def test_control_serialization(self, nand_circuit, timepoint, iptg,
dummy_control_decoder):
c1 = Control(
name='positive_gfp',
sample=Sample(
subject=nand_circuit,
treatments=[
TreatmentReference.create_from(
treatment=timepoint,
value=Value(
value=18,
unit=Unit(
reference=
'http://purl.obolibrary.org/obo/UO_0000032'))),
TreatmentReference.create_from(
treatment=iptg,
value=Value(
value=0,
unit=Unit(
reference=
'http://purl.obolibrary.org/obo/UO_0000064')))
]))
c_json = json.dumps(c1, cls=ControlEncoder)
c2 = json.loads(c_json, cls=dummy_control_decoder)
assert c1 == c2
def test_simple_treatment(self):
t1 = Treatment.create_from(
attribute=Attribute.create_from(
name='temperature',
value=Value(
value=1,
unit=Unit(
reference='http://purl.obolibrary.org/obo/UO_0000027')
))
)
assert t1.is_bound()
t2 = Treatment.create_from(
attribute=Attribute.create_from(
name='temperature',
value=Value(
value=1,
unit=Unit(
reference='http://purl.obolibrary.org/obo/UO_0000027')
))
)
assert t1 == t1
assert t1 == t2
assert t1 != {}
assert repr(
t1) == "AttributeTreatment(attribute=BoundAttribute(name='temperature', value=Value(value=1, unit=Unit(reference='http://purl.obolibrary.org/obo/UO_0000027'))))"
def test_generate_block_serialization(self, iptg,
dummy_definition_decoder):
b1 = GenerateBlock(
treatment=iptg,
attribute_name='concentration',
values=[
Value(value=0,
unit=Unit(
reference='http://purl.obolibrary.org/obo/UO_0000064'
)),
Value(value=0.25,
unit=Unit(
reference='http://purl.obolibrary.org/obo/UO_0000064'
)),
Value(value=2.5,
unit=Unit(
reference='http://purl.obolibrary.org/obo/UO_0000064'
)),
Value(value=25,
unit=Unit(
reference='http://purl.obolibrary.org/obo/UO_0000064'
)),
Value(
value=250,
unit=Unit(
reference='http://purl.obolibrary.org/obo/UO_0000064'))
])
b_json = json.dumps(b1, cls=BlockDefinitionEncoder)
b2 = json.loads(b_json, cls=dummy_definition_decoder)
assert b1 == b2
def test_generate_block(self, iptg):
b1 = GenerateBlock(
treatment=iptg,
attribute_name='concentration',
values=[
Value(value=0,
unit=Unit(
reference='http://purl.obolibrary.org/obo/UO_0000064'
)),
Value(value=0.25,
unit=Unit(
reference='http://purl.obolibrary.org/obo/UO_0000064'
)),
Value(value=2.5,
unit=Unit(
reference='http://purl.obolibrary.org/obo/UO_0000064'
)),
Value(value=25,
unit=Unit(
reference='http://purl.obolibrary.org/obo/UO_0000064'
)),
Value(
value=250,
unit=Unit(
reference='http://purl.obolibrary.org/obo/UO_0000064'))
])
b2 = GenerateBlock(
treatment=iptg,
attribute_name='concentration',
values=[
Value(value=0,
unit=Unit(
reference='http://purl.obolibrary.org/obo/UO_0000064'
)),
Value(value=0.25,
unit=Unit(
reference='http://purl.obolibrary.org/obo/UO_0000064'
)),
Value(value=2.5,
unit=Unit(
reference='http://purl.obolibrary.org/obo/UO_0000064'
)),
Value(value=25,
unit=Unit(
reference='http://purl.obolibrary.org/obo/UO_0000064'
)),
Value(
value=250,
unit=Unit(
reference='http://purl.obolibrary.org/obo/UO_0000064'))
])
assert b1 == b1
assert b1 == b2
assert b1 != {}
assert repr(
b1
