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 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_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_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 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 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 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_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 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_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 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 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 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))
def main():
temperature_unit = Unit(
reference='http://purl.obolibrary.org/obo/UO_0000027')
hour_unit = Unit(reference='http://purl.obolibrary.org/obo/UO_0000032')
micromolar_unit = Unit(
reference='http://purl.obolibrary.org/obo/UO_0000064')
microgram_per_milliliter_unit = Unit(
reference='http://purl.obolibrary.org/obo/UO_0000274')
nand_circuit = NamedEntity(
name="MG1655_NAND_Circuit",
reference="https://hub.sd2e.org/user/sd2e/design/MG1655_NAND_Circuit/1"
)
empty_landing_pads = NamedEntity(
name="MG1655_empty_landing_pads",
reference="https://hub.sd2e.org/user/sd2e/design/MG1655_empty_landing_pads/1"
)
temperature = Treatment.create_from(
attribute=Attribute.create_from(
name='temperature',
value=Value(
value=37.0,
unit=temperature_unit
)))
timepoint = Treatment.create_from(
attribute=Attribute.create_from(
name='timepoint',
unit=hour_unit)
)
media = Treatment.create_from(
entity=NamedEntity(
name="M9 Glucose CAA",
reference="https://hub.sd2e.org/user/sd2e/design/M9_glucose_CAA/1"
))
iptg = 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)
])
)
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)
])
)
kan = 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)
])
)
strain_block = DesignBlock(
label='strains',
definition=SumBlock(block_list=[
ProductBlock(block_list=[
SubjectReference(entity=nand_circuit),
TreatmentReference(treatment=kan)
]),
SubjectReference(entity=empty_landing_pads)
])
)
temperature_block = DesignBlock(
label='temperature-media',
definition=ProductBlock(block_list=[
TreatmentReference(treatment=temperature),
TreatmentReference(treatment=media)
])
)
condition_block = 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)
]),
])
)
experiment_block = 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)
]
),
])
)
flow_measurement = 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=hour_unit)),
TreatmentReference.create_from(
treatment=iptg,
value=Value(
value=0,
unit=micromolar_unit))
]
)
),
Control(
name='negative_gfp',
sample=Sample(subject=empty_landing_pads)
)
],
performers=['Ginkgo']
)
plate_reader_measurement = Measurement(
type='PLATE_READER',
block=BlockReference(block=experiment_block),
performers=['Ginkgo']
)
rnaseq_measurement = Measurement(
type='RNA_SEQ',
block=BlockReference(block=experiment_block),
performers=['Ginkgo']
)
proteomic_measurement = Measurement(
type='PROTEOMICS',
block=BlockReference(block=experiment_block),
performers=['Ginkgo']
)
request = ExperimentalRequest(
cp_name='NOVEL_CHASSIS',
reference_name='NovelChassis-NAND-Ecoli-Titration',
reference_url='https://docs.google.com/document/d/1oMC5VM3XcFn6zscxLKLUe4U-TXbBsz8H6OQwHal1h4g',
version=Version(major=1, minor=0, patch=0),
subjects=[
nand_circuit,
empty_landing_pads
],
treatments=[
iptg,
kan,
l_arabinose,
media,
temperature,
timepoint
],
designs=[
strain_block,
temperature_block,
condition_block,
experiment_block
],
measurements=[
flow_measurement,
plate_reader_measurement,
rnaseq_measurement,
proteomic_measurement
]
)
with open('nc_titration_generated.json', 'w') as file:
json.dump(request, file, cls=ExperimentEncoder, indent=2)