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'])
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 ProtocolFormatterTest(unittest.TestCase):
maxDiff = None
json = """
{
"info": {
"name": "Test Protocol",
"author": "Michelle Steigerwalt",
"description": "A protocol to test JSON output.",
"created": "Thu Aug 11 20:19:55 2016",
"updated": ""
},
"instruments": {
"p10_a": {
"axis": "A",
"name": "p10"
},
"p200_b": {
"axis": "B",
"name": "p200"
}
},
"containers": [
{
"name": "microplate.96",
"label": "Ingredients",
"slot": "A1"
},
{
"name": "microplate.96",
"label": "Output",
"slot": "B1"
}
],
"instructions": [
{
"command": "transfer",
"start": "Ingredients:A1",
"end": "Output:B1",
"volume": 10,
"tool": "p10",
"blowout": true,
"touchtip": true
},
{
"command": "transfer_group",
"tool": "p10",
"transfers": [
{
"start": "Ingredients:A3",
"end": "Output:B3",
"volume": 3,
"blowout": true,
"touchtip": true
},
{
"start": "Ingredients:A4",
"end": "Output:B4",
"volume": 10,
"blowout": true,
"touchtip": true
},
{
"start": "Ingredients:A5",
"end": "Output:C1",
"volume": 10,
"blowout": true,
"touchtip": true
}
]
},
{
"command": "consolidate",
"tool": "p10",
"end": "Output:B3",
"transfers": [
{
"start": "Ingredients:A3",
"volume": 3,
"blowout": true,
"touchtip": true
},
{
"start": "Ingredients:A4",
"volume": 10,
"blowout": true,
"touchtip": true
},
{
"start": "Ingredients:A5",
"volume": 10,
"blowout": true,
"touchtip": true
}
]
},
{
"command": "distribute",
"tool": "p10",
"start": "Ingredients:A1",
"transfers": [
{
"end": "Output:A1",
"volume": 3,
"blowout": true,
"touchtip": true
},
{
"end": "Output:A2",
"volume": 10,
"blowout": true,
"touchtip": true
},
{
"end": "Output:A3",
"volume": 10,
"blowout": true,
"touchtip": true
}
]
},
{
"command": "mix",
"start": "Output:A1",
"volume": 50,
"tool": "p200",
"repetitions": 30,
"blowout": true,
"touchtip": true
}
]
}
"""
def setUp(self):
self.protocol = Protocol()
self.stub_info = {
'name': "Test Protocol",
'description': "A protocol to test JSON output.",
'author': "Michelle Steigerwalt",
'created': "Thu Aug 11 20:19:55 2016"
}
# Same definitions as the protocol JSON above.
self.protocol.set_info(**self.stub_info)
self.protocol.add_instrument('A', 'p10')
self.protocol.add_instrument('B', 'p200')
self.protocol.add_container('A1', 'microplate.96', label="Ingredients")
self.protocol.add_container('B1', 'microplate.96', label="Output")
self.protocol.transfer('A1:A1', 'B1:B1', ul=10, tool='p10')
self.protocol.transfer_group(
('A1:A3', 'B1:B3', {'ul': 3}),
('INGREDIENTS:A4', 'B1:B4'),
('A1:A5', 'B1:C1'),
tool='p10',
ul=10
)
self.protocol.consolidate(
'Output:B3',
('A1:A3', {'ul': 3}),
'INGREDIENTS:A4',
'A1:A5',
tool='p10',
ul=10
)
self.protocol.distribute(
'Ingredients:A1',
('Output:A1', {'ul': 3}),
'Output:A2',
'Output:A3',
tool='p10',
ul=10
)
self.protocol.mix('Output:A1', ul=50, repetitions=30)
def test_json_export(self):
result = json.loads(self.protocol.export(JSONFormatter))
expected = json.loads(self.json)
self.assertEqual(self.protocol.version, '0.0.1')
for k, v in self.stub_info.items():
self.assertEqual(v, result['info'][k])
self.assertEqual(result["info"]["version"], self.protocol.version)
self.assertEqual(result["info"]["version_hash"], self.protocol.hash)
expected['info'] = ""
result['info'] = ""
self.assertEqual(expected, result)
def test_invalid_json(self):
with self.assertRaises(x.ContainerMissing):
# This fails because there's no tiprack or trash.
self.protocol.export(JSONFormatter, validate_run=True)
def test_load_json(self):
start = self.json
f = JSONLoader(self.json)
dump = f.protocol.export(JSONFormatter)
result = json.loads(dump)
expected = json.loads(start)
expected['info'] = ""
result['info'] = ""
self.assertEqual(expected, result) # ✨ OMG isomorphic! ✨
def test_equal_hashing(self):
p = JSONLoader(self.json).protocol
# Hashes of all protocol run-related data within the JSON and manually
# defined protcol are equal.
self.assertEqual(self.protocol, p)
# Make a modification of the original protocol.
p.add_instrument('B', 'p20')
