=10
)
expected = [{'mix': {
'tool': 'p10',
'start': ((0, 0), (0, 0)), # A1:A1
'blowout': True,
'volume': 50,
'reps': 10
}}]
self.assertEqual(self.instructions, expected)
def test_protocol_run_twice(self):
""" Run a protocol twice without error. """
self.protocol.add_instrument('A', 'p200')
self.protocol.add_container('C1', 'tiprack.p200')
self.protocol.add_container('A1', 'microplate.96')
self.protocol.calibrate('A1', x=1, y=2, z=3)
self.protocol.calibrate_instrument('A', top=0, blowout=10)
self.protocol.transfer('A1:A1', 'A1:A2', ul=100)
self.protocol.transfer('A1:A2', 'A1:A3', ul=80)
self.protocol.run_all()
self.protocol.run_all()
class ProtocolRequirementsTest(unittest.TestCase):
def setUp(self):
self.protocol = Protocol()
def assertRequirements(self, expected, reqs=None):
reqs = reqs or self.protocol.run_requirements
ouch = []
extra = deepcopy(reqs)
missing = deepcopy(expected)
for ei, e in enumerate(expected):
for ri, r in enumerate(reqs):
try:
self.assertEqual(e, r)
except AssertionError:
continue
extra[ri] = None
missing[ei] = None
extra = [x for x in extra if x is not None]
missing = [x for x in missing if x is not None]
if len(extra) > 0:
ouch.append("Found {} extra items: {}".format(len(extra), extra))
if len(missing) > 0:
ouch.append("Missing items: {}".format(missing))
if len(ouch) > 0:
assert False, "\n".join(ouch)
def test_requirements_assertion(self):
self.assertRequirements(
[{'foo': 'bar'}, {'bizz': 'buzz'}],
[{'foo': 'bar'}, {'bizz': 'buzz'}]
)
with self.assertRaises(AssertionError):
self.assertRequirements(
[{'foo': 'bar'}],
[{'foo': 'bar'}, {'bizz': 'buzz'}]
)
with self.assertRaises(AssertionError):
self.assertRequirements(
[{'foo': 'bar'}, {'bizz': 'buzz'}],
[{'foo': 'bar'}]
)
def test_require_instrument_calibration(self):
self.protocol.add_instrument('A', 'p20')
self.protocol.add_container('A1', 'microplate')
self.protocol.add_container('A2', 'tiprack.p20')
self.protocol.transfer('A1:A1', 'A1:A2', ul=10)
reqs = [
{'type': 'calibrate_instrument', 'axis': 'A', 'instrument_name': 'p20'},
{'type': 'calibrate_container', 'axis': 'A', 'address': (0, 0),
'container_name': 'microplate', 'instrument_name': 'p20'},
{'type': 'calibrate_container', 'axis': 'A', 'address': (0, 1),
'container_name': 'tiprack.p20', 'instrument_name': 'p20'}
]
self.assertRequirements(reqs)
self.protocol.calibrate_instrument(axis='A', top=10, bottom=10, blowout=10)
reqs.pop(0)
self.assertRequirements(reqs)
self.protocol.calibrate('A1', axis='A')
reqs.pop(0)
self.assertRequirements(reqs)
self.protocol.calibrate('A2', axis='A')
reqs.pop(0)
self.assertRequirements(reqs)
def test_requirements_calibration_multiple_racks(self):
self.protocol.add_instrument('A', 'p20')
self.protocol.add_container('A1', 'microplate')
self.protocol.add_container('A2', 'tiprack.p20')
self.protocol.add_container('A3', 'tiprack.p20')
for _ in range(50):
self.protocol.transfer('A1:A1', 'A1:A2', ul=10)
self.protocol.transfer('A1:A2', 'A1:A1', ul=10)
reqs = [
{'type': 'calibrate_instrument', 'axis': 'A', 'instrument_name': 'p20'},
{'type': 'calibrate_container', 'axis': 'A', 'address': (0, 0),
'container_name': 'microplate', 'instrument_name': 'p20'},
{'type': 'calibrate_container', 'axis': 'A', 'address': (0, 1),
