def run_case(call_file,
antimony_str,
phrasedml_str,
py_code=False,
working_dir=None):
""" Run one of the example phrasedml cases.
:param case_id:
:param antimony_str:
:param phrasedml_str:
:return:
"""
# run as omex
# FIXME: convert to combine archive
inline_omex = '\n'.join([antimony_str, phrasedml_str])
# output dir relative to call file
if not working_dir:
working_dir = os.path.join(os.path.dirname(call_file), './results')
if not os.path.exists(working_dir):
os.makedirs(working_dir)
# FIXME: not working
# write python code
if py_code:
fname = os.path.basename(call_file)
py_file = os.path.join(working_dir, fname + 'code.py')
print(py_file)
with open(py_file, 'w') as f:
f.write(exp._toPython(phrasedml_str, workingDir=working_dir))
# execute python
te.executeInlineOmex(inline_omex)
def run_case(call_file, antimony_str, phrasedml_str, py_code=False, working_dir=None):
""" Run one of the example phrasedml cases.
:param case_id:
:param antimony_str:
:param phrasedml_str:
:return:
"""
# run as omex
# FIXME: convert to combine archive
inline_omex = '\n'.join([antimony_str, phrasedml_str])
# output dir relative to call file
if not working_dir:
working_dir = os.path.join(os.path.dirname(call_file), './results')
if not os.path.exists(working_dir):
os.makedirs(working_dir)
# FIXME: not working
# write python code
if py_code:
fname = os.path.basename(call_file)
py_file = os.path.join(working_dir, fname + 'code.py')
print(py_file)
with open(py_file, 'w') as f:
f.write(exp._toPython(phrasedml_str, workingDir=working_dir))
# execute python
te.executeInlineOmex(inline_omex)
def test_repressilatorToInlineOmex(self):
importer = convert_omex.inlineOmexImporter.fromFile(OMEX_REPRESSILATOR)
assert importer is not None
inline_omex = importer.toInlineOmex()
assert inline_omex is not None
print(inline_omex)
te.executeInlineOmex(inline_omex)
def test_kisao_rk45_2(self):
p = """
model0 = model "m1"
sim0 = simulate uniform(0, 10, 100)
sim0.algorithm = kisao.435
task0 = run sim0 on model0
plot task0.time vs task0.S1
"""
inline_omex = '\n'.join([self.a1, p])
self.checkKisaoIntegrator(inline_omex, 'KISAO:0000435', 'rk45')
te.executeInlineOmex(inline_omex)
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
"""
inline_omex = '\n'.join([self.a1, p])
self.checkKisaoIntegrator(inline_omex, 'KISAO:0000241', 'gillespie')
te.executeInlineOmex(inline_omex)
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
"""
inline_omex = '\n'.join([self.a1, p])
self.checkKisaoIntegrator(inline_omex, 'KISAO:0000019', 'cvode')
te.executeInlineOmex(inline_omex)
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
"""
inline_omex = '\n'.join([self.a1, p])
self.checkKisaoAlgorithmParameter(inline_omex, 'KISAO:0000107', 'variable_step_size', True)
te.executeInlineOmex(inline_omex)
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
"""
inline_omex = '\n'.join([self.a1, p])
self.checkKisaoIntegrator(inline_omex, 'KISAO:0000241', 'gillespie')
te.executeInlineOmex(inline_omex)
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
"""
inline_omex = '\n'.join([self.a1, p])
self.checkKisaoIntegrator(inline_omex, 'KISAO:0000019', 'cvode')
te.executeInlineOmex(inline_omex)
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
"""
inline_omex = '\n'.join([self.a1, p])
self.checkKisaoAlgorithmParameter(inline_omex, 'KISAO:0000332', 'initial_time_step', 0.01)
te.executeInlineOmex(inline_omex)
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
"""
inline_omex = '\n'.join([self.a1, p])
self.checkKisaoAlgorithmParameter(inline_omex, 'KISAO:0000211', 'absolute_tolerance', 1E-8)