) == "GenerateBlock(treatment=EntityTreatment(entity=NamedEntity(name='IPTG', reference='https://hub.sd2e.org/user/sd2e/design/IPTG/1', attributes=[UnboundAttribute(name='concentration', unit=Unit(reference='http://purl.obolibrary.org/obo/UO_0000064'))])), attribute_name='concentration', values=[Value(value=0, unit=Unit(reference='http://purl.obolibrary.org/obo/UO_0000064')), Value(value=0.25, unit=Unit(reference='http://purl.obolibrary.org/obo/UO_0000064')), Value(value=2.5, unit=Unit(reference='http://purl.obolibrary.org/obo/UO_0000064')), Value(value=25, unit=Unit(reference='http://purl.obolibrary.org/obo/UO_0000064')), Value(value=250, unit=Unit(reference='http://purl.obolibrary.org/obo/UO_0000064'))])"
def test_methods(self):
u1 = Unit(reference="http://purl.obolibrary.org/obo/UO_0000064")
u2 = Unit(reference="http://purl.obolibrary.org/obo/UO_0000064")
assert u1 == u2
assert u1 != {}
assert repr(
u1
) == "Unit(reference='http://purl.obolibrary.org/obo/UO_0000064')"
assert str(u1) == "http://purl.obolibrary.org/obo/UO_0000064"
def test_value(self):
v1 = Value(
value=37,
unit=Unit(reference='http://purl.obolibrary.org/obo/UO_0000027'))
v2 = Value(
value=37,
unit=Unit(reference='http://purl.obolibrary.org/obo/UO_0000027'))
assert v1 == v1
assert v1 == v2
assert v1 != {}
assert repr(
v1
) == "Value(value=37, unit=Unit(reference='http://purl.obolibrary.org/obo/UO_0000027'))"
def test_entity_unbound_attributes(self):
concentration = Attribute.create_from(
name='concentration',
value=Value(
value=0.25,
unit=Unit(
reference='http://purl.obolibrary.org/obo/UO_0000064')))
timepoint = Attribute.create_from(
name='timepoint',
unit=Unit(reference='http://purl.obolibrary.org/obo/UO_0000027'))
e1 = NamedEntity(name="one",
reference="http://one.one",
attributes=[concentration, timepoint])
assert not e1.is_bound()
def test_entity_attributes(self):
concentration = Attribute.create_from(
name='concentration',
value=Value(
value=0.25,
unit=Unit(
reference='http://purl.obolibrary.org/obo/UO_0000064')))
e1 = NamedEntity(name="one",
reference="http://one.one",
attributes=[concentration])
assert e1.is_bound()
e2 = NamedEntity(name="one",
reference="http://one.one",
attributes=[concentration])
assert e1 == e1
assert e1 == e2
assert e1 != {}
assert repr(
e1
) == "NamedEntity(name='one', reference='http://one.one', attributes=[BoundAttribute(name='concentration', value=Value(value=0.25, unit=Unit(reference='http://purl.obolibrary.org/obo/UO_0000064')))])"
assert str(
e1
) == "NamedEntity(name='one', reference='http://one.one', attributes=[BoundAttribute(name='concentration', value=Value(value=0.25, unit=Unit(reference='http://purl.obolibrary.org/obo/UO_0000064')))])"
def test_entity_attribute(self):
concentration = Attribute.create_from(
name='concentration',
unit=Unit(
reference='http://purl.obolibrary.org/obo/UO_0000064'
)
)
t1 = Treatment.create_from(
entity=NamedEntity(
name='IPTG',
reference='https://hub.sd2e.org/user/sd2e/design/IPTG/1',
attributes=[
concentration
])
)
assert not t1.is_bound()
t2 = Treatment.create_from(
entity=NamedEntity(
name='IPTG',
reference='https://hub.sd2e.org/user/sd2e/design/IPTG/1',
attributes=[
concentration
])
)
assert t1 == t1
assert t1 == t2
assert t1 != {}
assert repr(
t1) == "EntityTreatment(entity=NamedEntity(name='IPTG', reference='https://hub.sd2e.org/user/sd2e/design/IPTG/1', attributes=[UnboundAttribute(name='concentration', unit=Unit(reference='http://purl.obolibrary.org/obo/UO_0000064'))]))"
