@Test
public void testClosure() throws Exception {
OWLGraphWrapper graph = null;
try {
graph = getGraph("graph/reg-of-ribosome-biogenesis.owl");
List<String> relations =
Arrays.asList(
"BFO:0000050",
"BFO:0000066",
"RO:0002211",
"RO:0002212",
"RO:0002213",
"RO:0002215",
"RO:0002216");
final OWLClass c1 =
graph.getOWLClassByIdentifier("GO:0090069"); // regulation of ribosome biogenesis
assertNotNull(c1);
List<String> result = graph.getRelationIDClosure(c1, relations);
assertTrue(result.contains("GO:0044087"));
assertTrue(result.contains("GO:0008150"));
assertTrue(result.contains("GO:0090069"));
assertTrue(result.contains("GO:0042254"));
assertTrue(result.contains("GO:0044085"));
assertTrue(result.contains("GO:0050789"));
assertTrue(result.contains("GO:0065007"));
assertTrue(result.contains("GO:0022613"));
assertTrue(result.contains("GO:0071840"));
} finally {
IOUtils.closeQuietly(graph);
}
}
@Test
public void testGetOnlyInTaxon() throws Exception {
OWLGraphWrapper graph = getGraph("graph/explainConstraints.owl");
OWLClass c1 = graph.getOWLClass(IRI.create("http://purl.obolibrary.org/obo/UBERON_0000001"));
Set<String> taxon1 = graph.getOnlyInTaxon(c1, Collections.<String>emptyList());
assertEquals(1, taxon1.size());
assertEquals("NCBITaxon:1", taxon1.iterator().next());
OWLClass c2 = graph.getOWLClass(IRI.create("http://purl.obolibrary.org/obo/UBERON_0000002"));
Set<String> taxon2 = graph.getOnlyInTaxon(c2, Collections.<String>emptyList());
assertEquals(1, taxon2.size());
assertEquals("NCBITaxon:2", taxon2.iterator().next());
Set<String> closure = graph.getOnlyInTaxonClosure(c2, Collections.<String>emptyList());
assertEquals(2, closure.size());
assertTrue(closure.contains("NCBITaxon:1"));
assertTrue(closure.contains("NCBITaxon:2"));
OWLClass c3 = graph.getOWLClass(IRI.create("http://purl.obolibrary.org/obo/UBERON_0000003"));
Set<String> taxon3 = graph.getOnlyInTaxon(c3, Collections.<String>emptyList());
assertEquals(0, taxon3.size());
}
@Test
public void testGetSvfClasses() throws Exception {
OWLGraphWrapper graph = getGraph("graph/explainConstraints.owl");
IRI onlyInTaxonIRI = IRI.create("http://purl.obolibrary.org/obo/RO_0002160");
OWLObjectProperty onlyInTaxon = graph.getDataFactory().getOWLObjectProperty(onlyInTaxonIRI);
OWLClass c1 = graph.getOWLClass(IRI.create("http://purl.obolibrary.org/obo/UBERON_0000001"));
OWLClass c2 = graph.getOWLClass(IRI.create("http://purl.obolibrary.org/obo/UBERON_0000002"));
OWLClass c3 = graph.getOWLClass(IRI.create("http://purl.obolibrary.org/obo/UBERON_0000003"));
Set<OWLClass> svf1 = graph.getSvfClasses(c1, onlyInTaxon);
Set<OWLClass> svf2 = graph.getSvfClasses(c2, onlyInTaxon);
Set<OWLClass> svf3 = graph.getSvfClasses(c3, onlyInTaxon);
assertEquals(1, svf1.size());
assertEquals(1, svf2.size());
assertEquals(0, svf3.size());
}