def test_tuple_block(self, condition_block, strain_block):
b1 = ProductBlock(block_list=[
BlockReference(block=strain_block),
BlockReference(block=condition_block)
])
b2 = ProductBlock(block_list=[
BlockReference(block=strain_block),
BlockReference(block=condition_block)
])
assert b1 == b1
assert b1 == b2
assert b1 != {}
assert repr(
b1
) == "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='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'))])])))])"
def test_replicate_block_serialization(self, condition_block,
dummy_definition_decoder):
b1 = ReplicateBlock(count=4,
block=BlockReference(block=condition_block))
b_json = json.dumps(b1, cls=BlockDefinitionEncoder)
assert b_json == '{"block_type": "replicate_block", "count": 4, "block": {"block_type": "block_reference", "reference": "conditions"}}'
b2 = json.loads(b_json, cls=dummy_definition_decoder)
assert b1 == b2
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 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_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 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)