def test_unbound_attribute(self):
t1 = Attribute.create_from(
name='timepoint',
unit=Unit(reference='http://purl.obolibrary.org/obo/UO_0000027'))
assert not t1.is_bound()
t2 = Attribute.create_from(
name='timepoint',
unit=Unit(reference='http://purl.obolibrary.org/obo/UO_0000027'))
assert t1 == t1
assert t1 == t2
assert t1 != {}
assert repr(
t1
) == "UnboundAttribute(name='timepoint', unit=Unit(reference='http://purl.obolibrary.org/obo/UO_0000027'))"
def test_value_serialization(self):
v1 = Value(
value=37,
unit=Unit(reference='http://purl.obolibrary.org/obo/UO_0000027'))
v_json = json.dumps(v1, cls=ValueEncoder)
v2 = json.loads(v_json, cls=ValueDecoder)
assert v1 == v2
def test_unbound_attribute_serialization(self):
t1 = Attribute.create_from(
name='timepoint',
unit=Unit(reference='http://purl.obolibrary.org/obo/UO_0000027'))
t_json = json.dumps(t1, cls=AttributeEncoder)
t2 = json.loads(t_json, cls=AttributeDecoder)
assert t1 == t2
def condition_block(iptg):
micromolar_unit = Unit(
reference='http://purl.obolibrary.org/obo/UO_0000064')
l_arabinose = Treatment.create_from(entity=NamedEntity(
name='L-arabinose',
reference='https://hub.sd2e.org/user/sd2e/design/Larabinose/1',
attributes=[
Attribute.create_from(name='concentration', unit=micromolar_unit)
]))
return DesignBlock(
label='conditions',
definition=ProductBlock(block_list=[
GenerateBlock(treatment=iptg,
attribute_name='concentration',
values=[
Value(value=0, unit=micromolar_unit),
Value(value=0.25, unit=micromolar_unit),
Value(value=2.5, unit=micromolar_unit),
Value(value=25, unit=micromolar_unit),
Value(value=250, unit=micromolar_unit)
]),
GenerateBlock(treatment=l_arabinose,
attribute_name='concentration',
values=[
Value(value=0, unit=micromolar_unit),
Value(value=5, unit=micromolar_unit),
Value(value=50, unit=micromolar_unit),
Value(value=500, unit=micromolar_unit),
Value(value=5000, unit=micromolar_unit),
Value(value=25000, unit=micromolar_unit)
]),
]))
def test_control(self, nand_circuit, timepoint, iptg):
c1 = Control(
name='positive_gfp',
sample=Sample(
subject=nand_circuit,
treatments=[
TreatmentReference.create_from(
treatment=timepoint,
value=Value(
value=18,
unit=Unit(
reference=
'http://purl.obolibrary.org/obo/UO_0000032'))),
TreatmentReference.create_from(
treatment=iptg,
value=Value(
value=0,
unit=Unit(
reference=
'http://purl.obolibrary.org/obo/UO_0000064')))
]))
c2 = Control(
name='positive_gfp',
sample=Sample(
subject=nand_circuit,
treatments=[
TreatmentReference.create_from(
treatment=timepoint,
value=Value(
value=18,
unit=Unit(
reference=
'http://purl.obolibrary.org/obo/UO_0000032'))),
TreatmentReference.create_from(
treatment=iptg,
value=Value(
value=0,
unit=Unit(
reference=
'http://purl.obolibrary.org/obo/UO_0000064')))
]))
assert c1 == c1
assert c1 == c2
assert c1 != {}
assert repr(
c1
