def checkKisaoIntegrator(self, inline_omex, kisao, name):
""" Helper function for checking kisao integrator. """
omex_file = os.path.join(self.test_dir, "test.omex")
te.exportInlineOmex(inline_omex, omex_file)
omex.extractCombineArchive(omex_file,
directory=self.test_dir,
method="zip")
locations = omex.getLocationsByFormat(omex_file, "sed-ml")
sedml_files = [os.path.join(self.test_dir, loc) for loc in locations]
sedml_file = sedml_files[0]
# check the SED-ML
doc = libsedml.readSedMLFromFile(sedml_file)
# test_str = libsedml.writeSedMLToString(doc)
# print(test_str)
simulation = doc.getSimulation('sim0')
algorithm = simulation.getAlgorithm()
assert algorithm.getKisaoID() == kisao
# check the generated code
pystr = tesedml.sedmlToPython(sedml_file, workingDir=self.test_dir)
# is integrator/solver set in python code
if simulation.getTypeCode() is libsedml.SEDML_SIMULATION_STEADYSTATE:
assert ".setSteadyStateSolver('{}')".format(name) in pystr
else:
assert ".setIntegrator('{}')".format(name) in pystr
def checkKisaoIntegrator(self, inline_omex, kisao, name):
""" Helper function for checking kisao integrator. """
omex_file = os.path.join(self.test_dir, "test.omex")
te.exportInlineOmex(inline_omex, omex_file)
omex.extractCombineArchive(omex_file, directory=self.test_dir, method="zip")
locations = omex.getLocationsByFormat(omex_file, "sed-ml")
sedml_files = [os.path.join(self.test_dir, loc) for loc in locations]
sedml_file = sedml_files[0]
# check the SED-ML
doc = libsedml.readSedMLFromFile(sedml_file)
# test_str = libsedml.writeSedMLToString(doc)
# print(test_str)
simulation = doc.getSimulation('sim0')
algorithm = simulation.getAlgorithm()
assert algorithm.getKisaoID() == kisao
# check the generated code
pystr = tesedml.sedmlToPython(sedml_file, workingDir=self.test_dir)
# is integrator/solver set in python code
if simulation.getTypeCode() is libsedml.SEDML_SIMULATION_STEADYSTATE:
assert ".setSteadyStateSolver('{}')".format(name) in pystr
else:
assert ".setIntegrator('{}')".format(name) in pystr
def checkKisaoAlgorithmParameter(self, inline_omex, kisao, name, value):
""" Helper function for checking kisao parameter. """
# check that set AlgorithmParameter set correctly in SED-ML
omex_file = os.path.join(self.test_dir, "test.omex")
te.exportInlineOmex(inline_omex, omex_file)
omex.extractCombineArchive(omex_file,
directory=self.test_dir,
method="zip")
locations = omex.getLocationsByFormat(omex_file, "sed-ml")
sedml_files = [os.path.join(self.test_dir, loc) for loc in locations]
sedml_file = sedml_files[0]
doc = libsedml.readSedMLFromFile(sedml_file)
simulation = doc.getSimulation('sim0')
algorithm = simulation.getAlgorithm()
pdict = {
p.getKisaoID(): p
for p in algorithm.getListOfAlgorithmParameters()
}
self.assertTrue(kisao in pdict)
pkey = tesedml.SEDMLCodeFactory.algorithmParameterToParameterKey(
pdict[kisao])
if pkey.dtype == str:
self.assertEqual(pkey.value, value)
else:
# numerical parameter
self.assertAlmostEqual(float(pkey.value), value)
# check that integrator is set in python code
pystr = tesedml.sedmlToPython(sedml_file, workingDir=self.test_dir)
print(simulation.getElementName())
print(pystr)
if simulation.getTypeCode() is libsedml.SEDML_SIMULATION_STEADYSTATE:
if pkey.dtype == str:
self.assertTrue(
".steadyStateSolver.setValue('{}', '{}')".format(
name, value) in pystr)
else:
# numerical parameter
self.assertTrue(".steadyStateSolver.setValue('{}', {})".format(
name, value) in pystr)
else:
if pkey.dtype == str:
self.assertTrue(".integrator.setValue('{}', '{}')".format(
name, value) in pystr)
else:
# numerical parameter
self.assertTrue(".integrator.setValue('{}', {})".format(
name, value) in pystr)
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 export_omex(self, antimony_str, phrasedml_str, **kwargs):
"""Generate COMBINE OMEX file.
