def writingAndReadingExecution(self):
antimonyStr = '''
model myModel
S1 -> S2; k1*S1;
S1 = 10; S2 = 0;
k1 = 1;
end
'''
phrasedmlStr = '''
model1 = model "myModel"
sim1 = simulate uniform(0, 5, 100)
task1 = run sim1 on model1
plot "Figure 1" time vs S1, S2
report time vs S1, S2
'''
import tellurium as te
# Create experiment
exp = te.experiment(antimonyStr, phrasedmlStr)
# Run and store with results
tmpdir = tempfile.mkdtemp()
exp.exportAsCombineWithOutputs(os.path.join(tmpdir, 'test.omex'))
# Execute the created archive
te.executeOMEX('test.omex', workingDir=tmpdir)
shutil.rmtree(tmpdir)
def test_2Model2PhrasedML(self):
""" Test multiple models and multiple phrasedml files. """
p1 = """
model1 = model "m1"
model2 = model "m2"
sim1 = simulate uniform(0, 6, 100)
task1 = run sim1 on model1
task2 = run sim1 on model2
plot task1.time vs task1.S1, task1.S2, task2.time vs task2.X1, task2.X2
"""
p2 = """
model1 = model "m1"
model2 = model "m2"
sim1 = simulate uniform(0, 20, 20)
task1 = run sim1 on model1
task2 = run sim1 on model2
plot task1.time vs task1.S1, task1.S2, task2.time vs task2.X1, task2.X2
"""
exp = te.experiment([self.a1, self.a2], [p1, p2])
# execute first
exp.execute(p1)
# execute second
exp.execute(p2)
# execute all
exp.execute()
def setUp(self):
# create a test instance
self.antimony = '''
model myModel
S1 -> S2; k1*S1
S1 = 10; S2 = 0
k1 = 1
end
'''
self.newAntimony = '''
model newAntimony
S1 -> S2; k1*S1
S1 = 10; S2 = 0
k1 = 1
end
'''
self.phrasedml = '''
model1 = model "myModel"
sim1 = simulate uniform(0, 5, 100)
task1 = run sim1 on model1
plot "Figure 1" time vs S1, S2
'''
self.newPhrasedml = '''
model1 = model "newAntimony"
sim1 = simulate uniform(0, 10, 100)
task1 = run sim1 on model1
plot "Figure 1" time vs S1, S2
'''
exp = te.experiment(self.antimony, self.phrasedml)
self.tmpdir = tempfile.mkdtemp()
self.tmparchive = os.path.join(self.tmpdir, 'test.zip')
exp.exportAsCombine(self.tmparchive)
self.com = te.combine(self.tmparchive)
def run_case(call_file, antimonyStr, phrasedmlStr, py_code=True):
""" Run one of the example phrasedml cases.
:param case_id:
:param antimonyStr:
:param phrasedmlStr:
:return:
"""
# phrasedml experiment
exp = te.experiment(antimonyStr, phrasedmlStr)
# output dir relative to call file
workingDir = os.path.join(os.path.dirname(call_file), './results')
if not os.path.exists(workingDir):
os.makedirs(workingDir)
# write python code
if py_code:
fname = os.path.basename(call_file)
py_file = os.path.join(workingDir, fname + 'code.py')
print(py_file)
with open(py_file, 'w') as f:
f.write(exp._toPython(phrasedmlStr, workingDir=workingDir))
# execute python
exp.execute(phrasedmlStr, workingDir=workingDir)
def test_kisao_maximum_adams_order_2(self):
p = """
model0 = model "m1"
sim0 = simulate uniform(0, 10, 100)
sim0.algorithm.219 = 5
task0 = run sim0 on model0
plot task0.time vs task0.S1
"""
exp = te.experiment(self.a1, p)
self.checkKisaoAlgorithmParameter(exp, 'KISAO:0000219', 'maximum_adams_order', 5)
exp.execute()
def test_kisao_minimum_damping_1(self):
p = """
model0 = model "m1"
sim0 = simulate steadystate
sim0.algorithm.minimum_damping = 1.0
