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 test_XMLTriple_create(self):
t = libsbml.XMLTriple()
self.assert_(t != None)
self.assert_(t.isEmpty() != False)
_dummyList = [t]
_dummyList[:] = []
del _dummyList
t = libsbml.XMLTriple("attr", "uri", "prefix")
self.assert_(("attr" != t.getName()) == False)
self.assert_(("uri" != t.getURI()) == False)
self.assert_(("prefix" != t.getPrefix()) == False)
self.assert_(("prefix:attr" != t.getPrefixedName()) == False)
self.assert_(t.isEmpty() == False)
_dummyList = [t]
_dummyList[:] = []
del _dummyList
t = libsbml.XMLTriple("attr", "uri", "")
self.assert_(("attr" != t.getName()) == False)
self.assert_(("uri" != t.getURI()) == False)
self.assert_(t.getPrefix() == "")
self.assert_(("attr" != t.getPrefixedName()) == False)
self.assert_(t.isEmpty() == False)
_dummyList = [t]
_dummyList[:] = []
del _dummyList
pass
def test_CVTerm_createFromNode(self):
qual_triple = libsbml.XMLTriple("is", "", "bqbiol")
bag_triple = libsbml.XMLTriple()
li_triple = libsbml.XMLTriple()
att = libsbml.XMLAttributes()
att.add("", "This is my resource")
att1 = libsbml.XMLAttributes()
li_token = libsbml.XMLToken(li_triple, att)
bag_token = libsbml.XMLToken(bag_triple, att1)
qual_token = libsbml.XMLToken(qual_triple, att1)
li = libsbml.XMLNode(li_token)
bag = libsbml.XMLNode(bag_token)
node = libsbml.XMLNode(qual_token)
bag.addChild(li)
node.addChild(bag)
term = libsbml.CVTerm(node)
self.assert_(term != None)
self.assert_(term.getQualifierType() == libsbml.BIOLOGICAL_QUALIFIER)
self.assert_(term.getBiologicalQualifierType() == libsbml.BQB_IS)
xa = term.getResources()
self.assert_(xa.getLength() == 1)
self.assert_(("rdf:resource" == xa.getName(0)))
self.assert_(("This is my resource" == xa.getValue(0)))
_dummyList = [qual_triple]
_dummyList[:] = []
del _dummyList
_dummyList = [bag_triple]
_dummyList[:] = []
del _dummyList
_dummyList = [li_triple]
_dummyList[:] = []
del _dummyList
_dummyList = [li_token]
_dummyList[:] = []
del _dummyList
_dummyList = [bag_token]
_dummyList[:] = []
del _dummyList
_dummyList = [qual_token]
_dummyList[:] = []
del _dummyList
_dummyList = [att]
_dummyList[:] = []
del _dummyList
_dummyList = [att1]
_dummyList[:] = []
del _dummyList
_dummyList = [term]
_dummyList[:] = []
del _dummyList
_dummyList = [node]
_dummyList[:] = []
del _dummyList
_dummyList = [bag]
_dummyList[:] = []
del _dummyList
_dummyList = [li]
_dummyList[:] = []
del _dummyList
pass
def test_XMLNode_clearAttributes(self):
triple = libsbml.XMLTriple("test","","")
attr = libsbml.XMLAttributes()
node = libsbml.XMLNode(triple,attr)
xt2 = libsbml.XMLTriple("name3", "http://name3.org/", "p3")
xt1 = libsbml.XMLTriple("name5", "http://name5.org/", "p5")
i = node.addAttr( "name1", "val1")
self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS )
self.assert_( node.getAttributes().getLength() == 1 )
i = node.addAttr( "name2", "val2", "http://name1.org/", "p1")
self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS )
self.assert_( node.getAttributes().getLength() == 2 )
i = node.addAttr(xt2, "val2")
self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS )
self.assert_( node.getAttributes().getLength() == 3 )
i = node.addAttr( "name4", "val4")
self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS )
self.assert_( node.getAttributes().getLength() == 4 )
i = node.clearAttributes()
self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS )
