def setUp(self):
self.model = dimerdecay()
self.mmmodel = MichaelisMenten()
# Create the model document using the API
self.modeldoc = StochMLDocument.fromModel(self.model)
def setUp(self):
self.model = dimerdecay()
self.mmmodel = MichaelisMenten()
# Create the model document using the API
self.modeldoc = StochMLDocument.fromModel(self.model)
class TestModelSerialization(unittest.TestCase):
def setUp(self):
self.model = dimerdecay()
self.mmmodel = MichaelisMenten()
# Create the model document using the API
self.modeldoc = StochMLDocument.fromModel(self.model)
def test_species(self):
""" Testing basic functionality of the Species class """
model = Model(name="testspecies")
S1 = Species(name="S1", initial_value=10)
S2 = Species(name="S2", initial_value=100)
S3 = Species(name="S3", initial_value=100)
# Both these calls should be supported
model.addSpecies(S1)
model.addSpecies([S2, S3])
# This should raise a ModelError since S1 is already in the list.
self.assertRaises(ModelError, model.addSpecies, S1)
def test_parameters(self):
""" Testing parameter evaluations. """
# Create a model to hold the list of parameters
model = Model(name="testparameters")
# Create a parameter with a scalar value
p1 = Parameter(name="p1", expression='0.1')
model.addParameter(p1)
# and a paramter defined as a function of p
p2 = Parameter("p2", expression='p1/10')
model.addParameter(p2)
# Make sure that p2 evaluates to 0.01
model.updateNamespace()
p2.evaluate(namespace=model.namespace)
self.assertEqual(p2.value, 0.01)
def test_massaction(self):
""" Testing auto-generation of mass-action propensities. """
S1 = Species('S1', 10)
S2 = Species('S2', 10)
S3 = Species('S3', 10)
c1 = Parameter(name="c1", expression='0.1')
c2 = Parameter(name="c2", expression='0.1')
c3 = Parameter(name="c3", expression='0.1')
# These are the allowed cases
# 1.) EmptySet->X
R = Reaction(name='R1',
products={S2.name: 1},
massaction=True,
rate=c1)
self.assertEqual(R.propensity_function, "c1")
# 2.) X1 -> Y (Or anything else)
R = Reaction(name='R1',
reactants={S1.name: 1},
products={S2.name: 1},
massaction=True,
rate=c1)
self.assertEqual(R.propensity_function, "c1*S1")
# 3.) 2X1 -> Y
R = Reaction(name='R1',
reactants={S1.name: 2},
products={S2.name: 1},
massaction=True,
rate=c2)
self.assertEqual(R.propensity_function, "0.5*c2*S1*(S1-1)")
# 4.) X1 + X2 -> Y
R = Reaction(name='R1',
reactants={
S1.name: 1,
S2.name: 1
},
products={S3.name: 1},
massaction=True,
rate=c2)
# We cannot guarantee the order of the species in the expression. This is not a problem
# for the actual simulation so both orders should be allowed.
valid_expressions = ["c2*S1*S2", "c2*S2*S1"]
iscorrect = R.propensity_function in valid_expressions
self.assertEqual(iscorrect, True)
def test_mmserialization(self):
""" Serializing MichaelisMenten example model to StochKit XML """
doc = self.mmmodel.serialize()
#model2 = doc1.toModel("MichaelisMenten")
#assertEqual(self.mmmodel.__dict__,model2.__dict__)
def test_read_dimer_decay(self):
""" Instantiate a model from dimer_decay.xml """
doc = StochMLDocument.fromFile("../examples/dimer_decay.xml")
model = doc.toModel("dimer_decay")
xmlstr = model.serialize()
