def test_Model_getNumSpeciesWithBoundaryCondition(self):
s1 = libsbml.Species(2, 4)
s2 = libsbml.Species(2, 4)
s3 = libsbml.Species(2, 4)
s1.setId("s1")
s2.setId("s2")
s3.setId("s3")
s1.setCompartment("c1")
s2.setCompartment("c2")
s3.setCompartment("c3")
s1.setBoundaryCondition(True)
s2.setBoundaryCondition(False)
s3.setBoundaryCondition(True)
self.assert_(self.M.getNumSpecies() == 0)
self.assert_(self.M.getNumSpeciesWithBoundaryCondition() == 0)
self.M.addSpecies(s1)
self.assert_(self.M.getNumSpecies() == 1)
self.assert_(self.M.getNumSpeciesWithBoundaryCondition() == 1)
self.M.addSpecies(s2)
self.assert_(self.M.getNumSpecies() == 2)
self.assert_(self.M.getNumSpeciesWithBoundaryCondition() == 1)
self.M.addSpecies(s3)
self.assert_(self.M.getNumSpecies() == 3)
self.assert_(self.M.getNumSpeciesWithBoundaryCondition() == 2)
pass
def test_Species_copyConstructor(self):
o1 = libsbml.Species(2,4)
o1.setId("c")
o1.setSpeciesType("c1")
self.assert_( o1.getId() == "c" )
self.assert_( o1.getSpeciesType() == "c1" )
o2 = libsbml.Species(o1)
self.assert_( o2.getId() == "c" )
self.assert_( o2.getSpeciesType() == "c1" )
self.assert_( o2.getParentSBMLObject() == o1.getParentSBMLObject() )
o2 = None
o1 = None
pass
def test_Species_assignmentOperator(self):
o1 = libsbml.Species(2,4)
o1.setId("c")
o1.setSpeciesType("c1")
self.assert_( o1.getId() == "c" )
self.assert_( o1.getSpeciesType() == "c1" )
o2 = libsbml.Species(2,4)
o2 = o1
self.assert_( o2.getId() == "c" )
self.assert_( o2.getSpeciesType() == "c1" )
self.assert_( o2.getParentSBMLObject() == o1.getParentSBMLObject() )
o2 = None
o1 = None
pass
def test_Model_getSpeciesById(self):
s1 = libsbml.Species(2, 4)
s2 = libsbml.Species(2, 4)
s1.setId("Glucose")
s2.setId("Glucose_6_P")
s1.setCompartment("c")
s2.setCompartment("c")
self.M.addSpecies(s1)
self.M.addSpecies(s2)
self.assert_(self.M.getNumSpecies() == 2)
self.assert_(self.M.getSpecies("Glucose") != s1)
self.assert_(self.M.getSpecies("Glucose_6_P") != s2)
self.assert_(self.M.getSpecies("Glucose2") == None)
pass
def test_Model_getSpecies(self):
s1 = libsbml.Species(2, 4)
s2 = libsbml.Species(2, 4)
s1.setId("Glucose")
s2.setId("Glucose_6_P")
s1.setCompartment("c")
s2.setCompartment("c")
self.M.addSpecies(s1)
self.M.addSpecies(s2)
self.assert_(self.M.getNumSpecies() == 2)
s1 = self.M.getSpecies(0)
s2 = self.M.getSpecies(1)
self.assert_(("Glucose" == s1.getId()))
self.assert_(("Glucose_6_P" == s2.getId()))
pass
def test_ListOf_remove(self): lo = libsbml.ListOf(2,4) sp = libsbml.Species(2,4) self.assert_( lo.size() == 0 ) lo.append(sp) lo.append(sp) lo.append(sp) lo.append(sp) lo.append(sp) self.assert_( lo.size() == 5 ) elem = lo.remove(0) _dummyList = [ elem ]; _dummyList[:] = []; del _dummyList elem = lo.remove(0) _dummyList = [ elem ]; _dummyList[:] = []; del _dummyList elem = lo.remove(0) _dummyList = [ elem ]; _dummyList[:] = []; del _dummyList elem = lo.remove(0) _dummyList = [ elem ]; _dummyList[:] = []; del _dummyList elem = lo.remove(0) _dummyList = [ elem ]; _dummyList[:] = []; del _dummyList self.assert_( lo.size() == 0 ) lo.append(sp) lo.append(sp) lo.append(sp) lo.append(sp) lo.appendAndOwn(sp) self.assert_( lo.size() == 5 ) _dummyList = [ lo ]; _dummyList[:] = []; del _dummyList pass
def test_Species_setSpatialSizeUnits4(self):
c = libsbml.Species(2,2)
i = c.setSpatialSizeUnits("")
self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS )
self.assertEqual( False, c.isSetSpatialSizeUnits() )
_dummyList = [ c ]; _dummyList[:] = []; del _dummyList
pass
def test_Species_setCharge2(self): c = libsbml.Species(2,2) i = c.setCharge(4) self.assert_( i == libsbml.LIBSBML_UNEXPECTED_ATTRIBUTE ) self.assertEqual( False, c.isSetCharge() ) _dummyList = [ c ]; _dummyList[:] = []; del _dummyList pass