te.executeInlineOmex(inline_omex)
def test_kisao_rk45_2(self):
p = """
model0 = model "m1"
sim0 = simulate uniform(0, 10, 100)
sim0.algorithm = kisao.435
task0 = run sim0 on model0
plot task0.time vs task0.S1
"""
inline_omex = '\n'.join([self.a1, p])
self.checkKisaoIntegrator(inline_omex, 'KISAO:0000435', 'rk45')
te.executeInlineOmex(inline_omex)
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
"""
inline_omex = '\n'.join([self.a1, p])
self.checkKisaoAlgorithmParameter(inline_omex, 'KISAO:0000219', 'maximum_adams_order', 5)
te.executeInlineOmex(inline_omex)
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
"""
inline_omex = '\n'.join([self.a1, p])
self.checkKisaoIntegrator(inline_omex, 'KISAO:0000241', 'gillespie')
te.executeInlineOmex(inline_omex)
def test_kisao_minimum_time_step_2(self):
p = """
model0 = model "m1"
sim0 = simulate uniform(0, 10, 100)
sim0.algorithm.485 = 1E-6
task0 = run sim0 on model0
plot task0.time vs task0.S1
"""
inline_omex = '\n'.join([self.a1, p])
self.checkKisaoAlgorithmParameter(inline_omex, 'KISAO:0000485', 'minimum_time_step', 1E-6)
te.executeInlineOmex(inline_omex)
def test_kisao_maximum_num_steps_1(self):
p = """
model0 = model "m1"
sim0 = simulate uniform(0, 10, 100)
sim0.algorithm.maximum_num_steps = 10000
task0 = run sim0 on model0
plot task0.time vs task0.S1
"""
inline_omex = '\n'.join([self.a1, p])
self.checkKisaoAlgorithmParameter(inline_omex, 'KISAO:0000415', 'maximum_num_steps', 10000)
te.executeInlineOmex(inline_omex)
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
"""
inline_omex = '\n'.join([self.a1, p])
self.checkKisaoIntegrator(inline_omex, 'KISAO:0000241', 'gillespie')
te.executeInlineOmex(inline_omex)
def test_kisao_minimum_damping_2(self):
p = """
model0 = model "m1"
sim0 = simulate steadystate
sim0.algorithm.487 = 1
task0 = run sim0 on model0
plot task0.time vs task0.S1
"""
inline_omex = '\n'.join([self.a1, p])
self.checkKisaoAlgorithmParameter(inline_omex, 'KISAO:0000487', 'minimum_damping', 1.0)
te.executeInlineOmex(inline_omex)
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
"""
inline_omex = '\n'.join([self.a1, p])
self.checkKisaoAlgorithmParameter(inline_omex, 'KISAO:0000486', 'maximum_iterations', 10)
te.executeInlineOmex(inline_omex)
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
"""
inline_omex = '\n'.join([self.a1, p])
self.checkKisaoAlgorithmParameter(inline_omex, 'KISAO:0000488', 'seed', 1234)
te.executeInlineOmex(inline_omex)
def test_kisao_maximum_num_steps_1(self):
p = """
model0 = model "m1"
sim0 = simulate uniform(0, 10, 100)
sim0.algorithm.maximum_num_steps = 10000
task0 = run sim0 on model0
plot task0.time vs task0.S1
"""
inline_omex = '\n'.join([self.a1, p])
self.checkKisaoAlgorithmParameter(inline_omex, 'KISAO:0000415',
'maximum_num_steps', 10000)
te.executeInlineOmex(inline_omex)
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
"""
inline_omex = '\n'.join([self.a1, p])
self.checkKisaoAlgorithmParameter(inline_omex, 'KISAO:0000332',
'initial_time_step', 0.01)
te.executeInlineOmex(inline_omex)
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
"""
inline_omex = '\n'.join([self.a1, p])
self.checkKisaoAlgorithmParameter(inline_omex, 'KISAO:0000488', 'seed',
1234)
te.executeInlineOmex(inline_omex)
def test_kisao_minimum_damping_2(self):
p = """
model0 = model "m1"
sim0 = simulate steadystate
sim0.algorithm.487 = 1
task0 = run sim0 on model0
plot task0.time vs task0.S1
"""
inline_omex = '\n'.join([self.a1, p])
self.checkKisaoAlgorithmParameter(inline_omex, 'KISAO:0000487',
'minimum_damping', 1.0)
te.executeInlineOmex(inline_omex)