# Run StochKit with the same seed for both the
# original model (diectly using the XML file) and using the file
# serialized from the imported model instance. They should result in
# the same output even if the format of the XML file is not identical.
means1, variances1, trajectories1 = stochkit(model,
job_id="test_dd_1",
seed=45367)
means2, variances2, trajectories2 = stochkit(
"../examples/dimer_decay.xml", job_id="test_dd_2", seed=45367)
isok = (means1 == means2).all()
self.assertEqual(isok, True)
def test_read_schlogl(self):
""" Instantiate a model from schlogl.xml """
doc = StochMLDocument.fromFile("../examples/schlogl.xml")
model = doc.toModel("schlogl")
xmlstr = model.serialize()
# Run StochKit
means1, variances1, trajectories1 = stochkit(model,
job_id="test_s_1",
seed=45367,
time=1.0)
means2, variances2, trajectories2 = stochkit("../examples/schlogl.xml",
job_id="test_s_2",
seed=45367,
time=1.0)
isok = (means1 == means2).all()
self.assertEqual(isok, True)
def test_read_simple1(self):
""" Instantiate a model from simple1.xml """
doc = StochMLDocument.fromFile("../examples/simple1.xml")
model = doc.toModel("simple1")
xmlstr = model.serialize()
# Run StochKit
means1, variances1, trajectories1 = stochkit(model,
job_id="test_1",
seed=45367)
means2, variances2, trajectories2 = stochkit("../examples/simple1.xml",
job_id="test_2",
seed=45367)
isok = (means1 == means2).all()
self.assertEqual(isok, True)
def test_read_simple1p(self):
""" Instantiate a model from simple1p.xml """
doc = StochMLDocument.fromFile("../examples/simple1p.xml")
model = doc.toModel("simple1p")
xmlstr = model.serialize()
# Run StochKit
means1, variances1, trajectories1 = stochkit(model,
job_id="test_1",
seed=45367)
means2, variances2, trajectories2 = stochkit(
"../examples/simple1p.xml", job_id="test_2", seed=45367)
isok = (means1 == means2).all()
self.assertEqual(isok, True)
def test_read_vilar(self):
""" Instantiate a model from vilar.xml """
doc = StochMLDocument.fromFile("../examples/vilar.xml")
model = doc.toModel("vilar")
xmlstr = model.serialize()
# Run StochKit
means1, variances1, trajectories1 = stochkit(model,
job_id="test_1",
seed=45367)
means2, variances2, trajectories2 = stochkit("../examples/vilar.xml",
job_id="test_2",
seed=45367)
isok = (means1 == means2).all()
self.assertEqual(isok, True)
def test_read_heat_shock_mixed(self):
""" Instantiate a model from heat_shock_mixed.xml """
doc = StochMLDocument.fromFile("../examples/heat_shock_mixed.xml")
model = doc.toModel("heat_shock_mixed")
xmlstr = model.serialize()
# Run StochKit
means1, variances1, trajectories1 = stochkit(model,
job_id="test_1",
seed=45367)
means2, variances2, trajectories2 = stochkit(
"../examples/heat_shock_mixed.xml", job_id="test_2", seed=45367)
isok = (means1 == means2).all()
self.assertEqual(isok, True)
def test_read_heat_shock_mass_action(self):
""" Instantiate a model from heat_shock_mass_action.xml """
doc = StochMLDocument.fromFile(
"../examples/heat_shock_mass_action.xml")
model = doc.toModel("heat_shock_mass_action")
xmlstr = model.serialize()
# Run StochKit
means1, variances1, trajectories1 = stochkit(model,
job_id="test_1",
seed=45367)
means2, variances2, trajectories2 = stochkit(
"../examples/heat_shock_mass_action.xml",
job_id="test_2",
seed=45367)
isok = (means1 == means2).all()
self.assertEqual(isok, True)
def test_read_heat_shock_10x(self):
""" Instantiate a model from heat_shock_10x.xml """
doc = StochMLDocument.fromFile("../examples/heat_shock_10x.xml")
model = doc.toModel("heat_shock_10x")
xmlstr = model.serialize()
# Run StochKit
means1, variances1, trajectories1 = stochkit(model,
job_id="test_1",
seed=45367)
means2, variances2, trajectories2 = stochkit(
"../examples/heat_shock_10x.xml", job_id="test_2", seed=45367)
isok = (means1 == means2).all()
self.assertEqual(isok, True)
# def test_readmodelfromstochmlfile(self):
# """ Initialize a model object from StochML. """
# Initialize a model object from the stochml document
# model2 = self.modeldoc2.toModel("Example 2")
# And write it to a new stochml document
#modeldoc2 = StochMLDocument.fromModel(model2)
#modelstr2 = modeldoc2.toString()
# Make sure that the documents are the same
#self.assertEqual(self.modeldoc.toString(),modeldoc2.toString())
def test_readandwritestochmlfiles(self):
""" Serialize to and from StochML. """
# Write the document to a file
modelstr = self.modeldoc.toString()
fhandle = open('test_model_doc.xml', 'w')
fhandle.write(modelstr)
fhandle.close()
# and then initialize new modeldocument from the file we just wrote
modeldoc2 = StochMLDocument.fromFile('test_model_doc.xml')
class TestModelSerialization(unittest.TestCase):
def setUp(self):
self.model = dimerdecay()
self.mmmodel = MichaelisMenten()
# Create the model document using the API
self.modeldoc = StochMLDocument.fromModel(self.model)
def test_species(self):
""" Testing basic functionality of the Species class """
model = Model(name="testspecies")
S1 = Species(name="S1",initial_value=10);
S2 = Species(name="S2",initial_value=100);
S3 = Species(name="S3",initial_value=100);
# Both these calls should be supported
model.addSpecies(S1)
model.addSpecies([S2,S3])
