private void print(XReferrable xr, Model m) {
System.out.println();
System.out.println(
"model="
+ m.contains(xr)
+ ":\t"
+ xr.getUri()
+ " is "
+ xr.getModelInterface().getSimpleName()
+ " and has xrefs: ");
for (Xref x : xr.getXref()) {
System.out.println(
"model="
+ m.contains(x)
+ ":\t"
+ " "
+ x
+ " is "
+ x.getModelInterface().getSimpleName()
+ " - "
+ x.getUri()
+ ", db="
+ x.getDb()
+ ", id="
+ x.getId()
+ ", idVer="
+ x.getIdVersion());
for (XReferrable rx : x.getXrefOf()) {
System.out.println("model=" + m.contains(rx) + ":\t" + " xrefOf: " + rx);
}
}
}
@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);
}
