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

Example 1 with Triple

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

the class GPADSPARQLTest method testGPADOutputWithNegation.

/**
 * Test whether the GPAD output contains all required entries and rows without any spurious results.
 * Example Input file: the owl dump from http://noctua-dev.berkeleybop.org/editor/graph/gomodel:59d1072300000074
 * <p>
 * Note on the GPAD file format and its contents:
 * 1. the number of entries in the GPAD output from this owl dump should be 6, not 7 (although there are 7 individuals/boxes)
 * because the edge/relationship "molecular_function" is a trivial one, which is supposed to be removed from the output.
 * 2. the 4th columns, which consists of the list of GO IDs attributed to the DB object ID (These should be GO:0005634, GO:0007267, GO:0007507, GO:0016301)
 * 3. the 2nd columns: the rest of entities in the noctua screen, i.e.  S000028630 (YFR032C-B Scer) or S000004724(SHH3 Scer)
 *
 * @throws Exception
 */
@Test
public void testGPADOutputWithNegation() throws Exception {
    Model model = ModelFactory.createDefaultModel();
    model.read(this.getClass().getResourceAsStream("/59d1072300000074.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"));
    /* Check the number of rows in GPAD output */
    String[] gpadOutputArr = gpad.split("\n", -1);
    /* 1 for header and 6 for the rest of the rows. the length should be  7 or 8.*/
    Assert.assertTrue("Should produce annotations", gpadOutputArr.length >= 1 + 6);
    /* Compare the output with the GPAD file that contains sample answers */
    List<String> lines = FileUtils.readLines(new File("src/test/resources/59d1072300000074.gpad"), "UTF-8");
    /* The order of the rows in the GPAD file can be different, so we compare rows by rows */
    for (String gpadOutputRow : gpadOutputArr) {
        /* Additionally check all rows's qualifier contains |NOT substring inside */
        String[] gpadRowArr = gpadOutputRow.split("\t");
        /* Skip checking the header; all rows need to contain NOT in its qualifier */
        if (gpadRowArr.length > 2) {
            Assert.assertTrue(gpadRowArr[2].contains("|NOT"));
        }
    }
}

Example 2 with Triple

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

the class GPADSPARQLTest method testFilterAnnotationsToRegulatedProcess.

@Test
public void testFilterAnnotationsToRegulatedProcess() throws Exception {
    HashMap<IRI, Set<IRI>> regulators = new HashMap<>();
    regulators.put(IRI.create("http://purl.obolibrary.org/obo/GO_0030511"), Collections.singleton(IRI.create("http://purl.obolibrary.org/obo/GO_0007179")));
    GPADSPARQLExport exporter = new GPADSPARQLExport(DefaultCurieHandler.getDefaultHandler(), new HashMap<IRI, String>(), new HashMap<IRI, String>(), regulators);
    Model model = ModelFactory.createDefaultModel();
    model.read(this.getClass().getResourceAsStream("/test_filter_regulated_process.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/mgi/MGI:2148811");
    IRI regulator = IRI.create("http://purl.obolibrary.org/obo/GO_0030511");
    IRI regulated = IRI.create("http://purl.obolibrary.org/obo/GO_0007179");
    Assert.assertTrue(annotations.stream().anyMatch(a -> a.getObject().equals(gene) && a.getOntologyClass().equals(regulator)));
    Assert.assertTrue(annotations.stream().noneMatch(a -> a.getObject().equals(gene) && a.getOntologyClass().equals(regulated)));
}

Example 3 with Triple

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

the class GPADSPARQLTest method testFilterRootMFWhenOtherMF.

@Test
public void testFilterRootMFWhenOtherMF() throws Exception {
    IRI rootMF = IRI.create("http://purl.obolibrary.org/obo/GO_0003674");
    IRI rootBP = IRI.create("http://purl.obolibrary.org/obo/GO_0008150");
    IRI rootCC = IRI.create("http://purl.obolibrary.org/obo/GO_0005575");
    Model model = ModelFactory.createDefaultModel();
    model.read(this.getClass().getResourceAsStream("/test_root_mf_filter.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/mgi/MGI:2153470");
    Assert.assertTrue(annotations.stream().noneMatch(a -> a.getObject().equals(gene) && a.getOntologyClass().equals(rootMF)));
    Model model2 = ModelFactory.createDefaultModel();
    model2.read(this.getClass().getResourceAsStream("/test_root_mf_filter2.ttl"), "", "ttl");
    Set<Triple> triples2 = model2.listStatements().toList().stream().map(s -> Bridge.tripleFromJena(s.asTriple())).collect(Collectors.toSet());
    WorkingMemory mem2 = arachne.processTriples(JavaConverters.asScalaSetConverter(triples2).asScala());
    Set<GPADData> annotations2 = exporter.getGPAD(mem2, IRI.create("http://test.org"));
    IRI gene2 = IRI.create("http://identifiers.org/mgi/MGI:98392");
    Assert.assertTrue(annotations2.stream().anyMatch(a -> a.getObject().equals(gene2) && a.getOntologyClass().equals(rootMF)));
    Assert.assertTrue(annotations2.stream().anyMatch(a -> a.getObject().equals(gene2) && a.getOntologyClass().equals(rootBP)));
    Model model3 = ModelFactory.createDefaultModel();
    model3.read(this.getClass().getResourceAsStream("/test_root_mf_filter3.ttl"), "", "ttl");
    Set<Triple> triples3 = model3.listStatements().toList().stream().map(s -> Bridge.tripleFromJena(s.asTriple())).collect(Collectors.toSet());
    WorkingMemory mem3 = arachne.processTriples(JavaConverters.asScalaSetConverter(triples3).asScala());
    Set<GPADData> annotations3 = exporter.getGPAD(mem3, IRI.create("http://test.org"));
    IRI gene3 = IRI.create("http://identifiers.org/sgd/S000002650");
    Assert.assertTrue(annotations3.stream().anyMatch(a -> a.getObject().equals(gene3) && a.getOntologyClass().equals(rootMF)));
    Assert.assertTrue(annotations3.stream().anyMatch(a -> a.getObject().equals(gene3) && a.getOntologyClass().equals(rootBP)));
    Assert.assertTrue(annotations3.stream().anyMatch(a -> a.getObject().equals(gene3) && a.getOntologyClass().equals(rootCC)));
}

Example 4 with Triple

use of org.geneontology.rules.engine.Triple 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 5 with Triple

use of org.geneontology.rules.engine.Triple 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)));
}