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 test_via_sedml_string(self):
"""Test SED-ML from string."""
sedml_string = """<?xml version="1.0" encoding="UTF-8"?>
<!-- Created by phraSED-ML version v0.5beta on 2016-01-31 22:02 with libSBML version 5.12.1. -->
<sedML xmlns="http://sed-ml.org/sed-ml/level1/version2" level="1" version="2">
<listOfSimulations>
<uniformTimeCourse id="sim1" initialTime="0" outputStartTime="0" outputEndTime="5" numberOfPoints="100">
<algorithm kisaoID="KISAO:0000019"/>
</uniformTimeCourse>
</listOfSimulations>
<listOfModels>
<model id="model1" language="urn:sedml:language:sbml.level-3.version-1" source="myModel"/>
</listOfModels>
<listOfTasks>
<task id="task1" modelReference="model1" simulationReference="sim1"/>
</listOfTasks>
<listOfDataGenerators>
<dataGenerator id="plot_0_0_0" name="time">
<listOfVariables>
<variable id="time" symbol="urn:sedml:symbol:time" taskReference="task1"/>
</listOfVariables>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> time </ci>
</math>
</dataGenerator>
<dataGenerator id="plot_0_0_1" name="S1">
<listOfVariables>
<variable id="S1" target="/sbml:sbml/sbml:model/descendant::*[@id='S1']" taskReference="task1" modelReference="model1"/>
</listOfVariables>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> S1 </ci>
</math>
</dataGenerator>
<dataGenerator id="plot_0_1_1" name="S2">
<listOfVariables>
<variable id="S2" target="/sbml:sbml/sbml:model/descendant::*[@id='S2']" taskReference="task1" modelReference="model1"/>
</listOfVariables>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> S2 </ci>
</math>
</dataGenerator>
</listOfDataGenerators>
<listOfOutputs>
<plot2D id="plot_0" name="Figure 1">
<listOfCurves>
<curve logX="false" logY="false" xDataReference="plot_0_0_0" yDataReference="plot_0_0_1"/>
<curve logX="false" logY="false" xDataReference="plot_0_0_0" yDataReference="plot_0_1_1"/>
</listOfCurves>
</plot2D>
</listOfOutputs>
</sedML>
"""
python_str = tesedml.sedmlToPython(sedml_string)
self.assertIsNotNone(python_str)
def test_via_sedml_string(self):
"""Test SED-ML from string."""
sedml_string = """<?xml version="1.0" encoding="UTF-8"?>
<!-- Created by phraSED-ML version v0.5beta on 2016-01-31 22:02 with libSBML version 5.12.1. -->
<sedML xmlns="http://sed-ml.org/sed-ml/level1/version2" level="1" version="2">
<listOfSimulations>
<uniformTimeCourse id="sim1" initialTime="0" outputStartTime="0" outputEndTime="5" numberOfPoints="100">
<algorithm kisaoID="KISAO:0000019"/>
</uniformTimeCourse>
</listOfSimulations>
<listOfModels>
<model id="model1" language="urn:sedml:language:sbml.level-3.version-1" source="myModel"/>
</listOfModels>
<listOfTasks>
<task id="task1" modelReference="model1" simulationReference="sim1"/>
</listOfTasks>
<listOfDataGenerators>
<dataGenerator id="plot_0_0_0" name="time">
<listOfVariables>
<variable id="time" symbol="urn:sedml:symbol:time" taskReference="task1"/>
</listOfVariables>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> time </ci>
</math>
</dataGenerator>
<dataGenerator id="plot_0_0_1" name="S1">
<listOfVariables>
<variable id="S1" target="/sbml:sbml/sbml:model/descendant::*[@id='S1']" taskReference="task1" modelReference="model1"/>
</listOfVariables>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> S1 </ci>
</math>
</dataGenerator>
<dataGenerator id="plot_0_1_1" name="S2">
<listOfVariables>
<variable id="S2" target="/sbml:sbml/sbml:model/descendant::*[@id='S2']" taskReference="task1" modelReference="model1"/>
</listOfVariables>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<ci> S2 </ci>
</math>
</dataGenerator>
</listOfDataGenerators>
<listOfOutputs>
<plot2D id="plot_0" name="Figure 1">
<listOfCurves>
<curve logX="false" logY="false" xDataReference="plot_0_0_0" yDataReference="plot_0_0_1"/>
<curve logX="false" logY="false" xDataReference="plot_0_0_0" yDataReference="plot_0_1_1"/>
</listOfCurves>
</plot2D>
</listOfOutputs>
</sedML>
"""
python_str = tesedml.sedmlToPython(sedml_string)
self.assertIsNotNone(python_str)
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 _toPython(self, phrasedmlStr, workingDir=None):
""" Create and return python script given phrasedml string.
:param phrasedmlStr: Name of PhraSEDML string defined in the code
:type phrasedmlStr: str
:returns: python string to execute
:rtype: str
"""
warnings.warn('Use inline_omex instead.', DeprecationWarning)
if phrasedmlStr is None:
phrasedmlStr = self._getDefaultPhrasedml()
# Models have to be resolved from phrasedml string and set as referenced
phrasedml.clearReferencedSBML()
self._setReferencedSBML(phrasedmlStr)
# check if conversion is possible
self._phrasedmlToSEDML(phrasedmlStr)
# create temporary working directory
import tempfile
isTmpDir = False
if workingDir is None:
workingDir = tempfile.mkdtemp(suffix="_sedml")
isTmpDir = True
# Export archive
expId = self.getId()
expArchive = os.path.join(workingDir, "{}.omex".format(expId))
self.exportAsCombine(expArchive)
# Create python code from archive
# This is the clean way to generate the code !
pycode = tesedml.sedmlToPython(expArchive)
# remove the temporary directory
if isTmpDir:
shutil.rmtree(workingDir)
return pycode
def single_check(self, f_sedml):
""" Test if python code can be generated from the
SED-ML file.
:param f_sedml:
:type f_sedml:
:return:
:rtype:
"""
directory = os.path.dirname(f_sedml)
basename = os.path.basename(f_sedml)
dir_results = os.path.join(directory, 'results')
python_str = tesedml.sedmlToPython(f_sedml)
self.assertIsNotNone(python_str)
# create the python code file
if not os.path.exists(dir_results):
os.mkdir(dir_results)
file_py = os.path.join(dir_results, basename + '.py')
with open(file_py, 'w') as f_py:
f_py.write(python_str)
def single_check(self, f_sedml):
""" Test if python code can be generated from the
SED-ML file.
:param f_sedml:
:type f_sedml:
:return:
:rtype:
"""
directory = os.path.dirname(f_sedml)
basename = os.path.basename(f_sedml)
dir_results = os.path.join(directory, 'results')
python_str = tesedml.sedmlToPython(f_sedml)
self.assertIsNotNone(python_str)
# create the python code file
if not os.path.exists(dir_results):
os.mkdir(dir_results)
file_py = os.path.join(dir_results, basename + '.py')
with open(file_py, 'w') as f_py:
f_py.write(python_str)
def single_check(self, f_sedml):
python_str = tesedml.sedmlToPython(f_sedml)
self.assertIsNotNone(python_str)
# create the python code file
with open(f_sedml+'.py', 'w') as f_py:
f_py.write(python_str)
def single_check(self, f_sedml):
python_str = tesedml.sedmlToPython(f_sedml)
self.assertIsNotNone(python_str)
# create the python code file
with open(f_sedml + '.py', 'w') as f_py:
f_py.write(python_str)