# This should raise a ModelError since S1 is already in the list.
self.assertRaises(ModelError,model.addSpecies,S1)
def test_parameters(self):
""" Testing parameter evaluations. """
# Create a model to hold the list of parameters
model = Model(name="testparameters")
# Create a parameter with a scalar value
p1 = Parameter(name="p1",expression='0.1')
model.addParameter(p1)
# and a paramter defined as a function of p
p2 = Parameter("p2",expression='p1/10')
model.addParameter(p2)
# Make sure that p2 evaluates to 0.01
model.updateNamespace()
p2.evaluate(namespace=model.namespace)
self.assertEqual(p2.value,0.01)
def test_massaction(self):
""" Testing auto-generation of mass-action propensities. """
S1 = Species('S1',10);
S2 = Species('S2',10);
S3 = Species('S3',10);
c1 = Parameter(name="c1",expression='0.1')
c2 = Parameter(name="c2",expression='0.1')
c3 = Parameter(name="c3",expression='0.1')
# These are the allowed cases
# 1.) EmptySet->X
R = Reaction(name='R1',products={S2.name:1},massaction=True,rate=c1)
self.assertEqual(R.propensity_function,"c1")
# 2.) X1 -> Y (Or anything else)
R = Reaction(name='R1',reactants={S1.name:1},products={S2.name:1},massaction=True,rate=c1)
self.assertEqual(R.propensity_function,"c1*S1")
# 3.) 2X1 -> Y
R = Reaction(name='R1',reactants={S1.name:2},products={S2.name:1},massaction=True,rate=c2)
self.assertEqual(R.propensity_function,"0.5*c2*S1*(S1-1)")
# 4.) X1 + X2 -> Y
R = Reaction(name='R1',reactants={S1.name:1,S2.name:1},products={S3.name:1},massaction=True,rate=c2)
# We cannot guarantee the order of the species in the expression. This is not a problem
# for the actual simulation so both orders should be allowed.
valid_expressions = ["c2*S1*S2","c2*S2*S1"]
iscorrect = R.propensity_function in valid_expressions
self.assertEqual(iscorrect,True)
def test_mmserialization(self):
""" Serializing MichaelisMenten example model to StochKit XML """
doc = self.mmmodel.serialize()
#model2 = doc1.toModel("MichaelisMenten")
#assertEqual(self.mmmodel.__dict__,model2.__dict__)
def test_read_dimer_decay(self):
""" Instantiate a model from dimer_decay.xml """
doc = StochMLDocument.fromFile("../examples/dimer_decay.xml")
model = doc.toModel("dimer_decay")
xmlstr = model.serialize()