# Hashes are different.
self.assertNotEqual(self.protocol, p)
class JSONLoader():
_protocol = None
def __init__(self, json_str):
data = json.loads(json_str)
self._protocol = Protocol()
self._load_info(data['info'])
self._load_containers(data['containers'])
self._load_instruments(data['instruments'])
self._load_instructions(data['instructions'])
def _load_info(self, info):
self._protocol.set_info(**info)
def _load_instruments(self, instruments):
for k, inst in instruments.items():
self._protocol.add_instrument(inst['axis'], inst['name'])
def _load_containers(self, deck):
for container in deck:
name = container.get('name', None)
label = container.get('label', None)
slot = container.get('slot', None)
self._protocol.add_container(
slot, name, label=label
)
def _load_instructions(self, instructions):
for i in copy.deepcopy(instructions):
command = i.pop('command')
meth = getattr(self, '_load_{}_command'.format(command), None)
if meth is None:
raise KeyError("Can't unpack command: {}".format(command))
meth(i)
def _load_transfer_command(self, inst):
volume = inst.pop('volume', None)
inst['ul'] = volume
start = inst.pop('start')
end = inst.pop('end')
self._protocol.transfer(start, end, **inst)
def _load_mix_command(self, inst):
volume = inst.pop('volume', None)
inst['ul'] = volume
start = inst.pop('start')
self._protocol.mix(start, **inst)
def _load_transfer_group_command(self, inst):
transfers = []
for t in inst.pop('transfers'):
start = t.pop('start')
end = t.pop('end')
t['ul'] = t.pop('volume')
transfers.append((start, end, t))
self._protocol.transfer_group(*transfers, tool=inst['tool'])
def _load_consolidate_command(self, inst):
transfers = []
for t in inst.pop('transfers'):
start = t.pop('start')
t['ul'] = t.pop('volume')
transfers.append((start, t))
self._protocol.consolidate(inst['end'], *transfers, tool=inst['tool'])
def _load_distribute_command(self, inst):
transfers = []
for t in inst.pop('transfers'):
start = t.pop('end')
t['ul'] = t.pop('volume')
transfers.append((start, t))
self._protocol.distribute(inst['start'], *transfers, tool=inst['tool'])
@property
def protocol(self):
return self._protocol
class JSONLoader():
_protocol = None
def __init__(self, json_str):
data = json.loads(json_str)
self._protocol = Protocol()
self._load_info(data['info'])
self._load_containers(data['containers'])
self._load_instruments(data['instruments'])
self._load_instructions(data['instructions'])
def _load_info(self, info):
self._protocol.set_info(**info)
def _load_instruments(self, instruments):
for k, inst in instruments.items():
self._protocol.add_instrument(inst['axis'], inst['name'])
def _load_containers(self, deck):
for container in deck:
name = container.get('name', None)
label = container.get('label', None)
slot = container.get('slot', None)
self._protocol.add_container(slot, name, label=label)
def _load_instructions(self, instructions):
for i in copy.deepcopy(instructions):
command = i.pop('command')
meth = getattr(self, '_load_{}_command'.format(command), None)
if meth is None:
raise KeyError("Can't unpack command: {}".format(command))
meth(i)
def _load_transfer_command(self, inst):
volume = inst.pop('volume', None)
inst['ul'] = volume
start = inst.pop('start')
end = inst.pop('end')
self._protocol.transfer(start, end, **inst)
def _load_mix_command(self, inst):
volume = inst.pop('volume', None)
inst['ul'] = volume
start = inst.pop('start')
self._protocol.mix(start, **inst)
def _load_transfer_group_command(self, inst):
transfers = []
for t in inst.pop('transfers'):
start = t.pop('start')
end = t.pop('end')
t['ul'] = t.pop('volume')
transfers.append((start, end, t))
self._protocol.transfer_group(*transfers, tool=inst['tool'])
def _load_consolidate_command(self, inst):
transfers = []
for t in inst.pop('transfers'):
start = t.pop('start')
t['ul'] = t.pop('volume')
transfers.append((start, t))
self._protocol.consolidate(inst['end'], *transfers, tool=inst['tool'])
def _load_distribute_command(self, inst):
transfers = []
for t in inst.pop('transfers'):
start = t.pop('end')
t['ul'] = t.pop('volume')
transfers.append((start, t))
self._protocol.distribute(inst['start'], *transfers, tool=inst['tool'])
@property
def protocol(self):
return self._protocol
def compile(*sequences, output=None):
"""
Takes a list of sequence arguments (RVD or DNA) and outputs a generated
protocol to make plasmids targetting those sequences.
"""
sequences = list(sequences)
# Limit right now is the number of tips in the static deck map we're
# using for this protocol.
if len(sequences) > 15:
raise ValueError(
"FusX compiler only supports up to 15 sequences."