self.assert_( node.getAttributes().getLength() == 0 )
_dummyList = [ xt1 ]; _dummyList[:] = []; del _dummyList
_dummyList = [ xt2 ]; _dummyList[:] = []; del _dummyList
_dummyList = [ triple ]; _dummyList[:] = []; del _dummyList
_dummyList = [ attr ]; _dummyList[:] = []; del _dummyList
_dummyList = [ node ]; _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 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_XMLToken_newSetters_setAttributes1(self):
triple = libsbml.XMLTriple("test", "", "")
attr = libsbml.XMLAttributes()
token = libsbml.XMLToken(triple, attr)
nattr = libsbml.XMLAttributes()
xt1 = libsbml.XMLTriple("name1", "http://name1.org/", "p1")
nattr.add(xt1, "val1")
i = token.setAttributes(nattr)
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assert_(token.isAttributesEmpty() == False)
_dummyList = [nattr]
_dummyList[:] = []
del _dummyList
_dummyList = [attr]
_dummyList[:] = []
del _dummyList
_dummyList = [triple]
_dummyList[:] = []
del _dummyList
_dummyList = [token]
_dummyList[:] = []
del _dummyList
_dummyList = [xt1]
_dummyList[:] = []
del _dummyList
pass
def test_XMLToken_newSetters_addAttributes2(self):
triple = libsbml.XMLTriple("test", "", "")
token = libsbml.XMLToken(triple)
xt2 = libsbml.XMLTriple("name3", "http://name3.org/", "p3")
i = token.addAttr("name1", "val1")
self.assert_(i == libsbml.LIBSBML_INVALID_XML_OPERATION)
self.assert_(token.getAttributesLength() == 0)
self.assert_(token.isAttributesEmpty() == True)
i = token.addAttr("name2", "val2", "http://name1.org/", "p1")
self.assert_(i == libsbml.LIBSBML_INVALID_XML_OPERATION)
self.assert_(token.getAttributesLength() == 0)
self.assert_(token.isAttributesEmpty() == True)
i = token.addAttr(xt2, "val2")
self.assert_(i == libsbml.LIBSBML_INVALID_XML_OPERATION)
self.assert_(token.getAttributesLength() == 0)
self.assert_(token.isAttributesEmpty() == True)
_dummyList = [xt2]
_dummyList[:] = []
del _dummyList
_dummyList = [triple]
_dummyList[:] = []
del _dummyList
_dummyList = [token]
_dummyList[:] = []
del _dummyList
pass
def test_XMLNode_removeAttributes(self):
triple = libsbml.XMLTriple("test", "", "")
attr = libsbml.XMLAttributes()
node = libsbml.XMLNode(triple, attr)
xt2 = libsbml.XMLTriple("name3", "http://name3.org/", "p3")
xt1 = libsbml.XMLTriple("name5", "http://name5.org/", "p5")
i = node.addAttr("name1", "val1")
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assert_(node.getAttributes().getLength() == 1)
i = node.addAttr("name2", "val2", "http://name1.org/", "p1")
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assert_(node.getAttributes().getLength() == 2)
i = node.addAttr(xt2, "val2")
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assert_(node.getAttributes().getLength() == 3)
i = node.addAttr("name4", "val4")
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assert_(node.getAttributes().getLength() == 4)
i = node.removeAttr(7)
self.assert_(i == libsbml.LIBSBML_INDEX_EXCEEDS_SIZE)
i = node.removeAttr("name7")
self.assert_(i == libsbml.LIBSBML_INDEX_EXCEEDS_SIZE)
i = node.removeAttr("name7", "namespaces7")
self.assert_(i == libsbml.LIBSBML_INDEX_EXCEEDS_SIZE)
i = node.removeAttr(xt1)
self.assert_(i == libsbml.LIBSBML_INDEX_EXCEEDS_SIZE)
self.assert_(node.getAttributes().getLength() == 4)
i = node.removeAttr(3)
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assert_(node.getAttributes().getLength() == 3)
i = node.removeAttr("name1")
