public void test_XMLNode_getChildForName()
{
string xmlstr = "<annotation>\n" + " <test xmlns=\"http://test.org/\" id=\"test\">test</test>\n" + "</annotation>";
XMLNode node = new XMLNode();
XMLNode annotation = node.getChild("test");
string name = annotation.getName();
assertTrue(name == "");
node = null;
node = XMLNode.convertStringToXMLNode(xmlstr, null);
annotation = node.getChild("test");
assertTrue(("test" != annotation.getName()) == false);
node = null;
}
public void test_XMLNode_attribute_set_clear()
{
XMLTriple triple = new XMLTriple("test", "", "");
XMLAttributes attr = new XMLAttributes();
XMLNode node = new XMLNode(triple, attr);
XMLAttributes nattr = new XMLAttributes();
XMLTriple xt1 = new XMLTriple("name1", "http://name1.org/", "p1");
XMLTriple xt2 = new XMLTriple("name2", "http://name2.org/", "p2");
XMLTriple xt3 = new XMLTriple("name3", "http://name3.org/", "p3");
XMLTriple xt4 = new XMLTriple("name4", "http://name4.org/", "p4");
XMLTriple xt5 = new 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");
node.setAttributes(nattr);
assertTrue(node.getAttributesLength() == 5);
assertTrue(node.isAttributesEmpty() == false);
assertTrue(("name1" != node.getAttrName(0)) == false);
assertTrue(("val1" != node.getAttrValue(0)) == false);
assertTrue(("http://name1.org/" != node.getAttrURI(0)) == false);
assertTrue(("p1" != node.getAttrPrefix(0)) == false);
assertTrue(("name2" != node.getAttrName(1)) == false);
assertTrue(("val2" != node.getAttrValue(1)) == false);
assertTrue(("http://name2.org/" != node.getAttrURI(1)) == false);
assertTrue(("p2" != node.getAttrPrefix(1)) == false);
assertTrue(("name3" != node.getAttrName(2)) == false);
assertTrue(("val3" != node.getAttrValue(2)) == false);
assertTrue(("http://name3.org/" != node.getAttrURI(2)) == false);
assertTrue(("p3" != node.getAttrPrefix(2)) == false);
assertTrue(("name4" != node.getAttrName(3)) == false);
assertTrue(("val4" != node.getAttrValue(3)) == false);
assertTrue(("http://name4.org/" != node.getAttrURI(3)) == false);
assertTrue(("p4" != node.getAttrPrefix(3)) == false);
assertTrue(("name5" != node.getAttrName(4)) == false);
assertTrue(("val5" != node.getAttrValue(4)) == false);
assertTrue(("http://name5.org/" != node.getAttrURI(4)) == false);
assertTrue(("p5" != node.getAttrPrefix(4)) == false);
XMLTriple ntriple = new XMLTriple("test2", "http://test2.org/", "p2");
node.setTriple(ntriple);
assertTrue(("test2" != node.getName()) == false);
assertTrue(("http://test2.org/" != node.getURI()) == false);
assertTrue(("p2" != node.getPrefix()) == false);
node.clearAttributes();
assertTrue(node.getAttributesLength() == 0);
assertTrue(node.isAttributesEmpty() != false);
triple = null;
ntriple = null;
node = null;
attr = null;
nattr = null;
xt1 = null;
xt2 = null;
xt3 = null;
xt4 = null;
xt5 = null;
}
public void test_Node_copyConstructor()
{
XMLAttributes att = new XMLAttributes();
XMLTriple t = new XMLTriple("sarah", "http://foo.org/", "bar");
XMLToken token = new XMLToken(t, att, 3, 4);
XMLNode node = new XMLNode(token);
XMLNode child = new XMLNode();
node.addChild(child);
assertTrue(node.getNumChildren() == 1);
assertTrue(node.getName() == "sarah");
assertTrue(node.getURI() == "http://foo.org/");
assertTrue(node.getPrefix() == "bar");
assertTrue(node.isEnd() == false);
assertTrue(node.isEOF() == false);
assertTrue(node.getLine() == 3);
assertTrue(node.getColumn() == 4);
XMLNode node2 = new XMLNode(node);
assertTrue(node2.getNumChildren() == 1);
assertTrue(node2.getName() == "sarah");
assertTrue(node2.getURI() == "http://foo.org/");
