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_Constraint_setMessage2() { XMLNode text = XMLNode.convertStringToXMLNode(" Some text ", null); XMLTriple triple = new XMLTriple("p", "http://www.w3.org/1999/xhtml", ""); XMLAttributes att = new XMLAttributes(); XMLNamespaces xmlns = new XMLNamespaces(); xmlns.add("http://www.w3.org/1999/xhtml", ""); XMLNode p = new XMLNode(triple, att, xmlns); p.addChild(text); XMLTriple triple1 = new XMLTriple("message", "", ""); XMLAttributes att1 = new XMLAttributes(); XMLNode node = new XMLNode(triple1, att1); node.addChild(p); int i = C.setMessage(node); assertTrue(i == libsbml.LIBSBML_OPERATION_SUCCESS); assertTrue(C.isSetMessage() == true); i = C.unsetMessage(); assertTrue(i == libsbml.LIBSBML_OPERATION_SUCCESS); assertEquals(false, C.isSetMessage()); if (C.getMessage() != null) { ; } { } node = null; }
public void test_SyntaxChecker_validXHTML() { SBMLNamespaces NS24 = new SBMLNamespaces(2, 4); SBMLNamespaces NS31 = new SBMLNamespaces(3, 1); XMLToken toptoken; XMLNode topnode; XMLTriple toptriple = new XMLTriple("notes", "", ""); XMLToken token; XMLNode node; XMLTriple triple = new XMLTriple("p", "", ""); XMLAttributes att = new XMLAttributes(); XMLNamespaces ns = new XMLNamespaces(); ns.add("http://www.w3.org/1999/xhtml", ""); XMLToken tt = new XMLToken("This is my text"); XMLNode n1 = new XMLNode(tt); toptoken = new XMLToken(toptriple, att); topnode = new XMLNode(toptoken); token = new XMLToken(triple, att, ns); node = new XMLNode(token); node.addChild(n1); topnode.addChild(node); assertTrue(SyntaxChecker.hasExpectedXHTMLSyntax(topnode, null) == true); assertTrue(SyntaxChecker.hasExpectedXHTMLSyntax(topnode, NS24) == true); assertTrue(SyntaxChecker.hasExpectedXHTMLSyntax(topnode, NS31) == true); triple = new XMLTriple("html", "", ""); token = new XMLToken(triple, att, ns); node = new XMLNode(token); node.addChild(n1); topnode.removeChild(0); topnode.addChild(node); assertTrue(SyntaxChecker.hasExpectedXHTMLSyntax(topnode, null) == true); assertTrue(SyntaxChecker.hasExpectedXHTMLSyntax(topnode, NS24) == false); assertTrue(SyntaxChecker.hasExpectedXHTMLSyntax(topnode, NS31) == true); triple = new XMLTriple("html", "", ""); ns.clear(); token = new XMLToken(triple, att, ns); node = new XMLNode(token); node.addChild(n1); topnode.removeChild(0); topnode.addChild(node); assertTrue(SyntaxChecker.hasExpectedXHTMLSyntax(topnode, null) == false); assertTrue(SyntaxChecker.hasExpectedXHTMLSyntax(topnode, NS24) == false); assertTrue(SyntaxChecker.hasExpectedXHTMLSyntax(topnode, NS31) == false); }
public void test_XMLNode_removeChildren() { XMLNode node = new XMLNode(); XMLNode node2 = new XMLNode(); XMLNode node3 = new XMLNode(); node.addChild(node2); node.addChild(node3); assertTrue(node.getNumChildren() == 2); int i = node.removeChildren(); assertTrue(i == libsbml.LIBSBML_OPERATION_SUCCESS); assertTrue(node.getNumChildren() == 0); node = null; node2 = null; node3 = null; }
public void test_XMLNode_addChild3() { XMLTriple triple = new XMLTriple("test", "", ""); XMLNode node = new XMLNode(triple); XMLNode node2 = new XMLNode(); int i = node.addChild(node2); assertTrue(i == libsbml.LIBSBML_INVALID_XML_OPERATION); assertTrue(node.getNumChildren() == 0); triple = null; node = null; node2 = null; }