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assert_(node.getAttributes().getLength() == 2)
i = node.removeAttr("name2", "http://name1.org/")
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assert_(node.getAttributes().getLength() == 1)
i = node.removeAttr(xt2)
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assert_(node.getAttributes().getLength() == 0)
_dummyList = [xt1]
_dummyList[:] = []
del _dummyList
_dummyList = [xt2]
_dummyList[:] = []
del _dummyList
_dummyList = [triple]
_dummyList[:] = []
del _dummyList
_dummyList = [attr]
_dummyList[:] = []
del _dummyList
_dummyList = [node]
_dummyList[:] = []
del _dummyList
pass
def test_Triple_copyConstructor(self):
t = libsbml.XMLTriple("sarah", "http://foo.org/", "bar")
self.assert_( t.getName() == "sarah" )
self.assert_( t.getURI() == "http://foo.org/" )
self.assert_( t.getPrefix() == "bar" )
t2 = libsbml.XMLTriple(t)
self.assert_( t2.getName() == "sarah" )
self.assert_( t2.getURI() == "http://foo.org/" )
self.assert_( t2.getPrefix() == "bar" )
t = None
t2 = None
pass
def test_Triple_assignmentOperator(self):
t = libsbml.XMLTriple("sarah", "http://foo.org/", "bar")
self.assert_( t.getName() == "sarah" )
self.assert_( t.getURI() == "http://foo.org/" )
self.assert_( t.getPrefix() == "bar" )
t2 = libsbml.XMLTriple()
t2 = t
self.assert_( t2.getName() == "sarah" )
self.assert_( t2.getURI() == "http://foo.org/" )
self.assert_( t2.getPrefix() == "bar" )
t = None
t2 = None
pass
def test_XMLNode_removeNamespaces(self):
triple = libsbml.XMLTriple("test","","")
attr = libsbml.XMLAttributes()
node = libsbml.XMLNode(triple,attr)
i = node.addNamespace( "http://test1.org/", "test1")
self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS )
nms = node.getNamespaces()
self.assert_( nms.getLength() == 1 )
i = node.addNamespace( "http://test2.org/", "test2")
self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS )
nms = node.getNamespaces()
self.assert_( nms.getLength() == 2 )
i = node.removeNamespace(7)
self.assert_( i == libsbml.LIBSBML_INDEX_EXCEEDS_SIZE )
nms = node.getNamespaces()
self.assert_( nms.getLength() == 2 )
i = node.removeNamespace( "name7")
self.assert_( i == libsbml.LIBSBML_INDEX_EXCEEDS_SIZE )
nms = node.getNamespaces()
self.assert_( nms.getLength() == 2 )
i = node.removeNamespace(0)
self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS )
nms = node.getNamespaces()
self.assert_( nms.getLength() == 1 )
i = node.removeNamespace( "test2")
self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS )
nms = node.getNamespaces()
self.assert_( nms.getLength() == 0 )
_dummyList = [ triple ]; _dummyList[:] = []; del _dummyList
_dummyList = [ attr ]; _dummyList[:] = []; del _dummyList
_dummyList = [ node ]; _dummyList[:] = []; del _dummyList
pass
def test_XMLNode_namespace_add(self):
triple = libsbml.XMLTriple("test", "", "")
attr = libsbml.XMLAttributes()
node = libsbml.XMLNode(triple, attr)
self.assert_(node.getNamespacesLength() == 0)
self.assert_(node.isNamespacesEmpty() == True)
node.addNamespace("http://test1.org/", "test1")
self.assert_(node.getNamespacesLength() == 1)
self.assert_(node.isNamespacesEmpty() == False)
node.addNamespace("http://test2.org/", "test2")
self.assert_(node.getNamespacesLength() == 2)
self.assert_(node.isNamespacesEmpty() == False)
node.addNamespace("http://test1.org/", "test1a")
self.assert_(node.getNamespacesLength() == 3)
self.assert_(node.isNamespacesEmpty() == False)
node.addNamespace("http://test1.org/", "test1a")