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
"""
inline_omex = '\n'.join([self.a1, p])
self.checkKisaoAlgorithmParameter(inline_omex, 'KISAO:0000486',
'maximum_iterations', 10)
te.executeInlineOmex(inline_omex)
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
"""
inline_omex = '\n'.join([self.a1, p])
self.checkKisaoAlgorithmParameter(inline_omex, 'KISAO:0000107',
'variable_step_size', True)
te.executeInlineOmex(inline_omex)
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
"""
inline_omex = '\n'.join([self.a1, p])
self.checkKisaoAlgorithmParameter(inline_omex, 'KISAO:0000211',
'absolute_tolerance', 1E-8)
te.executeInlineOmex(inline_omex)
def test_kisao_minimum_time_step_2(self):
p = """
model0 = model "m1"
sim0 = simulate uniform(0, 10, 100)
sim0.algorithm.485 = 1E-6
task0 = run sim0 on model0
plot task0.time vs task0.S1
"""
inline_omex = '\n'.join([self.a1, p])
self.checkKisaoAlgorithmParameter(inline_omex, 'KISAO:0000485',
'minimum_time_step', 1E-6)
te.executeInlineOmex(inline_omex)
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
"""
inline_omex = '\n'.join([self.a1, p])
self.checkKisaoAlgorithmParameter(inline_omex, 'KISAO:0000219',
'maximum_adams_order', 5)
te.executeInlineOmex(inline_omex)
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
"""
inline_omex = '\n'.join([self.a1, self.a2, p1])
te.executeInlineOmex(inline_omex)
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
"""
inline_omex = '\n'.join([self.a1, self.a2, p1])
te.executeInlineOmex(inline_omex)
def test_1Model1PhrasedML(self):
""" Minimal example which should work. """
antimony_str = """
model test
J0: S1 -> S2; k1*S1;
S1 = 10.0; S2=0.0;
k1 = 0.1;
end
"""
phrasedml_str = """
model0 = model "test"
sim0 = simulate uniform(0, 10, 100)
task0 = run sim0 on model0
plot task0.time vs task0.S1
"""
inline_omex = '\n'.join([antimony_str, phrasedml_str])
te.executeInlineOmex(inline_omex)
def test_1Model1PhrasedML(self):
""" Minimal example which should work. """
antimony_str = """
model test
J0: S1 -> S2; k1*S1;
S1 = 10.0; S2=0.0;
k1 = 0.1;
end
"""
phrasedml_str = """
model0 = model "test"
sim0 = simulate uniform(0, 10, 100)
task0 = run sim0 on model0
plot task0.time vs task0.S1
"""
inline_omex = '\n'.join([antimony_str, phrasedml_str])
te.executeInlineOmex(inline_omex)
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
"""
inline_omex = '\n'.join([self.a1, p])
self.checkKisaoIntegrator(inline_omex, 'KISAO:0000280', 'cvode')
te.executeInlineOmex(inline_omex)
omex_file = os.path.join(self.test_dir, "test.omex")
te.exportInlineOmex(inline_omex, omex_file)
pycode_dict = tesedml.combineArchiveToPython(omex_file)
pycode = six.next(six.itervalues(pycode_dict))
print(pycode)
self.assertTrue("integrator.setValue('stiff', False)" in pycode)
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
"""
inline_omex = '\n'.join([self.a1, p])
self.checkKisaoIntegrator(inline_omex, 'KISAO:0000280', 'cvode')
te.executeInlineOmex(inline_omex)
omex_file = os.path.join(self.test_dir, "test.omex")
te.exportInlineOmex(inline_omex, omex_file)
pycode_dict = tesedml.combineArchiveToPython(omex_file)
pycode = six.next(six.itervalues(pycode_dict))
print(pycode)
self.assertTrue("integrator.setValue('stiff', False)" in pycode)
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
"""
inline_omex = '\n'.join([self.a1, self.a2, p1, p2])
te.executeInlineOmex(inline_omex)
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
"""
inline_omex = '\n'.join([self.a1, self.a2, p1, p2])
te.executeInlineOmex(inline_omex)
def export_omex(self, antimony_str, phrasedml_str, **kwargs):
"""Generate COMBINE OMEX file.
