def test_Reaction_addProduct1(self):
m = libsbml.Reaction(2, 2)
p = libsbml.SpeciesReference(2, 2)
p1 = libsbml.SpeciesReference(2, 2)
p1.setSpecies("k")
p1.setId("k1")
i = m.addProduct(p)
self.assert_(i == libsbml.LIBSBML_INVALID_OBJECT)
p.setSpecies("k")
p.setId("k1")
i = m.addProduct(p)
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assert_(m.getNumProducts() == 1)
i = m.addProduct(p1)
self.assert_(i == libsbml.LIBSBML_DUPLICATE_OBJECT_ID)
self.assert_(m.getNumProducts() == 1)
_dummyList = [p]
_dummyList[:] = []
del _dummyList
_dummyList = [p1]
_dummyList[:] = []
del _dummyList
_dummyList = [m]
_dummyList[:] = []
del _dummyList
pass
def test_SpeciesReference_copyConstructor(self):
o1 = libsbml.SpeciesReference(2,4)
o1.setId("c")
self.assert_( o1.getId() == "c" )
o2 = libsbml.SpeciesReference(o1)
self.assert_( o2.getId() == "c" )
self.assert_( o2.getParentSBMLObject() == o1.getParentSBMLObject() )
o2 = None
o1 = None
pass
def test_SpeciesReference_assignmentOperator(self):
o1 = libsbml.SpeciesReference(2,4)
o1.setId("c")
self.assert_( o1.getId() == "c" )
o2 = libsbml.SpeciesReference(2,4)
o2 = o1
self.assert_( o2.getId() == "c" )
self.assert_( o2.getParentSBMLObject() == o1.getParentSBMLObject() )
o2 = None
o1 = None
pass
def test_SpeciesReference_setId3(self):
c = libsbml.SpeciesReference(2, 1)
i = c.setId("cell")
_dummyList = [c]
_dummyList[:] = []
del _dummyList
pass
def test_SpeciesReference(self):
sr = libsbml.SpeciesReference(2, 4)
self.assertEqual(False, (sr.hasRequiredAttributes()))
sr.setSpecies("sr")
self.assertEqual(True, sr.hasRequiredAttributes())
sr = None
pass
def setProducts(self, productIDString):
if self.Type != TYPE.REACTION: # can only do this for Reactions
return False
productIDs = productIDString.replace(" ", "").split(",")
if productIDs is None or len(productIDs) == 0:
return False
productRefs = self.Item.getListOfProducts()
IDsToRemove = []
for productRef in productRefs:
orgID = productRef.getSpecies()
IDsToRemove.append(orgID)
for ID in IDsToRemove:
logging.info("Removing Product: %s" % ID)
self.Item.removeProduct(ID)
for ID in productIDs:
if self.speciesIDExists(ID):
speciesRef = libsbml.SpeciesReference(self.Item.getLevel(), self.Item.getVersion())
speciesRef.setSpecies(ID)
self.Item.addProduct(speciesRef)
return True
def test_SpeciesReference_setSpecies2(self): c = libsbml.SpeciesReference(2,2) i = c.setSpecies( "1cell") self.assert_( i == libsbml.LIBSBML_INVALID_ATTRIBUTE_VALUE ) self.assertEqual( False, c.isSetSpecies() ) _dummyList = [ c ]; _dummyList[:] = []; del _dummyList pass
def test_SpeciesReference_setName3(self): c = libsbml.SpeciesReference(2,1) i = c.setName( "cell") self.assert_( i == libsbml.LIBSBML_UNEXPECTED_ATTRIBUTE ) self.assertEqual( False, c.isSetName() ) _dummyList = [ c ]; _dummyList[:] = []; del _dummyList pass
def setReactants(self, reactantIDString):
if self.Type != TYPE.REACTION: # can only do this for Reactions
return False
reactantIDs = reactantIDString.replace(" ", "").split(",")
if reactantIDs is None or len(reactantIDs) == 0:
return False
reactantRefs = self.Item.getListOfReactants()
IDsToRemove = []
for reactantRef in reactantRefs:
orgID = reactantRef.getSpecies()
IDsToRemove.append(orgID)
for ID in IDsToRemove:
logging.debug("Removing Reactant: %s" % ID)
self.Item.removeReactant(ID)
for ID in reactantIDs:
if self.speciesIDExists(ID):
speciesRef = libsbml.SpeciesReference(self.Item.getLevel(),
self.Item.getVersion())
speciesRef.setSpecies(ID)
self.Item.addReactant(speciesRef)
return True
def test_SpeciesReference_setStoichiometry2(self): c = libsbml.SpeciesReference(2,2) i = c.setStoichiometry(4) self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS ) self.assert_( c.getStoichiometry() == 4.0 ) _dummyList = [ c ]; _dummyList[:] = []; del _dummyList pass
def test_L3_SpeciesReference_createWithNS(self): xmlns = libsbml.XMLNamespaces() xmlns.add( "http://www.sbml.org", "testsbml") sbmlns = libsbml.SBMLNamespaces(3,1) sbmlns.addNamespaces(xmlns) sr = libsbml.SpeciesReference(sbmlns) self.assert_( sr.getTypeCode() == libsbml.SBML_SPECIES_REFERENCE ) self.assert_( sr.getMetaId() == "" ) self.assert_( sr.getNotes() == None ) self.assert_( sr.getAnnotation() == None ) self.assert_( sr.getLevel() == 3 ) self.assert_( sr.getVersion() == 1 ) self.assert_( sr.getNamespaces() != None ) self.assert_( sr.getNamespaces().getLength() == 2 ) self.assert_( sr.getId() == "" ) self.assert_( sr.getName() == "" ) self.assert_( sr.getSpecies() == "" ) self.assertEqual( True, isnan(sr.getStoichiometry()) ) self.assert_( sr.getConstant() == False ) self.assertEqual( False, sr.isSetId() ) self.assertEqual( False, sr.isSetName() ) self.assertEqual( False, sr.isSetSpecies() ) self.assertEqual( False, sr.isSetStoichiometry() ) self.assertEqual( False, sr.isSetConstant() ) _dummyList = [ sr ]; _dummyList[:] = []; del _dummyList pass
def test_SpeciesReference_setDenominator2(self): c = libsbml.SpeciesReference(2,2) i = c.setDenominator(4) self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS ) self.assert_( c.getDenominator() == 4 ) _dummyList = [ c ]; _dummyList[:] = []; del _dummyList pass
def test_SpeciesReference_setStoichiometryMath7(self):
sr1 = libsbml.SpeciesReference(1, 2)
i = sr1.unsetStoichiometryMath()
self.assert_(i == libsbml.LIBSBML_UNEXPECTED_ATTRIBUTE)
_dummyList = [sr1]
_dummyList[:] = []
del _dummyList
pass
def test_SpeciesReference_setSpecies3(self): c = libsbml.SpeciesReference(2,2) i = c.setSpecies( "mole") self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS ) self.assert_(( "mole" == c.getSpecies() )) self.assertEqual( True, c.isSetSpecies() ) _dummyList = [ c ]; _dummyList[:] = []; del _dummyList pass
def test_StoichiometryMath_parent_add(self):
m = libsbml.StoichiometryMath(2, 4)
m.setMath(libsbml.parseFormula("1"))
sr = libsbml.SpeciesReference(2, 4)
sr.setStoichiometryMath(m)
m = None
self.assert_(sr == sr.getStoichiometryMath().getParentSBMLObject())
sr = None
pass