'container_name': 'tiprack.p20', 'instrument_name': 'p20'},
{'type': 'calibrate_container', 'axis': 'A', 'address': (0, 2),
'container_name': 'tiprack.p20', 'instrument_name': 'p20'}
]
self.assertRequirements(reqs)
def test_no_errors_from_commands(self):
self.protocol.add_instrument('B', 'p200')
self.protocol.add_container('A1', 'microplate.96')
self.protocol.add_container('B1', 'tiprack.p200')
self.protocol.add_container('C1', 'point.trash')
self.protocol.calibrate('A1')
self.protocol.calibrate('B1')
self.protocol.calibrate('C1')
self.protocol.calibrate('A1', x=1, y=2, top=3, bottom=13)
self.protocol.calibrate_instrument('B', top=0, blowout=10, droptip=25)
self.protocol.transfer('A1:A1', 'A1:A2', ul=100)
self.protocol.transfer_group(
('A1:A1', 'A1:A2', {'ul': 100})
)
self.protocol.consolidate(
'A1:A1',
('A1:A2', {'ul':100}),
('A1:A2', {'ul':150})
)
self.protocol.distribute(
'A1:A1',
('A1:A2', {'ul':100}),
('A1:A2', {'ul':150})
)
self.protocol.mix('A1:A2', ul=100, repetitions=5)
self.protocol.run_requirements
from flask_socketio import SocketIO, emit
import logging
import math
protocol = Protocol()
motor_handler = protocol.attach_motor()
protocol.add_instrument('B', 'p200')
protocol.add_container('A1', 'microplate.96')
protocol.add_container('C1', 'tiprack.p200')
protocol.add_container('B2', 'point.trash')
protocol.calibrate('A1', x=1, y=2, top=3, bottom=13)
protocol.calibrate('A1:A2', bottom=5)
protocol.calibrate('C1', x=100, y=100, top=50)
protocol.calibrate('B2', x=200, y=250, top=15)
protocol.calibrate_instrument('B', top=0, blowout=10, droptip=25)
protocol.transfer('A1:A1', 'A1:A2', ul=100)
protocol.transfer('A1:A2', 'A1:A3', ul=80)
logging.basicConfig(
level=logging.DEBUG,
format='%(asctime)s %(levelname)-8s %(message)s',
datefmt='%d-%m-%y %H:%M:%S'
)
app = Flask(__name__)
socketio = SocketIO(app, async_mode='gevent')
@app.route('/')
def index():
class MotorHandlerTest(unittest.TestCase):
def setUp(self):
self.protocol = Protocol()
def test_basic_transfer(self):
""" Basic transfer. """
motor = self.protocol.attach_motor()
output_log = motor._driver
self.protocol.add_instrument('A', 'p20')
self.protocol.add_instrument('B', 'p200')
self.protocol.add_container('A1', 'microplate.96')
self.protocol.add_container('C1', 'tiprack.p200')
self.protocol.add_container('B1', 'tiprack.p20')
self.protocol.add_container('B2', 'point.trash')
self.protocol.calibrate('A1', axis="A", x=1, y=2, top=3, bottom=10)
self.protocol.calibrate('B1', axis="A", x=4, y=5, top=6, bottom=15)
self.protocol.calibrate('B2', axis="A", x=50, y=60, top=70)
self.protocol.calibrate('A1:A2', axis="B", bottom=5)
self.protocol.calibrate('C1', axis="B", x=100, y=100, top=50)
self.protocol.calibrate('B2', axis="B", x=200, y=250, top=15)
self.protocol.calibrate('A1', axis="B", x=1, y=2, top=3, bottom=13)
self.protocol.calibrate_instrument('A', top=0, blowout=1, droptip=2)
self.protocol.calibrate_instrument('B', top=0, blowout=10, droptip=25)
self.protocol.transfer('A1:A1', 'A1:A2', ul=10)
self.protocol.transfer('A1:A2', 'A1:A3', ul=80)
prog_out = []
for progress in self.protocol.run():
prog_out.append(progress)
expected = [
# Transfer 1.
{'x': 4, 'y': 5}, # Pickup tip.
