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

Example 31 with TaxonImpl

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

the class LinkerOpenTreeOfLifeTest method copyAndLink.

@Test
public void copyAndLink() {
    final TaxonImpl taxon = new TaxonImpl();
    taxon.setExternalId("GBIF:123");
    final Taxon linkedTaxon = LinkerOpenTreeOfLife.copyAndLinkToOpenTreeTaxon(taxon, 555L);
    assertThat(linkedTaxon.getExternalId(), is("OTT:555"));
    assertThat(linkedTaxon.getExternalUrl(), is("https://tree.opentreeoflife.org/opentree/ottol@555"));
}

Example 32 with TaxonImpl

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

the class LinkerOpenTreeOfLifeTest method assertOTTLink.

protected void assertOTTLink(String name, int expectedCount, String ottId) throws NodeFactoryException, PropertyEnricherException {
    OpenTreeTaxonIndex index = null;
    try {
        index = new OpenTreeTaxonIndex(getClass().getResource("taxonomy-small.tsv"));
        taxonIndex.getOrCreateTaxon(new TaxonImpl(name, null));
        new LinkerTermMatcher(getGraphDb()).link();
        new LinkerOpenTreeOfLife(getGraphDb(), index).link();
        Collection<String> externalIds = LinkerTestUtil.assertHasOther(name, expectedCount, taxonIndex, RelTypes.SAME_AS);
        assertThat(externalIds, hasItem(TaxonomyProvider.OPEN_TREE_OF_LIFE.getIdPrefix() + ottId));
    } finally {
        if (index != null) {
            index.destroy();
        }
    }
}

Example 33 with TaxonImpl

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

the class LinkerTaxonIndexTest method findByStringWithWhitespaces.

@Test
public void findByStringWithWhitespaces() throws NodeFactoryException {
    NonResolvingTaxonIndex taxonService = new NonResolvingTaxonIndex(getGraphDb());
    taxonService.getOrCreateTaxon(setTaxonProps(new TaxonImpl("Homo sapiens")));
    resolveNames();
    new LinkerTaxonIndex(getGraphDb()).link();
    assertThat(getGraphDb().index().existsForNodes("taxonNameSuggestions"), is(true));
    Index<Node> index = getGraphDb().index().forNodes("taxonNameSuggestions");
    Query query = new TermQuery(new Term("name", "name"));
    IndexHits<Node> hits = index.query(query);
    assertThat(hits.size(), is(1));
    hits = index.query("name", "s nme~");
    assertThat(hits.size(), is(1));
    hits = index.query("name", "geRman~");
    assertThat(hits.size(), is(1));
    hits = index.query("name:geRman~ AND name:som~");
    assertThat(hits.size(), is(1));
    hits = index.query("name:hmo~ AND name:SApiens~");
    assertThat(hits.size(), is(1));
    hits = index.query("name:hmo~ AND name:sapiens~");
    assertThat(hits.size(), is(1));
    // queries are case sensitive . . . should all be lower cased.
    hits = index.query("name:HMO~ AND name:saPIENS~");
    assertThat(hits.size(), is(0));
}

Example 34 with TaxonImpl

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

the class NameResolverTest method iNaturalistTaxon.

@Test
public void iNaturalistTaxon() throws NodeFactoryException {
    Specimen someOtherOrganism = nodeFactory.createSpecimen(nodeFactory.createStudy(new StudyImpl("bla", null, null, null)), new TaxonImpl("Blaus bla", "INAT_TAXON:58831"));
    Specimen someOtherOrganism2 = nodeFactory.createSpecimen(nodeFactory.createStudy(new StudyImpl("bla", null, null, null)), new TaxonImpl("Redus rha", "INAT_TAXON:126777"));
    someOtherOrganism.ate(someOtherOrganism2);
    final NameResolver nameResolver = new NameResolver(getGraphDb(), new NonResolvingTaxonIndex(getGraphDb()));
    nameResolver.setBatchSize(1L);
    nameResolver.resolve();
    Taxon resolvedTaxon = taxonIndex.findTaxonById("INAT_TAXON:58831");
    assertThat(resolvedTaxon, is(notNullValue()));
    assertThat(resolvedTaxon.getExternalId(), is("INAT_TAXON:58831"));
    assertThat(resolvedTaxon.getName(), is("Blaus bla"));
    Taxon resolvedTaxon2 = taxonIndex.findTaxonByName("Blaus bla");
    assertThat(resolvedTaxon2, is(notNullValue()));
    assertThat(resolvedTaxon2.getExternalId(), is("INAT_TAXON:58831"));
}

Example 35 with TaxonImpl

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

the class LinkerTermMatcherTest method hasFishBaseLinks.

@Test
public void hasFishBaseLinks() throws NodeFactoryException, PropertyEnricherException {
    taxonIndex.getOrCreateTaxon(new TaxonImpl("Ariopsis felis", null));
    new LinkerTermMatcher(getGraphDb()).link();
    Collection<String> ids = LinkerTestUtil.assertHasOther("Ariopsis felis", 8, taxonIndex, RelTypes.SAME_AS);
    assertThat(ids, hasItem("FBC:FB:SpecCode:947"));
    assertThat(ids, hasItem("INAT_TAXON:94635"));
}