def test_NS_copyConstructor(self): ns = libsbml.XMLNamespaces() ns.add("http://test1.org/", "test1") self.assert_( ns.getLength() == 1 ) self.assert_( ns.isEmpty() == False ) self.assert_( ns.getPrefix(0) == "test1" ) self.assert_( ns.getURI("test1") == "http://test1.org/" ) ns2 = libsbml.XMLNamespaces(ns) self.assert_( ns2.getLength() == 1 ) self.assert_( ns2.isEmpty() == False ) self.assert_( ns2.getPrefix(0) == "test1" ) self.assert_( ns2.getURI("test1") == "http://test1.org/" ) ns2 = None ns = None 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_L3_Compartment_createWithNS(self): xmlns = libsbml.XMLNamespaces() xmlns.add("http://www.sbml.org", "testsbml") sbmlns = libsbml.SBMLNamespaces(3, 1) sbmlns.addNamespaces(xmlns) c = libsbml.Compartment(sbmlns) self.assert_(c.getTypeCode() == libsbml.SBML_COMPARTMENT) self.assert_(c.getMetaId() == "") self.assert_(c.getNotes() == None) self.assert_(c.getAnnotation() == None) self.assert_(c.getLevel() == 3) self.assert_(c.getVersion() == 1) self.assert_(c.getNamespaces() != None) self.assert_(c.getNamespaces().getLength() == 2) self.assert_(c.getId() == "") self.assert_(c.getName() == "") self.assert_(c.getUnits() == "") self.assert_(c.getOutside() == "") self.assertEqual(True, isnan(c.getSpatialDimensionsAsDouble())) self.assertEqual(True, isnan(c.getVolume())) self.assert_(c.getConstant() == True) self.assertEqual(False, c.isSetId()) self.assertEqual(False, c.isSetSpatialDimensions()) self.assertEqual(False, c.isSetName()) self.assertEqual(False, c.isSetSize()) self.assertEqual(False, c.isSetVolume()) self.assertEqual(False, c.isSetUnits()) self.assertEqual(False, c.isSetOutside()) self.assertEqual(False, c.isSetConstant()) _dummyList = [c] _dummyList[:] = [] del _dummyList pass
def test_L3_Unit_createWithNS(self): xmlns = libsbml.XMLNamespaces() xmlns.add("http://www.sbml.org", "testsbml") sbmlns = libsbml.SBMLNamespaces(3, 1) sbmlns.addNamespaces(xmlns) u = libsbml.Unit(sbmlns) self.assert_(u.getTypeCode() == libsbml.SBML_UNIT) self.assert_(u.getMetaId() == "") self.assert_(u.getNotes() == None) self.assert_(u.getAnnotation() == None) self.assert_(u.getLevel() == 3) self.assert_(u.getVersion() == 1) self.assert_(u.getNamespaces() != None) self.assert_(u.getNamespaces().getLength() == 2) self.assert_(u.getKind() == libsbml.UNIT_KIND_INVALID) self.assertEqual(True, isnan(u.getExponentAsDouble())) self.assertEqual(True, isnan(u.getMultiplier())) self.assertEqual(False, u.isSetKind()) self.assertEqual(False, u.isSetExponent()) self.assertEqual(False, u.isSetMultiplier()) self.assertEqual(False, u.isSetScale()) _dummyList = [u] _dummyList[:] = [] del _dummyList pass
def test_Constraint_setMessage(self): text = libsbml.XMLNode.convertStringToXMLNode(" Some text ", None) triple = libsbml.XMLTriple("p", "http://www.w3.org/1999/xhtml", "") att = libsbml.XMLAttributes() xmlns = libsbml.XMLNamespaces() xmlns.add("http://www.w3.org/1999/xhtml", "") p = libsbml.XMLNode(triple, att, xmlns) p.addChild(text) triple1 = libsbml.XMLTriple("message", "", "") att1 = libsbml.XMLAttributes() node = libsbml.XMLNode(triple1, att1) node.addChild(p) self.C.setMessage(node) self.assert_(self.C.getMessage() != node) self.assert_(self.C.isSetMessage() == True) self.C.setMessage(self.C.getMessage()) self.assert_(self.C.getMessage() != node) self.assert_(self.C.getMessageString() != None) self.C.unsetMessage() self.assertEqual(False, self.C.isSetMessage()) if (self.C.getMessage() != None): pass _dummyList = [node] _dummyList[:] = [] del _dummyList pass