task0 = run sim0 on model0
plot task0.time vs task0.S1
"""
exp = te.experiment(self.a1, p)
self.checkKisaoAlgorithmParameter(exp, 'KISAO:0000487', 'minimum_damping', 1.0)
exp.execute()
def test_kisao_variable_step_size_2(self):
p = """
model0 = model "m1"
sim0 = simulate uniform(0, 10, 100)
sim0.algorithm.107 = true
task0 = run sim0 on model0
plot task0.time vs task0.S1
"""
exp = te.experiment(self.a1, p)
self.checkKisaoAlgorithmParameter(exp, 'KISAO:0000107', 'variable_step_size', True)
exp.execute()
def test_kisao_maximum_iterations_2(self):
p = """
model0 = model "m1"
sim0 = simulate steadystate
sim0.algorithm.486 = 10
task0 = run sim0 on model0
plot task0.time vs task0.S1
"""
exp = te.experiment(self.a1, p)
self.checkKisaoAlgorithmParameter(exp, 'KISAO:0000486', 'maximum_iterations', 10)
exp.execute()
def test_kisao_minimum_time_step_2(self):
p = """
model0 = model "m1"
sim0 = simulate uniform(0, 10, 100)
sim0.algorithm.485 = 1E-5
task0 = run sim0 on model0
plot task0.time vs task0.S1
"""
exp = te.experiment(self.a1, p)
self.checkKisaoAlgorithmParameter(exp, 'KISAO:0000485', 'minimum_time_step', 1E-5)
exp.execute()
def test_exportAsCombine(self):
""" Test exportAsCombine. """
exp = te.experiment(self.antimony, self.phrasedml)
tmpdir = tempfile.mkdtemp()
tmparchive = os.path.join(tmpdir, 'test.zip')
exp.exportAsCombine(tmparchive)
# try to re
import zipfile
zip = zipfile.ZipFile(tmparchive)
zip.close()
shutil.rmtree(tmpdir)
def test_kisao_maximum_num_steps_2(self):
p = """
model0 = model "m1"
sim0 = simulate uniform(0, 10, 100)
sim0.algorithm.415 = 10000
task0 = run sim0 on model0
plot task0.time vs task0.S1
"""
exp = te.experiment(self.a1, p)
self.checkKisaoAlgorithmParameter(exp, 'KISAO:0000415', 'maximum_num_steps', 10000)
exp.execute()
def test_kisao_gillespie_3(self):
""" Default of uniform_stochastic is gillespie."""
p = """
model0 = model "m1"
sim0 = simulate uniform_stochastic(0, 10, 100)
task0 = run sim0 on model0
plot task0.time vs task0.S1
"""
exp = te.experiment(self.a1, p)
self.checkKisaoIntegrator(exp, 'KISAO:0000241', 'gillespie')
exp.execute()
def test_kisao_absolute_tolerance_2(self):
p = """
model0 = model "m1"
sim0 = simulate uniform(0, 10, 100)
sim0.algorithm.211 = 1E-8
task0 = run sim0 on model0
plot task0.time vs task0.S1
"""
exp = te.experiment(self.a1, p)
self.checkKisaoAlgorithmParameter(exp, 'KISAO:0000211', 'absolute_tolerance', 1E-8)
exp.execute()
def test_kisao_rk4_2(self):
p = """
model0 = model "m1"
sim0 = simulate uniform(0, 10, 100)
sim0.algorithm = kisao.32
task0 = run sim0 on model0
plot task0.time vs task0.S1
"""
exp = te.experiment(self.a1, p)
self.checkKisaoIntegrator(exp, 'KISAO:0000032', 'rk4')
exp.execute()
def test_kisao_gillespie_1(self):
p = """
model0 = model "m1"
sim0 = simulate uniform(0, 10, 100)
sim0.algorithm = gillespie
task0 = run sim0 on model0
plot task0.time vs task0.S1
"""
exp = te.experiment(self.a1, p)
self.checkKisaoIntegrator(exp, 'KISAO:0000241', 'gillespie')
exp.execute()
def test_kisao_cvode_4(self):
""" Default of onestep is cvode. """
p = """
model0 = model "m1"
sim0 = simulate onestep(10)
