Examples with TaxonImpl org.eol.globi.domain.TaxonImpl used on opensource projects

Example 51 with TaxonImpl

use of org.eol.globi.domain.TaxonImpl in project eol-globi-data by jhpoelen.

the class TaxonUtilTest method copyTaxonPrefillExternalURL.

@Test
public void copyTaxonPrefillExternalURL() {
    Taxon src = new TaxonImpl("name", "GBIF:123");
    src.setStatus(new TermImpl("statusId", "statusLabel"));
    Taxon target = new TaxonImpl();
    TaxonUtil.copy(src, target);
    assertThat(target.getStatus().getId(), is("statusId"));
    assertThat(target.getStatus().getName(), is("statusLabel"));
    assertThat(target.getExternalUrl(), is("http://www.gbif.org/species/123"));
}

Example 52 with TaxonImpl

use of org.eol.globi.domain.TaxonImpl in project eol-globi-data by jhpoelen.

the class TaxonUtilTest method homonymNull.

@Test
public void homonymNull() {
    TaxonImpl otherTaxon = new TaxonImpl();
    otherTaxon.setName("Lestes");
    otherTaxon.setPath("Mammalia|Mesonychidae|Lestes");
    otherTaxon.setPathNames("class|family|genus");
    assertFalse(TaxonUtil.likelyHomonym(null, otherTaxon));
    assertFalse(TaxonUtil.likelyHomonym(otherTaxon, null));
}

Example 53 with TaxonImpl

use of org.eol.globi.domain.TaxonImpl in project eol-globi-data by jhpoelen.

the class ImageLinkerTest method linkTaxonWithFunnyID.

@Test
public void linkTaxonWithFunnyID() throws NodeFactoryException {
    Taxon taxon = taxonIndex.getOrCreateTaxon(new TaxonImpl("Donald duckus", "DUCK:123"));
    assertNotNull(taxon);
    new ImageLinker(getGraphDb(), System.out).link();
    Taxon enrichedTaxon = taxonIndex.findTaxonById("DUCK:123");
    assertThat(enrichedTaxon.getThumbnailUrl(), is(nullValue()));
    assertThat(enrichedTaxon.getExternalUrl(), is(nullValue()));
}

Example 54 with TaxonImpl

use of org.eol.globi.domain.TaxonImpl in project eol-globi-data by jhpoelen.

the class IndexInteractionsTest method indexInteractions.

