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