task0 = run sim0 on model0
plot task0.time vs task0.S1
"""
exp = te.experiment(self.a1, p)
self.checkKisaoIntegrator(exp, 'KISAO:0000019', 'cvode')
exp.execute()
def test_kisao_seed_2(self):
p = """
model0 = model "m1"
sim0 = simulate uniform_stochastic(0, 10, 100)
sim0.algorithm.488 = 1234
task0 = run sim0 on model0
plot task0.time vs task0.S1
"""
exp = te.experiment(self.a1, p)
self.checkKisaoAlgorithmParameter(exp, 'KISAO:0000488', 'seed', 1234)
exp.execute()
def test_kisao_initial_time_step_2(self):
p = """
model0 = model "m1"
sim0 = simulate uniform(0, 10, 100)
sim0.algorithm.332 = 0.01
task0 = run sim0 on model0
plot task0.time vs task0.S1
"""
exp = te.experiment(self.a1, p)
self.checkKisaoAlgorithmParameter(exp, 'KISAO:0000332', 'initial_time_step', 0.01)
exp.execute()
def test_2Model1PhrasedML(self):
""" Test multiple models and multiple phrasedml files. """
p1 = """
model1 = model "m1"
model2 = model "m2"
model3 = model model1 with S1=S2+20
sim1 = simulate uniform(0, 6, 100)
task1 = run sim1 on model1
task2 = run sim1 on model2
plot "Timecourse test1" task1.time vs task1.S1, task1.S2
plot "Timecourse test2" task2.time vs task2.X1, task2.X2
"""
exp = te.experiment([self.a1, self.a2], p1)
exp.execute(p1)
def test_kisao_adams(self):
p = """
model0 = model "m1"
sim0 = simulate uniform(0, 10, 100)
sim0.algorithm = nonstiff
task0 = run sim0 on model0
plot task0.time vs task0.S1
"""
exp = te.experiment(self.a1, p)
self.checkKisaoIntegrator(exp, 'KISAO:0000280', 'cvode')
exp.execute()
pycode = exp._toPython(p)
print(pycode)
self.assertTrue("integrator.setValue('stiff', False)" in pycode)
def test_1Model1PhrasedML(self):
""" Minimal example which should work. """
antimonyStr = """
model test
J0: S1 -> S2; k1*S1;
S1 = 10.0; S2=0.0;
k1 = 0.1;
end
"""
phrasedmlStr = """
model0 = model "test"
sim0 = simulate uniform(0, 10, 100)
task0 = run sim0 on model0
plot task0.time vs task0.S1
"""
exp = te.experiment(antimonyStr, phrasedmlStr)
exp.execute(phrasedmlStr)
def test_1Model2PhrasedML(self):
""" Test multiple models and multiple phrasedml files. """
p1 = """
model1 = model "m1"
sim1 = simulate uniform(0, 6, 100)
task1 = run sim1 on model1
plot task1.time vs task1.S1, task1.S2
"""
p2 = """
model1 = model "m1"
model2 = model model1 with S1=S2+20
sim1 = simulate uniform(0, 6, 100)
task1 = run sim1 on model2
plot task1.time vs task1.S1, task1.S2
"""
exp = te.experiment(self.a1, [p1, p2])
# execute first
exp.execute(p1)
# execute second
exp.execute(p2)
# execute all
exp.execute()
J0: S1 -> S2; k1*S1-k2*S2
S1 = 10.0; S2 = 0.0;
k1 = 0.5; k2=0.4
end
'''
phrasedmlStr = '''
mod1 = model "case_03"
mod2 = model mod1 with S2=S1+4
sim1 = simulate uniform(0, 10, 100)
task1 = run sim1 on mod1
task2 = run sim1 on mod2
plot "ComputeChanges" task1.time vs task1.S1, task1.S2, task2.S1, task2.S2
report task1.time vs task1.S1, task1.S2, task2.S1, task2.S2
'''
# phrasedml experiment
exp = te.experiment(antimonyStr, phrasedmlStr)
# write python code
realPath = os.path.realpath(__file__)
workingDir = os.path.dirname(realPath)
with open(realPath + 'code.py', 'w') as f:
f.write(exp._toPython(phrasedmlStr, workingDir=workingDir))