) == "Control(name='positive_gfp', sample=Sample(subject=NamedEntity(name='MG1655_NAND_Circuit', reference='https://hub.sd2e.org/user/sd2e/design/MG1655_NAND_Circuit/1'), treatments=[TreatmentValueReference(treatment=AttributeTreatment(attribute=UnboundAttribute(name='timepoint', unit=Unit(reference='http://purl.obolibrary.org/obo/UO_0000032'))), value=Value(value=18, unit=Unit(reference='http://purl.obolibrary.org/obo/UO_0000032'))), TreatmentValueReference(treatment=EntityTreatment(entity=NamedEntity(name='IPTG', reference='https://hub.sd2e.org/user/sd2e/design/IPTG/1', attributes=[UnboundAttribute(name='concentration', unit=Unit(reference='http://purl.obolibrary.org/obo/UO_0000064'))])), value=Value(value=0, unit=Unit(reference='http://purl.obolibrary.org/obo/UO_0000064')))]))"
def iptg():
micromolar_unit = Unit(
reference='http://purl.obolibrary.org/obo/UO_0000064')
return Treatment.create_from(entity=NamedEntity(
name='IPTG',
reference='https://hub.sd2e.org/user/sd2e/design/IPTG/1',
attributes=[
Attribute.create_from(name='concentration', unit=micromolar_unit)
]))
def test_bound_attribute_serialization(self):
a1 = Attribute.create_from(
name='temperature',
value=Value(
value='',
unit=Unit(
reference='http://purl.obolibrary.org/obo/UO_0000027')))
a_json = json.dumps(a1, cls=AttributeEncoder)
a2 = json.loads(a_json, cls=AttributeDecoder)
assert a1 == a2
def kan():
microgram_per_milliliter_unit = Unit(
reference='http://purl.obolibrary.org/obo/UO_0000274')
return Treatment.create_from(entity=NamedEntity(
name='Kan',
reference='https://hub.sd2e.org/user/sd2e/design/Kan/1',
attributes=[
Attribute.create_from(name='concentration',
unit=microgram_per_milliliter_unit)
]))
def test_treatment_attribute_value_reference(self, iptg):
r1 = TreatmentReference.create_from(
treatment=iptg,
value=Value(
value=0,
unit=Unit(
reference='http://purl.obolibrary.org/obo/UO_0000064')))
r2 = TreatmentReference.create_from(
treatment=iptg,
value=Value(
value=0,
unit=Unit(
reference='http://purl.obolibrary.org/obo/UO_0000064')))
assert r1 == r1
assert r1 == r2
assert r1 != {}
assert repr(
r1
) == "TreatmentValueReference(treatment=EntityTreatment(entity=NamedEntity(name='IPTG', reference='https://hub.sd2e.org/user/sd2e/design/IPTG/1', attributes=[UnboundAttribute(name='concentration', unit=Unit(reference='http://purl.obolibrary.org/obo/UO_0000064'))])), value=Value(value=0, unit=Unit(reference='http://purl.obolibrary.org/obo/UO_0000064')))"
def test_treatment_attribute_value_reference_serialization(
self, iptg, dummy_definition_decoder):
r1 = TreatmentReference.create_from(
treatment=iptg,
value=Value(
value=0,
unit=Unit(
reference='http://purl.obolibrary.org/obo/UO_0000064')))
r_json = json.dumps(r1, cls=BlockDefinitionEncoder)
r2 = json.loads(r_json, cls=dummy_definition_decoder)
assert r1 == r2
def test_bound_attribute(self):
a1 = Attribute.create_from(
name='temperature',
value=Value(
value=37.2,
unit=Unit(
reference='http://purl.obolibrary.org/obo/UO_0000027')))
assert a1.is_bound()
a2 = Attribute.create_from(
name='temperature',
value=Value(
value=37.2,
unit=Unit(
reference='http://purl.obolibrary.org/obo/UO_0000027')))
assert a1 == a1
assert a1 == a2
assert a1 != {}
assert repr(
a1
) == "BoundAttribute(name='temperature', value=Value(value=37.2, unit=Unit(reference='http://purl.obolibrary.org/obo/UO_0000027')))"
def test_simple_treatment_serialization(self):
t1 = Treatment.create_from(
attribute=Attribute.create_from(
name='temperature',
value=Value(
value=1,
unit=Unit(
reference='http://purl.obolibrary.org/obo/UO_0000027')