def test_Species_setCharge3(self): c = libsbml.Species(2,1) i = c.unsetCharge() self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS ) self.assertEqual( False, c.isSetCharge() ) _dummyList = [ c ]; _dummyList[:] = []; del _dummyList pass
def test_Species_setConstant2(self): c = libsbml.Species(2,2) i = c.setConstant(True) self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS ) self.assert_( c.getConstant() == True ) _dummyList = [ c ]; _dummyList[:] = []; del _dummyList pass
def test_Model_addSpecies(self):
s = libsbml.Species(2, 4)
s.setId("s")
s.setCompartment("c")
self.M.addSpecies(s)
self.assert_(self.M.getNumSpecies() == 1)
pass
def test_ListOf_clear(self): lo = libsbml.ListOf(2,4) sp = libsbml.Species(2,4) lo.append(sp) lo.append(sp) lo.append(sp) lo.append(sp) lo.append(sp) self.assert_( lo.size() == 5 ) lo.clear(True) self.assert_( lo.size() == 0 ) lo.append(sp) lo.append(sp) lo.append(sp) lo.append(sp) lo.appendAndOwn(sp) self.assert_( lo.size() == 5 ) elem = lo.get(0) _dummyList = [ elem ]; _dummyList[:] = []; del _dummyList elem = lo.get(1) _dummyList = [ elem ]; _dummyList[:] = []; del _dummyList elem = lo.get(2) _dummyList = [ elem ]; _dummyList[:] = []; del _dummyList elem = lo.get(3) _dummyList = [ elem ]; _dummyList[:] = []; del _dummyList elem = lo.get(4) _dummyList = [ elem ]; _dummyList[:] = []; del _dummyList lo.clear(False) self.assert_( lo.size() == 0 ) _dummyList = [ lo ]; _dummyList[:] = []; del _dummyList pass
def test_Species_setSubstanceUnits2(self): c = libsbml.Species(2,2) i = c.setSubstanceUnits( "1cell") self.assert_( i == libsbml.LIBSBML_INVALID_ATTRIBUTE_VALUE ) self.assertEqual( False, c.isSetSubstanceUnits() ) _dummyList = [ c ]; _dummyList[:] = []; del _dummyList pass
def test_Species_setSubstanceUnits3(self): c = libsbml.Species(2,2) i = c.setSubstanceUnits( "mole") self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS ) self.assert_(( "mole" == c.getSubstanceUnits() )) self.assertEqual( True, c.isSetSubstanceUnits() ) _dummyList = [ c ]; _dummyList[:] = []; del _dummyList pass
def test_Species_setId3(self): c = libsbml.Species(2,2) i = c.setId( "cell") self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS ) self.assertEqual( True, c.isSetId() ) self.assert_(( "cell" == c.getId() )) _dummyList = [ c ]; _dummyList[:] = []; del _dummyList pass
def __init__(self, model, met=None):
if met is None:
self._sbml = libsbml.Species(3, 1)
model.getListOfSpecies().append(self._sbml)
else:
self._sbml = met
if not self.meta_id:
self.meta_id = self.id
def test_Species(self):
s = libsbml.Species(2, 4)
self.assertEqual(False, (s.hasRequiredAttributes()))
s.setId("s")
self.assertEqual(False, (s.hasRequiredAttributes()))
s.setCompartment("c")
self.assertEqual(True, s.hasRequiredAttributes())
s = None
pass
def test_Species_setHasOnlySubstanceUnits2(self): c = libsbml.Species(2,2) i = c.setHasOnlySubstanceUnits(False) self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS ) self.assert_( c.getHasOnlySubstanceUnits() == False ) i = c.setHasOnlySubstanceUnits(True) self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS ) self.assert_( c.getHasOnlySubstanceUnits() == True ) _dummyList = [ c ]; _dummyList[:] = []; del _dummyList pass
def test_Species_setSpeciesType2(self): c = libsbml.Species(2,2) i = c.setSpeciesType( "1cell") self.assert_( i == libsbml.LIBSBML_INVALID_ATTRIBUTE_VALUE ) self.assertEqual( False, c.isSetSpeciesType() ) i = c.unsetSpeciesType() self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS ) self.assertEqual( False, c.isSetSpeciesType() ) _dummyList = [ c ]; _dummyList[:] = []; del _dummyList pass
def test_Species_setName2(self): c = libsbml.Species(2,2) i = c.setName( "1cell") self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS ) self.assertEqual( True, c.isSetName() ) i = c.unsetName() self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS ) self.assertEqual( False, c.isSetName() ) _dummyList = [ c ]; _dummyList[:] = []; del _dummyList pass
