@Test
public final void testNormalizeInoh() {
// there're two Protein objects that have entityReference
// rdf:ID="IMR_0100366_G_alpha_s_Canonical" (in fact a generic ProteinReference inproperly
// defined);
// and that PR has two UniProt UnificationXref: P63092 (human), P63095 (rat).
// Identifiers.org URI for the PR should NOT be generated.
//
// Also, there was a bug when replacing the PR's URI (warning: IllegalBioPAXArgumentException:
// Incompatible type!..)
// The cause is that there was a (weird, invalid) PublicationXref having db:id as UniProt:P63092
// that gets the same URI!
// To avoid such issues altogether (despite illegal pub. xrefs), the Normalizer won't use
// Identifiers.org for PublicationXrefs anymore.
Model model = simpleIO.convertFromOWL(getClass().getResourceAsStream("/test-inoh.owl"));
Normalizer normalizer = new Normalizer();
normalizer.setXmlBase("");
normalizer.normalize(model);
// A weird PublicationXref that uses a UniProt ID won't be normalized:
assertFalse(model.containsID("http://identifiers.org/uniprot/P63092"));
// A PR with two UniProt IDs/unif.xrefs - human, rat - won't be normalized!
assertTrue(model.containsID(model.getXmlBase() + "IMR_0100366_G_alpha_s_Canonical"));
assertEquals(
"ProteinReference",
model
.getByID(model.getXmlBase() + "IMR_0100366_G_alpha_s_Canonical")
.getModelInterface()
.getSimpleName());
}