))
)
t_json = json.dumps(t1, cls=TreatmentEncoder)
t2 = json.loads(t_json, cls=TreatmentDecoder)
assert t1 == t2
def test_entity_attribute_serialization(self):
concentration = Attribute.create_from(
name='concentration',
value=Value(
value=0.25,
unit=Unit(
reference='http://purl.obolibrary.org/obo/UO_0000064')))
e1 = NamedEntity(name="one",
reference="http://one.one",
attributes=[concentration])
e_json = json.dumps(e1, cls=NamedEntityEncoder)
e2 = json.loads(e_json, cls=NamedEntityDecoder)
assert e1 == e2
def temperature_block():
temperature_unit = Unit(
reference='http://purl.obolibrary.org/obo/UO_0000027')
media = Treatment.create_from(entity=NamedEntity(
name="M9 Glucose CAA",
reference="https://hub.sd2e.org/user/sd2e/design/M9_glucose_CAA/1"))
temperature = Treatment.create_from(attribute=Attribute.create_from(
name='temperature', value=Value(value=37.0, unit=temperature_unit)))
return DesignBlock(label='temperature-media',
definition=ProductBlock(block_list=[
TreatmentReference(treatment=temperature),
TreatmentReference(treatment=media)
]))
def test_sample_serialization(self, nand_circuit, timepoint, iptg,
dummy_sample_decoder):
s1 = Sample(
subject=nand_circuit,
treatments=[
TreatmentReference.create_from(
treatment=timepoint,
value=Value(
value=18,
unit=Unit(
reference=
'http://purl.obolibrary.org/obo/UO_0000032'))),
TreatmentReference.create_from(
treatment=iptg,
value=Value(
value=0,
unit=Unit(
reference=
'http://purl.obolibrary.org/obo/UO_0000064')))
])
s_json = json.dumps(s1, cls=SampleEncoder)
s2 = json.loads(s_json, cls=dummy_sample_decoder)
assert s1 == s2
def test_measurement_serialization(self, nand_circuit, timepoint, iptg,
empty_landing_pads, experiment_block,
dummy_measurement_decoder):
m1 = Measurement(
type='FLOW',
block=BlockReference(block=experiment_block),
controls=[
Control(
name='positive_gfp',
sample=Sample(
subject=nand_circuit,
treatments=[
TreatmentReference.create_from(
treatment=timepoint,
value=Value(
value=18,
unit=Unit(
reference=
'http://purl.obolibrary.org/obo/UO_0000032'
))),
TreatmentReference.create_from(
treatment=iptg,
value=Value(
value=0,
unit=Unit(
reference=
'http://purl.obolibrary.org/obo/UO_0000064'
)))
])),
Control(name='negative_gfp',
sample=Sample(subject=empty_landing_pads))
],
performers=['Ginkgo'])
m_json = json.dumps(m1, cls=MeasurementEncoder)
m2 = json.loads(m_json, cls=dummy_measurement_decoder)
assert m1 == m2
def test_entity_attribute_serialization(self):
concentration = Attribute.create_from(
name='concentration',
unit=Unit(
reference='http://purl.obolibrary.org/obo/UO_0000064')
)
t1 = Treatment.create_from(
entity=NamedEntity(
name='IPTG',
reference='https://hub.sd2e.org/user/sd2e/design/IPTG/1',
attributes=[
concentration
])
)
t_json = json.dumps(t1, cls=TreatmentEncoder)
t2 = json.loads(t_json, cls=TreatmentDecoder)
assert t1 == t2
def experiment_block(strain_block, temperature_block, condition_block,
timepoint):
hour_unit = Unit(reference='http://purl.obolibrary.org/obo/UO_0000032')
return DesignBlock(
label='experiment',
definition=ProductBlock(block_list=[
ReplicateBlock(count=4,
block=ProductBlock(block_list=[
BlockReference(block=strain_block),
BlockReference(block=temperature_block),