def test_L3_Model_createWithNS(self): xmlns = libsbml.XMLNamespaces() xmlns.add("http://www.sbml.org", "testsbml") sbmlns = libsbml.SBMLNamespaces(3, 1) sbmlns.addNamespaces(xmlns) m = libsbml.Model(sbmlns) self.assert_(m.getTypeCode() == libsbml.SBML_MODEL) self.assert_(m.getMetaId() == "") self.assert_(m.getNotes() == None) self.assert_(m.getAnnotation() == None) self.assert_(m.getLevel() == 3) self.assert_(m.getVersion() == 1) self.assert_(m.getNamespaces() != None) self.assert_(m.getNamespaces().getLength() == 2) self.assert_(m.getId() == "") self.assert_(m.getName() == "") self.assert_(m.getSubstanceUnits() == "") self.assert_(m.getTimeUnits() == "") self.assert_(m.getVolumeUnits() == "") self.assert_(m.getAreaUnits() == "") self.assert_(m.getLengthUnits() == "") self.assert_(m.getConversionFactor() == "") self.assertEqual(False, m.isSetId()) self.assertEqual(False, m.isSetName()) self.assertEqual(False, m.isSetSubstanceUnits()) self.assertEqual(False, m.isSetTimeUnits()) self.assertEqual(False, m.isSetVolumeUnits()) self.assertEqual(False, m.isSetAreaUnits()) self.assertEqual(False, m.isSetLengthUnits()) self.assertEqual(False, m.isSetConversionFactor()) _dummyList = [m] _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 add_annotation_complex(model, model_id, participants): species = model.getSpecies(model_id) xmlns = libsbml.XMLNamespaces() xmlns.add('http://www.w3.org/1999/02/22-rdf-syntax-ns#', 'rdf') rdf_triple = libsbml.XMLTriple( 'RDF', 'http://www.w3.org/1999/02/22-rdf-syntax-ns#', 'rdf') rdf_token = libsbml.XMLToken(rdf_triple, libsbml.XMLAttributes(), xmlns) annotation = libsbml.XMLNode(rdf_token) if species: participants_xml_triple = libsbml.XMLTriple( 'Participants', 'http://www.w3.org/1999/02/22-rdf-syntax-ns#', 'rdf') participants_xml_token = \ libsbml.XMLToken(participants_xml_triple, libsbml.XMLAttributes()) participants_xml_node = libsbml.XMLNode(participants_xml_token) participant_xml_triple = libsbml.XMLTriple( 'Participant', 'http://www.w3.org/1999/02/22-rdf-syntax-ns#', 'rdf') for iii in participants: resource_att = libsbml.XMLAttributes() resource_att.add('participant', str(iii)) subject_token = libsbml.XMLToken(participant_xml_triple, resource_att) subject_token.setEnd() participants_xml_node.addChild(libsbml.XMLNode(subject_token)) annotation.addChild(participants_xml_node) species.appendAnnotation(annotation)
def test_L3_Reaction_createWithNS(self): xmlns = libsbml.XMLNamespaces() xmlns.add("http://www.sbml.org", "testsbml") sbmlns = libsbml.SBMLNamespaces(3, 1) sbmlns.addNamespaces(xmlns) r = libsbml.Reaction(sbmlns) self.assert_(r.getTypeCode() == libsbml.SBML_REACTION) self.assert_(r.getMetaId() == "") self.assert_(r.getNotes() == None) self.assert_(r.getAnnotation() == None) self.assert_(r.getLevel() == 3) self.assert_(r.getVersion() == 1) self.assert_(r.getNamespaces() != None) self.assert_(r.getNamespaces().getLength() == 2) self.assert_(r.getId() == "") self.assert_(r.getName() == "") self.assert_(r.getCompartment() == "") self.assert_(r.getFast() == False) self.assert_(r.getReversible() == True) self.assertEqual(False, r.isSetId()) self.assertEqual(False, r.isSetName()) self.assertEqual(False, r.isSetCompartment()) self.assertEqual(False, r.isSetFast()) self.assertEqual(False, r.isSetReversible()) _dummyList = [r] _dummyList[:] = [] del _dummyList pass