{'z': 6},
{'z': 0}, # Move to well.
{'x': 1, 'y': 2},
{'z': 3},
{'a': 0.5}, # Plunge.
{'x': 1, 'y': 2},
{'z': 10}, # Move into well.
{'a': 0}, # Release.
{'z': 0}, # Move up.
{'x': 1, 'y': 11}, # Move to well.
{'z': 3},
{'x': 1, 'y': 11},
{'z': 10}, # Move into well.
{'a': 1}, # Blowout.
{'z': 0}, # Move up.
{'a': 0}, # Release.
{'x': 50, 'y': 60}, # Dispose tip.
{'z': 70},
{'a': 2},
{'a': 0},
# Transfer 2.
{'x': 100, 'y': 100},
{'z': 50},
{'z': 0},
{'x': 1, 'y': 11},
{'z': 3},
{'b': 4.0},
{'x': 1, 'y': 11},
{'z': 5},
{'b': 0},
{'z': 0},
{'x': 1, 'y': 20},
{'z': 3},
{'x': 1, 'y': 20},
{'z': 13},
{'b': 10},
{'z': 0},
{'b': 0},
{'x': 200, 'y': 250},
{'z': 15},
{'b': 25},
{'b': 0}
]
self.assertEqual(expected, output_log.movements)
self.assertEqual([(0, 2), (1, 2), (2, 2)], prog_out)
def test_calibrate_without_axis(self):
self.protocol.add_instrument('A', 'p20')
self.protocol.add_instrument('B', 'p200')
with self.assertRaises(x.DataMissing):
self.protocol.calibrate('A1', top=0, bottom=0)
def test_transfer_without_tiprack(self):
""" Raise error when no tiprack found. """
self.protocol.attach_motor()
self.protocol.add_instrument('B', 'p200')
self.protocol.add_container('A1', 'microplate.96')
self.protocol.calibrate('A1', top=0, bottom=0)
self.protocol.calibrate_instrument('B', top=0, blowout=10)
self.protocol.transfer('A1:A1', 'A1:A2', ul=100)
with self.assertRaises(x.ContainerMissing):
self.protocol.run_all()
def test_transfer_without_dispose_point(self):
""" Raise when no dispose point set. """
self.protocol.attach_motor()
self.protocol.add_instrument('B', 'p200')
self.protocol.add_container('A1', 'microplate.96')
self.protocol.add_container('C1', 'tiprack.p200')
self.protocol.calibrate('A1')
self.protocol.calibrate('C1')
self.protocol.calibrate_instrument('B', top=0, blowout=10)
self.protocol.transfer('A1:A1', 'A1:A2', ul=100)
self.protocol.transfer('A1:A2', 'A1:A3', ul=80)
with self.assertRaises(x.ContainerMissing):
self.protocol.run_all()
def test_instrument_missing(self):
with self.assertRaises(x.InstrumentMissing):
m = self.protocol.attach_motor()
m.get_pipette(has_volume=1000)
def test_no_errors_from_commands(self):
self.protocol.add_instrument('B', 'p200')
self.protocol.add_container('A1', 'microplate.96')
self.protocol.add_container('B1', 'tiprack.p200')
self.protocol.add_container('C1', 'point.trash')
self.protocol.calibrate('A1')
self.protocol.calibrate('B1')
self.protocol.calibrate('C1')
self.protocol.calibrate('A1', x=1, y=2, top=3, bottom=13)
self.protocol.calibrate_instrument('B', top=0, blowout=10, droptip=25)
self.protocol.transfer('A1:A1', 'A1:A2', ul=100)
self.protocol.transfer_group(
('A1:A1', 'A1:A2', {'ul': 100})
)
self.protocol.consolidate(
'A1:A1',
('A1:A2', {'ul':100}),
('A1:A2', {'ul':150})
)
self.protocol.distribute(
'A1:A1',
('A1:A2', {'ul':100}),
('A1:A2', {'ul':150})
)
self.protocol.mix('A1:A2', ul=100, repetitions=5)
motor = self.protocol.attach_motor()