)
# Argument normalization.
normalized = []
for i, s in enumerate(sequences):
try:
normalized.append(_normalize_sequence(s))
except ValueError as e:
raise ValueError("Sequence #{}: {}".format(i + 1, e))
# Make the transfers for every sequence.
buffers = []
tals = []
enzymes = []
well_map = {}
for n, s in enumerate(normalized):
n = n + 1
if n > 12:
well = 'B{}'.format(n - 12)
else:
well = 'A{}'.format(n)
# We're going to do all the buffers at the start...
buffers += [('Ingredients:A1', 'FusX Output:' + well, 10)]
# TALs in the middle...
tals += _get_tal_transfers(s, well=well)
# Enzyme (BsmBI) at the end.
enzymes += [("Ingredients:B1", 'FusX Output:' + well, 10)]
# For printing an output map.
well_map[well] = sequences[n - 1] # Map to original input.
# Nicely formatted well map for the description.
output_map = []
for well in sorted(well_map):
output_map.append("{}: {}".format(well, well_map[well]))
protocol = Protocol()
protocol.set_info(
name="FusX Transfer",
created=str(datetime.date.today()),
description="; ".join(output_map)
)
protocol.add_instrument('A', 'p10')
protocol.add_instrument('B', 'p200')
protocol.add_container('A1', 'tuberack.15-50ml', label='Ingredients')
protocol.add_container('E1', 'microplate.96', label='Fusx Output')
protocol.add_container('A2', 'point.trash')
protocol.add_container('E3', 'microplate.96') # Cool deck.
protocol.add_container('B2', 'tiprack.p10')
protocol.add_container('B1', 'tiprack.p10')
protocol.add_container('B3', 'tiprack.p10')
protocol.add_container('C1', 'microplate.96', label='TALE1')
protocol.add_container('D1', 'microplate.96', label='TALE2')
protocol.add_container('C2', 'microplate.96', label='TALE3')
protocol.add_container('D2', 'microplate.96', label='TALE4')
protocol.add_container('C3', 'microplate.96', label='TALE5')
# Take our three transfer groups and make them into a consolidated
# transfer list.
# Buffers
group = []
for start, end, volume in buffers:
group.append((start, end, {'ul': volume}))
protocol.transfer_group(*group, tool="p10")
# TALS
for start, end, volume in tals:
protocol.transfer(start, end, ul=volume)
# Enzymes
for start, end, volume in enzymes:
protocol.transfer(start, end, ul=volume)
compiled = protocol.export(JSONFormatter)
if output:
with open(output, 'w') as f:
f.write(compiled)
return compiled
def compile(*sequences, output=None):
"""
Takes a list of sequence arguments (RVD or DNA) and outputs a generated
protocol to make plasmids targetting those sequences.
"""
sequences = list(sequences)
# Limit right now is the number of tips in the static deck map we're
# using for this protocol.
if len(sequences) > 15:
raise ValueError("FusX compiler only supports up to 15 sequences.")
# Argument normalization.
normalized = []
for i, s in enumerate(sequences):
try:
normalized.append(_normalize_sequence(s))
except ValueError as e:
raise ValueError("Sequence #{}: {}".format(i + 1, e))
# Make the transfers for every sequence.
buffers = []
tals = []
enzymes = []
well_map = {}
for n, s in enumerate(normalized):
n = n + 1
if n > 12:
well = 'B{}'.format(n - 12)
else:
well = 'A{}'.format(n)
# We're going to do all the buffers at the start...
buffers += [('Ingredients:A1', 'FusX Output:' + well, 10)]
# TALs in the middle...
tals += _get_tal_transfers(s, well=well)
# Enzyme (BsmBI) at the end.
enzymes += [("Ingredients:B1", 'FusX Output:' + well, 10)]
# For printing an output map.
well_map[well] = sequences[n - 1] # Map to original input.
# Nicely formatted well map for the description.
output_map = []
for well in sorted(well_map):
output_map.append("{}: {}".format(well, well_map[well]))
protocol = Protocol()
protocol.set_info(name="FusX Transfer",
created=str(datetime.date.today()),
description="; ".join(output_map))
protocol.add_instrument('A', 'p10')
protocol.add_instrument('B', 'p200')
protocol.add_container('A1', 'tuberack.15-50ml', label='Ingredients')
protocol.add_container('E1', 'microplate.96', label='Fusx Output')
protocol.add_container('A2', 'point.trash')
protocol.add_container('E3', 'microplate.96') # Cool deck.
protocol.add_container('B2', 'tiprack.p10')
protocol.add_container('B1', 'tiprack.p10')
protocol.add_container('B3', 'tiprack.p10')
protocol.add_container('C1', 'microplate.96', label='TALE1')
protocol.add_container('D1', 'microplate.96', label='TALE2')
protocol.add_container('C2', 'microplate.96', label='TALE3')
protocol.add_container('D2', 'microplate.96', label='TALE4')
protocol.add_container('C3', 'microplate.96', label='TALE5')
# Take our three transfer groups and make them into a consolidated
# transfer list.
# Buffers
group = []
for start, end, volume in buffers:
group.append((start, end, {'ul': volume}))
protocol.transfer_group(*group, tool="p10")
# TALS
for start, end, volume in tals:
protocol.transfer(start, end, ul=volume)
# Enzymes
for start, end, volume in enzymes:
protocol.transfer(start, end, ul=volume)
compiled = protocol.export(JSONFormatter)
if output:
with open(output, 'w') as f:
f.write(compiled)
return compiled
