def test_two_behaviors(self):
#############################################
# set up the document
print('Setting up document')
doc = sbol3.Document()
sbol3.set_namespace('https://bbn.com/scratch/')
#############################################
# Create the behavior and constraints
print('Creating Constraints')
a = paml.Primitive("a")
b = paml.Primitive("b")
# Constrain start of b to follow end of a by [10, 15]
follows_constraint = pamlt.precedes(a, [10, 15], b, units=tyto.OM.hour)
doc.add(a)
# doc.add(follows_constraint)
########################################
# Validate and write the document
print('Validating and writing time')
v = doc.validate()
assert not v.errors and not v.warnings, "".join(
str(e) for e in doc.validate().errors)
def test_single_behavior(self):
#############################################
# set up the document
print('Setting up document')
doc = sbol3.Document()
sbol3.set_namespace('https://bbn.com/scratch/')
#############################################
# Create the behavior and constraints
print('Creating Constraints')
a = paml.Primitive("a")
# Constrain start time of a to [0, 10]
start_a = pamlt.startTime(a, [0, 10], units=tyto.OM.hour)
# Constrain end time of a to [10, 15]
end_a = pamlt.endTime(a, [10, 15], units=tyto.OM.hour)
# Constrain duration of a to [1, 5]
duration_a = pamlt.duration(a, [1, 5], units=tyto.OM.hour)
constraint = pamlt.And([start_a, end_a, duration_a])
time_constraints = pamlt.TimeConstraints("small_protocol_constraints",
constraints=[constraint])
doc.add(a)
doc.add(time_constraints)
########################################
# Validate and write the document
print('Validating and writing time')
v = doc.validate()
assert not v.errors and not v.warnings, "".join(
str(e) for e in doc.validate().errors)
def test_expressions(self):
#############################################
# set up the document
print('Setting up document')
doc = sbol3.Document()
sbol3.set_namespace('https://bbn.com/scratch/')
#############################################
# Create the Expressions
print('Creating Protocol')
# expression e1: 60s * duration(a1)
a1 = paml.Primitive("a1")
d1 = uml.Duration(observation=uml.DurationObservation(event=[a1]))
m1 = pamlt.TimeMeasure(expr=sbol3.Measure(60, tyto.OM.second))
e1 = uml.Expression(symbol="*", is_ordered=False, operand=[m1, d1])
#doc.add(e1)
# expression lt1: e1 < e2
e2 = pamlt.TimeMeasure(expr=sbol3.Measure(120, tyto.OM.second))
lt1 = uml.Expression(symbol="<", is_ordered=True, operand=[e1, e2])
#doc.add(lt1)
# c1: Not(lt1)
c1 = pamlt.Not(constrained_elements=lt1)
# doc.add(c1)
########################################
# Validate and write the document
print('Validating and writing time')
v = doc.validate()
assert not v.errors and not v.warnings, "".join(
str(e) for e in doc.validate().errors)
def test_two_element_library(self):
#############################################
# Set up the document
doc = sbol3.Document()
sbol3.set_namespace('https://example.org/test')
#############################################
# Create the primitives
print('Making primitives for test library')
p = paml.Primitive('Provision')
p.description = 'Place a measured amount (mass or volume) of a specified component into a location.'
