public void test_XMLNode_convert() {
String xmlstr =
"<annotation>\n"
+ " <test xmlns=\"http://test.org/\" id=\"test\">test</test>\n"
+ "</annotation>";
XMLNode node;
XMLNode child, gchild;
XMLAttributes attr;
XMLNamespaces ns;
node = XMLNode.convertStringToXMLNode(xmlstr, null);
child = node.getChild(0);
gchild = child.getChild(0);
attr = child.getAttributes();
ns = child.getNamespaces();
assertTrue(!node.getName().equals("annotation") == false);
assertTrue(!child.getName().equals("test") == false);
assertTrue(!gchild.getCharacters().equals("test") == false);
assertTrue(!attr.getName(0).equals("id") == false);
assertTrue(!attr.getValue(0).equals("test") == false);
assertTrue(!ns.getURI(0).equals("http://test.org/") == false);
assertTrue(ns.getPrefix(0).equals("") == true);
String toxmlstring = node.toXMLString();
assertTrue(!toxmlstring.equals(xmlstr) == 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(!node.getAttrName(0).equals("name1") == false);
assertTrue(!node.getAttrValue(0).equals("val1") == false);
assertTrue(!node.getAttrURI(0).equals("http://name1.org/") == false);
assertTrue(!node.getAttrPrefix(0).equals("p1") == false);
assertTrue(!node.getAttrName(1).equals("name2") == false);
assertTrue(!node.getAttrValue(1).equals("val2") == false);
assertTrue(!node.getAttrURI(1).equals("http://name2.org/") == false);
assertTrue(!node.getAttrPrefix(1).equals("p2") == false);
assertTrue(!node.getAttrName(2).equals("name3") == false);
assertTrue(!node.getAttrValue(2).equals("val3") == false);
assertTrue(!node.getAttrURI(2).equals("http://name3.org/") == false);
assertTrue(!node.getAttrPrefix(2).equals("p3") == false);
assertTrue(!node.getAttrName(3).equals("name4") == false);
assertTrue(!node.getAttrValue(3).equals("val4") == false);
assertTrue(!node.getAttrURI(3).equals("http://name4.org/") == false);
assertTrue(!node.getAttrPrefix(3).equals("p4") == false);
assertTrue(!node.getAttrName(4).equals("name5") == false);
assertTrue(!node.getAttrValue(4).equals("val5") == false);
assertTrue(!node.getAttrURI(4).equals("http://name5.org/") == false);
assertTrue(!node.getAttrPrefix(4).equals("p5") == false);
XMLTriple ntriple = new XMLTriple("test2", "http://test2.org/", "p2");
node.setTriple(ntriple);
assertTrue(!node.getName().equals("test2") == false);
assertTrue(!node.getURI().equals("http://test2.org/") == false);
assertTrue(!node.getPrefix().equals("p2") == 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_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(!node.getCharacters().equals("This is a test") == 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(!node.getName().equals("attr") == false);
assertTrue(!node.getURI().equals("uri") == false);
assertTrue(!node.getPrefix().equals("prefix") == false);
XMLAttributes returnattr = node.getAttributes();
assertTrue(!returnattr.getName(0).equals("attr2") == false);
assertTrue(!returnattr.getValue(0).equals("value") == 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 static void main(String[] args) {
System.loadLibrary("sbmlj");
if (args.length != 2) {
System.out.println(" usage: addingEvidenceCodes_2 <input-filename> <output-filename>");
System.out.println(" Adds controlled vocabulary term to a species");
System.out.println();
System.exit(2);
}
SBMLDocument d = libsbml.readSBML(args[0]);
long errors = d.getNumErrors();
if (errors > 0) {
System.out.println("Read Error(s):");
d.printErrors();
System.out.println("Correct the above and re-run.");
} else {
long n = d.getModel().getNumSpecies();
if (n <= 0) {
System.out.println("Model has no species.\n Cannot add CV terms\n");
} else {
Species s = d.getModel().getSpecies(0);
/*
* check that the species has a metaid no CVTerms will be added
* if there is no metaid to reference
*/
if (!s.isSetMetaId()) s.setMetaId("metaid_0000052");
CVTerm cv1 = new CVTerm(libsbml.BIOLOGICAL_QUALIFIER);
cv1.setBiologicalQualifierType(libsbml.BQB_OCCURS_IN);
cv1.addResource("urn:miriam:obo.go:GO%3A0005764");
s.addCVTerm(cv1);
// now create the additional annotation
// <rdf:Statement>
// <rdf:subject rdf:resource="#metaid_0000052"/>
// <rdf:predicate
// rdf:resource="http://biomodels.net/biology-qualifiers/occursIn"/>
// <rdf:object rdf:resource="urn:miriam:obo.go:GO%3A0005764"/>
// <bqbiol:isDescribedBy>
// <rdf:Bag>
// <rdf:li rdf:resource="urn:miriam:obo.eco:ECO%3A0000004"/>
// <rdf:li rdf:resource="urn:miriam:pubmed:7017716"/>
// </rdf:Bag>
// </bqbiol:isDescribedBy>
// </rdf:Statement>
/* attributes */
XMLAttributes blank_att = new XMLAttributes();
XMLAttributes resource_att = new XMLAttributes();
/* create the outer statement node */
XMLTriple statement_triple =
new XMLTriple("Statement", "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf");
XMLToken statement_token = new XMLToken(statement_triple, blank_att);
XMLNode statement = new XMLNode(statement_token);
/* create the subject node */
XMLTriple subject_triple =