def test_L3_SpeciesReference_hasRequiredAttributes(self): sr = libsbml.SpeciesReference(3,1) self.assertEqual( False, sr.hasRequiredAttributes() ) sr.setSpecies( "id") self.assertEqual( False, sr.hasRequiredAttributes() ) sr.setConstant(False) self.assertEqual( True, sr.hasRequiredAttributes() ) _dummyList = [ sr ]; _dummyList[:] = []; del _dummyList pass
def test_SpeciesReference_Reactant_parent_add(self):
sr = libsbml.SpeciesReference(2, 4)
r = libsbml.Reaction(2, 4)
sr.setSpecies("s")
r.addReactant(sr)
sr = None
lo = r.getListOfReactants()
self.assert_(lo == r.getReactant(0).getParentSBMLObject())
self.assert_(r == lo.getParentSBMLObject())
pass
def test_SpeciesReference_clone(self):
o1 = libsbml.SpeciesReference(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_Reaction_addReactant(self):
sr = libsbml.SpeciesReference(2, 4)
sr.setSpecies("s")
self.R.addReactant(sr)
self.assert_(self.R.getNumReactants() == 1)
self.assert_(self.R.getNumProducts() == 0)
self.assert_(self.R.getNumModifiers() == 0)
_dummyList = [sr]
_dummyList[:] = []
del _dummyList
pass
def test_StoichiometryMath_ancestor_create(self): sr = libsbml.SpeciesReference(2,4) sm = sr.createStoichiometryMath() self.assert_( sm.getAncestorOfType(libsbml.SBML_SPECIES_REFERENCE) == sr ) self.assert_( sm.getAncestorOfType(libsbml.SBML_DOCUMENT) == None ) self.assert_( sm.getAncestorOfType(libsbml.SBML_COMPARTMENT) == None ) obj = sr.getStoichiometryMath() self.assert_( obj.getAncestorOfType(libsbml.SBML_SPECIES_REFERENCE) == sr ) self.assert_( obj.getAncestorOfType(libsbml.SBML_DOCUMENT) == None ) self.assert_( obj.getAncestorOfType(libsbml.SBML_COMPARTMENT) == None ) pass
def test_Reaction_getReactantById(self):
sr1 = libsbml.SpeciesReference(2, 4)
sr1.setSpecies("R1")
sr2 = libsbml.SpeciesReference(2, 4)
sr2.setSpecies("R2")
self.R.addReactant(sr1)
self.R.addReactant(sr2)
self.assert_(self.R.getNumReactants() == 2)
self.assert_(self.R.getNumProducts() == 0)
self.assert_(self.R.getNumModifiers() == 0)
self.assert_(self.R.getReactant("R1") != sr1)
self.assert_(self.R.getReactant("R2") != sr2)
self.assert_(self.R.getReactant("R3") == None)
_dummyList = [sr1]
_dummyList[:] = []
del _dummyList
_dummyList = [sr2]
_dummyList[:] = []
del _dummyList
pass
def test_Reaction_getReactant(self):
sr1 = libsbml.SpeciesReference(2, 4)
sr2 = libsbml.SpeciesReference(2, 4)
sr1.setSpecies("R1")
sr2.setSpecies("R2")
self.R.addReactant(sr1)
self.R.addReactant(sr2)
_dummyList = [sr1]
_dummyList[:] = []
del _dummyList
_dummyList = [sr2]
_dummyList[:] = []
del _dummyList
self.assert_(self.R.getNumReactants() == 2)
self.assert_(self.R.getNumProducts() == 0)
self.assert_(self.R.getNumModifiers() == 0)
sr1 = self.R.getReactant(0)
sr2 = self.R.getReactant(1)
self.assert_(("R1" == sr1.getSpecies()))
self.assert_(("R2" == sr2.getSpecies()))
pass
def test_StoichiometryMath_ancestor_add(self):
m = libsbml.StoichiometryMath(2,4)
m.setMath(libsbml.parseFormula("1"))
sr = libsbml.SpeciesReference(2,4)
sr.setStoichiometryMath(m)
m = None
obj = sr.getStoichiometryMath()
self.assert_( obj.getAncestorOfType(libsbml.SBML_SPECIES_REFERENCE) == sr )
self.assert_( obj.getAncestorOfType(libsbml.SBML_MODEL) == None )
