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_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 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_namespace_add(self):
triple = libsbml.XMLTriple("test", "", "")
attr = libsbml.XMLAttributes()
token = libsbml.XMLToken(triple, attr)
self.assert_(token.getNamespacesLength() == 0)
self.assert_(token.isNamespacesEmpty() == True)
token.addNamespace("http://test1.org/", "test1")
self.assert_(token.getNamespacesLength() == 1)
self.assert_(token.isNamespacesEmpty() == False)
token.addNamespace("http://test2.org/", "test2")
self.assert_(token.getNamespacesLength() == 2)
self.assert_(token.isNamespacesEmpty() == False)
token.addNamespace("http://test1.org/", "test1a")
self.assert_(token.getNamespacesLength() == 3)
self.assert_(token.isNamespacesEmpty() == False)
token.addNamespace("http://test1.org/", "test1a")
self.assert_(token.getNamespacesLength() == 3)
self.assert_(token.isNamespacesEmpty() == False)
self.assert_(
(token.getNamespaceIndex("http://test1.org/") == -1) == False)
_dummyList = [token]
_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 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_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_XMLToken_newSetters_setEOF(self):
token = libsbml.XMLToken()
self.assert_(token.isEnd() == False)
i = token.setEOF()
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assert_(token.isEnd() == False)
self.assert_(token.isStart() == False)
self.assert_(token.isText() == False)
_dummyList = [token]
_dummyList[:] = []
del _dummyList
pass
def test_XMLToken_chars(self):
token = libsbml.XMLToken("This is text")
self.assert_(token.isElement() == False)
self.assert_(token.isEnd() == False)
self.assert_(token.isStart() == False)
self.assert_(token.isText() == True)
self.assert_(token.isEOF() == False)
self.assert_(("This is text" != token.getCharacters()) == False)
_dummyList = [token]
_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_Token_copyConstructor(self):
t = libsbml.XMLTriple("sarah", "http://foo.org/", "bar")
token = libsbml.XMLToken(t,3,4)
self.assert_( token.getName() == "sarah" )
self.assert_( token.getURI() == "http://foo.org/" )
self.assert_( token.getPrefix() == "bar" )
self.assert_( token.isEnd() == True )
self.assert_( token.isEOF() == False )
self.assert_( token.getLine() == 3 )
self.assert_( token.getColumn() == 4 )
token2 = libsbml.XMLToken(token)
self.assert_( token2.getName() == "sarah" )
self.assert_( token2.getURI() == "http://foo.org/" )
self.assert_( token2.getPrefix() == "bar" )
self.assert_( token2.isEnd() == True )
self.assert_( token2.isEOF() == False )
self.assert_( token2.getLine() == 3 )
self.assert_( token2.getColumn() == 4 )
t = None
token = None
token2 = None
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_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_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_XMLToken_newSetters_removeAttributes1(self):
triple = libsbml.XMLTriple("test", "", "")
attr = libsbml.XMLAttributes()
token = libsbml.XMLToken(triple, attr)
xt2 = libsbml.XMLTriple("name3", "http://name3.org/", "p3")
xt1 = libsbml.XMLTriple("name5", "http://name5.org/", "p5")
i = token.addAttr("name1", "val1")
i = token.addAttr("name2", "val2", "http://name1.org/", "p1")
i = token.addAttr(xt2, "val2")
i = token.addAttr("name4", "val4")
self.assert_(token.getAttributes().getLength() == 4)
i = token.removeAttr(7)
self.assert_(i == libsbml.LIBSBML_INDEX_EXCEEDS_SIZE)
i = token.removeAttr("name7")
self.assert_(i == libsbml.LIBSBML_INDEX_EXCEEDS_SIZE)
i = token.removeAttr("name7", "namespaces7")
self.assert_(i == libsbml.LIBSBML_INDEX_EXCEEDS_SIZE)
i = token.removeAttr(xt1)
self.assert_(i == libsbml.LIBSBML_INDEX_EXCEEDS_SIZE)
self.assert_(token.getAttributes().getLength() == 4)
i = token.removeAttr(3)
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assert_(token.getAttributes().getLength() == 3)
i = token.removeAttr("name1")
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assert_(token.getAttributes().getLength() == 2)
i = token.removeAttr("name2", "http://name1.org/")
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assert_(token.getAttributes().getLength() == 1)
