Examples with WorkingMemory org.geneontology.rules.engine.WorkingMemory used on opensource projects

Example 6 with WorkingMemory

use of org.geneontology.rules.engine.WorkingMemory in project minerva by geneontology.

the class GPADSPARQLTest method testSuppressUberonExtensionsWhenEMAPA.

/**
 * This test needs improvements; the current background axioms used in the tests are resulting in the Uberon inference we're trying to avoid
 *
 * @throws Exception
 */
@Test
public void testSuppressUberonExtensionsWhenEMAPA() throws Exception {
    Model model = ModelFactory.createDefaultModel();
    model.read(this.getClass().getResourceAsStream("/no_uberon_with_emapa.ttl"), "", "ttl");
    Set<Triple> triples = model.listStatements().toList().stream().map(s -> Bridge.tripleFromJena(s.asTriple())).collect(Collectors.toSet());
    WorkingMemory mem = arachne.processTriples(JavaConverters.asScalaSetConverter(triples).asScala());
    Set<GPADData> annotations = exporter.getGPAD(mem, IRI.create("http://test.org"));
    Assert.assertTrue(annotations.stream().anyMatch(a -> a.getAnnotationExtensions().stream().anyMatch(e -> e.getFiller().toString().startsWith("http://purl.obolibrary.org/obo/EMAPA_"))));
    Assert.assertTrue(annotations.stream().noneMatch(a -> a.getAnnotationExtensions().stream().anyMatch(e -> e.getFiller().toString().startsWith("http://purl.obolibrary.org/obo/UBERON_"))));
}

Example 7 with WorkingMemory

use of org.geneontology.rules.engine.WorkingMemory in project minerva by geneontology.

the class GPADSPARQLTest method testGPADContainsAcceptedAndCreatedDates.

@Test
@Ignore
public void testGPADContainsAcceptedAndCreatedDates() throws Exception {
    Model model = ModelFactory.createDefaultModel();
    model.read(this.getClass().getResourceAsStream("/created-date-test.ttl"), "", "ttl");
    Set<Triple> triples = model.listStatements().toList().stream().map(s -> Bridge.tripleFromJena(s.asTriple())).collect(Collectors.toSet());
    WorkingMemory mem = arachne.processTriples(JavaConverters.asScalaSetConverter(triples).asScala());
    Set<GPADData> annotations = exporter.getGPAD(mem, IRI.create("http://test.org"));
    IRI gene = IRI.create("http://identifiers.org/wormbase/WBGene00001326");
    Pair<String, String> creationDate = Pair.of("creation-date", "2021-05-13");
    Assert.assertTrue(annotations.stream().anyMatch(a -> a.getObject().equals(gene) && a.getAnnotations().contains(creationDate)));
}

Example 8 with WorkingMemory

use of org.geneontology.rules.engine.WorkingMemory in project minerva by geneontology.

the class GPADSPARQLTest method testGPADOutput.

@Test
public void testGPADOutput() throws Exception {
    Model model = ModelFactory.createDefaultModel();
    model.read(this.getClass().getResourceAsStream("/581e072c00000473.ttl"), "", "ttl");
    Set<Triple> triples = model.listStatements().toList().stream().map(s -> Bridge.tripleFromJena(s.asTriple())).collect(Collectors.toSet());
    WorkingMemory mem = arachne.processTriples(JavaConverters.asScalaSetConverter(triples).asScala());
    String gpad = exporter.exportGPAD(mem, IRI.create("http://test.org"));
    int lines = gpad.split("\n", -1).length;
    // TODO test contents of annotations; dumb test for now
    Assert.assertTrue(gpad.contains("model-state=production"));
    Assert.assertTrue("Should produce annotations", lines > 2);
}

Example 9 with WorkingMemory

use of org.geneontology.rules.engine.WorkingMemory in project minerva by geneontology.

the class CoreMolecularModelManager method createCanonicalInferredModel.

public WorkingMemory createCanonicalInferredModel(IRI modelId) {
    // swap out any non-canonical types
    OWLOntology source_abox = getModelAbox(modelId);
    OWLOntologyManager aman = OWLManager.createOWLOntologyManager();
    OWLDataFactory df = aman.getOWLDataFactory();
    OWLAnnotationProperty canonical_record = df.getOWLAnnotationProperty(IRI.create("http://geneontology.org/lego/canonical_record"));
    OWLReasonerFactory reasonerFactory = new StructuralReasonerFactory();
    try {
        OWLOntology abox = aman.copyOntology(source_abox, OntologyCopy.DEEP);
        OWLReasoner abox_reasoner = reasonerFactory.createReasoner(abox);
        // convert to canonical wherever possible
        abox.getIndividualsInSignature().forEach(i -> {
            Set<OWLClass> types = abox_reasoner.getTypes(i, true).getFlattened();
            for (OWLClass type : types) {
                Collection<OWLAnnotation> canons = EntitySearcher.getAnnotationObjects(type, tbox, canonical_record);
                // more correct to create new instances for each
                if (canons != null && canons.size() > 0) {
                    for (OWLAnnotation canon : canons) {
                        if (canon.getValue().asIRI().isPresent()) {
                            OWLClass canonical = df.getOWLClass(canon.getValue().asIRI().get());
                            // direct swap
                            // remove the old one
                            OWLClassAssertionAxiom original = df.getOWLClassAssertionAxiom(type, i);
                            aman.removeAxiom(abox, original);
                            // add the new one
                            OWLClassAssertionAxiom canonical_type = df.getOWLClassAssertionAxiom(canonical, i);
                            aman.addAxiom(abox, canonical_type);
                        }
                    }
                }
            }
        });
        WorkingMemory inferred = createInferredModel(abox, modelId);
        abox_reasoner.dispose();
        aman.removeOntology(abox);
        return inferred;
    } catch (OWLOntologyCreationException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
        return createInferredModel(source_abox, modelId);
    }
}