# Run StochKit with the same seed for both the
# original model (diectly using the XML file) and using the file
# serialized from the imported model instance. They should result in
# the same output even if the format of the XML file is not identical.
means1,variances1,trajectories1 = stochkit(model,job_id="test_dd_1",seed=45367)
means2,variances2,trajectories2 = stochkit("../examples/dimer_decay.xml",job_id="test_dd_2",seed=45367)
isok = (means1==means2).all()
self.assertEqual(isok,True)
def test_read_schlogl(self):
""" Instantiate a model from schlogl.xml """
doc = StochMLDocument.fromFile("../examples/schlogl.xml")
model = doc.toModel("schlogl")
xmlstr = model.serialize()
# Run StochKit
means1,variances1,trajectories1 = stochkit(model,job_id="test_s_1",seed=45367,time=1.0)
means2,variances2,trajectories2 = stochkit("../examples/schlogl.xml",job_id="test_s_2",seed=45367,time=1.0)
isok = (means1==means2).all()
self.assertEqual(isok,True)
def test_read_simple1(self):
""" Instantiate a model from simple1.xml """
doc = StochMLDocument.fromFile("../examples/simple1.xml")
model = doc.toModel("simple1")
xmlstr = model.serialize()
# Run StochKit
means1,variances1,trajectories1 = stochkit(model,job_id="test_1",seed=45367)
means2,variances2,trajectories2 = stochkit("../examples/simple1.xml",job_id="test_2",seed=45367)
isok = (means1==means2).all()
self.assertEqual(isok,True)
def test_read_simple1p(self):
""" Instantiate a model from simple1p.xml """
doc = StochMLDocument.fromFile("../examples/simple1p.xml")
model = doc.toModel("simple1p")
xmlstr = model.serialize()
# Run StochKit
means1,variances1,trajectories1 = stochkit(model,job_id="test_1",seed=45367)
means2,variances2,trajectories2 = stochkit("../examples/simple1p.xml",job_id="test_2",seed=45367)
isok = (means1==means2).all()
self.assertEqual(isok,True)
def test_read_vilar(self):
""" Instantiate a model from vilar.xml """
doc = StochMLDocument.fromFile("../examples/vilar.xml")
model = doc.toModel("vilar")
xmlstr = model.serialize()
# Run StochKit
means1,variances1,trajectories1 = stochkit(model,job_id="test_1",seed=45367)
means2,variances2,trajectories2 = stochkit("../examples/vilar.xml",job_id="test_2",seed=45367)
isok = (means1==means2).all()
self.assertEqual(isok,True)
def test_read_heat_shock_mixed(self):
""" Instantiate a model from heat_shock_mixed.xml """
doc = StochMLDocument.fromFile("../examples/heat_shock_mixed.xml")
model = doc.toModel("heat_shock_mixed")
xmlstr = model.serialize()
# Run StochKit
means1,variances1,trajectories1 = stochkit(model,job_id="test_1",seed=45367)
means2,variances2,trajectories2 = stochkit("../examples/heat_shock_mixed.xml",job_id="test_2",seed=45367)
isok = (means1==means2).all()
self.assertEqual(isok,True)
def test_read_heat_shock_mass_action(self):
""" Instantiate a model from heat_shock_mass_action.xml """
doc = StochMLDocument.fromFile("../examples/heat_shock_mass_action.xml")
model = doc.toModel("heat_shock_mass_action")
xmlstr = model.serialize()
# Run StochKit
means1,variances1,trajectories1 = stochkit(model,job_id="test_1",seed=45367)
means2,variances2,trajectories2 = stochkit("../examples/heat_shock_mass_action.xml",job_id="test_2",seed=45367)
isok = (means1==means2).all()
self.assertEqual(isok,True)
def test_read_heat_shock_10x(self):
""" Instantiate a model from heat_shock_10x.xml """
doc = StochMLDocument.fromFile("../examples/heat_shock_10x.xml")
model = doc.toModel("heat_shock_10x")
xmlstr = model.serialize()
# Run StochKit
means1,variances1,trajectories1 = stochkit(model,job_id="test_1",seed=45367)
means2,variances2,trajectories2 = stochkit("../examples/heat_shock_10x.xml",job_id="test_2",seed=45367)
isok = (means1==means2).all()
self.assertEqual(isok,True)
# def test_readmodelfromstochmlfile(self):
# """ Initialize a model object from StochML. """
# Initialize a model object from the stochml document
# model2 = self.modeldoc2.toModel("Example 2")
# And write it to a new stochml document
#modeldoc2 = StochMLDocument.fromModel(model2)
#modelstr2 = modeldoc2.toString()
# Make sure that the documents are the same
#self.assertEqual(self.modeldoc.toString(),modeldoc2.toString())
def test_readandwritestochmlfiles(self):
""" Serialize to and from StochML. """
# Write the document to a file
modelstr = self.modeldoc.toString()
fhandle = open('test_model_doc.xml','w')
fhandle.write(modelstr)
fhandle.close()
# and then initialize new modeldocument from the file we just wrote
modeldoc2 = StochMLDocument.fromFile('test_model_doc.xml')