i = token.removeAttr(xt2)
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assert_(token.getAttributes().getLength() == 0)
_dummyList = [xt1]
_dummyList[:] = []
del _dummyList
_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_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_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
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_XMLToken_fields(self):
triple = libsbml.XMLTriple("attr", "uri", "prefix")
token = libsbml.XMLToken(triple)
self.assert_(token.isElement() == True)
self.assert_(token.isEnd() == True)
self.assert_(token.isStart() == False)
self.assert_(token.isText() == False)
self.assert_(token.isEOF() == False)
self.assert_(("attr" != token.getName()) == False)
self.assert_(("uri" != token.getURI()) == False)
self.assert_(("prefix" != token.getPrefix()) == False)
_dummyList = [token]
_dummyList[:] = []
del _dummyList
_dummyList = [triple]
_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_XMLNode_createFromToken(self):
triple = libsbml.XMLTriple("attr", "uri", "prefix")
token = libsbml.XMLToken(triple)
node = libsbml.XMLNode(token)
self.assert_(node != None)
self.assert_(node.getNumChildren() == 0)
self.assert_(("attr" != node.getName()) == False)
self.assert_(("prefix" != node.getPrefix()) == False)
self.assert_(("uri" != node.getURI()) == False)
self.assert_(node.getChild(1) != None)
_dummyList = [token]
_dummyList[:] = []
del _dummyList
_dummyList = [triple]
_dummyList[:] = []
del _dummyList
_dummyList = [node]
_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_removeNamespaces1(self):
triple = libsbml.XMLTriple("test", "", "")
attr = libsbml.XMLAttributes()
token = libsbml.XMLToken(triple, attr)
token.addNamespace("http://test1.org/", "test1")
self.assert_(token.getNamespacesLength() == 1)
i = token.removeNamespace("test2")
self.assert_(i == libsbml.LIBSBML_INDEX_EXCEEDS_SIZE)
self.assert_(token.getNamespacesLength() == 1)
i = token.removeNamespace("test1")
self.assert_(i == libsbml.LIBSBML_OPERATION_SUCCESS)
self.assert_(token.getNamespacesLength() == 0)
_dummyList = [token]
_dummyList[:] = []
del _dummyList
_dummyList = [triple]
_dummyList[:] = []
del _dummyList
_dummyList = [attr]
_dummyList[:] = []
del _dummyList
pass
def convertSBMLNotes(notesSBML='unset', notesDict='unset'):
"""
Function that translates notes sbml node to Dictionary and vice-versa
"""
# We use 'unset' instead of None as the deault here because sometimes None is given as a valid input value for notesSBML,
# and we want to return an empty dictionary for that.
# The following functions are used to convert to and from the types of records that
# can be conveyed in an SBML notes object.
rPassthrough = lambda line: line
rToInt = lambda line: int(line)
rToStrippedStr = lambda line: line.strip()
rToTrue = lambda line: True
rFromNumber = lambda numb: [str(numb)]
rGetAbbrev = lambda GCMS: GCMS.abbrev
def rFromLinesInDict(fragDict):
lines = []
for abbrev in fragDict:
lines.append(fragDict[abbrev].line)
return lines
# looks like e.g. [[0,1],[2,3]]. It means first fragment has carbon 0 and 1 eliminated and second fragment carbons 2 and 3
def rToDestInfo(line):
indsnew = []
inds = line.split(';')
for ind in inds:
indsnew.append(ind.strip().split(','))
return indsnew
def rFromDestInfo(carbonsOut):
if carbonsOut is None:
return []
newgroups = []
for group in carbonsOut:
newgroups.append(','.join(group))
return [';'.join(newgroups)]
def rToFlux(line):
# Examples of acceptable inputs:
# <flux forward="240.34" backward="5.0" net="[230:235.34:237.004]" exchange="5.0" />
# Or:
# "240.34, 5.0, [230:235.34:237.004], 5.0"
# Or:
# "240.34, 5.0, 235.34, 5.0"
if isinstance(line, libsbml.XMLNode):
forward = None
backward = None
net = None
exchange = None
if line.hasAttr("forward"):
forward = line.getAttrValue("forward")
if line.hasAttr("backward"):
backward = line.getAttrValue("backward")
if line.hasAttr("net"):
net = line.getAttrValue("net")
if line.hasAttr("exchange"):
exchange = line.getAttrValue("exchange")
else:
v = line.split(',')
if len(v) != 4:
raise Exception('Wrong input for flux value from SBML')
forward = v[0]
backward = v[1]
net = v[2]
exchange = v[3]
processed = []
for item in [forward, backward, net, exchange]:
# If they look like rangedNumbers, turn them into rangedNumber objects
# before passing them to the flux instantiator.
if isinstance(item, str):
item = item.strip()
if core.rangedNumber.looks_like_rangedNumber(item):
item = core.rangedNumber.from_string(item)
else:
if utils.is_float(item):
item = float(item)
processed.append(item)
forward = processed[0]
backward = processed[1]
net = processed[2]
exchange = processed[3]
flux = core.flux(for_back_tup=(forward, backward),
net_exc_tup=(net, exchange))
return flux
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]
# A dictionary of note headers, providing three things:
# 1. A function to use for input from SBML line into dictionary key,
# 2. An inverse function to use for obtaining SBML line from dict element,
# 3. A function to produce a label for dictionary in the case of multiple entries (e.g. GCMS)
noteTypes = {
'GCMSLabelData':
(labeling.GCMSLabelData, rFromLinesInDict, rGetAbbrev),
'GCMSLabelData(fit)':
(labeling.GCMSLabelData, rFromLinesInDict, rGetAbbrev),
'LCMSLabelData':
(labeling.LCMSLabelData, rFromLinesInDict, rGetAbbrev),
'LCMSLabelData(fit)':
(labeling.LCMSLabelData, rFromLinesInDict, rGetAbbrev),
'CEMSLabelData': (labeling.CEMSLabelData, rFromLinesInDict,
rGetAbbrev),
'CEMSLabelData(fit)': (labeling.CEMSLabelData, rFromLinesInDict,
rGetAbbrev),
'DENS': (rPassthrough, '', ''),
'CARBON TRANSITIONS TYPE': (rPassthrough, '', ''),
'CARBON_TRANSITIONS': (rToStrippedStr, '', ''),
'LABELING_DEST': (rToDestInfo, rFromDestInfo, ''),
'LABELING_SOURCE': (rToTrue, '', ''),
'EXCLUDED': (rToTrue, '', ''),
'FEED': (rPassthrough, '', ''),
'CARBON NUMBER': (rToInt, rFromNumber, ''),
'FLUX VALUE': (rToFlux, rFromFlux, ''),
'SUBSYSTEM': (rPassthrough, '', ''),
'GENE_ASSOCIATION': (rPassthrough, '', ''),
'PROTEIN_ASSOCIATION': (rPassthrough, '', ''),
'FORMULA': (rPassthrough, '', '')
}
# SBML Notes to notesDict
if notesSBML != 'unset':
notesDict = {}
if not notesSBML:
return notesDict
notesBody = notesSBML
if notesSBML.hasChild('body'):
notesBody = notesSBML.getChild(0)
for i in range(notesBody.getNumChildren()):
nElement = notesBody.getChild(i)
string = nElement.getChild(0).toXMLString()
try:
noteHead, noteContent = string.split(':', 1)
except ValueError:
continue
# If there is an additional XML object inside the note element, past the
# text string, use that as the note content, rather than the remainder of the string.
if (nElement.getNumChildren() > 1):
noteContent = nElement.getChild(1)
header = noteHead.strip()
if header in noteTypes:
recordImportFunction, recordExportFunction, labelGeneratorFunc = noteTypes[
header]
# Eliminate header (e.g. GCMS :) from string
object = recordImportFunction(noteContent)
else:
labelGeneratorFunc = ''
object = noteContent
# Store
# This object is meant to return a dictionary, store as a list for the moment
if labelGeneratorFunc != '':
if header in notesDict:
notesDict[header].append(object)
else:
notesDict[header] = [object]
# One entry
else:
notesDict[header] = object
# Convert lists into dictionaries if labelGeneratorFunc has been provided
for header in notesDict:
if header in noteTypes:
recordImportFunction, recordExportFunction, labelGeneratorFunc = noteTypes[
header]
# if there is a function and it is a list (iterable object)
if labelGeneratorFunc and getattr(notesDict[header],
'__iter__', False):
dict = {}
list = notesDict[header]
for object in list:
dict[labelGeneratorFunc(object)] = object
notesDict[header] = dict
return notesDict
# notesDict to SBML Notes
elif notesDict != 'unset':
notesSBML = libsbml.XMLNode()
triple = libsbml.XMLTriple("body", "", "")
att = libsbml.XMLAttributes()
ns = libsbml.XMLNamespaces()
ns.add("http://www.w3.org/1999/xhtml", "")
token = libsbml.XMLToken(triple, att, ns)
notesBodyNode = libsbml.XMLNode(token)
ns.clear()
triple = libsbml.XMLTriple("p", "", "")
token = libsbml.XMLToken(triple, att, ns)
for header in notesDict:
object = notesDict[header]
lines = [object]
if header in noteTypes:
recordImportFunction, recordExportFunction, labelGeneratorFunc = noteTypes[
header]
if recordExportFunction:
lines = recordExportFunction(object)
# Processing all lines
for line in lines:
# If the result of the export function was None, don't bother embedding the note
if line is None:
continue
node = libsbml.XMLNode(token)
if isinstance(line, libsbml.XMLNode):
tt = libsbml.XMLToken(header + ': ')
n1 = libsbml.XMLNode(tt)
node.addChild(n1)
node.addChild(line)
else:
tt = libsbml.XMLToken(header + ': ' + str(line))
n1 = libsbml.XMLNode(tt)
node.addChild(n1)
notesBodyNode.addChild(node)
notesSBML.addChild(notesBodyNode)
return notesSBML
raise Exception('convertSBMLNotes called with no valid input')
def test_XMLToken_attribute_set_clear(self):
triple = libsbml.XMLTriple("test", "", "")
attr = libsbml.XMLAttributes()
token = libsbml.XMLToken(triple, attr)
nattr = libsbml.XMLAttributes()
xt1 = libsbml.XMLTriple("name1", "http://name1.org/", "p1")
xt2 = libsbml.XMLTriple("name2", "http://name2.org/", "p2")
xt3 = libsbml.XMLTriple("name3", "http://name3.org/", "p3")
xt4 = libsbml.XMLTriple("name4", "http://name4.org/", "p4")
xt5 = libsbml.XMLTriple("name5", "http://name5.org/", "p5")
nattr.add(xt1, "val1")
nattr.add(xt2, "val2")
nattr.add(xt3, "val3")
nattr.add(xt4, "val4")
nattr.add(xt5, "val5")
token.setAttributes(nattr)
self.assert_(token.getAttributesLength() == 5)
self.assert_(token.isAttributesEmpty() == False)
self.assert_(("name1" != token.getAttrName(0)) == False)
self.assert_(("val1" != token.getAttrValue(0)) == False)
self.assert_(("http://name1.org/" != token.getAttrURI(0)) == False)
self.assert_(("p1" != token.getAttrPrefix(0)) == False)
self.assert_(("name2" != token.getAttrName(1)) == False)
self.assert_(("val2" != token.getAttrValue(1)) == False)
self.assert_(("http://name2.org/" != token.getAttrURI(1)) == False)
self.assert_(("p2" != token.getAttrPrefix(1)) == False)
self.assert_(("name3" != token.getAttrName(2)) == False)
self.assert_(("val3" != token.getAttrValue(2)) == False)
self.assert_(("http://name3.org/" != token.getAttrURI(2)) == False)
self.assert_(("p3" != token.getAttrPrefix(2)) == False)
