@Test
public final void testNormalize2() {
Model model = BioPAXLevel.L3.getDefaultFactory().createModel();
Xref ref = model.addNew(UnificationXref.class, "Xref1");
ref.setDb("uniprotkb"); // will be converted to 'uniprot'
ref.setId("Q0VCL1");
Xref uniprotX = ref;
ProteinReference pr = model.addNew(ProteinReference.class, "ProteinReference");
pr.setDisplayName("ProteinReference");
pr.addXref(uniprotX);
ref = model.addNew(RelationshipXref.class, "Xref2");
ref.setDb("refseq");
ref.setId("NP_001734");
pr.addXref(ref);
// normalizer won't merge diff. types of xref with the same db:id
ref = model.addNew(PublicationXref.class, "Xref3");
ref.setDb("pubmed");
ref.setId("2549346"); // the same id
pr.addXref(ref);
ref = model.addNew(RelationshipXref.class, "Xref4");
ref.setDb("pubmed");
ref.setId("2549346"); // the same id
pr.addXref(ref);
Normalizer normalizer = new Normalizer();
normalizer.normalize(model);
ProteinReference e = (ProteinReference) model.getByID("http://identifiers.org/uniprot/Q0VCL1");
assertNotNull(e);
assertEquals(4, e.getXref().size());
// print(e, model);
}
@Test
public final void testNormalize3() {
Model model = BioPAXLevel.L3.getDefaultFactory().createModel();
Xref ref = model.addNew(UnificationXref.class, "Xref1");
ref.setDb("uniprotkb"); // will be converted to 'uniprot'
ref.setId("Q0VCL1");
ProteinReference pr = model.addNew(ProteinReference.class, "ProteinReference1");
pr.setDisplayName("A ProteinReference");
pr.addXref(ref);
assertEquals(1, ref.getXrefOf().size());
// System.out.println("Before the model is normalized - ");
// print(pr, model);
// go normalize!
Normalizer normalizer = new Normalizer();
normalizer.normalize(model);
// System.out.println("After the model is normalized - ");
// print(pr, model);
assertFalse(model.contains(pr)); // replaced by new norm. PR in the model
assertFalse(model.contains(ref)); // replaced by new norm. xref in the model
// now xrefOf is consistent with xref for all objects inn the model (since after some paxtools
// 4.1.3 snapshot)
assertEquals(0, pr.getXref().size()); // old PR has xref removed!
assertEquals(
0, ref.getXrefOf().size()); // because the old xref was replaced in all parent elements!
ProteinReference e = (ProteinReference) model.getByID("http://identifiers.org/uniprot/Q0VCL1");
assertNotNull(e);
assertEquals(1, e.getXref().size());
String normUri = Normalizer.uri(model.getXmlBase(), "UNIPROT", "Q0VCL1", UnificationXref.class);
ref = (UnificationXref) model.getByID(normUri);
assertNotNull(ref);
assertEquals(1, ref.getXrefOf().size());
// print(e, model);
}
