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_entity(self):
e1 = NamedEntity(name="one", reference="http://one.one")
e2 = NamedEntity(name="one", reference="http://one.one")
assert e1 == e2
assert e1 != {}
assert repr(
e1) == "NamedEntity(name='one', reference='http://one.one')"
assert str(e1) == "NamedEntity(name='one', reference='http://one.one')"
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(self):
t1 = Treatment.create_from(entity=NamedEntity(
name='M9 Glucose CAA',
reference='https://hub.sd2e.org/user/sd2e/design/M9_glucose_CAA/1'
))
assert t1.is_bound()
t2 = Treatment.create_from(entity=NamedEntity(
name='M9 Glucose CAA',
reference='https://hub.sd2e.org/user/sd2e/design/M9_glucose_CAA/1'
))
assert t1 == t1
assert t1 == t2
assert t1 != {}
assert repr(
t1) == "EntityTreatment(entity=NamedEntity(name='M9 Glucose CAA', reference='https://hub.sd2e.org/user/sd2e/design/M9_glucose_CAA/1'))"
def test_entity_serialization(self):
t1 = Treatment.create_from(entity=NamedEntity(
name='M9 Glucose CAA',
reference='https://hub.sd2e.org/user/sd2e/design/M9_glucose_CAA/1'
))
t_json = json.dumps(t1, cls=TreatmentEncoder)
t2 = json.loads(t_json, cls=TreatmentDecoder)
assert t1 == t2
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 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_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 main():
base_library = NamedEntity(
name='NODS4 in PetconV4 B1A2',
reference='https://hub.sd2e.org/user/sd2e/design/NODS40x20in0x20PetconV40x20B1A2/1'
)
ladder = NamedEntity(
name='Protein Design Ladder 1 PetconV4 B1A2',
reference='https://hub.sd2e.org/user/sd2e/design/Protein0x20Design0x20Ladder0x2010x20PetconV40x20B1A2/1'
)
library = NamedEntity(
name='NODS4 with Protein Design Ladder 1 in PetconV4 B1A2',
reference='https://hub.sd2e.org/user/sd2e/design/NODS40x20with0x20Protein0x20Design0x20Ladder0x2010x20in0x20PetconV40x20B1A2/1'
)
request = ExperimentalRequest(
cp_name='PROTEIN_DESIGN',
reference_name='',
reference_url='',
version=Version(major=1, minor=0, patch=0),
subjects=[base_library, ladder, library],
treatments=[
Treatment.create_from(
entity=NamedEntity(
name='SDO -His -Trp -Ura',
reference='https://hub.sd2e.org/user/sd2e/design/SDO0x200x2DHis0x200x2DTrp0x200x2DUra/1'
)
),
Treatment.create_from(
entity=NamedEntity(
name='SDO + 2% Galactose -His -Trp -Ura',
reference='https://hub.sd2e.org/user/sd2e/design/SDO0x200x2B0x2020x250x20Galactose0x200x2DHis0x200x2DTrp0x200x2DUra/1'
)
),
Treatment.create_from(
entity=NamedEntity(
name='Chymotrypsin',
reference='https://hub.sd2e.org/user/sd2e/design/Chymotrypsin/1'
)
),
Treatment.create_from(
entity=NamedEntity(
name='Anti-c-myc-FITC',
reference='https://hub.sd2e.org/user/sd2e/design/Anti0x2Dc0x2Dmyc0x2DFITC/1'
)
),
Treatment.create_from(
entity=NamedEntity(
name='TBS',
reference='https://hub.sd2e.org/user/sd2e/design/Tris0x20Buffered0x20Saline/1'
)
),
Treatment.create_from(
entity=NamedEntity(
name='TBSF',
reference='https://hub.sd2e.org/user/sd2e/design/Tris0x20Buffered0x20Saline0x200x2B0x2010x250x20BSA/1'
)
),
Treatment.create_from(
entity=NamedEntity(
name='PBS',
reference='https://hub.sd2e.org/user/sd2e/design/pbs/1'
)
),
Treatment.create_from(
entity=NamedEntity(
name='PBSF',
reference='https://hub.sd2e.org/user/sd2e/design/Phosphate0x20Buffered0x20Saline0x200x2B0x2010x250x20BSA/1'
)
),
Treatment.create_from(
entity=NamedEntity(
name='Trypsin',
reference='https://hub.sd2e.org/user/sd2e/design/Trypsin/1'
)
),
Treatment.create_from(
entity=NamedEntity(
name='AMA1-best',
reference='https://hub.sd2e.org/user/sd2e/design/UWBF_21171/1'
)
),
Treatment.create_from(
entity=NamedEntity(
name='EBY100 + PETCONv3_baker',
reference='https://hub.sd2e.org/user/sd2e/design/UWBF_21535/1'
))],
designs=[],
measurements=[]
)
with open('nc_titration_generated.json', 'w') as file:
json.dump(request, file, cls=ExperimentEncoder, indent=2)
def empty_landing_pads():
ref = "https://hub.sd2e.org/user/sd2e/design/MG1655_empty_landing_pads/1"
return NamedEntity(name="MG1655_empty_landing_pads", reference=ref)
def nand_circuit():
return NamedEntity(
name="MG1655_NAND_Circuit",
reference="https://hub.sd2e.org/user/sd2e/design/MG1655_NAND_Circuit/1"
)
def test_serialization(self):
e1 = NamedEntity(name="one", reference="http://one.one")
e_json = json.dumps(e1, cls=NamedEntityEncoder)
e2 = json.loads(e_json, cls=NamedEntityDecoder)
assert e1 == e2
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)