def test_XMLToken_newSetters_setNamespaces1(self): triple = libsbml.XMLTriple("test", "", "") attr = libsbml.XMLAttributes() token = libsbml.XMLToken(triple, attr) ns = libsbml.XMLNamespaces() self.assert_(token.getNamespacesLength() == 0) self.assert_(token.isNamespacesEmpty() == True) ns.add("http://test1.org/", "test1") i = token.setNamespaces(ns) self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS) self.assert_(token.getNamespacesLength() == 1) self.assert_(token.isNamespacesEmpty() == False) _dummyList = [attr] _dummyList[:] = [] del _dummyList _dummyList = [triple] _dummyList[:] = [] del _dummyList _dummyList = [token] _dummyList[:] = [] del _dummyList _dummyList = [ns] _dummyList[:] = [] del _dummyList pass
def _setThresholdXml(self, value): """ Uses the value to update the internal libsbml.XMLNode structure. If there is a reference to an existing XML node (from loading the file) it is used. Otherwise, it's created. @since: 2011-05-23 """ if not self.thresholdNode: # have to create the XML node thresholdNodeTriplet = libsbml.XMLTriple(XML_SCALE, XML_THRESHOLD_NAMESPACE, "") thresholdNodeAttribute = libsbml.XMLAttributes() thresholdNodeAttribute.add(XML_THRESHOLD_VALUE, str(value)) self.thresholdNode = libsbml.XMLNode(thresholdNodeTriplet, thresholdNodeAttribute) namespace = libsbml.XMLNamespaces( ) # seems to be necessary to do this again namespace.add(XML_THRESHOLD_NAMESPACE) self.thresholdNode.setNamespaces(namespace) self.Item.appendAnnotation(self.thresholdNode) else: thresholdNodeAttribute = libsbml.XMLAttributes() thresholdNodeAttribute.add(XML_THRESHOLD_VALUE, str(value)) self.thresholdNode.setAttributes(thresholdNodeAttribute)
def test_Constraint_copyConstructor(self): o1 = libsbml.Constraint(2,4) o1.setMetaId("c") self.assert_( o1.getMetaId() == "c" ) text = libsbml.XMLNode.convertStringToXMLNode(" Some text ") triple = libsbml.XMLTriple("p", "http://www.w3.org/1999/xhtml", "") att = libsbml.XMLAttributes() xmlns = libsbml.XMLNamespaces() xmlns.add("http://www.w3.org/1999/xhtml") p = libsbml.XMLNode(triple,att,xmlns) p.addChild(text) triple1 = libsbml.XMLTriple("message", "", "") att1 = libsbml.XMLAttributes() message = libsbml.XMLNode(triple1,att1) message.addChild(p) math = libsbml.ASTNode(libsbml.AST_CONSTANT_PI) o1.setMath(math) o1.setMessage(message) math = None message = None self.assert_( o1.getMath() != None ) msg = o1.getMessage() self.assert_( msg != None ) o2 = libsbml.Constraint(o1) self.assert_( o2.getMetaId() == "c" ) self.assert_( o2.getMath() != None ) msg = o2.getMessage() self.assert_( msg != None ) self.assert_( o2.getParentSBMLObject() == o1.getParentSBMLObject() ) o2 = None o1 = None pass