assertTrue(node2.getPrefix() == "bar");
assertTrue(node2.isEnd() == false);
assertTrue(node2.isEOF() == false);
assertTrue(node2.getLine() == 3);
assertTrue(node2.getColumn() == 4);
t = null;
token = null;
node = null;
node2 = null;
}
public void test_RDFAnnotation_C_delete()
{
SBase obj = m.getCompartment(0);
XMLNode node = RDFAnnotationParser.parseCVTerms(obj);
XMLNode n1 = RDFAnnotationParser.deleteRDFAnnotation(node);
assertTrue(n1.getNumChildren() == 0);
assertTrue(("annotation" == n1.getName()));
node = null;
}
public void test_RDFAnnotation_delete()
{
XMLNode node = RDFAnnotationParser.parseCVTerms(m.getCompartment(0));
XMLNode n1 = RDFAnnotationParser.deleteRDFAnnotation(node);
string expected = "<annotation/>";
assertTrue( n1.getNumChildren() == 0 );
assertTrue( n1.getName() == "annotation" );
assertEquals( true, equals(expected,n1.toXMLString()) );
node = null;
}
public void test_RDFAnnotation_C_parseCVTerms()
{
SBase obj = m.getCompartment(0);
XMLNode node = RDFAnnotationParser.parseCVTerms(obj);
assertTrue(node.getNumChildren() == 1);
XMLNode rdf = node.getChild(0);
assertTrue(("RDF" == rdf.getName()));
assertTrue(("rdf" == rdf.getPrefix()));
assertTrue(("http://www.w3.org/1999/02/22-rdf-syntax-ns#" == rdf.getURI()));
assertTrue(rdf.getNumChildren() == 1);
XMLNode desc = rdf.getChild(0);
assertTrue(("Description" == desc.getName()));
assertTrue(("rdf" == desc.getPrefix()));
assertTrue(("http://www.w3.org/1999/02/22-rdf-syntax-ns#" == desc.getURI()));
assertTrue(desc.getNumChildren() == 1);
XMLNode is1 = desc.getChild(0);
assertTrue(("is" == is1.getName()));
assertTrue(("bqbiol" == is1.getPrefix()));
assertTrue(is1.getNumChildren() == 1);
XMLNode Bag = is1.getChild(0);
assertTrue(("Bag" == Bag.getName()));
assertTrue(("rdf" == Bag.getPrefix()));
assertTrue(("http://www.w3.org/1999/02/22-rdf-syntax-ns#" == Bag.getURI()));
assertTrue(Bag.getNumChildren() == 4);
XMLNode li = Bag.getChild(0);
assertTrue(("li" == li.getName()));
assertTrue(("rdf" == li.getPrefix()));
assertTrue(("http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li.getURI()));
assertTrue(li.getNumChildren() == 0);
XMLNode li1 = Bag.getChild(1);
assertTrue(("li" == li1.getName()));
assertTrue(("rdf" == li1.getPrefix()));
assertTrue(("http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li1.getURI()));
assertTrue(li1.getNumChildren() == 0);
XMLNode li2 = Bag.getChild(2);
assertTrue(("li" == li2.getName()));
assertTrue(("rdf" == li2.getPrefix()));
assertTrue(("http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li2.getURI()));
assertTrue(li2.getNumChildren() == 0);
XMLNode li3 = Bag.getChild(3);
assertTrue(("li" == li3.getName()));
assertTrue(("rdf" == li3.getPrefix()));
assertTrue(("http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li3.getURI()));
assertTrue(li3.getNumChildren() == 0);
node = null;
}
public void test_L3ModelHistory_delete_Model()
{
XMLNode node = RDFAnnotationParser.parseModelHistory(m);
XMLNode n1 = RDFAnnotationParser.deleteRDFAnnotation(node);
string expected = "<annotation/>";
assertTrue(n1.getNumChildren() == 0);
assertTrue(n1.getName() == "annotation");
assertEquals(true, equals(expected, n1.toXMLString()));
node = null;
}
public void test_XMLNode_createFromToken()
{
XMLToken token;
XMLTriple triple;
XMLNode node;
triple = new XMLTriple("attr", "uri", "prefix");
token = new XMLToken(triple);
node = new XMLNode(token);
assertTrue(node != null);
assertTrue(node.getNumChildren() == 0);
assertTrue(("attr" != node.getName()) == false);
assertTrue(("prefix" != node.getPrefix()) == false);
assertTrue(("uri" != node.getURI()) == false);