self.assert_(("name4" != token.getAttrName(3)) == False)
self.assert_(("val4" != token.getAttrValue(3)) == False)
self.assert_(("http://name4.org/" != token.getAttrURI(3)) == False)
self.assert_(("p4" != token.getAttrPrefix(3)) == False)
self.assert_(("name5" != token.getAttrName(4)) == False)
self.assert_(("val5" != token.getAttrValue(4)) == False)
self.assert_(("http://name5.org/" != token.getAttrURI(4)) == False)
self.assert_(("p5" != token.getAttrPrefix(4)) == False)
ntriple = libsbml.XMLTriple("test2", "http://test2.org/", "p2")
token.setTriple(ntriple)
self.assert_(("test2" != token.getName()) == False)
self.assert_(("http://test2.org/" != token.getURI()) == False)
self.assert_(("p2" != token.getPrefix()) == False)
token.clearAttributes()
self.assert_(token.getAttributesLength() == 0)
self.assert_(token.isAttributesEmpty() != False)
_dummyList = [nattr]
_dummyList[:] = []
del _dummyList
_dummyList = [triple]
_dummyList[:] = []
del _dummyList
_dummyList = [ntriple]
_dummyList[:] = []
del _dummyList
_dummyList = [attr]
_dummyList[:] = []
del _dummyList
_dummyList = [token]
_dummyList[:] = []
del _dummyList
_dummyList = [xt1]
_dummyList[:] = []
del _dummyList
_dummyList = [xt2]
_dummyList[:] = []
del _dummyList
_dummyList = [xt3]
_dummyList[:] = []
del _dummyList
_dummyList = [xt4]
_dummyList[:] = []
del _dummyList
_dummyList = [xt5]
_dummyList[:] = []
del _dummyList
pass
def test_XMLToken_attribute_add_remove(self):
triple = libsbml.XMLTriple("test", "", "")
attr = libsbml.XMLAttributes()
token = libsbml.XMLToken(triple, attr)
xt1 = libsbml.XMLTriple("name1", "http://name1.org/", "p1")
xt2 = libsbml.XMLTriple("name2", "http://name2.org/", "p2")
xt3 = libsbml.XMLTriple("name3", "http://name3.org/", "p3")
xt1a = libsbml.XMLTriple("name1", "http://name1a.org/", "p1a")
xt2a = libsbml.XMLTriple("name2", "http://name2a.org/", "p2a")
token.addAttr("name1", "val1", "http://name1.org/", "p1")
token.addAttr(xt2, "val2")
self.assert_(token.getAttributesLength() == 2)
self.assert_(token.isAttributesEmpty() == False)
self.assert_(("name1" != token.getAttrName(0)) == False)
self.assert_(("val1" != token.getAttrValue(0)) == False)
self.assert_(("http://name1.org/" != token.getAttrURI(0)) == False)
self.assert_(("p1" != token.getAttrPrefix(0)) == False)
self.assert_(("name2" != token.getAttrName(1)) == False)
self.assert_(("val2" != token.getAttrValue(1)) == False)
self.assert_(("http://name2.org/" != token.getAttrURI(1)) == False)
self.assert_(("p2" != token.getAttrPrefix(1)) == False)
self.assert_(token.getAttrValue("name1") == "")
self.assert_(token.getAttrValue("name2") == "")
self.assert_(
("val1" != token.getAttrValue("name1", "http://name1.org/")
) == False)
self.assert_(
("val2" != token.getAttrValue("name2", "http://name2.org/")
) == False)
self.assert_(("val1" != token.getAttrValue(xt1)) == False)
self.assert_(("val2" != token.getAttrValue(xt2)) == False)
self.assert_(token.hasAttr(-1) == False)
self.assert_(token.hasAttr(2) == False)
self.assert_(token.hasAttr(0) == True)
self.assert_(token.hasAttr("name1", "http://name1.org/") == True)
self.assert_(token.hasAttr("name2", "http://name2.org/") == True)
self.assert_(token.hasAttr("name3", "http://name3.org/") == False)
self.assert_(token.hasAttr(xt1) == True)
self.assert_(token.hasAttr(xt2) == True)
self.assert_(token.hasAttr(xt3) == False)
token.addAttr("noprefix", "val3")
self.assert_(token.getAttributesLength() == 3)
self.assert_(token.isAttributesEmpty() == False)
self.assert_(("noprefix" != token.getAttrName(2)) == False)
self.assert_(("val3" != token.getAttrValue(2)) == False)
self.assert_(token.getAttrURI(2) == "")
self.assert_(token.getAttrPrefix(2) == "")
self.assert_(("val3" != token.getAttrValue("noprefix")) == False)
self.assert_(("val3" != token.getAttrValue("noprefix", "")) == False)
self.assert_(token.hasAttr("noprefix") == True)
self.assert_(token.hasAttr("noprefix", "") == True)
