Examples with NonResolvingTaxonIndex org.eol.globi.taxon.NonResolvingTaxonIndex used on opensource projects

Example 6 with NonResolvingTaxonIndex

use of org.eol.globi.taxon.NonResolvingTaxonIndex in project eol-globi-data by jhpoelen.

the class TaxonInteractionIndexerTest method buildTaxonInterIndex.

@Test
public void buildTaxonInterIndex() throws NodeFactoryException, PropertyEnricherException {
    Specimen human = nodeFactory.createSpecimen(nodeFactory.createStudy(new StudyImpl("bla", null, null, null)), new TaxonImpl("Homo sapiens", "NCBI:9606"));
    Specimen animal = nodeFactory.createSpecimen(nodeFactory.createStudy(new StudyImpl("bla", null, null, null)), new TaxonImpl("Canis lupus", "WORMS:2"));
    human.ate(animal);
    for (int i = 0; i < 10; i++) {
        Specimen fish = nodeFactory.createSpecimen(nodeFactory.createStudy(new StudyImpl("bla", null, null, null)), new TaxonImpl("Arius felis", "WORMS:158711"));
        human.ate(fish);
    }
    assertNull(taxonIndex.findTaxonById("WORMS:2"));
    assertNull(taxonIndex.findTaxonByName("Homo sapiens"));
    new NameResolver(getGraphDb(), new NonResolvingTaxonIndex(getGraphDb())).resolve();
    new TaxonInteractionIndexer(getGraphDb()).index();
    Taxon homoSapiens = taxonIndex.findTaxonByName("Homo sapiens");
    assertNotNull(homoSapiens);
    Iterable<Relationship> rels = ((NodeBacked) homoSapiens).getUnderlyingNode().getRelationships(Direction.OUTGOING, NodeUtil.asNeo4j(InteractType.ATE));
    List<String> humanFood = new ArrayList<String>();
    List<Long> counts = new ArrayList<Long>();
    List<String> labels = new ArrayList<>();
    for (Relationship rel : rels) {
        humanFood.add((String) rel.getEndNode().getProperty("name"));
        counts.add((Long) rel.getProperty("count"));
        labels.add((String) rel.getProperty("label"));
    }
    assertThat(humanFood.size(), is(4));
    assertThat(humanFood, hasItems("Arius felis", "Canis lupus"));
    assertThat(counts, hasItems(10L, 1L));
    assertThat(labels, hasItems("eats"));
}

Example 7 with NonResolvingTaxonIndex

use of org.eol.globi.taxon.NonResolvingTaxonIndex in project eol-globi-data by jhpoelen.

the class NameResolverTest method doNameResolving.

@Test
public void doNameResolving() throws NodeFactoryException, PropertyEnricherException {
    Specimen human = nodeFactory.createSpecimen(nodeFactory.createStudy(new StudyImpl("bla", null, null, null)), new TaxonImpl("Homo sapiens", "NCBI:9606"));
    Specimen animal = nodeFactory.createSpecimen(nodeFactory.createStudy(new StudyImpl("bla", null, null, null)), new TaxonImpl("Animalia", "WORMS:2"));
    human.ate(animal);
    Specimen fish = nodeFactory.createSpecimen(nodeFactory.createStudy(new StudyImpl("bla", null, null, null)), new TaxonImpl("Arius felis", "WORMS:158711"));
    human.ate(fish);
    assertNull(taxonIndex.findTaxonById("NCBI:9606"));
    assertNull(taxonIndex.findTaxonByName("Homo sapiens"));
    final NameResolver nameResolver = new NameResolver(getGraphDb(), new NonResolvingTaxonIndex(getGraphDb()));
    nameResolver.setBatchSize(1L);
    nameResolver.resolve();
    assertAnimalia(taxonIndex.findTaxonById("WORMS:2"));
    assertThat(taxonIndex.findTaxonByName("Arius felis"), is(notNullValue()));
    Taxon homoSapiens = taxonIndex.findTaxonByName("Homo sapiens");
    assertNotNull(homoSapiens);
    assertThat(homoSapiens.getExternalId(), is("NCBI:9606"));
}

Example 8 with NonResolvingTaxonIndex

use of org.eol.globi.taxon.NonResolvingTaxonIndex in project eol-globi-data by jhpoelen.

the class LinkerTermMatcherTest method lestesExcludeSuspectedHomonyms.

@Test
public void lestesExcludeSuspectedHomonyms() throws NodeFactoryException, PropertyEnricherException {
    taxonIndex = new NonResolvingTaxonIndex(getGraphDb());
    Taxon lestes = taxonIndex.getOrCreateTaxon(addProps(new TaxonImpl("Lestes", null)));
    assertThat(lestes.getPath(), is("Animalia | Insecta | Lestes"));
    new LinkerTermMatcher(getGraphDb()).link();
    Collection<String> ids = LinkerTestUtil.assertHasOther("Lestes", 7, taxonIndex, RelTypes.SAME_AS);
    assertThat(ids, hasItems("NCBI:181491", "ITIS:102061", "IRMNG:1320006", "GBIF:1423980", "OTT:1090993"));
    assertThat(ids, hasItems("INAT_TAXON:89475"));
}