:param antimony_str: represent the SBML
:type antimony_str: str
:param phrasedml_str: represent the SEDML
:type phrasedml_str: str
:return: omex inline
:rtype: str
:Keyword Arguments:
* *outputfile*: specify outputfile
"""
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.get_omexfilename()
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
def checkKisaoAlgorithmParameter(self, inline_omex, kisao, name, value):
""" Helper function for checking kisao parameter. """
# check that set AlgorithmParameter set correctly in SED-ML
omex_file = os.path.join(self.test_dir, "test.omex")
te.exportInlineOmex(inline_omex, omex_file)
omex.extractCombineArchive(omex_file, directory=self.test_dir, method="zip")
locations = omex.getLocationsByFormat(omex_file, "sed-ml")
sedml_files = [os.path.join(self.test_dir, loc) for loc in locations]
sedml_file = sedml_files[0]
doc = libsedml.readSedMLFromFile(sedml_file)
simulation = doc.getSimulation('sim0')
algorithm = simulation.getAlgorithm()
pdict = {p.getKisaoID(): p for p in algorithm.getListOfAlgorithmParameters()}
self.assertTrue(kisao in pdict)
pkey = tesedml.SEDMLCodeFactory.algorithmParameterToParameterKey(pdict[kisao])
if pkey.dtype == str:
self.assertEqual(pkey.value, value)
else:
# numerical parameter
self.assertAlmostEqual(float(pkey.value), value)
# check that integrator is set in python code
pystr = tesedml.sedmlToPython(sedml_file, workingDir=self.test_dir)
print(simulation.getElementName())
print(pystr)
if simulation.getTypeCode() is libsedml.SEDML_SIMULATION_STEADYSTATE:
if pkey.dtype == str:
self.assertTrue(".steadyStateSolver.setValue('{}', '{}')".format(name, value) in pystr)
else:
# numerical parameter
self.assertTrue(".steadyStateSolver.setValue('{}', {})".format(name, value) in pystr)
else:
if pkey.dtype == str:
self.assertTrue(".integrator.setValue('{}', '{}')".format(name, value) in pystr)
else:
# numerical parameter
self.assertTrue(".integrator.setValue('{}', {})".format(name, value) in pystr)
import tellurium as te
# works
# inline_omex = te.convertCombineArchive('out_sedml.omex')
# doesn't work
inline_omex = te.convertCombineArchive('out_phrasedml.omex')
print('inline omex:')
print(inline_omex)
te.exportInlineOmex(inline_omex, 'out_tellurium.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'))
def Combinecreator(core_model, settings, Plot_Variable, outputpath, KISAO_algorithm):
'''
Generates and outputs COMBINE OMEX file.
:param core_model: core model database of model
:param settings: settings database of model
:param Plot_Variable: Variables to be plotted in list format
:param outputpath: filepath to output OMEX file in OS path format
:param KISAO_algorithm: Kinetic Simulation Algorithm Ontology number in string format
:return combine_filename : OMEX file name in string format
:return total_scenarios : Total number of scenarios in string format
'''
#--- Extract data from settings and clean up units ---
number_init = len(settings['init'])
number_parameters = len(settings['parameters'])
addparam = settings['parameters']
unit_model = sbmlgen.unitlookup(settings)
total_scenarios = number_init * number_parameters
#print(total_scenarios)
scenario_name = core_model["system_type"]
scenario_name = scenario_name.replace(", ", "_")
modelname_file = []
antimony_final = []
#--- Generates SBML string and adds to list
#based on the number of combinations with init
#and parameter amts ---
for j in range(number_init): #Cycle through number of init
for k in range(number_parameters): #Cycle through number of parameters
sbmlstr = sbmlgen.SBMLcreation(core_model, settings, unit_model, addparam, j, k)
antimony_final.append(te.sbmlToAntimony(sbmlstr))
#--- Generates the scenario name for each SBML string generated ---
scenario_placeholder = []
for l in range(total_scenarios):
for j in range(number_init): #Cycle through number of init
for k in range(number_parameters):
temp_scenario_name = '_' + str(j+1)+ '_' + str(k+1)
scenario_placeholder.append(temp_scenario_name)
#--- Names the models in antimony string according the scenario ---
inline_omex = '\n'
for l in range(total_scenarios):
scenario_name = scenario_name + scenario_placeholder[l]
modelname_file.append(scenario_name)
antimony_final[l] = antimony_final[l].replace('*doc0', modelname_file[l])
scenario_name = scenario_name.replace(scenario_placeholder[l], "")
inline_omex = inline_omex + str(antimony_final[l])
#print("This is antimony_final", scenario_number,": \n", antimony_final[l])
#--- Generates phrasedml file ---
phrasedml_final = gen_phrasedml(settings, modelname_file, Plot_Variable, KISAO_algorithm)
#--- Generates and outputs OMEX file---
inline_omex = inline_omex + phrasedml_final
combine_filename = 'COMBINE_' + scenario_name + '.omex'
archive = os.path.join(outputpath, combine_filename)
print('COMBINE Archive output: ', archive)
te.exportInlineOmex(inline_omex, archive)
return combine_filename, total_scenarios
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'))
def test_exportAsCombine(self):
""" Test exportAsCombine. """
inline_omex = '\n'.join([self.antimony, self.phrasedml])
tmpdir = tempfile.mkdtemp()
te.exportInlineOmex(inline_omex, os.path.join(tmpdir, 'archive.omex'))
shutil.rmtree(tmpdir)
def test_exportAsCombine(self):
""" Test exportAsCombine. """
inline_omex = '\n'.join([self.antimony, self.phrasedml])
tmpdir = tempfile.mkdtemp()
te.exportInlineOmex(inline_omex, os.path.join(tmpdir, 'archive.omex'))
shutil.rmtree(tmpdir)