def _setConstraintsXml(self, type, lower, upper): """ @since: 2012-01-25 """ if not self._constraintsXmlNode: # have to create the XML node constraintsNodeTriplet = libsbml.XMLTriple(XML_CONSTRAINTS, XML_CONSTRAINTS_NAMESPACE, "") constraintsNodeAttribute = libsbml.XMLAttributes() constraintsNodeAttribute.add(XML_CONSTRAINTS_TYPE, str(type)) constraintsNodeAttribute.add(XML_CONSTRAINTS_LOWERBOUND, str(lower)) constraintsNodeAttribute.add(XML_CONSTRAINTS_UPPERBOUND, str(upper)) self._constraintsXmlNode = libsbml.XMLNode(constraintsNodeTriplet, constraintsNodeAttribute) namespace = libsbml.XMLNamespaces() # seems to be necessary to do this again namespace.add(XML_CONSTRAINTS_NAMESPACE) self._constraintsXmlNode.setNamespaces(namespace) self.Item.appendAnnotation(self._constraintsXmlNode) else: constraintsNodeAttribute = libsbml.XMLAttributes() constraintsNodeAttribute.add(XML_CONSTRAINTS_TYPE, str(type)) constraintsNodeAttribute.add(XML_CONSTRAINTS_LOWERBOUND, str(lower)) constraintsNodeAttribute.add(XML_CONSTRAINTS_UPPERBOUND, str(upper)) self._constraintsXmlNode.setAttributes(constraintsNodeAttribute)
def test_FunctionDefinition_createWithNS(self): xmlns = libsbml.XMLNamespaces() xmlns.add( "http://www.sbml.org", "testsbml") sbmlns = libsbml.SBMLNamespaces(2,1) sbmlns.addNamespaces(xmlns) object = libsbml.FunctionDefinition(sbmlns) self.assert_( object.getTypeCode() == libsbml.SBML_FUNCTION_DEFINITION ) 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_Constraint_createWithNS(self): xmlns = libsbml.XMLNamespaces() xmlns.add( "http://www.sbml.org", "testsbml") sbmlns = libsbml.SBMLNamespaces(2,2) sbmlns.addNamespaces(xmlns) object = libsbml.Constraint(sbmlns) self.assert_( object.getTypeCode() == libsbml.SBML_CONSTRAINT ) self.assert_( object.getMetaId() == "" ) self.assert_( object.getNotes() == None ) self.assert_( object.getAnnotation() == None ) self.assert_( object.getLevel() == 2 ) self.assert_( object.getVersion() == 2 ) self.assert_( object.getNamespaces() != None ) self.assert_( object.getNamespaces().getLength() == 2 ) _dummyList = [ object ]; _dummyList[:] = []; del _dummyList pass
def test_EventAssignment_createWithNS(self): xmlns = libsbml.XMLNamespaces() xmlns.add( "http://www.sbml.org", "testsbml") sbmlns = libsbml.SBMLNamespaces(2,1) sbmlns.addNamespaces(xmlns) object = libsbml.EventAssignment(sbmlns) self.assert_( object.getTypeCode() == libsbml.SBML_EVENT_ASSIGNMENT ) 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_StoichiometryMath_createWithNS(self): xmlns = libsbml.XMLNamespaces() xmlns.add( "http://www.sbml.org", "testsbml") sbmlns = libsbml.SBMLNamespaces(2,1) sbmlns.addNamespaces(xmlns) object = libsbml.StoichiometryMath(sbmlns) self.assert_( object.getTypeCode() == libsbml.SBML_STOICHIOMETRY_MATH ) 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_XMLToken_namespace_set_clear(self): triple = libsbml.XMLTriple("test", "", "") attr = libsbml.XMLAttributes() token = libsbml.XMLToken(triple, attr) ns = libsbml.XMLNamespaces() self.assert_(token.getNamespacesLength() == 0) self.assert_(token.isNamespacesEmpty() == True) ns.add("http://test1.org/", "test1") ns.add("http://test2.org/", "test2") ns.add("http://test3.org/", "test3") ns.add("http://test4.org/", "test4") ns.add("http://test5.org/", "test5") token.setNamespaces(ns) self.assert_(token.getNamespacesLength() == 