def test_Species_parent_add(self):
ia = libsbml.Species(2, 4)
ia.setId("s")
ia.setCompartment("c")
m = libsbml.Model(2, 4)
m.addSpecies(ia)
ia = None
lo = m.getListOfSpecies()
self.assert_(lo == m.getSpecies(0).getParentSBMLObject())
self.assert_(m == lo.getParentSBMLObject())
pass
def test_Species_setInitialConcentration2(self): c = libsbml.Species(2,2) i = c.setInitialConcentration(4) self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS ) self.assert_( c.getInitialConcentration() == 4 ) self.assertEqual( True, c.isSetInitialConcentration() ) i = c.unsetInitialConcentration() self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS ) self.assertEqual( False, c.isSetInitialConcentration() ) _dummyList = [ c ]; _dummyList[:] = []; del _dummyList pass
def test_Species_setInitialAmount2(self):
c = libsbml.Species(2, 2)
i = c.setInitialAmount(4)
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assert_(c.getInitialAmount() == 4.0)
self.assertEqual(True, c.isSetInitialAmount())
i = c.unsetInitialAmount()
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assertEqual(False, c.isSetInitialAmount())
_dummyList = [c]
_dummyList[:] = []
del _dummyList
pass
def test_Species_setSpeciesType4(self):
c = libsbml.Species(2, 2)
i = c.setSpeciesType("cell")
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assertEqual(True, c.isSetSpeciesType())
self.assert_(("cell" == c.getSpeciesType()))
i = c.setSpeciesType("")
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assertEqual(False, c.isSetSpeciesType())
_dummyList = [c]
_dummyList[:] = []
del _dummyList
pass
def test_ListOf_copyConstructor(self):
o1 = libsbml.ListOf(2,1)
s = libsbml.Species(2,1)
s.setId("species_1")
o1.append(s)
s = None
o2 = libsbml.ListOf(o1)
self.assert_( o2.size() == 1 )
self.assert_( o2.get(0).getId() == "species_1" )
self.assert_( o2.getParentSBMLObject() == o1.getParentSBMLObject() )
o2 = None
o1 = None
pass
def test_Species_ancestor_add(self):
ia = libsbml.Species(2,4)
m = libsbml.Model(2,4)
ia.setId("s")
ia.setCompartment("c")
m.addSpecies(ia)
ia = None
lo = m.getListOfSpecies()
obj = m.getSpecies(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_species(self):
d = libsbml.SBMLDocument(2,4)
s = libsbml.Species(2,4)
d.setLevelAndVersion(1,2,False)
m = d.createModel()
c = m.createCompartment()
c.setId("c")
s.setCompartment("c")
s.setId("s")
s.setMetaId("mmm")
m.addSpecies(s)
errors = d.checkInternalConsistency()
self.assert_( errors == 0 )
d = None
pass
def test_Model_addSpecies5(self):
m = libsbml.Model(2, 2)
s = libsbml.Species(2, 2)
s.setId("s")
s.setCompartment("c")
s1 = libsbml.Species(2, 2)
s1.setId("s")
s1.setCompartment("c")
i = m.addSpecies(s)
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assert_(m.getNumSpecies() == 1)
i = m.addSpecies(s1)
self.assert_(i == libsbml.LIBSBML_DUPLICATE_OBJECT_ID)
self.assert_(m.getNumSpecies() == 1)
_dummyList = [s]
_dummyList[:] = []
del _dummyList
_dummyList = [s1]
_dummyList[:] = []
del _dummyList
_dummyList = [m]
_dummyList[:] = []
del _dummyList
pass
def test_Model_addSpecies2(self):
m = libsbml.Model(2, 2)
s = libsbml.Species(2, 1)
s.setId("s")
s.setCompartment("c")
i = m.addSpecies(s)
self.assert_(i == libsbml.LIBSBML_VERSION_MISMATCH)
self.assert_(m.getNumSpecies() == 0)
_dummyList = [s]
_dummyList[:] = []
del _dummyList
_dummyList = [m]
_dummyList[:] = []
del _dummyList
pass
def test_SBMLConvert_convertToL1_Species_Amount(self): d = libsbml.SBMLDocument(2,1) m = d.createModel() sid = "C"; c = libsbml.Compartment(2,4) s = libsbml.Species(2,4) c.setId(sid) m.addCompartment(c) s.setCompartment(sid) s.setInitialAmount(2.34) m.addSpecies(s) self.assert_( d.setLevelAndVersion(1,2,True) == True ) self.assert_( s.getInitialAmount() == 2.34 ) _dummyList = [ d ]; _dummyList[:] = []; del _dummyList pass
