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