@Test
public void indexInteractions() throws NodeFactoryException {
    TaxonIndex taxonIndex = getOrCreateTaxonIndex();
    // see https://github.com/jhpoelen/eol-globi-data/wiki/Nanopubs
    StudyImpl study = new StudyImpl("some study", "some source", "http://doi.org/123.23/222", "some study citation");
    NodeFactoryWithDatasetContext factory = new NodeFactoryWithDatasetContext(nodeFactory, new DatasetImpl("some/namespace", URI.create("https://some.uri")));
    Study interaction = factory.getOrCreateStudy(study);
    TaxonImpl donaldTaxon = new TaxonImpl("donald duck", "NCBI:1234");
    Specimen donald = factory.createSpecimen(interaction, donaldTaxon);
    donald.classifyAs(taxonIndex.getOrCreateTaxon(donaldTaxon));
    TaxonImpl mickeyTaxon = new TaxonImpl("mickey mouse", "NCBI:4444");
    Taxon mickeyTaxonNCBI = taxonIndex.getOrCreateTaxon(new TaxonImpl("mickey mouse", "EOL:567"));
    NodeUtil.connectTaxa(mickeyTaxon, (TaxonNode) mickeyTaxonNCBI, getGraphDb(), RelTypes.SAME_AS);
    Specimen mickey = factory.createSpecimen(interaction, mickeyTaxon);
    mickey.classifyAs(taxonIndex.getOrCreateTaxon(mickeyTaxon));
    donald.ate(mickey);
    new IndexInteractions(getGraphDb()).link();
    NodeFactoryNeo4j nodeFactoryNeo4j = new NodeFactoryNeo4j(getGraphDb());
    StudyImpl study1 = new StudyImpl("some study", "some source", null, "come citation");
    study1.setOriginatingDataset(new DatasetImpl("some/namespace", URI.create("some:uri")));
    StudyNode someStudy = nodeFactoryNeo4j.getOrCreateStudy(study1);
    assertThat(interaction.getOriginatingDataset().getNamespace(), is(someStudy.getOriginatingDataset().getNamespace()));
    assertThat(interaction.getTitle(), is(someStudy.getTitle()));
    Iterable<Relationship> specimens = NodeUtil.getSpecimens(someStudy);
    RelationshipType hasParticipant = NodeUtil.asNeo4j(RelTypes.HAS_PARTICIPANT);
    Set<Long> ids = new HashSet<>();
    List<Long> idList = new ArrayList<>();
    for (Relationship specimen : specimens) {
        assertThat(specimen.getEndNode().hasRelationship(Direction.INCOMING, hasParticipant), Is.is(true));
        Relationship singleRelationship = specimen.getEndNode().getSingleRelationship(hasParticipant, Direction.INCOMING);
        long id = singleRelationship.getStartNode().getId();
        ids.add(id);
        idList.add(id);
    }
    assertThat(ids.size(), Is.is(1));
    assertThat(idList.size(), Is.is(2));
    Node interactionNode = getGraphDb().getNodeById(idList.get(0));
    assertTrue(interactionNode.hasRelationship(Direction.OUTGOING, NodeUtil.asNeo4j(RelTypes.DERIVED_FROM)));
    assertTrue(interactionNode.hasRelationship(Direction.OUTGOING, NodeUtil.asNeo4j(RelTypes.ACCESSED_AT)));
}

Example 55 with TaxonImpl

use of org.eol.globi.domain.TaxonImpl in project eol-globi-data by jhpoelen.

the class ResolvingTaxonIndexTest method synonymsAddedToIndexOnce.

@Test
public final void synonymsAddedToIndexOnce() throws NodeFactoryException {
    ResolvingTaxonIndex taxonService = createTaxonService(getGraphDb());
    taxonService.setEnricher(new PropertyEnricher() {

        private boolean firstTime = true;

        @Override
        public Map<String, String> enrich(Map<String, String> properties) throws PropertyEnricherException {
            Taxon taxon = TaxonUtil.mapToTaxon(properties);
            if ("not pref".equals(taxon.getName())) {
                if (!firstTime) {
                    fail("should already have indexed [" + taxon.getName() + "]...");
                }
                taxon.setName("preferred");
                taxon.setExternalId("bla:123");
                taxon.setPath("one | two | three");
                taxon.setPathIds("1 | 2 | 3");
                firstTime = false;
            }
            return TaxonUtil.taxonToMap(taxon);
        }

        @Override
        public void shutdown() {
        }
    });
    this.taxonService = taxonService;
    Taxon taxon2 = new TaxonImpl("not pref", null);
    taxon2.setPath(null);
    TaxonNode first = this.taxonService.getOrCreateTaxon(taxon2);
    assertThat(first.getName(), is("preferred"));
    assertThat(first.getPath(), is("one | two | three"));
    assertThat(first.getPathIds(), is("1 | 2 | 3"));
    Taxon taxon1 = new TaxonImpl("not pref", null);
    taxon1.setPath(null);
    TaxonNode second = this.taxonService.getOrCreateTaxon(taxon1);
    assertThat(second.getNodeID(), is(first.getNodeID()));
    TaxonNode third = this.taxonService.getOrCreateTaxon(new TaxonImpl("not pref"));
    assertThat(third.getNodeID(), is(first.getNodeID()));
    TaxonNode foundTaxon = this.taxonService.findTaxonByName("not pref");
    assertThat(foundTaxon.getNodeID(), is(first.getNodeID()));
    foundTaxon = this.taxonService.findTaxonByName("preferred");
    assertThat(foundTaxon.getNodeID(), is(first.getNodeID()));
}