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 test_getLocationsByFormat4_zip():
locations = omex.getLocationsByFormat(omexPath=OMEX_SHOWCASE, formatKey="sed-ml", method="zip")
assert len(locations) == 2
# in case of zip files no master file exists, so the order of the entries depends on
# filenames and how they are returned from the zip
assert "experiment/Calzone2007-simulation-figure-1B.xml" in locations
assert "experiment/Calzone2007-default-simulation.xml" in locations
def test_getLocationsByFormat4():
locations = omex.getLocationsByFormat(omexPath=OMEX_SHOWCASE, formatKey="sed-ml")
assert len(locations) == 2
# master=True file first
assert locations[0].endswith("Calzone2007-simulation-figure-1B.xml")
# master=False afterwards
assert locations[1].endswith("Calzone2007-default-simulation.xml")
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 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_getLocationsByFormat3_zip():
locations = omex.getLocationsByFormat(omexPath=OMEX_SHOWCASE, formatKey="cellml", method="zip")
assert len(locations) == 1
def test_getLocationsByFormat2():
locations = omex.getLocationsByFormat(omexPath=OMEX_SHOWCASE, formatKey="sbml")
assert len(locations) == 1