def test_KineticLaw_getParameterById(self):
k1 = libsbml.Parameter(2, 4)
k2 = libsbml.Parameter(2, 4)
k1.setId("k1")
k2.setId("k2")
k1.setValue(3.14)
k2.setValue(2.72)
self.M.addParameter(k1)
self.M.addParameter(k2)
r1 = libsbml.Reaction(2, 4)
r1.setId("reaction_1")
kl = libsbml.KineticLaw(2, 4)
kl.setFormula("k1 * X0")
k3 = libsbml.Parameter(2, 4)
k4 = libsbml.Parameter(2, 4)
k3.setId("k1")
k4.setId("k2")
k3.setValue(2.72)
k4.setValue(3.14)
kl.addParameter(k3)
kl.addParameter(k4)
r1.setKineticLaw(kl)
self.M.addReaction(r1)
kl1 = self.M.getReaction(0).getKineticLaw()
self.assert_(kl1.getParameter("k1") != k3)
self.assert_(kl1.getParameter("k1") != k1)
self.assert_(kl1.getParameter("k2") != k4)
self.assert_(kl1.getParameter("k3") == None)
pass
def test_Parameter_copyConstructor(self):
o1 = libsbml.Parameter(2,4)
o1.setId("c")
self.assert_( o1.getId() == "c" )
o2 = libsbml.Parameter(o1)
self.assert_( o2.getId() == "c" )
self.assert_( o2.getParentSBMLObject() == o1.getParentSBMLObject() )
o2 = None
o1 = None
pass
def test_Parameter_assignmentOperator(self):
o1 = libsbml.Parameter(2,4)
o1.setId("c")
self.assert_( o1.getId() == "c" )
o2 = libsbml.Parameter(2,4)
o2 = o1
self.assert_( o2.getId() == "c" )
self.assert_( o2.getParentSBMLObject() == o1.getParentSBMLObject() )
o2 = None
o1 = None
pass
def test_Model_getParameterById(self):
p1 = libsbml.Parameter(2, 4)
p2 = libsbml.Parameter(2, 4)
p1.setId("Km1")
p2.setId("Km2")
self.M.addParameter(p1)
self.M.addParameter(p2)
self.assert_(self.M.getNumParameters() == 2)
self.assert_(self.M.getParameter("Km1") != p1)
self.assert_(self.M.getParameter("Km2") != p2)
self.assert_(self.M.getParameter("Km3") == None)
pass
def test_Model_getParameter(self):
p1 = libsbml.Parameter(2, 4)
p2 = libsbml.Parameter(2, 4)
p1.setId("Km1")
p2.setId("Km2")
self.M.addParameter(p1)
self.M.addParameter(p2)
self.assert_(self.M.getNumParameters() == 2)
p1 = self.M.getParameter(0)
p2 = self.M.getParameter(1)
self.assert_(("Km1" == p1.getId()))
self.assert_(("Km2" == p2.getId()))
pass
def test_Parameter_setValue2(self): p = libsbml.Parameter(2,2) i = p.unsetValue() self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS ) self.assertEqual( False, p.isSetValue() ) _dummyList = [ p ]; _dummyList[:] = []; del _dummyList pass
def test_L3_KineticLaw_addParameter1(self):
kl = libsbml.KineticLaw(3, 1)
p = libsbml.Parameter(3, 1)
i = self.KL.addParameter(p)
self.assert_(i == libsbml.LIBSBML_INVALID_OBJECT)
p.setId("p")
i = self.KL.addParameter(p)
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assert_(self.KL.getNumParameters() == 1)
self.assert_(self.KL.getNumLocalParameters() == 1)
self.assert_(kl.getNumParameters() == 0)
self.assert_(kl.getNumLocalParameters() == 0)
i = kl.addParameter(p)
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assert_(self.KL.getNumParameters() == 1)
self.assert_(self.KL.getNumLocalParameters() == 1)
self.assert_(kl.getNumParameters() == 1)
self.assert_(kl.getNumLocalParameters() == 1)
_dummyList = [p]