5) self.assert_(token.isNamespacesEmpty() == False) self.assert_(("test1" != token.getNamespacePrefix(0)) == False) self.assert_(("test2" != token.getNamespacePrefix(1)) == False) self.assert_(("test3" != token.getNamespacePrefix(2)) == False) self.assert_(("test4" != token.getNamespacePrefix(3)) == False) self.assert_(("test5" != token.getNamespacePrefix(4)) == False) self.assert_( ("http://test1.org/" != token.getNamespaceURI(0)) == False) self.assert_( ("http://test2.org/" != token.getNamespaceURI(1)) == False) self.assert_( ("http://test3.org/" != token.getNamespaceURI(2)) == False) self.assert_( ("http://test4.org/" != token.getNamespaceURI(3)) == False) self.assert_( ("http://test5.org/" != token.getNamespaceURI(4)) == False) token.clearNamespaces() self.assert_(token.getNamespacesLength() == 0) _dummyList = [ns] _dummyList[:] = [] del _dummyList _dummyList = [token] _dummyList[:] = [] del _dummyList _dummyList = [triple] _dummyList[:] = [] del _dummyList _dummyList = [attr] _dummyList[:] = [] del _dummyList pass
def test_Delay_createWithNS(self): xmlns = libsbml.XMLNamespaces() xmlns.add("http://www.sbml.org", "testsbml") sbmlns = libsbml.SBMLNamespaces(2, 1) sbmlns.addNamespaces(xmlns) object = libsbml.Delay(sbmlns) self.assert_(object.getTypeCode() == libsbml.SBML_DELAY) 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_CompartmentType_createWithNS(self): xmlns = libsbml.XMLNamespaces() xmlns.add("http://www.sbml.org", "testsbml") sbmlns = libsbml.SBMLNamespaces(2, 2) sbmlns.addNamespaces(xmlns) object = libsbml.CompartmentType(sbmlns) self.assert_(object.getTypeCode() == libsbml.SBML_COMPARTMENT_TYPE) self.assert_(object.getMetaId() == "") self.assert_(object.getNotes() == None) self.assert_(object.getAnnotation() == None) self.assert_(object.getLevel() == 2) self.assert_(object.getVersion() == 2) self.assert_(object.getNamespaces() != None) self.assert_(object.getNamespaces().getLength() == 2) _dummyList = [object] _dummyList[:] = [] del _dummyList pass
def test_AlgebraicRule_createWithNS(self): xmlns = libsbml.XMLNamespaces() xmlns.add("http://www.sbml.org", "testsbml") sbmlns = libsbml.SBMLNamespaces(2, 3) sbmlns.addNamespaces(xmlns) r = libsbml.AlgebraicRule(sbmlns) self.assert_(r.getTypeCode() == libsbml.SBML_ALGEBRAIC_RULE) self.assert_(r.getMetaId() == "") self.assert_(r.getNotes() == None) self.assert_(r.getAnnotation() == None) self.assert_(r.getLevel() == 2) self.assert_(r.getVersion() == 3) self.assert_(r.getNamespaces() != None) self.assert_(r.getNamespaces().getLength() == 2) _dummyList = [r] _dummyList[:] = [] del _dummyList pass
def rFromFlux(flux): fluxSBML = libsbml.XMLNode() triple = libsbml.XMLTriple("flux", "", "") att = libsbml.XMLAttributes() att.add( "forward", str(flux.forward) ) # Forcing string conversion to invoke __str__ for rangedNumber att.add("backward", str(flux.backward)) att.add("net", str(flux.net)) att.add("exchange", str(flux.exchange)) ns = libsbml.XMLNamespaces() token = libsbml.XMLToken(triple, att, ns) fluxNode = libsbml.XMLNode(token) fluxSBML.addChild(fluxNode) return [fluxSBML]
def test_ModifierSpeciesReference_createWithNS(self): xmlns = libsbml.XMLNamespaces() xmlns.add("http://www.sbml.org", "testsbml") sbmlns = libsbml.SBMLNamespaces(2, 1) sbmlns.addNamespaces(xmlns) object = libsbml.ModifierSpeciesReference(sbmlns) self.assert_( object.getTypeCode() == libsbml.SBML_MODIFIER_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) n = object.getNamespaces() self.assert_(n.getLength() == 2) _dummyList = [object] _dummyList[:] = [] del _dummyList pass