p.add_input('resource', sbol3.SBOL_COMPONENT)
p.add_input('destination', 'http://bioprotocols.org/paml#Location')
p.add_input('amount', sbol3.OM_MEASURE) # Can be mass or volume
p.add_input('dispenseVelocity', sbol3.OM_MEASURE, True)
p.add_output('samples', 'http://bioprotocols.org/paml#LocatedSamples')
doc.add(p)
p = paml.Primitive('Transfer')
p.description = 'Move a measured volume taken from a collection of source samples to a location'
p.add_input('source', 'http://bioprotocols.org/paml#LocatedSamples')
p.add_input('destination', 'http://bioprotocols.org/paml#Location')
p.add_input('amount', sbol3.OM_MEASURE) # Must be volume
p.add_input('dispenseVelocity', sbol3.OM_MEASURE, True)
p.add_output('samples', 'http://bioprotocols.org/paml#LocatedSamples')
doc.add(p)
print('Library construction complete')
########################################
# Validate and write the document
print('Validating and writing protocol')
v = doc.validate()
assert len(v) == 0, "".join(f'\n {e}' for e in v)
temp_name = os.path.join(tempfile.gettempdir(), 'mini_library.nt')
doc.write(temp_name, sbol3.SORTED_NTRIPLES)
print(f'Wrote file as {temp_name}')
comparison_file = os.path.join(
os.path.dirname(os.path.realpath(__file__)), 'testfiles',
'mini_library.nt')
print(f'Comparing against {comparison_file}')
assert filecmp.cmp(temp_name,
comparison_file), "Files are not identical"
print('File identical with test file')
import sbol3
import paml
#############################################
# Set up the document
doc = sbol3.Document()
LIBRARY_NAME = 'spectrophotometry'
sbol3.set_namespace('https://bioprotocols.org/paml/primitives/' + LIBRARY_NAME)
#############################################
# Create the primitives
print('Making primitives for ' + LIBRARY_NAME)
p = paml.Primitive('MeasureAbsorbance')
p.description = 'Measure absorbance at a given wavelength from a set of samples'
p.add_input('samples', 'http://bioprotocols.org/paml#SampleCollection')
p.add_input('wavelength', sbol3.OM_MEASURE)
p.add_input('numFlashes', 'http://www.w3.org/2001/XMLSchema#integer', True)
p.add_output('measurements', 'http://bioprotocols.org/paml#SampleData')
doc.add(p)
p = paml.Primitive('MeasureFluorescence')
p.description = 'Measure fluorescence intensity from a set of samples stimulated by a given wavelength, with an optional bandpass or lowpass filter'
p.add_input('samples', 'http://bioprotocols.org/paml#SampleCollection')
p.add_input('excitationWavelength', sbol3.OM_MEASURE)
p.add_input('emissionBandpassWavelength', sbol3.OM_MEASURE, True)
p.add_input(
'emissionBandpassWidth', sbol3.OM_MEASURE, True
) # measured in total range, e.g., 450nm wavelength, 50nm width = 425nm - 475nm
p.add_input('emissionLowpassCutoff', sbol3.OM_MEASURE, True) # e.g., 750LP
p.add_input('numFlashes', 'http://www.w3.org/2001/XMLSchema#integer', True)
import sbol3
import paml
#############################################
# Set up the document
doc = sbol3.Document()
LIBRARY_NAME = 'liquid_handling'
sbol3.set_namespace('https://bioprotocols.org/paml/primitives/' + LIBRARY_NAME)
#############################################
# Create the primitives
print('Making primitives for ' + LIBRARY_NAME)
p = paml.Primitive('Provision')
p.description = 'Place a measured amount (mass or volume) of a specified component into a location, where it may then be used in executing the protocol.'
p.add_input('resource', sbol3.SBOL_COMPONENT)
p.add_input(
'destination', 'http://bioprotocols.org/paml#SampleCollection'
) # TODO: change these URIs to constants on resolution of pySBOL issue #228
p.add_input('amount', sbol3.OM_MEASURE) # Can be mass or volume
p.add_input('dispenseVelocity', sbol3.OM_MEASURE, True)
doc.add(p)
p = paml.Primitive('Dispense')
p.description = 'Move a measured volume of liquid from one source sample to create samples at multiple destination locations'
p.add_input('source', 'http://bioprotocols.org/paml#SampleCollection')
p.add_input('destination', 'http://bioprotocols.org/paml#SampleCollection')
p.add_input('amount', sbol3.OM_MEASURE) # Must be volume
p.add_input('dispenseVelocity', sbol3.OM_MEASURE, True)
doc.add(p)
import sbol3
import paml
#############################################
# Set up the document
doc = sbol3.Document()
LIBRARY_NAME = 'culturing'
sbol3.set_namespace('https://bioprotocols.org/paml/primitives/'+LIBRARY_NAME)
#############################################
# Create the primitives
print('Making primitives for '+LIBRARY_NAME)
p = paml.Primitive('Transform')
p.description = 'Transform competent cells.'
p.add_input('host', sbol3.SBOL_COMPONENT)
p.add_input('dna', sbol3.SBOL_COMPONENT)
p.add_input('amount', sbol3.OM_MEASURE, True) # Can be mass or volume
p.add_input('selection_medium', sbol3.SBOL_COMPONENT)
p.add_output('transformants', 'http://bioprotocols.org/paml#SampleArray')
doc.add(p)
p = paml.Primitive('Culture')
p.description = 'Inoculate and grow cells in a growth medium.'
