Examples with GraphServiceFactoryProxy org.eol.globi.db.GraphServiceFactoryProxy used on opensource projects

Example 6 with GraphServiceFactoryProxy

use of org.eol.globi.db.GraphServiceFactoryProxy in project eol-globi-data by jhpoelen.

the class LinkerTaxonIndexTest method linkingWithIdOnlyNoPath.

@Test
public void linkingWithIdOnlyNoPath() throws NodeFactoryException {
    Taxon taxonFound = new TaxonImpl(null, "some id");
    taxonIndex.getOrCreateTaxon(taxonFound);
    resolveNames();
    new LinkerTaxonIndex(new GraphServiceFactoryProxy(getGraphDb())).index();
    IndexHits<Node> hits = getGraphDb().index().forNodes(LinkerTaxonIndex.INDEX_TAXON_NAMES_AND_IDS).query("path:\"some id\"");
    assertThat(hits.hasNext(), is(true));
    Node next = hits.next();
    assertThat(new TaxonNode(next).getExternalId(), is("some id"));
    assertThat(hits.hasNext(), is(false));
    hits.close();
}

Example 7 with GraphServiceFactoryProxy

use of org.eol.globi.db.GraphServiceFactoryProxy 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();
    resolveNames();
    new LinkerTaxonIndex(new GraphServiceFactoryProxy(getGraphDb())).index();
    assertThat(getGraphDb().index().existsForNodes(TaxonFuzzySearchIndex.TAXON_NAME_SUGGESTIONS), is(true));
    Index<Node> index = getGraphDb().index().forNodes(TaxonFuzzySearchIndex.TAXON_NAME_SUGGESTIONS);
    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 8 with GraphServiceFactoryProxy

use of org.eol.globi.db.GraphServiceFactoryProxy in project eol-globi-data by jhpoelen.

the class LinkerTaxonIndexTest method indexTaxaWithLiteratureLink.

private void indexTaxaWithLiteratureLink() throws NodeFactoryException {
    Taxon taxonFound = new TaxonImpl("Homo sapiens", "bar:123");
    taxonFound.setPath("Animalia | Mammalia | Homo sapiens");
    Taxon taxon = taxonIndex.getOrCreateTaxon(taxonFound);
    TaxonImpl taxon1 = new TaxonImpl("doi:10.123/456", "doi:10.123/456");
    taxon1.setPath("doi:10.123/456");
    taxon1.setPathIds("doi:10.123/456");
    NodeUtil.connectTaxa(taxon1, (TaxonNode) taxon, getGraphDb(), RelTypes.SAME_AS);
    resolveNames();
    new LinkerTaxonIndex(new GraphServiceFactoryProxy(getGraphDb())).index();
}

Example 9 with GraphServiceFactoryProxy

use of org.eol.globi.db.GraphServiceFactoryProxy in project eol-globi-data by jhpoelen.

the class NameResolverTest method literatureTaxon.

@Test
public void literatureTaxon() throws NodeFactoryException {
    Specimen someOtherOrganism = nodeFactory.createSpecimen(nodeFactory.createStudy(new StudyImpl("bla", null, null)), new TaxonImpl("foo", "foo:123"));
    Specimen someOtherOrganism2 = nodeFactory.createSpecimen(nodeFactory.createStudy(new StudyImpl("bla", null, null)), new TaxonImpl("bar", "bar:456"));
    someOtherOrganism.ate(someOtherOrganism2);
    final NameResolver nameResolver = new NameResolver(new GraphServiceFactoryProxy(getGraphDb()), new ResolvingTaxonIndex(new PropertyEnricher() {

        @Override
        public Map<String, String> enrichFirstMatch(Map<String, String> properties) throws PropertyEnricherException {
            return enrichAllMatches(properties).get(0);
        }

        @Override
        public List<Map<String, String>> enrichAllMatches(Map<String, String> properties) throws PropertyEnricherException {
            TaxonImpl literature = new TaxonImpl("doi:10.678/901", "doi:10.678/901");
            literature.setPath("some | other | path");
            TaxonImpl concept = new TaxonImpl("Donald duckus", "foo:XXX");
            concept.setPath("some | path");
            return Arrays.asList(TaxonUtil.taxonToMap(literature), TaxonUtil.taxonToMap(concept));
        }

        @Override
        public void shutdown() {
        }
    }, getGraphDb()));
    nameResolver.setBatchSize(1L);
    nameResolver.index();
    Taxon resolvedTaxon = taxonIndex.findTaxonById("foo:123");
    assertThat(resolvedTaxon, is(notNullValue()));
    assertThat(resolvedTaxon.getExternalId(), is("foo:XXX"));
    assertThat(resolvedTaxon.getName(), is("Donald duckus"));
    Taxon resolvedTaxon2 = taxonIndex.findTaxonByName("foo");
    assertThat(resolvedTaxon2.getExternalId(), is("foo:XXX"));
    assertThat(resolvedTaxon2.getName(), is("Donald duckus"));
}

Example 10 with GraphServiceFactoryProxy

use of org.eol.globi.db.GraphServiceFactoryProxy 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)), new TaxonImpl("Blaus bla", "INAT_TAXON:58831"));
    Specimen someOtherOrganism2 = nodeFactory.createSpecimen(nodeFactory.createStudy(new StudyImpl("bla", null, null)), new TaxonImpl("Redus rha", "INAT_TAXON:126777"));
    someOtherOrganism.ate(someOtherOrganism2);
    GraphServiceFactory graphServiceFactory = new GraphServiceFactoryProxy(getGraphDb());
    final NameResolver nameResolver = new NameResolver(graphServiceFactory, new NonResolvingTaxonIndex(getGraphDb()));
    nameResolver.setBatchSize(1L);
    nameResolver.index();
    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"));
}