def test_methods(self):
version = Version(major=1, minor=0, patch=2)
version2 = Version(major=1, minor=0, patch=2)
version3 = Version(major=3, minor=0, patch=2)
assert repr(version) == "Version(major=1, minor=0, patch=2)"
assert str(version) == "1.0.2"
assert version == version2
assert version != version3
assert version.major == 1
assert version.minor == 0
assert version.patch == 2
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)
def test_serialization(self):
v = Version(major=1, minor=0, patch=2)
json_string = json.dumps(v, cls=VersionEncoder)
assert json_string == '{"major": 1, "minor": 0, "patch": 2}'
v_load = json.loads(json_string, cls=VersionDecoder)
assert v_load == v
def test_equals(self):
v = Version(major=1, minor=0, patch=2)
assert v != {}
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)