_dummyList[:] = []
del _dummyList
_dummyList = [kl]
_dummyList[:] = []
del _dummyList
pass
def test_L3_Parameter_createWithNS(self): xmlns = libsbml.XMLNamespaces() xmlns.add( "http://www.sbml.org", "testsbml") sbmlns = libsbml.SBMLNamespaces(3,1) sbmlns.addNamespaces(xmlns) p = libsbml.Parameter(sbmlns) self.assert_( p.getTypeCode() == libsbml.SBML_PARAMETER ) self.assert_( p.getMetaId() == "" ) self.assert_( p.getNotes() == None ) self.assert_( p.getAnnotation() == None ) self.assert_( p.getLevel() == 3 ) self.assert_( p.getVersion() == 1 ) self.assert_( p.getNamespaces() != None ) self.assert_( p.getNamespaces().getLength() == 2 ) self.assert_( p.getId() == "" ) self.assert_( p.getName() == "" ) self.assert_( p.getUnits() == "" ) self.assertEqual( True, isnan(p.getValue()) ) self.assert_( p.getConstant() == True ) self.assertEqual( False, p.isSetId() ) self.assertEqual( False, p.isSetName() ) self.assertEqual( False, p.isSetValue() ) self.assertEqual( False, p.isSetUnits() ) self.assertEqual( False, p.isSetConstant() ) _dummyList = [ p ]; _dummyList[:] = []; del _dummyList pass
def test_Parameter(self):
p = libsbml.Parameter(2, 4)
self.assertEqual(False, (p.hasRequiredAttributes()))
p.setId("p")
self.assertEqual(True, p.hasRequiredAttributes())
p = None
pass
def test_Parameter_setConstant2(self): p = libsbml.Parameter(2,2) i = p.setConstant(False) self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS ) self.assert_( p.getConstant() == False ) _dummyList = [ p ]; _dummyList[:] = []; del _dummyList pass
def test_L3_Parameter_hasRequiredAttributes(self): p = libsbml.Parameter(3,1) self.assertEqual( False, p.hasRequiredAttributes() ) p.setId( "id") self.assertEqual( False, p.hasRequiredAttributes() ) p.setConstant(False) self.assertEqual( True, p.hasRequiredAttributes() ) _dummyList = [ p ]; _dummyList[:] = []; del _dummyList pass
def test_KineticLaw_addParameter(self):
p = libsbml.Parameter(2, 4)
p.setId("p")
self.kl.addParameter(p)
self.assert_(self.kl.getNumParameters() == 1)
_dummyList = [p]
_dummyList[:] = []
del _dummyList
pass
def test_Parameter_L1V1(self):
p = libsbml.Parameter(1, 1)
self.assertEqual(False, (p.hasRequiredAttributes()))
p.setId("p")
self.assertEqual(False, (p.hasRequiredAttributes()))
p.setValue(12)
self.assertEqual(True, p.hasRequiredAttributes())
p = None
pass
def test_KineticLaw_addParameter3(self): self.kl = libsbml.KineticLaw(2,2) p = libsbml.Parameter(1,2) p.setId( "p") i = self.kl.addParameter(p) self.assert_( i == libsbml.LIBSBML_LEVEL_MISMATCH ) self.assert_( self.kl.getNumParameters() == 0 ) _dummyList = [ p ]; _dummyList[:] = []; del _dummyList _dummyList = [ self.kl ]; _dummyList[:] = []; del _dummyList pass
def test_Parameter_clone(self):
o1 = libsbml.Parameter(2,4)
o1.setId("c")
self.assert_( o1.getId() == "c" )
o2 = o1.clone()
self.assert_( o2.getId() == "c" )
self.assert_( o2.getParentSBMLObject() == o1.getParentSBMLObject() )
o2 = None
o1 = None
pass
def test_Parameter_parent_add(self):
