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 ); }