self.assert_(node.getNamespacesLength() == 3)
self.assert_(node.isNamespacesEmpty() == False)
self.assert_(
(node.getNamespaceIndex("http://test1.org/") == -1) == False)
_dummyList = [node]
_dummyList[:] = []
del _dummyList
_dummyList = [triple]
_dummyList[:] = []
del _dummyList
_dummyList = [attr]
_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 test_Node_assignmentOperator(self):
att = libsbml.XMLAttributes()
t = libsbml.XMLTriple("sarah", "http://foo.org/", "bar")
token = libsbml.XMLToken(t,att,3,4)
node = libsbml.XMLNode(token)
child = libsbml.XMLNode()
node.addChild(child)
self.assert_( node.getNumChildren() == 1 )
self.assert_( node.getName() == "sarah" )
self.assert_( node.getURI() == "http://foo.org/" )
self.assert_( node.getPrefix() == "bar" )
self.assert_( node.isEnd() == False )
self.assert_( node.isEOF() == False )
self.assert_( node.getLine() == 3 )
self.assert_( node.getColumn() == 4 )
node2 = libsbml.XMLNode()
node2 = node
self.assert_( node2.getNumChildren() == 1 )
self.assert_( node2.getName() == "sarah" )
self.assert_( node2.getURI() == "http://foo.org/" )
self.assert_( node2.getPrefix() == "bar" )
self.assert_( node2.isEnd() == False )
self.assert_( node2.isEOF() == False )
self.assert_( node2.getLine() == 3 )
self.assert_( node2.getColumn() == 4 )
t = None
token = None
node = None
node2 = None
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_XMLToken_create(self):
token = libsbml.XMLToken()
self.assert_(token != None)
_dummyList = [token]
_dummyList[:] = []
del _dummyList
triple = libsbml.XMLTriple("attr", "uri", "prefix")
token = libsbml.XMLToken(triple)
self.assert_(token != None)
self.assert_(("attr" != token.getName()) == False)
self.assert_(("prefix" != token.getPrefix()) == False)
self.assert_(("uri" != token.getURI()) == False)
_dummyList = [token]
_dummyList[:] = []
del _dummyList
attr = libsbml.XMLAttributes()
self.assert_(attr != None)
attr.add("attr2", "value")
token = libsbml.XMLToken(triple, attr)
self.assert_(token != None)
returnattr = token.getAttributes()
self.assert_(("attr2" != returnattr.getName(0)) == False)
_dummyList = [token]
_dummyList[:] = []
del _dummyList
_dummyList = [triple]
_dummyList[:] = []
del _dummyList
_dummyList = [attr]
_dummyList[:] = []
del _dummyList
pass
def test_XMLNode_clearNamespaces(self):
triple = libsbml.XMLTriple("test", "", "")
attr = libsbml.XMLAttributes()
node = libsbml.XMLNode(triple, attr)
i = node.addNamespace("http://test1.org/", "test1")
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
nms = node.getNamespaces()
self.assert_(nms.getLength() == 1)
i = node.addNamespace("http://test2.org/", "test2")
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
nms = node.getNamespaces()
self.assert_(nms.getLength() == 2)
i = node.clearNamespaces()
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
nms = node.getNamespaces()
self.assert_(nms.getLength() == 0)
_dummyList = [triple]
_dummyList[:] = []
del _dummyList
_dummyList = [attr]
_dummyList[:] = []
del _dummyList
_dummyList = [node]
_dummyList[:] = []
del _dummyList
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_XMLAttributes_remove1(self):
xa = libsbml.XMLAttributes()
xt2 = libsbml.XMLTriple("name2", "http://name2.org/", "p2")
i = xa.add("name1", "val1", "http://name1.org/", "p1")
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
i = xa.add(xt2, "val2")
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