ia = libsbml.Parameter(2, 4)
m = libsbml.Model(2, 4)
ia.setId("p")
m.addParameter(ia)
ia = None
lo = m.getListOfParameters()
self.assert_(lo == m.getParameter(0).getParentSBMLObject())
self.assert_(m == lo.getParentSBMLObject())
pass
def test_Parameter_setName3(self):
p = libsbml.Parameter(1,2)
i = p.setName( "11pp")
self.assert_( i == libsbml.LIBSBML_INVALID_ATTRIBUTE_VALUE )
self.assertEqual( False, p.isSetName() )
i = p.setName("")
self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS )
self.assertEqual( False, p.isSetName() )
_dummyList = [ p ]; _dummyList[:] = []; del _dummyList
pass
def test_KineticLaw_addParameter1(self): self.kl = libsbml.KineticLaw(2,2) p = libsbml.Parameter(2,2) i = self.kl.addParameter(p) self.assert_( i == libsbml.LIBSBML_INVALID_OBJECT ) p.setId( "p") i = self.kl.addParameter(p) self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS ) self.assert_( self.kl.getNumParameters() == 1 ) _dummyList = [ p ]; _dummyList[:] = []; del _dummyList _dummyList = [ self.kl ]; _dummyList[:] = []; del _dummyList pass
def test_internal_consistency_check_99911_param(self):
d = libsbml.SBMLDocument(2,4)
m = d.createModel()
p = libsbml.Parameter(2,4)
d.setLevelAndVersion(2,1,False)
p.setId("p")
p.setSBOTerm(2)
m.addParameter(p)
errors = d.checkInternalConsistency()
self.assert_( errors == 0 )
d = None
pass
def test_Parameter_setName2(self):
p = libsbml.Parameter(2, 2)
i = p.setName("1cell")
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assertEqual(True, p.isSetName())
i = p.unsetName()
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assertEqual(False, p.isSetName())
_dummyList = [p]
_dummyList[:] = []
del _dummyList
pass
def test_KineticLaw_Parameter_parent_add(self):
kl = libsbml.KineticLaw(2, 4)
p = libsbml.Parameter(2, 4)
p.setId("jake")
kl.addParameter(p)
p = None
self.assert_(kl.getNumParameters() == 1)
self.assert_(kl.getParameter(0).getId() == "jake")
lop = kl.getListOfParameters()
self.assert_(kl == lop.getParentSBMLObject())
self.assert_(lop == kl.getParameter(0).getParentSBMLObject())
kl = None
pass
def test_Model_addParameter5(self):
m = libsbml.Model(2, 2)
p = libsbml.Parameter(2, 2)
p.setId("p")
p1 = libsbml.Parameter(2, 2)
p1.setId("p")
i = m.addParameter(p)
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assert_(m.getNumParameters() == 1)
i = m.addParameter(p1)
self.assert_(i == libsbml.LIBSBML_DUPLICATE_OBJECT_ID)
self.assert_(m.getNumParameters() == 1)
_dummyList = [p]
_dummyList[:] = []
del _dummyList
_dummyList = [p1]
_dummyList[:] = []
del _dummyList
_dummyList = [m]
_dummyList[:] = []
del _dummyList
pass
def test_Parameter_ancestor_add(self):
ia = libsbml.Parameter(2,4)
m = libsbml.Model(2,4)
ia.setId("p")
m.addParameter(ia)
ia = None
lo = m.getListOfParameters()
obj = m.getParameter(0)
self.assert_( obj.getAncestorOfType(libsbml.SBML_MODEL) == m )
self.assert_( obj.getAncestorOfType(libsbml.SBML_LIST_OF) == lo )
self.assert_( obj.getAncestorOfType(libsbml.SBML_DOCUMENT) == None )