# execute python
exp.execute(phrasedmlStr, workingDir=workingDir)
# remove sedx (not hashable due to timestamp)
os.remove(os.path.join(workingDir, 'case_03.sedx'))
''' Lorenz attractor This is a sample file that demonstrates the use of Antimony and phraSEDML to simulate Lorenz attractor. This script requires Tellurium (http://tellurium.analogmachine.org/) to run. ''' import tellurium as te antimonyStr = ''' model lorenz x' = sigma*(y - x); y' = x*(rho - z) - y; z' = x*y - beta*z; x = 0.96259; y = 2.07272; z = 18.65888; sigma = 10; rho = 28; beta = 2.67; end ''' phrasedmlStr = ''' model1 = model "lorenz" sim1 = simulate uniform(0,15,2000) task1 = run sim1 on model1 plot task1.z vs task1.x ''' exp = te.experiment(antimonyStr, phrasedmlStr) exp.execute(phrasedmlStr)
# -*- coding: utf-8 -*- """ Testing phrasedml. """ from __future__ import print_function import tellurium as te ant = ''' model myModel S1 -> S2; k1*S1 S1 = 10; S2 = 0 k1 = 1 end ''' phrasedml = ''' model1 = model "myModel" sim1 = simulate uniform(0, 5, 100) task1 = run sim1 on model1 plot "Figure 1" time vs S1, S2 ''' # create experiment exp = te.experiment(ant, phrasedml) exp.execute() exp.printPython()
antimony = ''' model myModel S1 -> S2; k1*S1 S1 = 10; S2 = 0 k1 = 1 end ''' phrasedml = ''' model1 = model "myModel" sim1 = simulate uniform(0, 5, 100) task1 = run sim1 on model1 plot "Figure 1" time vs S1, S2 ''' import tellurium as te exp = te.experiment(antimony, phrasedml) exp.execute() exp.printpython() ### export testing - put the full path of zip file you want to create #exp.exportAsCombine()
model test()
J0: S1 -> S2; k1*S1;
S1 = 10.0; S2=0.0;
k1 = 0.1;
end
"""
phrasedmlStr = """
model0 = model "test"
sim0 = simulate uniform(0, 6, 100)
task0 = run sim0 on model0
plot "Timecourse test model" task0.time vs task0.S1
"""
# phrasedml experiment
exp = te.experiment(antimonyStr, phrasedmlStr)
exp.execute(phrasedmlStr)
# create Combine Archive
import tempfile
f = tempfile.NamedTemporaryFile()
exp.exportAsCombine(f.name)
# print the content of the Combine Archive
import zipfile
zip=zipfile.ZipFile(f.name)
print(zip.namelist())
# ### Create combine archive
# TODO
J8_V9 = 0.5;
J8_KK9 = 15;
J9_V10 = 0.5;
J9_KK10 = 15;
// Other declarations:
const compartment_, J0_V1, J0_Ki, J0_n, J0_K1, J1_V2, J1_KK2, J2_k3, J2_KK3;
const J3_k4, J3_KK4, J4_V5, J4_KK5, J5_V6, J5_KK6, J6_k7, J6_KK7, J7_k8;
const J7_KK8, J8_V9, J8_KK9, J9_V10, J9_KK10;
end
'''
# Describe the simulations we want to carry out
PhrasedMLstr = '''
// Created by libphrasedml v0.5beta
// Models
model1 = model "BorisEJB"
// Simulations
timecourse1 = simulate uniform(0, 9000, 9000)
// Tasks
task1 = run timecourse1 on model1
// Outputs
plot "Figure 5A" time vs MAPK, MAPK_PP
'''
import tellurium as te
# Package up the model and model simulations into a COMBINE archive.
exp = te.experiment([AntimonyModel], [PhrasedMLstr])
exp.execute(PhrasedMLstr)
exp.exportAsCombine('./BorisEJB.omex')
def test_experiment(self):
"""Test experiment."""
exp = te.experiment(self.antimony, self.phrasedml)
pstr = exp._toPython(self.phrasedml)
self.assertIsNotNone(pstr)