def test_XMLToken_newSetters_setNamespaces2(self): triple = libsbml.XMLTriple("test", "", "") token = libsbml.XMLToken(triple) ns = libsbml.XMLNamespaces() self.assert_(token.getNamespacesLength() == 0) self.assert_(token.isNamespacesEmpty() == True) ns.add("http://test1.org/", "test1") i = token.setNamespaces(ns) self.assert_(i == libsbml.LIBSBML_INVALID_XML_OPERATION) self.assert_(token.getNamespacesLength() == 0) self.assert_(token.isNamespacesEmpty() == True) _dummyList = [triple] _dummyList[:] = [] del _dummyList _dummyList = [token] _dummyList[:] = [] del _dummyList _dummyList = [ns] _dummyList[:] = [] del _dummyList pass
def test_Compartment_createWithNS(self): xmlns = libsbml.XMLNamespaces() xmlns.add("http://www.sbml.org", "testsbml") sbmlns = libsbml.SBMLNamespaces(2, 1) sbmlns.addNamespaces(xmlns) c = libsbml.Compartment(sbmlns) self.assert_(c.getTypeCode() == libsbml.SBML_COMPARTMENT) self.assert_(c.getMetaId() == "") self.assert_(c.getNotes() == None) self.assert_(c.getAnnotation() == None) self.assert_(c.getLevel() == 2) self.assert_(c.getVersion() == 1) self.assert_(c.getNamespaces() != None) self.assert_(c.getNamespaces().getLength() == 2) self.assert_(c.getName() == "") self.assert_(c.getSpatialDimensions() == 3) self.assert_(c.getConstant() == True) _dummyList = [c] _dummyList[:] = [] del _dummyList pass
def test_SyntaxChecker_validXHTML(self): NS24 = libsbml.SBMLNamespaces(2,4) NS31 = libsbml.SBMLNamespaces(3,1) toptriple = libsbml.XMLTriple("notes", "", "") triple = libsbml.XMLTriple("p", "", "") att = libsbml.XMLAttributes() ns = libsbml.XMLNamespaces() ns.add( "http://www.w3.org/1999/xhtml", "") tt = libsbml.XMLToken("This is my text") n1 = libsbml.XMLNode(tt) toptoken = libsbml.XMLToken(toptriple,att) topnode = libsbml.XMLNode(toptoken) token = libsbml.XMLToken(triple,att,ns) node = libsbml.XMLNode(token) node.addChild(n1) topnode.addChild(node) self.assert_( libsbml.SyntaxChecker.hasExpectedXHTMLSyntax(topnode,None) == True ) self.assert_( libsbml.SyntaxChecker.hasExpectedXHTMLSyntax(topnode,NS24) == True ) self.assert_( libsbml.SyntaxChecker.hasExpectedXHTMLSyntax(topnode,NS31) == True ) triple = libsbml.XMLTriple("html", "", "") token = libsbml.XMLToken(triple,att,ns) node = libsbml.XMLNode(token) node.addChild(n1) topnode.removeChild(0) topnode.addChild(node) self.assert_( libsbml.SyntaxChecker.hasExpectedXHTMLSyntax(topnode,None) == True ) self.assert_( libsbml.SyntaxChecker.hasExpectedXHTMLSyntax(topnode,NS24) == False ) self.assert_( libsbml.SyntaxChecker.hasExpectedXHTMLSyntax(topnode,NS31) == True ) triple = libsbml.XMLTriple("html", "", "") ns.clear() token = libsbml.XMLToken(triple,att,ns) node = libsbml.XMLNode(token) node.addChild(n1) topnode.removeChild(0) topnode.addChild(node) self.assert_( libsbml.SyntaxChecker.hasExpectedXHTMLSyntax(topnode,None) == False ) self.assert_( libsbml.SyntaxChecker.hasExpectedXHTMLSyntax(topnode,NS24) == False ) self.assert_( libsbml.SyntaxChecker.hasExpectedXHTMLSyntax(topnode,NS31) == False ) pass