Parameters:
antimony_str: represent the SBML
phrasedml_str: represent the SEDML
Returns:
execute the omex and export omex archive
"""
model = re.search("model (.*)\n", antimony_str)
if model.group(1)[0] == "*":
model = self.find_between(model.group(1), "*", "()")
phrasedml_str = phrasedml_str.format(model)
else:
phrasedml_str = phrasedml_str.format(model.group(1))
inline_omex = "\n".join([antimony_str, phrasedml_str])
if "outputfile" in kwargs:
filepath = kwargs["outputfile"]
else:
dirName = self.getOMEXfilename()
try:
os.mkdir(dirName)
print("Directory ", dirName, " Created ")
except FileExistsError:
print("Directory ", dirName, " already exists")
workingDir = os.path.join(self.workingdir0, dirName)
filepath = os.path.join(workingDir, "archive.omex")
print("The output file path: ", filepath)
te.exportInlineOmex(inline_omex, filepath)
return inline_omex, te.executeInlineOmex(inline_omex)
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
"""
inline_omex = '\n'.join([self.a1, p1])
te.executeInlineOmex(inline_omex)
inline_omex = '\n'.join([self.a1, p2])
te.executeInlineOmex(inline_omex)
inline_omex = '\n'.join([self.a1, p1, p2])
te.executeInlineOmex(inline_omex)
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
"""
inline_omex = '\n'.join([self.a1, p1])
te.executeInlineOmex(inline_omex)
inline_omex = '\n'.join([self.a1, p2])
te.executeInlineOmex(inline_omex)
inline_omex = '\n'.join([self.a1, p1, p2])
te.executeInlineOmex(inline_omex)
def test_execute(self):
"""Test execute."""
inline_omex = '\n'.join([self.antimony, self.phrasedml])
te.executeInlineOmex(inline_omex)
def execute_inlineomex(inline_omex):
"""Execute the inline omex and generate the simulation figures.
"""
return te.executeInlineOmex(inline_omex)
def test_execute(self):
"""Test execute."""
inline_omex = '\n'.join([self.antimony, self.phrasedml])
te.executeInlineOmex(inline_omex)
model myModel S1 -> S2; k1*S1 S1 = 10; S2 = 0 k1 = 1 end ''' phrasedml_str = ''' model1 = model "myModel" sim1 = simulate uniform(0, 5, 100) task1 = run sim1 on model1 plot "Figure 1" time vs S1, S2 ''' # create an inline OMEX (inline representation of a COMBINE archive) # from the antimony and phrasedml strings inline_omex = '\n'.join([antimony_str, phrasedml_str]) # execute the inline OMEX te.executeInlineOmex(inline_omex) # export to a COMBINE archive workingDir = tempfile.mkdtemp(suffix="_omex") te.exportInlineOmex(inline_omex, os.path.join(workingDir, 'archive.omex')) # In[2]: te.executeCombineArchive(os.path.join(workingDir, 'archive.omex'))
get_ipython().magic(u'matplotlib inline') antimony_str = ''' model myModel S1 -> S2; k1*S1 S1 = 10; S2 = 0 k1 = 1 end ''' phrasedml_str = ''' model1 = model "myModel" sim1 = simulate uniform(0, 5, 100) task1 = run sim1 on model1 plot "Figure 1" time vs S1, S2 ''' # create an inline OMEX (inline representation of a COMBINE archive) # from the antimony and phrasedml strings inline_omex = '\n'.join([antimony_str, phrasedml_str]) # execute the inline OMEX te.executeInlineOmex(inline_omex) # export to a COMBINE archive workingDir = tempfile.mkdtemp(suffix="_omex") te.exportInlineOmex(inline_omex, os.path.join(workingDir, 'archive.omex')) # In[2]: te.executeCombineArchive(os.path.join(workingDir, 'archive.omex'))