assertTrue(node.getChild(1) != null);
token = null;
triple = null;
node = null;
}
public void test_XMLNode_getters()
{
XMLToken token;
XMLNode node;
XMLTriple triple;
XMLAttributes attr;
XMLNamespaces NS;
NS = new XMLNamespaces();
NS.add("http://test1.org/", "test1");
token = new XMLToken("This is a test");
node = new XMLNode(token);
assertTrue(node != null);
assertTrue(node.getNumChildren() == 0);
assertTrue(("This is a test" != node.getCharacters()) == false);
assertTrue(node.getChild(1) != null);
attr = new XMLAttributes();
assertTrue(attr != null);
attr.add("attr2", "value");
triple = new XMLTriple("attr", "uri", "prefix");
token = new XMLToken(triple, attr);
assertTrue(token != null);
node = new XMLNode(token);
assertTrue(("attr" != node.getName()) == false);
assertTrue(("uri" != node.getURI()) == false);
assertTrue(("prefix" != node.getPrefix()) == false);
XMLAttributes returnattr = node.getAttributes();
assertTrue(("attr2" != returnattr.getName(0)) == false);
assertTrue(("value" != returnattr.getValue(0)) == false);
token = new XMLToken(triple, attr, NS);
node = new XMLNode(token);
XMLNamespaces returnNS = node.getNamespaces();
assertTrue(returnNS.getLength() == 1);
assertTrue(returnNS.isEmpty() == false);
triple = null;
token = null;
node = null;
}
public void test_L3ModelHistory_parseModelHistory_Model()
{
XMLNode node = RDFAnnotationParser.parseModelHistory(m);
assertTrue(node.getNumChildren() == 1);
XMLNode rdf = node.getChild(0);
assertTrue(("RDF" == rdf.getName()));
assertTrue(("rdf" == rdf.getPrefix()));
assertTrue(("http://www.w3.org/1999/02/22-rdf-syntax-ns#" == rdf.getURI()));
assertTrue(rdf.getNumChildren() == 1);
XMLNode desc = rdf.getChild(0);
assertTrue(("Description" == desc.getName()));
assertTrue(("rdf" == desc.getPrefix()));
assertTrue(("http://www.w3.org/1999/02/22-rdf-syntax-ns#" == desc.getURI()));
assertTrue(desc.getNumChildren() == 4);
XMLNode creator = desc.getChild(0);
assertTrue(("creator" == creator.getName()));
assertTrue(("dcterms" == creator.getPrefix()));
assertTrue(creator.getNumChildren() == 1);
XMLNode Bag = creator.getChild(0);
assertTrue(("Bag" == Bag.getName()));
assertTrue(("rdf" == Bag.getPrefix()));
assertTrue(("http://www.w3.org/1999/02/22-rdf-syntax-ns#" == Bag.getURI()));
assertTrue(Bag.getNumChildren() == 1);
XMLNode li = Bag.getChild(0);
assertTrue(("li" == li.getName()));
assertTrue(("rdf" == li.getPrefix()));
assertTrue(("http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li.getURI()));
assertTrue(li.getNumChildren() == 3);
XMLNode N = li.getChild(0);
assertTrue(("N" == N.getName()));
assertTrue(("vCard" == N.getPrefix()));
assertTrue(("http://www.w3.org/2001/vcard-rdf/3.0#" == N.getURI()));
assertTrue(N.getNumChildren() == 2);
XMLNode Family = N.getChild(0);
assertTrue(("Family" == Family.getName()));
assertTrue(("vCard" == Family.getPrefix()));
assertTrue(("http://www.w3.org/2001/vcard-rdf/3.0#" == Family.getURI()));
assertTrue(Family.getNumChildren() == 1);
XMLNode Given = N.getChild(1);
assertTrue(("Given" == Given.getName()));
assertTrue(("vCard" == Given.getPrefix()));
assertTrue(("http://www.w3.org/2001/vcard-rdf/3.0#" == Given.getURI()));
assertTrue(Given.getNumChildren() == 1);
XMLNode EMAIL = li.getChild(1);
assertTrue(("EMAIL" == EMAIL.getName()));
assertTrue(("vCard" == EMAIL.getPrefix()));
assertTrue(("http://www.w3.org/2001/vcard-rdf/3.0#" == EMAIL.getURI()));
assertTrue(EMAIL.getNumChildren() == 1);
XMLNode ORG = li.getChild(2);
assertTrue(("ORG" == ORG.getName()));
assertTrue(("vCard" == ORG.getPrefix()));