self.assert_( obj.getAncestorOfType(libsbml.SBML_EVENT) == None )
pass
def test_internal_consistency_check_99904_param(self):
d = libsbml.SBMLDocument(2,4)
p = libsbml.Parameter(2,4)
d.setLevelAndVersion(1,2,False)
m = d.createModel()
c = m.createCompartment()
c.setId("cc")
p.setId("p")
p.setMetaId("mmm")
m.addParameter(p)
errors = d.checkInternalConsistency()
self.assert_( errors == 0 )
d = None
pass
def test_KineticLaw_getParameterById(self):
k1 = libsbml.Parameter(2, 4)
k2 = libsbml.Parameter(2, 4)
k1.setId("k1")
k2.setId("k2")
k1.setValue(3.14)
k2.setValue(2.72)
self.kl.addParameter(k1)
self.kl.addParameter(k2)
_dummyList = [k1]
_dummyList[:] = []
del _dummyList
_dummyList = [k2]
_dummyList[:] = []
del _dummyList
self.assert_(self.kl.getNumParameters() == 2)
k1 = self.kl.getParameter("k1")
k2 = self.kl.getParameter("k2")
self.assert_(("k1" == k1.getId()))
self.assert_(("k2" == k2.getId()))
self.assert_(k1.getValue() == 3.14)
self.assert_(k2.getValue() == 2.72)
pass
def test_KineticLaw_addParameter2(self):
self.kl = libsbml.KineticLaw(2, 2)
p = libsbml.Parameter(2, 1)
p.setId("p")
i = self.kl.addParameter(p)
self.assert_(i == libsbml.LIBSBML_VERSION_MISMATCH)
self.assert_(self.kl.getNumParameters() == 0)
_dummyList = [p]
_dummyList[:] = []
del _dummyList
_dummyList = [self.kl]
_dummyList[:] = []
del _dummyList
pass
def test_KineticLaw_Parameter_ancestor_add(self):
kl = libsbml.KineticLaw(2,4)
p = libsbml.Parameter(2,4)
p.setId("jake")
kl.addParameter(p)
p = None
lop = kl.getListOfParameters()
obj = kl.getParameter(0)
self.assert_( obj.getAncestorOfType(libsbml.SBML_KINETIC_LAW) == kl )
self.assert_( obj.getAncestorOfType(libsbml.SBML_LIST_OF) == lop )
self.assert_( obj.getAncestorOfType(libsbml.SBML_DOCUMENT) == None )
self.assert_( obj.getAncestorOfType(libsbml.SBML_COMPARTMENT) == None )
kl = None
pass
def test_Model_addParameter3(self):
m = libsbml.Model(2, 2)
p = libsbml.Parameter(1, 2)
p.setId("p")
i = m.addParameter(p)
self.assert_(i == libsbml.LIBSBML_LEVEL_MISMATCH)
self.assert_(m.getNumParameters() == 0)
_dummyList = [p]
_dummyList[:] = []
del _dummyList
_dummyList = [m]
_dummyList[:] = []
del _dummyList
pass
def test_KineticLaw_copyConstructor(self):
o1 = libsbml.KineticLaw(2,4)
p = libsbml.Parameter(2,4)
p.setId("jake")
o1.addParameter(p)
p = None
self.assert_( o1.getNumParameters() == 1 )
self.assert_( o1.getParameter(0).getId() == "jake" )
o2 = libsbml.KineticLaw(o1)
self.assert_( o2.getNumParameters() == 1 )
self.assert_( o2.getParameter(0).getId() == "jake" )
self.assert_( o2.getParentSBMLObject() == o1.getParentSBMLObject() )
o2 = None
o1 = None
pass
def test_Model_addParameter1(self):
m = libsbml.Model(2, 2)
p = libsbml.Parameter(2, 2)
i = m.addParameter(p)
self.assert_(i == libsbml.LIBSBML_INVALID_OBJECT)
p.setId("p")
i = m.addParameter(p)
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assert_(m.getNumParameters() == 1)
_dummyList = [p]
_dummyList[:] = []
del _dummyList
_dummyList = [m]
_dummyList[:] = []
del _dummyList
pass