BlockReference(block=condition_block)
])),
GenerateBlock(treatment=timepoint,
attribute_name='timepoint',
values=[
Value(value=5, unit=hour_unit),
Value(value=6.5, unit=hour_unit),
Value(value=8, unit=hour_unit),
Value(value=18, unit=hour_unit)
]),
]))
def temperature():
temperature_unit = Unit(
reference='http://purl.obolibrary.org/obo/UO_0000027')
return Treatment.create_from(attribute=Attribute.create_from(
name='temperature', value=Value(value=37.0, unit=temperature_unit)))
def test_measurement(self, nand_circuit, iptg, timepoint,
empty_landing_pads, experiment_block):
m1 = Measurement(
type='FLOW',
block=BlockReference(block=experiment_block),
controls=[
Control(
name='positive_gfp',
sample=Sample(
subject=nand_circuit,
treatments=[
TreatmentReference.create_from(
treatment=timepoint,
value=Value(
value=18,
unit=Unit(
reference=
'http://purl.obolibrary.org/obo/UO_0000032'
))),
TreatmentReference.create_from(
treatment=iptg,
value=Value(
value=0,
unit=Unit(
reference=
'http://purl.obolibrary.org/obo/UO_0000064'
)))
])),
Control(name='negative_gfp',
sample=Sample(subject=empty_landing_pads))
],
performers=['Ginkgo'])
m2 = Measurement(
type='FLOW',
block=BlockReference(block=experiment_block),
controls=[
Control(
name='positive_gfp',
sample=Sample(
subject=nand_circuit,
treatments=[
TreatmentReference.create_from(
treatment=timepoint,
value=Value(
value=18,
unit=Unit(
reference=
'http://purl.obolibrary.org/obo/UO_0000032'
))),
TreatmentReference.create_from(
treatment=iptg,
value=Value(
value=0,
unit=Unit(
reference=
'http://purl.obolibrary.org/obo/UO_0000064'
)))
])),
Control(name='negative_gfp',
sample=Sample(subject=empty_landing_pads))
],
performers=['Ginkgo'])
assert m1 == m1
assert m1 == m2
assert m1 != {}
# TODO: figure out why this fails
assert repr(
m1
) == "Measurement(type='FLOW', block=BlockReference(block=DesignBlock(label='experiment', definition=ProductBlock(block_list=[ReplicateBlock(count=4, block=ProductBlock(block_list=[BlockReference(block=DesignBlock(label='strains', definition=SumBlock(block_list=[ProductBlock(block_list=[SubjectReference(entity=NamedEntity(name='MG1655_NAND_Circuit', reference='https://hub.sd2e.org/user/sd2e/design/MG1655_NAND_Circuit/1')), TreatmentReference(treatment=EntityTreatment(entity=NamedEntity(name='Kan', reference='https://hub.sd2e.org/user/sd2e/design/Kan/1', attributes=[UnboundAttribute(name='concentration', unit=Unit(reference='http://purl.obolibrary.org/obo/UO_0000274'))])))]), SubjectReference(entity=NamedEntity(name='MG1655_empty_landing_pads', reference='https://hub.sd2e.org/user/sd2e/design/MG1655_empty_landing_pads/1'))]))), BlockReference(block=DesignBlock(label='temperature-media', definition=ProductBlock(block_list=[TreatmentReference(treatment=AttributeTreatment(attribute=BoundAttribute(name='temperature', value=Value(value=37.0, unit=Unit(reference='http://purl.obolibrary.org/obo/UO_0000027'))))), TreatmentReference(treatment=EntityTreatment(entity=NamedEntity(name='M9 Glucose