public void test_XMLNode_create() { XMLNode node = new XMLNode(); assertTrue(node != null); assertTrue(node.getNumChildren() == 0); node = null; node = new XMLNode(); assertTrue(node != null); XMLNode node2 = new XMLNode(); assertTrue(node2 != null); node.addChild(node2); assertTrue(node.getNumChildren() == 1); XMLNode node3 = new XMLNode(); assertTrue(node3 != null); node.addChild(node3); assertTrue(node.getNumChildren() == 2); node = null; node2 = null; node3 = null; }
public void test_XMLNode_addChild2() { XMLTriple triple = new XMLTriple("test", "", ""); XMLAttributes attr = new XMLAttributes(); XMLNode node = new XMLNode(triple, attr); XMLNode node2 = new XMLNode(); int i = node.addChild(node2); assertTrue(i == libsbml.LIBSBML_OPERATION_SUCCESS); assertTrue(node.getNumChildren() == 1); triple = null; attr = null; node = null; node2 = null; }
public void test_Constraint_assignmentOperator() { Constraint o1 = new Constraint(2, 4); o1.setMetaId("c"); assertTrue(o1.getMetaId() == "c"); XMLNode text = XMLNode.convertStringToXMLNode(" Some text "); XMLTriple triple = new XMLTriple("p", "http://www.w3.org/1999/xhtml", ""); XMLAttributes att = new XMLAttributes(); XMLNamespaces xmlns = new XMLNamespaces(); xmlns.add("http://www.w3.org/1999/xhtml"); XMLNode p = new XMLNode(triple, att, xmlns); p.addChild(text); XMLTriple triple1 = new XMLTriple("message", "", ""); XMLAttributes att1 = new XMLAttributes(); XMLNode message = new XMLNode(triple1, att1); message.addChild(p); ASTNode math = new ASTNode(libsbml.AST_CONSTANT_PI); o1.setMath(math); o1.setMessage(message); math = null; message = null; XMLNode msg; assertTrue(o1.getMath() != null); msg = o1.getMessage(); assertTrue(msg != null); Constraint o2 = new Constraint(2, 4); o2 = o1; assertTrue(o2.getMetaId() == "c"); assertTrue(o2.getMath() != null); msg = o2.getMessage(); assertTrue(msg != null); assertTrue(o2.getParentSBMLObject() == o1.getParentSBMLObject()); o2 = null; o1 = null; }
public void test_CVTerm_createFromNode() { XMLAttributes xa; XMLTriple qual_triple = new XMLTriple("is", "", "bqbiol"); XMLTriple bag_triple = new XMLTriple(); XMLTriple li_triple = new XMLTriple(); XMLAttributes att = new XMLAttributes(); att.add("", "This is my resource"); XMLAttributes att1 = new XMLAttributes(); XMLToken li_token = new XMLToken(li_triple, att); XMLToken bag_token = new XMLToken(bag_triple, att1); XMLToken qual_token = new XMLToken(qual_triple, att1); XMLNode li = new XMLNode(li_token); XMLNode bag = new XMLNode(bag_token); XMLNode node = new XMLNode(qual_token); bag.addChild(li); node.addChild(bag); CVTerm term = new CVTerm(node); assertTrue(term != null); assertTrue(term.getQualifierType() == libsbml.BIOLOGICAL_QUALIFIER); assertTrue(term.getBiologicalQualifierType() == libsbml.BQB_IS); xa = term.getResources(); assertTrue(xa.getLength() == 1); assertTrue(("rdf:resource" == xa.getName(0))); assertTrue(("This is my resource" == xa.getValue(0))); qual_triple = null; bag_triple = null; li_triple = null; li_token = null; bag_token = null; qual_token = null; att = null; att1 = null; term = null; node = null; bag = null; li = null; }
public static int Main(string[] args) { if (args.Length != 2) { Console.WriteLine(" usage: addingEvidenceCodes_2 <input-filename> <output-filename>"); Console.WriteLine(" Adds controlled vocabulary term to a species"); Console.WriteLine(); return(2); } SBMLDocument d = libsbml.readSBML(args[0]); long errors = d.getNumErrors(); if (errors > 0) { Console.WriteLine("Read Error(s):"); d.printErrors(); Console.WriteLine("Correct the above and re-run."); } else { long n = d.getModel().getNumSpecies(); if (n <= 0) { Console.WriteLine("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]); } } return((int)errors); }