i = xa.add("noprefix", "val3")
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
i = xa.add("name4", "val4", "http://name4.org/", "p1")
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assert_(xa.getLength() == 4)
i = xa.remove(4)
self.assert_(i == libsbml.LIBSBML_INDEX_EXCEEDS_SIZE)
i = xa.remove(3)
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assert_(xa.getLength() == 3)
i = xa.remove("noprefix")
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assert_(xa.getLength() == 2)
i = xa.remove(xt2)
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assert_(xa.getLength() == 1)
i = xa.remove("name1", "http://name1.org/")
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assert_(xa.getLength() == 0)
_dummyList = [xa]
_dummyList[:] = []
del _dummyList
_dummyList = [xt2]
_dummyList[:] = []
del _dummyList
pass
def test_XMLToken_namespace_get(self):
triple = libsbml.XMLTriple("test", "", "")
attr = libsbml.XMLAttributes()
token = libsbml.XMLToken(triple, attr)
token.addNamespace("http://test1.org/", "test1")
token.addNamespace("http://test2.org/", "test2")
token.addNamespace("http://test3.org/", "test3")
token.addNamespace("http://test4.org/", "test4")
token.addNamespace("http://test5.org/", "test5")
token.addNamespace("http://test6.org/", "test6")
token.addNamespace("http://test7.org/", "test7")
token.addNamespace("http://test8.org/", "test8")
token.addNamespace("http://test9.org/", "test9")
self.assert_(token.getNamespacesLength() == 9)
self.assert_(token.getNamespaceIndex("http://test1.org/") == 0)
self.assert_(("test2" != token.getNamespacePrefix(1)) == False)
self.assert_((
"test1" != token.getNamespacePrefix("http://test1.org/")) == False)
self.assert_(
("http://test2.org/" != token.getNamespaceURI(1)) == False)
self.assert_(
("http://test2.org/" != token.getNamespaceURI("test2")) == False)
self.assert_(token.getNamespaceIndex("http://test1.org/") == 0)
self.assert_(token.getNamespaceIndex("http://test2.org/") == 1)
self.assert_(token.getNamespaceIndex("http://test5.org/") == 4)
self.assert_(token.getNamespaceIndex("http://test9.org/") == 8)
self.assert_(token.getNamespaceIndex("http://testX.org/") == -1)
self.assert_(token.hasNamespaceURI("http://test1.org/") != False)
self.assert_(token.hasNamespaceURI("http://test2.org/") != False)
self.assert_(token.hasNamespaceURI("http://test5.org/") != False)
self.assert_(token.hasNamespaceURI("http://test9.org/") != False)
self.assert_(token.hasNamespaceURI("http://testX.org/") == False)
self.assert_(token.getNamespaceIndexByPrefix("test1") == 0)
self.assert_(token.getNamespaceIndexByPrefix("test5") == 4)
self.assert_(token.getNamespaceIndexByPrefix("test9") == 8)
self.assert_(token.getNamespaceIndexByPrefix("testX") == -1)
self.assert_(token.hasNamespacePrefix("test1") != False)
self.assert_(token.hasNamespacePrefix("test5") != False)
self.assert_(token.hasNamespacePrefix("test9") != False)
self.assert_(token.hasNamespacePrefix("testX") == False)
self.assert_(
token.hasNamespaceNS("http://test1.org/", "test1") != False)
self.assert_(
token.hasNamespaceNS("http://test5.org/", "test5") != False)
self.assert_(
token.hasNamespaceNS("http://test9.org/", "test9") != False)
self.assert_(
token.hasNamespaceNS("http://testX.org/", "testX") == False)
_dummyList = [token]
_dummyList[:] = []
del _dummyList
_dummyList = [triple]
_dummyList[:] = []
del _dummyList
_dummyList = [attr]
_dummyList[:] = []