assertTrue(("http://www.w3.org/2001/vcard-rdf/3.0#" == ORG.getURI()));
assertTrue(ORG.getNumChildren() == 1);
XMLNode Orgname = ORG.getChild(0);
assertTrue(("Orgname" == Orgname.getName()));
assertTrue(("vCard" == Orgname.getPrefix()));
assertTrue(("http://www.w3.org/2001/vcard-rdf/3.0#" == Orgname.getURI()));
assertTrue(Orgname.getNumChildren() == 1);
XMLNode created = desc.getChild(1);
assertTrue(("created" == created.getName()));
assertTrue(("dcterms" == created.getPrefix()));
assertTrue(("http://purl.org/dc/terms/" == created.getURI()));
assertTrue(created.getNumChildren() == 1);
XMLNode cr_date = created.getChild(0);
assertTrue(("W3CDTF" == cr_date.getName()));
assertTrue(("dcterms" == cr_date.getPrefix()));
assertTrue(("http://purl.org/dc/terms/" == cr_date.getURI()));
assertTrue(cr_date.getNumChildren() == 1);
XMLNode modified = desc.getChild(2);
assertTrue(("modified" == modified.getName()));
assertTrue(("dcterms" == modified.getPrefix()));
assertTrue(("http://purl.org/dc/terms/" == modified.getURI()));
assertTrue(modified.getNumChildren() == 1);
XMLNode mo_date = created.getChild(0);
assertTrue(("W3CDTF" == mo_date.getName()));
assertTrue(("dcterms" == mo_date.getPrefix()));
assertTrue(("http://purl.org/dc/terms/" == mo_date.getURI()));
assertTrue(mo_date.getNumChildren() == 1);
node = null;
}
public void test_RDFAnnotation_parseCVTerms()
{
XMLNode node = RDFAnnotationParser.parseCVTerms(m.getCompartment(0));
assertTrue(node.getNumChildren() == 1);
XMLNode rdf = node.getChild(0);
assertTrue(("RDF" == rdf.getName()));
assertTrue(("rdf" == rdf.getPrefix()));
assertTrue(("http://www.w3.org/1999/02/22-rdf-syntax-ns#" == rdf.getURI()));
assertTrue(rdf.getNumChildren() == 1);
XMLNode desc = rdf.getChild(0);
assertTrue(("Description" == desc.getName()));
assertTrue(("rdf" == desc.getPrefix()));
assertTrue(("http://www.w3.org/1999/02/22-rdf-syntax-ns#" == desc.getURI()));
assertTrue(desc.getNumChildren() == 1);
XMLNode is1 = desc.getChild(0);
assertTrue(("is" == is1.getName()));
assertTrue(("bqbiol" == is1.getPrefix()));
assertTrue(is1.getNumChildren() == 1);
XMLNode Bag = is1.getChild(0);
assertTrue(("Bag" == Bag.getName()));
assertTrue(("rdf" == Bag.getPrefix()));
assertTrue(("http://www.w3.org/1999/02/22-rdf-syntax-ns#" == Bag.getURI()));
assertTrue(Bag.getNumChildren() == 4);
XMLNode li = Bag.getChild(0);
assertTrue(("li" == li.getName()));
assertTrue(("rdf" == li.getPrefix()));
assertTrue(("http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li.getURI()));
assertTrue(li.getNumChildren() == 0);
XMLNode li1 = Bag.getChild(1);
assertTrue(("li" == li1.getName()));
assertTrue(("rdf" == li1.getPrefix()));
assertTrue(("http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li1.getURI()));
assertTrue(li1.getNumChildren() == 0);
XMLNode li2 = Bag.getChild(2);
assertTrue(("li" == li2.getName()));
assertTrue(("rdf" == li2.getPrefix()));
assertTrue(("http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li2.getURI()));
assertTrue(li2.getNumChildren() == 0);
XMLNode li3 = Bag.getChild(3);
assertTrue(("li" == li3.getName()));
assertTrue(("rdf" == li3.getPrefix()));
assertTrue(("http://www.w3.org/1999/02/22-rdf-syntax-ns#" == li3.getURI()));
assertTrue(li3.getNumChildren() == 0);
node = null;
XMLNode node1 = RDFAnnotationParser.parseCVTerms(null);
assertTrue(node1 == null);
node1 = RDFAnnotationParser.createCVTerms(null);
assertTrue(node1 == null);
node1 = RDFAnnotationParser.parseCVTerms(m.getCompartment(2));
assertTrue(node1 == null);
node1 = RDFAnnotationParser.createCVTerms(m.getCompartment(2));
assertTrue(node1 == null);