public void test_XMLNode_remove() { XMLAttributes attr = new XMLAttributes(); XMLTriple trp_p = new XMLTriple("parent", "", ""); XMLTriple trp_c1 = new XMLTriple("child1", "", ""); XMLTriple trp_c2 = new XMLTriple("child2", "", ""); XMLTriple trp_c3 = new XMLTriple("child3", "", ""); XMLTriple trp_c4 = new XMLTriple("child4", "", ""); XMLTriple trp_c5 = new XMLTriple("child5", "", ""); XMLNode p = new XMLNode(trp_p, attr); XMLNode c1 = new XMLNode(trp_c1, attr); XMLNode c2 = new XMLNode(trp_c2, attr); XMLNode c3 = new XMLNode(trp_c3, attr); XMLNode c4 = new XMLNode(trp_c4, attr); XMLNode c5 = new XMLNode(trp_c5, attr); XMLNode r; p.addChild(c1); p.addChild(c2); p.addChild(c3); p.addChild(c4); p.addChild(c5); r = p.removeChild(5); assertTrue(r == null); r = p.removeChild(1); assertTrue(p.getNumChildren() == 4); assertTrue(("child2" != r.getName()) == false); r = null; r = p.removeChild(3); assertTrue(p.getNumChildren() == 3); assertTrue(("child5" != r.getName()) == false); r = null; r = p.removeChild(0); assertTrue(p.getNumChildren() == 2); assertTrue(("child1" != r.getName()) == false); r = null; r = p.removeChild(1); assertTrue(p.getNumChildren() == 1); assertTrue(("child4" != r.getName()) == false); r = null; r = p.removeChild(0); assertTrue(p.getNumChildren() == 0); assertTrue(("child3" != r.getName()) == false); r = null; p.addChild(c1); p.addChild(c2); p.addChild(c3); p.addChild(c4); p.addChild(c5); r = p.removeChild(4); assertTrue(p.getNumChildren() == 4); assertTrue(("child5" != r.getName()) == false); r = null; r = p.removeChild(3); assertTrue(p.getNumChildren() == 3); assertTrue(("child4" != r.getName()) == false); r = null; r = p.removeChild(2); assertTrue(p.getNumChildren() == 2); assertTrue(("child3" != r.getName()) == false); r = null; r = p.removeChild(1); assertTrue(p.getNumChildren() == 1); assertTrue(("child2" != r.getName()) == false); r = null; r = p.removeChild(0); assertTrue(p.getNumChildren() == 0); assertTrue(("child1" != r.getName()) == false); r = null; p.addChild(c1); p.addChild(c2); p.addChild(c3); p.addChild(c4); p.addChild(c5); r = p.removeChild(0); assertTrue(p.getNumChildren() == 4); assertTrue(("child1" != r.getName()) == false); r = null; r = p.removeChild(0); assertTrue(p.getNumChildren() == 3); assertTrue(("child2" != r.getName()) == false); r = null; r = p.removeChild(0); assertTrue(p.getNumChildren() == 2); assertTrue(("child3" != r.getName()) == false); r = null; r = p.removeChild(0); assertTrue(p.getNumChildren() == 1); assertTrue(("child4" != r.getName()) == false); r = null; r = p.removeChild(0); assertTrue(p.getNumChildren() == 0); assertTrue(("child5" != r.getName()) == false); r = null; p.addChild(c1); p.addChild(c2); p.addChild(c3); p.addChild(c4); p.addChild(c5); r = p.removeChild(0); assertTrue(("child1" != r.getName()) == false); p.insertChild(0, r); assertTrue(p.getNumChildren() == 5); assertTrue(("child1" != p.getChild(0).getName()) == false); r = null; r = p.removeChild(1); assertTrue(("child2" != r.getName()) == false); p.insertChild(1, r); assertTrue(p.getNumChildren() == 5); assertTrue(("child2" != p.getChild(1).getName()) == false); r = null; r = p.removeChild(2); assertTrue(("child3" != r.getName()) == false); p.insertChild(2, r); assertTrue(p.getNumChildren() == 5); assertTrue(("child3" != p.getChild(2).getName()) == false); r = null; r = p.removeChild(3); assertTrue(("child4" != r.getName()) == false); p.insertChild(3, r); assertTrue(p.getNumChildren() == 5); assertTrue(("child4" != p.getChild(3).getName()) == false); r = null; r = p.removeChild(4); assertTrue(("child5" != r.getName()) == false); p.insertChild(4, r); assertTrue(p.getNumChildren() == 5); assertTrue(("child5" != p.getChild(4).getName()) == false); r = null; p = null; c1 = null; c2 = null; c3 = null; c4 = null; c5 = null; attr = null; trp_p = null; trp_c1 = null; trp_c2 = null; trp_c3 = null; trp_c4 = null; trp_c5 = null; }