del _dummyList
pass
def test_XMLNode_addChild3(self):
triple = libsbml.XMLTriple("test","","")
node = libsbml.XMLNode(triple)
node2 = libsbml.XMLNode()
i = node.addChild(node2)
self.assert_( i == libsbml.LIBSBML_INVALID_XML_OPERATION )
self.assert_( node.getNumChildren() == 0 )
_dummyList = [ triple ]; _dummyList[:] = []; del _dummyList
_dummyList = [ node ]; _dummyList[:] = []; del _dummyList
_dummyList = [ node2 ]; _dummyList[:] = []; del _dummyList
pass
def test_XMLToken_newSetters_setTriple2(self):
triple = libsbml.XMLTriple("test", "", "")
token = libsbml.XMLToken("This is text")
i = token.setTriple(triple)
self.assert_(i == libsbml.LIBSBML_INVALID_XML_OPERATION)
_dummyList = [triple]
_dummyList[:] = []
del _dummyList
_dummyList = [token]
_dummyList[:] = []
del _dummyList
pass
def test_XMLToken_newSetters_addAttributes1(self):
triple = libsbml.XMLTriple("test", "", "")
attr = libsbml.XMLAttributes()
token = libsbml.XMLToken(triple, attr)
xt2 = libsbml.XMLTriple("name3", "http://name3.org/", "p3")
i = token.addAttr("name1", "val1")
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assert_(token.getAttributesLength() == 1)
self.assert_(token.isAttributesEmpty() == False)
self.assert_(("name1" != token.getAttrName(0)) == False)
self.assert_(("val1" != token.getAttrValue(0)) == False)
i = token.addAttr("name2", "val2", "http://name1.org/", "p1")
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assert_(token.getAttributesLength() == 2)
self.assert_(token.isAttributesEmpty() == False)
self.assert_(("name2" != token.getAttrName(1)) == False)
self.assert_(("val2" != token.getAttrValue(1)) == False)
self.assert_(("http://name1.org/" != token.getAttrURI(1)) == False)
self.assert_(("p1" != token.getAttrPrefix(1)) == False)
i = token.addAttr(xt2, "val2")
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assert_(token.getAttributesLength() == 3)
self.assert_(token.isAttributesEmpty() == False)
self.assert_(("name3" != token.getAttrName(2)) == False)
self.assert_(("val2" != token.getAttrValue(2)) == False)
self.assert_(("http://name3.org/" != token.getAttrURI(2)) == False)
self.assert_(("p3" != token.getAttrPrefix(2)) == False)
_dummyList = [xt2]
_dummyList[:] = []
del _dummyList
_dummyList = [triple]
_dummyList[:] = []
del _dummyList
_dummyList = [attr]
_dummyList[:] = []
del _dummyList
_dummyList = [token]
_dummyList[:] = []
del _dummyList
pass
def test_XMLToken_newSetters_setTriple1(self):
triple = libsbml.XMLTriple("test", "", "")
token = libsbml.XMLToken()
i = token.setTriple(triple)
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assert_(("test" == token.getName()))
_dummyList = [triple]
_dummyList[:] = []
del _dummyList
_dummyList = [token]
_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_XMLNode_addChild2(self):
triple = libsbml.XMLTriple("test","","")
attr = libsbml.XMLAttributes()
node = libsbml.XMLNode(triple,attr)
node2 = libsbml.XMLNode()
i = node.addChild(node2)
self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS )
self.assert_( node.getNumChildren() == 1 )
_dummyList = [ triple ]; _dummyList[:] = []; del _dummyList
_dummyList = [ attr ]; _dummyList[:] = []; del _dummyList
_dummyList = [ node ]; _dummyList[:] = []; del _dummyList
_dummyList = [ node2 ]; _dummyList[:] = []; del _dummyList
pass
def test_XMLToken_newSetters_addNamespaces2(self):
triple = libsbml.XMLTriple("test", "", "")
token = libsbml.XMLToken(triple)