p.add_input('inoculum', sbol3.SBOL_COMPONENT)
p.add_input('replicates', 'http://bioprotocols.org/uml#ValueSpecification', optional=True)
p.add_input('growth_medium', sbol3.SBOL_COMPONENT)
p.add_input('volume', sbol3.OM_MEASURE, True)
p.add_input('duration', sbol3.OM_MEASURE)
p.add_input('orbital_shake_speed', sbol3.OM_MEASURE, True) # Should be rpm
import sbol3
import paml
#############################################
# Set up the document
doc = sbol3.Document()
LIBRARY_NAME = 'liquid_handling'
sbol3.set_namespace('https://bioprotocols.org/paml/primitives/' + LIBRARY_NAME)
#############################################
# Create the primitives
print('Making primitives for ' + LIBRARY_NAME)
p = paml.Primitive('Provision')
p.description = 'Place a measured amount (mass or volume) of a specified component into a location, where it may then be used in executing the protocol.'
p.add_input('resource', sbol3.SBOL_COMPONENT)
p.add_input(
'destination', 'http://bioprotocols.org/paml#SampleCollection'
) # TODO: change these URIs to constants on resolution of pySBOL issue #228
p.add_input('amount', sbol3.OM_MEASURE) # Can be mass or volume
p.add_input('dispenseVelocity', sbol3.OM_MEASURE, True)
doc.add(p)
p = paml.Primitive('Dispense')
p.description = 'Move a measured volume of liquid from one source sample to create samples at multiple destination locations'
p.add_input('source', 'http://bioprotocols.org/paml#SampleCollection')
p.add_input('destination', 'http://bioprotocols.org/paml#SampleCollection')
p.add_input('amount', sbol3.OM_MEASURE) # Must be volume
p.add_input('dispenseVelocity', sbol3.OM_MEASURE, True)
doc.add(p)
import sbol3
import paml
#############################################
# Set up the document
doc = sbol3.Document()
LIBRARY_NAME = 'sample_arrays'
sbol3.set_namespace('https://bioprotocols.org/paml/primitives/' + LIBRARY_NAME)
#############################################
# Create the primitives
print('Making primitives for ' + LIBRARY_NAME)
p = paml.Primitive('EmptyContainer')
p.description = 'Allocate a sample array with size and type based on an empty container'
p.add_input('specification', sbol3.SBOL_IDENTIFIED)
p.add_output('samples', 'http://bioprotocols.org/paml#SampleArray')
doc.add(p)
p = paml.Primitive('PlateCoordinates')
p.description = 'Select only the samples with specified row/column combination from a sample collection'
p.add_input('source', 'http://bioprotocols.org/paml#SampleCollection')
p.add_input('coordinates', 'http://bioprotocols.org/uml#ValueSpecification')
p.add_output('samples', 'http://bioprotocols.org/paml#SampleCollection')
doc.add(p)
p = paml.Primitive('Rows')
p.description = 'Select only the samples with specified rows from a sample collection'
p.add_input('source', 'http://bioprotocols.org/paml#SampleCollection')
p.add_input('row', 'http://bioprotocols.org/uml#ValueSpecification')
p.add_output('samples', 'http://bioprotocols.org/paml#SampleCollection')
import sbol3
import paml
#############################################
# Set up the document
doc = sbol3.Document()
LIBRARY_NAME = 'plate_handling'
sbol3.set_namespace('https://bioprotocols.org/paml/primitives/'+LIBRARY_NAME)
#############################################
# Create the primitives
print('Making primitives for '+LIBRARY_NAME)
# Note: plate handling primitives operate on whole arrays only, not just fragments
p = paml.Primitive('Cover')
p.description = 'Cover a set of samples to keep materials from entering or exiting'
p.add_input('location', 'http://bioprotocols.org/paml#SampleArray')
p.add_input('type', 'http://www.w3.org/2001/XMLSchema#anyURI')
doc.add(p)
p = paml.Primitive('Seal')
p.description = 'Seal a collection of samples fixing the seal using a user-selected method, in order to guarantee isolation from the external environment'
p.add_input('location', 'http://bioprotocols.org/paml#SampleArray')
p.add_input('type', 'http://www.w3.org/2001/XMLSchema#anyURI') # e.g., breathable vs. non-breathable
doc.add(p)
p = paml.Primitive('AdhesiveSeal')
p.description = 'Seal a collection of samples using adhesive to fix the seal, in order to guarantee isolation from the external environment'
p.add_input('location', 'http://bioprotocols.org/paml#SampleArray')
p.add_input('type', 'http://www.w3.org/2001/XMLSchema#anyURI') # e.g., breathable vs. non-breathable