CAA', reference='https://hub.sd2e.org/user/sd2e/design/M9_glucose_CAA/1')))]))), BlockReference(block=DesignBlock(label='conditions', definition=ProductBlock(block_list=[GenerateBlock(treatment=EntityTreatment(entity=NamedEntity(name='IPTG', reference='https://hub.sd2e.org/user/sd2e/design/IPTG/1', attributes=[UnboundAttribute(name='concentration', unit=Unit(reference='http://purl.obolibrary.org/obo/UO_0000064'))])), attribute_name='concentration', values=[Value(value=0, unit=Unit(reference='http://purl.obolibrary.org/obo/UO_0000064')), Value(value=0.25, unit=Unit(reference='http://purl.obolibrary.org/obo/UO_0000064')), Value(value=2.5, unit=Unit(reference='http://purl.obolibrary.org/obo/UO_0000064')), Value(value=25, unit=Unit(reference='http://purl.obolibrary.org/obo/UO_0000064')), Value(value=250, unit=Unit(reference='http://purl.obolibrary.org/obo/UO_0000064'))]), GenerateBlock(treatment=EntityTreatment(entity=NamedEntity(name='L-arabinose', reference='https://hub.sd2e.org/user/sd2e/design/Larabinose/1', attributes=[UnboundAttribute(name='concentration', unit=Unit(reference='http://purl.obolibrary.org/obo/UO_0000064'))])), attribute_name='concentration', values=[Value(value=0, unit=Unit(reference='http://purl.obolibrary.org/obo/UO_0000064')), Value(value=5, unit=Unit(reference='http://purl.obolibrary.org/obo/UO_0000064')), Value(value=50, unit=Unit(reference='http://purl.obolibrary.org/obo/UO_0000064')), Value(value=500, unit=Unit(reference='http://purl.obolibrary.org/obo/UO_0000064')), Value(value=5000, unit=Unit(reference='http://purl.obolibrary.org/obo/UO_0000064')), Value(value=25000, unit=Unit(reference='http://purl.obolibrary.org/obo/UO_0000064'))])])))])), GenerateBlock(treatment=AttributeTreatment(attribute=UnboundAttribute(name='timepoint', unit=Unit(reference='http://purl.obolibrary.org/obo/UO_0000032'))), attribute_name='timepoint', values=[Value(value=5, unit=Unit(reference='http://purl.obolibrary.org/obo/UO_0000032')), Value(value=6.5, unit=Unit(reference='http://purl.obolibrary.org/obo/UO_0000032')), Value(value=8, unit=Unit(reference='http://purl.obolibrary.org/obo/UO_0000032')), Value(value=18, unit=Unit(reference='http://purl.obolibrary.org/obo/UO_0000032'))])]))), controls=[Control(name='positive_gfp', sample=Sample(subject=NamedEntity(name='MG1655_NAND_Circuit', reference='https://hub.sd2e.org/user/sd2e/design/MG1655_NAND_Circuit/1'), treatments=[TreatmentValueReference(treatment=AttributeTreatment(attribute=UnboundAttribute(name='timepoint', unit=Unit(reference='http://purl.obolibrary.org/obo/UO_0000032'))), value=Value(value=18, unit=Unit(reference='http://purl.obolibrary.org/obo/UO_0000032'))), TreatmentValueReference(treatment=EntityTreatment(entity=NamedEntity(name='IPTG', reference='https://hub.sd2e.org/user/sd2e/design/IPTG/1', attributes=[UnboundAttribute(name='concentration', unit=Unit(reference='http://purl.obolibrary.org/obo/UO_0000064'))])), value=Value(value=0, unit=Unit(reference='http://purl.obolibrary.org/obo/UO_0000064')))])), Control(name='negative_gfp', sample=Sample(subject=NamedEntity(name='MG1655_empty_landing_pads', reference='https://hub.sd2e.org/user/sd2e/design/MG1655_empty_landing_pads/1'), treatments=[]))], performers=['Ginkgo'])"
def timepoint():
hour_unit = Unit(reference='http://purl.obolibrary.org/obo/UO_0000032')
return Treatment.create_from(
attribute=Attribute.create_from(name='timepoint', unit=hour_unit))