new XMLTriple("subject", "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf");
resource_att.clear();
resource_att.add("rdf:resource", "#" + s.getMetaId());
XMLToken subject_token = new XMLToken(subject_triple, resource_att);
XMLNode subject = new XMLNode(subject_token);
/* create the predicate node */
XMLTriple predicate_triple =
new XMLTriple("predicate", "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf");
resource_att.clear();
resource_att.add("rdf:resource", "http://biomodels.net/biology-qualifiers/occursIn");
XMLToken predicate_token = new XMLToken(predicate_triple, resource_att);
XMLNode predicate = new XMLNode(predicate_token);
/* create the object node */
XMLTriple object_triple =
new XMLTriple("object", "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf");
resource_att.clear();
resource_att.add("rdf:resource", "urn:miriam:obo.go:GO%3A0005764");
XMLToken object_token = new XMLToken(object_triple, resource_att);
XMLNode object_ = new XMLNode(object_token);
/* create the bqbiol node */
XMLTriple bqbiol_triple =
new XMLTriple("isDescribedBy", "http://biomodels.net/biology-qualifiers/", "bqbiol");
XMLToken bqbiol_token = new XMLToken(bqbiol_triple, blank_att);
XMLNode bqbiol = new XMLNode(bqbiol_token);
/* create the bag node */
XMLTriple bag_triple =
new XMLTriple("Bag", "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf");
XMLToken bag_token = new XMLToken(bag_triple, blank_att);
XMLNode bag = new XMLNode(bag_token);
/* create each li node and add to the bag */
XMLTriple li_triple =
new XMLTriple("li", "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf");
resource_att.clear();
resource_att.add("rdf:resource", "urn:miriam:obo.eco:ECO%3A0000004");
XMLToken li_token = new XMLToken(li_triple, resource_att);
li_token.setEnd();
XMLNode li = new XMLNode(li_token);
bag.addChild(li);
resource_att.clear();
resource_att.add("rdf:resource", "urn:miriam:pubmed:7017716");
li_token = new XMLToken(li_triple, resource_att);
li_token.setEnd();
li = new XMLNode(li_token);
bag.addChild(li);
/* add the bag to bqbiol */
bqbiol.addChild(bag);
/* add subject, predicate, object and bqbiol to statement */
statement.addChild(subject);
statement.addChild(predicate);
statement.addChild(object_);
statement.addChild(bqbiol);
/*
* create a top-level RDF element this will ensure correct
* merging
*/
XMLNamespaces xmlns = new XMLNamespaces();
xmlns.add("http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf");
xmlns.add("http://purl.org/dc/elements/1.1/", "dc");
xmlns.add("http://purl.org/dc/terms/", "dcterms");
xmlns.add("http://www.w3.org/2001/vcard-rdf/3.0#", "vCard");
xmlns.add("http://biomodels.net/biology-qualifiers/", "bqbiol");
xmlns.add("http://biomodels.net/model-qualifiers/", "bqmodel");
XMLTriple RDF_triple =
new XMLTriple("RDF", "http://www.w3.org/1999/02/22-rdf-syntax-ns#", "rdf");
XMLToken RDF_token = new XMLToken(RDF_triple, blank_att, xmlns);
XMLNode annotation = new XMLNode(RDF_token);
/* add the staement node to the RDF node */
annotation.addChild(statement);
s.appendAnnotation(annotation);
libsbml.writeSBML(d, args[1]);
}
}
System.exit((int) errors);
}
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(!snode.getName().equals(name) == false);
assertTrue(!snode.getPrefix().equals(prefix) == false);
assertTrue(!snode.getURI().equals(uri) == 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(!cattr.getName(0).equals("id") == false);
assertTrue(!cattr.getValue(0).equals("value") == false);
assertTrue(!cattr.getPrefix(0).equals(prefix) == false);
assertTrue(!cattr.getURI(0).equals(uri) == 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(!snode.getName().equals("test") == false);
assertTrue(snode.getPrefix().equals("") == true);
assertTrue(snode.getURI().equals("") == true);
assertTrue(snode.isElement() == true);
assertTrue(snode.isStart() == true);
assertTrue(snode.isEnd() == false);
assertTrue(snode.isText() == false);
cattr = snode.getAttributes();
assertTrue(cattr != null);
assertTrue(!cattr.getName(0).equals("id") == false);
assertTrue(!cattr.getValue(0).equals("value") == false);
assertTrue(cattr.getPrefix(0).equals("") == true);
assertTrue(cattr.getURI(0).equals("") == true);
enode = new XMLNode(triple);
assertTrue(enode != null);
assertTrue(enode.getNumChildren() == 0);
assertTrue(!enode.getName().equals("test") == false);
assertTrue(enode.getPrefix().equals("") == true);
assertTrue(enode.getURI().equals("") == true);
assertTrue(enode.isElement() == true);
assertTrue(enode.isStart() == false);
assertTrue(enode.isEnd() == true);
assertTrue(enode.isText() == false);
tnode = new XMLNode(text);
assertTrue(tnode != null);
assertTrue(!tnode.getCharacters().equals(text) == false);
assertTrue(tnode.getNumChildren() == 0);
assertTrue(tnode.getName().equals("") == true);
assertTrue(tnode.getPrefix().equals("") == true);
assertTrue(tnode.getURI().equals("") == true);
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;
}