node1 = RDFAnnotationParser.parseCVTerms(m);
assertTrue(node1 == null);
node1 = RDFAnnotationParser.createCVTerms(m);
assertTrue(node1 == null);
Compartment c = new Compartment(3, 1);
c.setMetaId("_002");
node1 = RDFAnnotationParser.parseCVTerms(c);
assertTrue(node1 == null);
node1 = RDFAnnotationParser.createCVTerms(c);
assertTrue(node1 == null);
CVTerm cv = new CVTerm(libsbml.BIOLOGICAL_QUALIFIER);
cv.setBiologicalQualifierType(23);
cv.addResource("http://myres");
c.addCVTerm(cv);
node1 = RDFAnnotationParser.createCVTerms(c);
assertTrue(node1 == null);
c = null;
Model m1 = new Model(3, 1);
m1.setMetaId("_002");
cv = new CVTerm(libsbml.MODEL_QUALIFIER);
cv.setModelQualifierType(23);
cv.addResource("http://myres");
m1.addCVTerm(cv);
node1 = RDFAnnotationParser.createCVTerms(m1);
assertTrue(node1 == null);
}
public void test_XMLNode_createElement()
{
XMLTriple triple;
XMLAttributes attr;
XMLNamespaces ns;
XMLNode snode, enode, tnode;
XMLAttributes cattr;
string name = "test";
string uri = "http://test.org/";
string prefix = "p";
string text = "text node";
triple = new XMLTriple(name, uri, prefix);
ns = new XMLNamespaces();
attr = new XMLAttributes();
ns.add(uri, prefix);
attr.add("id", "value", uri, prefix);
snode = new XMLNode(triple, attr, ns);
assertTrue(snode != null);
assertTrue(snode.getNumChildren() == 0);
assertTrue((name != snode.getName()) == false);
assertTrue((prefix != snode.getPrefix()) == false);
assertTrue((uri != snode.getURI()) == false);
assertTrue(snode.isElement() == true);
assertTrue(snode.isStart() == true);
assertTrue(snode.isEnd() == false);
assertTrue(snode.isText() == false);
snode.setEnd();
assertTrue(snode.isEnd() == true);
snode.unsetEnd();
assertTrue(snode.isEnd() == false);
cattr = snode.getAttributes();
assertTrue(cattr != null);
assertTrue(("id" != cattr.getName(0)) == false);
assertTrue(("value" != cattr.getValue(0)) == false);
assertTrue((prefix != cattr.getPrefix(0)) == false);
assertTrue((uri != cattr.getURI(0)) == false);
triple = null;
attr = null;
ns = null;
snode = null;
attr = new XMLAttributes();
attr.add("id", "value");
triple = new XMLTriple(name, "", "");
snode = new XMLNode(triple, attr);
assertTrue(snode != null);
assertTrue(snode.getNumChildren() == 0);
assertTrue(("test" != snode.getName()) == false);
assertTrue(snode.getPrefix() == "");
assertTrue(snode.getURI() == "");
assertTrue(snode.isElement() == true);
assertTrue(snode.isStart() == true);
assertTrue(snode.isEnd() == false);
assertTrue(snode.isText() == false);
cattr = snode.getAttributes();
assertTrue(cattr != null);
assertTrue(("id" != cattr.getName(0)) == false);
assertTrue(("value" != cattr.getValue(0)) == false);
assertTrue(cattr.getPrefix(0) == "");
assertTrue(cattr.getURI(0) == "");
enode = new XMLNode(triple);
assertTrue(enode != null);
assertTrue(enode.getNumChildren() == 0);
assertTrue(("test" != enode.getName()) == false);
assertTrue(enode.getPrefix() == "");
assertTrue(enode.getURI() == "");
assertTrue(enode.isElement() == true);
assertTrue(enode.isStart() == false);
assertTrue(enode.isEnd() == true);
assertTrue(enode.isText() == false);
tnode = new XMLNode(text);
assertTrue(tnode != null);
assertTrue((text != tnode.getCharacters()) == false);
assertTrue(tnode.getNumChildren() == 0);
assertTrue(tnode.getName() == "");
assertTrue(tnode.getPrefix() == "");
assertTrue(tnode.getURI() == "");
assertTrue(tnode.isElement() == false);
assertTrue(tnode.isStart() == false);
assertTrue(tnode.isEnd() == false);
assertTrue(tnode.isText() == true);
triple = null;
attr = null;
snode = null;
enode = null;
tnode = null;
}