def test_L3_Species_createWithNS(self): xmlns = libsbml.XMLNamespaces() xmlns.add("http://www.sbml.org", "testsbml") sbmlns = libsbml.SBMLNamespaces(3, 1) sbmlns.addNamespaces(xmlns) s = libsbml.Species(sbmlns) self.assert_(s.getTypeCode() == libsbml.SBML_SPECIES) self.assert_(s.getMetaId() == "") self.assert_(s.getNotes() == None) self.assert_(s.getAnnotation() == None) self.assert_(s.getLevel() == 3) self.assert_(s.getVersion() == 1) self.assert_(s.getNamespaces() != None) self.assert_(s.getNamespaces().getLength() == 2) self.assert_(s.getId() == "") self.assert_(s.getName() == "") self.assert_(s.getCompartment() == "") self.assertEqual(True, isnan(s.getInitialAmount())) self.assertEqual(True, isnan(s.getInitialConcentration())) self.assert_(s.getSubstanceUnits() == "") self.assert_(s.getHasOnlySubstanceUnits() == False) self.assert_(s.getBoundaryCondition() == False) self.assert_(s.getConstant() == False) self.assert_(s.getConversionFactor() == "") self.assertEqual(False, s.isSetId()) self.assertEqual(False, s.isSetName()) self.assertEqual(False, s.isSetCompartment()) self.assertEqual(False, s.isSetInitialAmount()) self.assertEqual(False, s.isSetInitialConcentration()) self.assertEqual(False, s.isSetSubstanceUnits()) self.assertEqual(False, s.isSetHasOnlySubstanceUnits()) self.assertEqual(False, s.isSetBoundaryCondition()) self.assertEqual(False, s.isSetConstant()) self.assertEqual(False, s.isSetConversionFactor()) _dummyList = [s] _dummyList[:] = [] del _dummyList pass
def test_XMLNode_getters(self): NS = libsbml.XMLNamespaces() NS.add("http://test1.org/", "test1") token = libsbml.XMLToken("This is a test") node = libsbml.XMLNode(token) self.assert_(node != None) self.assert_(node.getNumChildren() == 0) self.assert_(("This is a test" != node.getCharacters()) == False) self.assert_(node.getChild(1) != None) attr = libsbml.XMLAttributes() self.assert_(attr != None) attr.add("attr2", "value") triple = libsbml.XMLTriple("attr", "uri", "prefix") token = libsbml.XMLToken(triple, attr) self.assert_(token != None) node = libsbml.XMLNode(token) self.assert_(("attr" != node.getName()) == False) self.assert_(("uri" != node.getURI()) == False) self.assert_(("prefix" != node.getPrefix()) == False) returnattr = node.getAttributes() self.assert_(("attr2" != returnattr.getName(0)) == False) self.assert_(("value" != returnattr.getValue(0)) == False) token = libsbml.XMLToken(triple, attr, NS) node = libsbml.XMLNode(token) returnNS = node.getNamespaces() self.assert_(returnNS.getLength() == 1) self.assert_(returnNS.isEmpty() == False) _dummyList = [triple] _dummyList[:] = [] del _dummyList _dummyList = [token] _dummyList[:] = [] del _dummyList _dummyList = [node] _dummyList[:] = [] del _dummyList pass
def test_L3_Event_createWithNS(self): xmlns = libsbml.XMLNamespaces() xmlns.add("http://www.sbml.org", "testsbml") sbmlns = libsbml.SBMLNamespaces(3, 1) sbmlns.addNamespaces(xmlns) e = libsbml.Event(sbmlns) self.assert_(e.getTypeCode() == libsbml.SBML_EVENT) self.assert_(e.getMetaId() == "") self.assert_(e.getNotes() == None) self.assert_(e.getAnnotation() == None) self.assert_(e.getLevel() == 3) self.assert_(e.getVersion() == 1) self.assert_(e.getNamespaces() != None) self.assert_(e.getNamespaces().getLength() == 2) self.assert_(e.getId() == "") self.assert_(e.getName() == "") self.assert_(e.getUseValuesFromTriggerTime() == True) self.assertEqual(False, e.isSetId()) self.assertEqual(False, e.isSetName()) self.assertEqual(False, e.isSetUseValuesFromTriggerTime()) _dummyList = [e] _dummyList[:] = [] del _dummyList pass