output_log = motor._driver
movements = output_log.movements
# We're not really testing anything except that it runs without
# errors.
self.protocol.run_all()
class MotorHandlerTest(unittest.TestCase):
def setUp(self):
self.protocol = Protocol()
def test_basic_transfer(self):
""" Basic transfer. """
motor = self.protocol.attach_motor()
output_log = motor._driver
self.protocol.add_instrument('B', 'p200')
self.protocol.add_container('A1', 'microplate.96')
self.protocol.add_container('C1', 'tiprack.p200')
self.protocol.add_container('B2', 'point.trash')
self.protocol.calibrate('A1', x=1, y=2, top=3, bottom=13)
self.protocol.calibrate('A1:A2', bottom=5)
self.protocol.calibrate('C1', x=100, y=100, top=50)
self.protocol.calibrate('B2', x=200, y=250, top=15)
self.protocol.calibrate_instrument('B', top=0, blowout=10, droptip=25)
self.protocol.transfer('A1:A1', 'A1:A2', ul=100)
self.protocol.transfer('A1:A2', 'A1:A3', ul=80)
prog_out = []
for progress in self.protocol.run():
prog_out.append(progress)
expected = [
# Transfer 1.
{'x': 100, 'y': 100}, # Pickup tip.
{'z': 50},
{'z': 0}, # Move to well.
{'x': 1, 'y': 2},
{'z': 3},
{'b': 5.0}, # Plunge.
{'x': 1, 'y': 2},
{'z': 13}, # Move into well.
{'b': 0}, # Release.
{'z': 0}, # Move up.
{'x': 1, 'y': 11}, # Move to well.
{'z': 3},
{'x': 1, 'y': 11},
{'z': 5}, # Move into well.
{'b': 10}, # Blowout.
{'z': 0}, # Move up.
{'b': 0}, # Release.
{'x': 200, 'y': 250}, # Dispose tip.
{'z': 15},
{'b': 25},
{'b': 0},
# Transfer 2.
{'x': 100, 'y': 109},
{'z': 50},
{'z': 0},
{'x': 1, 'y': 11},
{'z': 3},
{'b': 4.0},
{'x': 1, 'y': 11},
{'z': 5},
{'b': 0},
{'z': 0},
{'x': 1, 'y': 20},
{'z': 3},
{'x': 1, 'y': 20},
{'z': 13},
{'b': 10},
{'z': 0},
{'b': 0},
{'x': 200, 'y': 250},
{'z': 15},
{'b': 25},
{'b': 0}
]
self.assertEqual(expected, output_log.movements)
self.assertEqual([(0, 2), (1, 2), (2, 2)], prog_out)
def test_transfer_without_tiprack(self):
""" Raise error when no tiprack found. """
self.protocol.attach_motor()
self.protocol.add_instrument('B', 'p200')
self.protocol.add_container('A1', 'microplate.96')
self.protocol.calibrate_instrument('B', top=0, blowout=10)
self.protocol.transfer('A1:A1', 'A1:A2', ul=100)
self.protocol.transfer('A1:A2', 'A1:A3', ul=80)
with self.assertRaises(KeyError):
for progress in self.protocol.run():
continue
def test_transfer_without_dispose_point(self):
""" Raise when no dispose point set. """
self.protocol.attach_motor()
self.protocol.add_instrument('B', 'p200')
self.protocol.add_container('A1', 'microplate.96')
self.protocol.add_container('C1', 'tiprack.p200')
self.protocol.calibrate_instrument('B', top=0, blowout=10)
self.protocol.transfer('A1:A1', 'A1:A2', ul=100)
self.protocol.transfer('A1:A2', 'A1:A3', ul=80)
with self.assertRaises(KeyError):
for progress in self.protocol.run():
continue
