public void test_RDFAnnotation_testMissingAbout()
{
string withAbout = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n" +
" <annotation>\n" +
" <rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:dc=\"http://purl.org/dc/elements/1.1/\" xmlns:dcterms=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n" +
" <rdf:Description rdf:about=\"#_000004\">\n" +
" <bqbiol:is>\n" +
" <rdf:Bag>\n" +
" <rdf:li rdf:resource=\"http://www.geneontology.org/#GO:0007274\"/>\n" +
" </rdf:Bag>\n" +
" </bqbiol:is>\n" +
" </rdf:Description>\n" +
" </rdf:RDF>\n" +
" </annotation>";
string emptyAbout = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n" +
" <annotation>\n" +
" <rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:dc=\"http://purl.org/dc/elements/1.1/\" xmlns:dcterms=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n" +
" <rdf:Description rdf:about=\"\">\n" +
" <bqbiol:is>\n" +
" <rdf:Bag>\n" +
" <rdf:li rdf:resource=\"http://www.geneontology.org/#GO:0007274\"/>\n" +
" </rdf:Bag>\n" +
" </bqbiol:is>\n" +
" </rdf:Description>\n" +
" </rdf:RDF>\n" +
" </annotation>";
string noAbout = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n" +
" <annotation>\n" +
" <rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:dc=\"http://purl.org/dc/elements/1.1/\" xmlns:dcterms=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n" +
" <rdf:Description>\n" +
" <bqbiol:is>\n" +
" <rdf:Bag>\n" +
" <rdf:li rdf:resource=\"http://www.geneontology.org/#GO:0007274\"/>\n" +
" </rdf:Bag>\n" +
" </bqbiol:is>\n" +
" </rdf:Description>\n" +
" </rdf:RDF>\n" +
" </annotation>";
CVTermList cvTerms = new CVTermList();
XMLInputStream stream = new XMLInputStream ( withAbout,false );
XMLNode node = new XMLNode ( stream );
RDFAnnotationParser.parseRDFAnnotation(node,cvTerms);
assertTrue( cvTerms.getSize() == 1 );
cvTerms = new CVTermList();
RDFAnnotationParser.parseRDFAnnotation(node,cvTerms );
assertTrue( cvTerms.getSize() == 1 );
cvTerms = null;
cvTerms = null;
cvTerms = new CVTermList();
XMLInputStream stream1 = new XMLInputStream ( emptyAbout,false );
XMLNode node1 = new XMLNode ( stream1 );
RDFAnnotationParser.parseRDFAnnotation(node1,cvTerms);
assertTrue( cvTerms.getSize() == 0 );
cvTerms = null;
cvTerms = null;
cvTerms = new CVTermList();
XMLInputStream stream2 = new XMLInputStream ( noAbout,false );
XMLNode node2 = new XMLNode ( stream2 );
RDFAnnotationParser.parseRDFAnnotation(node2,cvTerms);
assertTrue( cvTerms.getSize() == 0 );
cvTerms = null;
cvTerms = 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(("dc" == creator.getPrefix()));
assertTrue(("http://purl.org/dc/elements/1.1/" == creator.getURI()));
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 );
}