self.assert_( obj.getAncestorOfType(libsbml.SBML_DOCUMENT) == None )
sr = None
pass
def test_SpeciesReference_Reactant_ancestor_add(self):
sr = libsbml.SpeciesReference(2,4)
r = libsbml.Reaction(2,4)
sr.setSpecies("s")
r.addReactant(sr)
sr = None
lo = r.getListOfReactants()
obj = r.getReactant(0)
self.assert_( obj.getAncestorOfType(libsbml.SBML_REACTION) == r )
self.assert_( obj.getAncestorOfType(libsbml.SBML_LIST_OF) == lo )
self.assert_( obj.getAncestorOfType(libsbml.SBML_DOCUMENT) == None )
self.assert_( obj.getAncestorOfType(libsbml.SBML_COMPARTMENT) == None )
pass
def test_Reaction_addProduct3(self):
m = libsbml.Reaction(2, 2)
p = libsbml.SpeciesReference(1, 2)
p.setSpecies("k")
i = m.addProduct(p)
self.assert_(i == libsbml.LIBSBML_LEVEL_MISMATCH)
self.assert_(m.getNumProducts() == 0)
_dummyList = [p]
_dummyList[:] = []
del _dummyList
_dummyList = [m]
_dummyList[:] = []
del _dummyList
pass
def test_Reaction_addReactant2(self):
m = libsbml.Reaction(2, 2)
p = libsbml.SpeciesReference(2, 1)
p.setSpecies("k")
i = m.addReactant(p)
self.assert_(i == libsbml.LIBSBML_VERSION_MISMATCH)
self.assert_(m.getNumReactants() == 0)
_dummyList = [p]
_dummyList[:] = []
del _dummyList
_dummyList = [m]
_dummyList[:] = []
del _dummyList
pass
def test_SpeciesReference_setStoichiometryMath5(self): sr1 = libsbml.SpeciesReference(1,2) sm = libsbml.StoichiometryMath(2,4) math = libsbml.ASTNode(libsbml.AST_TIMES) a = libsbml.ASTNode() b = libsbml.ASTNode() a.setName( "a") b.setName( "b") math.addChild(a) math.addChild(b) sm.setMath(math) i = sr1.setStoichiometryMath(sm) self.assert_( i == libsbml.LIBSBML_UNEXPECTED_ATTRIBUTE ) self.assertEqual( False, sr1.isSetStoichiometryMath() ) _dummyList = [ sm ]; _dummyList[:] = []; del _dummyList _dummyList = [ sr1 ]; _dummyList[:] = []; del _dummyList pass
def test_SpeciesReference_createWithNS(self):
xmlns = libsbml.XMLNamespaces()
xmlns.add("http://www.sbml.org", "testsbml")
sbmlns = libsbml.SBMLNamespaces(2, 1)
sbmlns.addNamespaces(xmlns)
object = libsbml.SpeciesReference(sbmlns)
self.assert_(object.getTypeCode() == libsbml.SBML_SPECIES_REFERENCE)
self.assert_(object.getMetaId() == "")
self.assert_(object.getNotes() == None)
self.assert_(object.getAnnotation() == None)
self.assert_(object.getLevel() == 2)
self.assert_(object.getVersion() == 1)
self.assert_(object.getNamespaces() != None)
self.assert_(object.getNamespaces().getLength() == 2)
_dummyList = [object]
_dummyList[:] = []
del _dummyList
pass
def test_internal_consistency_check_99904_speciesRef(self):
d = libsbml.SBMLDocument(2,4)
sr = libsbml.SpeciesReference(2,4)
d.setLevelAndVersion(1,2,False)
m = d.createModel()
c = m.createCompartment()
c.setId("c")
s = m.createSpecies()
s.setId("s")
s.setCompartment("c")
r = m.createReaction()
r.setId("r")
sr.setSpecies("s")
sr.setMetaId("mmm")
r.addProduct(sr)
errors = d.checkInternalConsistency()
self.assert_( errors == 1 )
self.assert_( d.getError(0).getErrorId() == 21101 )
d = None
pass
def setUp(self):
self.sr = libsbml.SpeciesReference(2,4)
if (self.sr == None):
pass
pass