public void test_XMLNode_insert() { XMLAttributes attr = new XMLAttributes(); XMLTriple trp_p = new XMLTriple("parent", "", ""); XMLTriple trp_c1 = new XMLTriple("child1", "", ""); XMLTriple trp_c2 = new XMLTriple("child2", "", ""); XMLTriple trp_c3 = new XMLTriple("child3", "", ""); XMLTriple trp_c4 = new XMLTriple("child4", "", ""); XMLTriple trp_c5 = new XMLTriple("child5", "", ""); XMLNode p = new XMLNode(trp_p, attr); XMLNode c1 = new XMLNode(trp_c1, attr); XMLNode c2 = new XMLNode(trp_c2, attr); XMLNode c3 = new XMLNode(trp_c3, attr); XMLNode c4 = new XMLNode(trp_c4, attr); XMLNode c5 = new XMLNode(trp_c5, attr); p.addChild(c2); p.addChild(c4); p.insertChild(0, c1); p.insertChild(2, c3); p.insertChild(4, c5); assertTrue(p.getNumChildren() == 5); assertTrue(("child1" != p.getChild(0).getName()) == false); assertTrue(("child2" != p.getChild(1).getName()) == false); assertTrue(("child3" != p.getChild(2).getName()) == false); assertTrue(("child4" != p.getChild(3).getName()) == false); assertTrue(("child5" != p.getChild(4).getName()) == false); p.removeChildren(); p.insertChild(0, c1); p.insertChild(0, c2); p.insertChild(0, c3); p.insertChild(0, c4); p.insertChild(0, c5); assertTrue(p.getNumChildren() == 5); assertTrue(("child5" != p.getChild(0).getName()) == false); assertTrue(("child4" != p.getChild(1).getName()) == false); assertTrue(("child3" != p.getChild(2).getName()) == false); assertTrue(("child2" != p.getChild(3).getName()) == false); assertTrue(("child1" != p.getChild(4).getName()) == false); p.removeChildren(); p.insertChild(1, c1); p.insertChild(2, c2); p.insertChild(3, c3); p.insertChild(4, c4); p.insertChild(5, c5); assertTrue(p.getNumChildren() == 5); assertTrue(("child1" != p.getChild(0).getName()) == false); assertTrue(("child2" != p.getChild(1).getName()) == false); assertTrue(("child3" != p.getChild(2).getName()) == false); assertTrue(("child4" != p.getChild(3).getName()) == false); assertTrue(("child5" != p.getChild(4).getName()) == false); p.removeChildren(); XMLNode tmp; tmp = p.insertChild(0, c1); assertTrue(("child1" != tmp.getName()) == false); tmp = p.insertChild(0, c2); assertTrue(("child2" != tmp.getName()) == false); tmp = p.insertChild(0, c3); assertTrue(("child3" != tmp.getName()) == false); tmp = p.insertChild(0, c4); assertTrue(("child4" != tmp.getName()) == false); tmp = p.insertChild(0, c5); assertTrue(("child5" != tmp.getName()) == false); p.removeChildren(); tmp = p.insertChild(1, c1); assertTrue(("child1" != tmp.getName()) == false); tmp = p.insertChild(2, c2); assertTrue(("child2" != tmp.getName()) == false); tmp = p.insertChild(3, c3); assertTrue(("child3" != tmp.getName()) == false); tmp = p.insertChild(4, c4); assertTrue(("child4" != tmp.getName()) == false); tmp = p.insertChild(5, c5); assertTrue(("child5" != tmp.getName()) == false); p = null; c1 = null; c2 = null; c3 = null; c4 = null; c5 = null; attr = null; trp_p = null; trp_c1 = null; trp_c2 = null; trp_c3 = null; trp_c4 = null; trp_c5 = null; }