token.addAttr(xt1, "mval1")
token.addAttr("name2", "mval2", "http://name2.org/", "p2")
self.assert_(token.getAttributesLength() == 3)
self.assert_(token.isAttributesEmpty() == False)
self.assert_(("name1" != token.getAttrName(0)) == False)
self.assert_(("mval1" != token.getAttrValue(0)) == False)
self.assert_(("http://name1.org/" != token.getAttrURI(0)) == False)
self.assert_(("p1" != token.getAttrPrefix(0)) == False)
self.assert_(("name2" != token.getAttrName(1)) == False)
self.assert_(("mval2" != token.getAttrValue(1)) == False)
self.assert_(("http://name2.org/" != token.getAttrURI(1)) == False)
self.assert_(("p2" != token.getAttrPrefix(1)) == False)
self.assert_(token.hasAttr(xt1) == True)
self.assert_(token.hasAttr("name1", "http://name1.org/") == True)
token.addAttr("noprefix", "mval3")
self.assert_(token.getAttributesLength() == 3)
self.assert_(token.isAttributesEmpty() == False)
self.assert_(("noprefix" != token.getAttrName(2)) == False)
self.assert_(("mval3" != token.getAttrValue(2)) == False)
self.assert_(token.getAttrURI(2) == "")
self.assert_(token.getAttrPrefix(2) == "")
self.assert_(token.hasAttr("noprefix") == True)
self.assert_(token.hasAttr("noprefix", "") == True)
token.addAttr(xt1a, "val1a")
token.addAttr(xt2a, "val2a")
self.assert_(token.getAttributesLength() == 5)
self.assert_(("name1" != token.getAttrName(3)) == False)
self.assert_(("val1a" != token.getAttrValue(3)) == False)
self.assert_(("http://name1a.org/" != token.getAttrURI(3)) == False)
self.assert_(("p1a" != token.getAttrPrefix(3)) == False)
self.assert_(("name2" != token.getAttrName(4)) == False)
self.assert_(("val2a" != token.getAttrValue(4)) == False)
self.assert_(("http://name2a.org/" != token.getAttrURI(4)) == False)
self.assert_(("p2a" != token.getAttrPrefix(4)) == False)
self.assert_(
("val1a" != token.getAttrValue("name1", "http://name1a.org/")
) == False)
self.assert_(
("val2a" != token.getAttrValue("name2", "http://name2a.org/")
) == False)
self.assert_(("val1a" != token.getAttrValue(xt1a)) == False)
self.assert_(("val2a" != token.getAttrValue(xt2a)) == False)
token.removeAttr(xt1a)
token.removeAttr(xt2a)
self.assert_(token.getAttributesLength() == 3)
token.removeAttr("name1", "http://name1.org/")
self.assert_(token.getAttributesLength() == 2)
self.assert_(token.isAttributesEmpty() == False)
self.assert_(("name2" != token.getAttrName(0)) == False)
self.assert_(("mval2" != token.getAttrValue(0)) == False)
self.assert_(("http://name2.org/" != token.getAttrURI(0)) == False)
self.assert_(("p2" != token.getAttrPrefix(0)) == False)
self.assert_(("noprefix" != token.getAttrName(1)) == False)
self.assert_(("mval3" != token.getAttrValue(1)) == False)
self.assert_(token.getAttrURI(1) == "")
self.assert_(token.getAttrPrefix(1) == "")
self.assert_(token.hasAttr("name1", "http://name1.org/") == False)
token.removeAttr(xt2)
self.assert_(token.getAttributesLength() == 1)
self.assert_(token.isAttributesEmpty() == False)
self.assert_(("noprefix" != token.getAttrName(0)) == False)
self.assert_(("mval3" != token.getAttrValue(0)) == False)
self.assert_(token.getAttrURI(0) == "")
self.assert_(token.getAttrPrefix(0) == "")
self.assert_(token.hasAttr(xt2) == False)
self.assert_(token.hasAttr("name2", "http://name2.org/") == False)
token.removeAttr("noprefix")
self.assert_(token.getAttributesLength() == 0)
self.assert_(token.isAttributesEmpty() == True)
self.assert_(token.hasAttr("noprefix") == False)
self.assert_(token.hasAttr("noprefix", "") == False)
_dummyList = [token]
_dummyList[:] = []
del _dummyList
_dummyList = [xt1]
_dummyList[:] = []
del _dummyList
_dummyList = [xt2]
_dummyList[:] = []
del _dummyList
_dummyList = [xt3]
_dummyList[:] = []
del _dummyList
_dummyList = [xt1a]
_dummyList[:] = []
del _dummyList
_dummyList = [xt2a]
_dummyList[:] = []
del _dummyList
_dummyList = [triple]
_dummyList[:] = []
del _dummyList
_dummyList = [attr]
_dummyList[:] = []
del _dummyList
pass