self.assert_(token.getNamespacesLength() == 0)
self.assert_(token.isNamespacesEmpty() == True)
i = token.addNamespace("http://test1.org/", "test1")
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
pass
def test_XMLNode_namespace_remove(self):
triple = libsbml.XMLTriple("test", "", "")
attr = libsbml.XMLAttributes()
node = libsbml.XMLNode(triple, attr)
node.addNamespace("http://test1.org/", "test1")
node.addNamespace("http://test2.org/", "test2")
node.addNamespace("http://test3.org/", "test3")
node.addNamespace("http://test4.org/", "test4")
node.addNamespace("http://test5.org/", "test5")
self.assert_(node.getNamespacesLength() == 5)
node.removeNamespace(4)
self.assert_(node.getNamespacesLength() == 4)
node.removeNamespace(3)
self.assert_(node.getNamespacesLength() == 3)
node.removeNamespace(2)
self.assert_(node.getNamespacesLength() == 2)
node.removeNamespace(1)
self.assert_(node.getNamespacesLength() == 1)
node.removeNamespace(0)
self.assert_(node.getNamespacesLength() == 0)
node.addNamespace("http://test1.org/", "test1")
node.addNamespace("http://test2.org/", "test2")
node.addNamespace("http://test3.org/", "test3")
node.addNamespace("http://test4.org/", "test4")
node.addNamespace("http://test5.org/", "test5")
self.assert_(node.getNamespacesLength() == 5)
node.removeNamespace(0)
self.assert_(node.getNamespacesLength() == 4)
node.removeNamespace(0)
self.assert_(node.getNamespacesLength() == 3)
node.removeNamespace(0)
self.assert_(node.getNamespacesLength() == 2)
node.removeNamespace(0)
self.assert_(node.getNamespacesLength() == 1)
node.removeNamespace(0)
self.assert_(node.getNamespacesLength() == 0)
_dummyList = [node]
_dummyList[:] = []
del _dummyList
_dummyList = [triple]
_dummyList[:] = []
del _dummyList
_dummyList = [attr]
_dummyList[:] = []
del _dummyList
pass
def test_XMLToken_namespace_remove(self):
triple = libsbml.XMLTriple("test", "", "")
attr = libsbml.XMLAttributes()
token = libsbml.XMLToken(triple, attr)
token.addNamespace("http://test1.org/", "test1")
token.addNamespace("http://test2.org/", "test2")
token.addNamespace("http://test3.org/", "test3")
token.addNamespace("http://test4.org/", "test4")
token.addNamespace("http://test5.org/", "test5")
self.assert_(token.getNamespacesLength() == 5)
token.removeNamespace(4)
self.assert_(token.getNamespacesLength() == 4)
token.removeNamespace(3)
self.assert_(token.getNamespacesLength() == 3)
token.removeNamespace(2)
self.assert_(token.getNamespacesLength() == 2)
token.removeNamespace(1)
self.assert_(token.getNamespacesLength() == 1)
token.removeNamespace(0)
self.assert_(token.getNamespacesLength() == 0)
token.addNamespace("http://test1.org/", "test1")
token.addNamespace("http://test2.org/", "test2")
token.addNamespace("http://test3.org/", "test3")
token.addNamespace("http://test4.org/", "test4")
token.addNamespace("http://test5.org/", "test5")
self.assert_(token.getNamespacesLength() == 5)
token.removeNamespace(0)
self.assert_(token.getNamespacesLength() == 4)
token.removeNamespace(0)
self.assert_(token.getNamespacesLength() == 3)
token.removeNamespace(0)
self.assert_(token.getNamespacesLength() == 2)
token.removeNamespace(0)
self.assert_(token.getNamespacesLength() == 1)
token.removeNamespace(0)
self.assert_(token.getNamespacesLength() == 0)
_dummyList = [token]
_dummyList[:] = []
del _dummyList
_dummyList = [triple]
_dummyList[:] = []
del _dummyList
_dummyList = [attr]
_dummyList[:] = []
del _dummyList
pass