def test_XMLNode_createElement(self): name = "test" uri = "http://test.org/" prefix = "p" text = "text node" triple = libsbml.XMLTriple(name, uri, prefix) ns = libsbml.XMLNamespaces() attr = libsbml.XMLAttributes() ns.add(uri, prefix) attr.add("id", "value", uri, prefix) snode = libsbml.XMLNode(triple, attr, ns) self.assert_(snode != None) self.assert_(snode.getNumChildren() == 0) self.assert_((name != snode.getName()) == False) self.assert_((prefix != snode.getPrefix()) == False) self.assert_((uri != snode.getURI()) == False) self.assert_(snode.isElement() == True) self.assert_(snode.isStart() == True) self.assert_(snode.isEnd() == False) self.assert_(snode.isText() == False) snode.setEnd() self.assert_(snode.isEnd() == True) snode.unsetEnd() self.assert_(snode.isEnd() == False) cattr = snode.getAttributes() self.assert_(cattr != None) self.assert_(("id" != cattr.getName(0)) == False) self.assert_(("value" != cattr.getValue(0)) == False) self.assert_((prefix != cattr.getPrefix(0)) == False) self.assert_((uri != cattr.getURI(0)) == False) _dummyList = [triple] _dummyList[:] = [] del _dummyList _dummyList = [attr] _dummyList[:] = [] del _dummyList _dummyList = [ns] _dummyList[:] = [] del _dummyList _dummyList = [snode] _dummyList[:] = [] del _dummyList attr = libsbml.XMLAttributes() attr.add("id", "value") triple = libsbml.XMLTriple(name, "", "") snode = libsbml.XMLNode(triple, attr) self.assert_(snode != None) self.assert_(snode.getNumChildren() == 0) self.assert_(("test" != snode.getName()) == False) self.assert_(snode.getPrefix() == "") self.assert_(snode.getURI() == "") self.assert_(snode.isElement() == True) self.assert_(snode.isStart() == True) self.assert_(snode.isEnd() == False) self.assert_(snode.isText() == False) cattr = snode.getAttributes() self.assert_(cattr != None) self.assert_(("id" != cattr.getName(0)) == False) self.assert_(("value" != cattr.getValue(0)) == False) self.assert_(cattr.getPrefix(0) == "") self.assert_(cattr.getURI(0) == "") enode = libsbml.XMLNode(triple) self.assert_(enode != None) self.assert_(enode.getNumChildren() == 0) self.assert_(("test" != enode.getName()) == False) self.assert_(enode.getPrefix() == "") self.assert_(enode.getURI() == "") self.assert_(enode.isElement() == True) self.assert_(enode.isStart() == False) self.assert_(enode.isEnd() == True) self.assert_(enode.isText() == False) tnode = libsbml.XMLNode(text) self.assert_(tnode != None) self.assert_((text != tnode.getCharacters()) == False) self.assert_(tnode.getNumChildren() == 0) self.assert_(tnode.getName() == "") self.assert_(tnode.getPrefix() == "") self.assert_(tnode.getURI() == "") self.assert_(tnode.isElement() == False) self.assert_(tnode.isStart() == False) self.assert_(tnode.isEnd() == False) self.assert_(tnode.isText() == True) _dummyList = [triple] _dummyList[:] = [] del _dummyList _dummyList = [attr] _dummyList[:] = [] del _dummyList _dummyList = [snode] _dummyList[:] = [] del _dummyList _dummyList = [enode] _dummyList[:] = [] del _dummyList _dummyList = [tnode] _dummyList[:] = [] del _dummyList pass