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

Example 16 with TaxonNode

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

the class NonResolvingTaxonIndexTest method assertNotIndexed.

private final void assertNotIndexed(String magicValue) throws NodeFactoryException {
    Taxon taxon1 = new TaxonImpl(magicValue, null);
    taxon1.setPath(null);
    TaxonNode taxon = taxonService.getOrCreateTaxon(taxon1);
    assertThat(taxon, is(notNullValue()));
    assertThat(taxonService.findTaxonByName(magicValue), is(nullValue()));
}

Example 17 with TaxonNode

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

the class NonResolvingTaxonIndexTest method createTaxonExternalIdIndex.

@Test
public final void createTaxonExternalIdIndex() throws NodeFactoryException {
    Taxon taxon1 = new TaxonImpl(null, "foo:123");
    taxon1.setPath(null);
    TaxonNode taxon = taxonService.getOrCreateTaxon(taxon1);
    assertThat(taxon, is(notNullValue()));
    assertThat(taxonService.findTaxonById("foo:123"), is(notNullValue()));
}

Example 18 with TaxonNode

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

the class NonResolvingTaxonIndexTest method createNullTaxon.

@Test
public final void createNullTaxon() throws NodeFactoryException {
    Taxon taxon1 = new TaxonImpl(null, "EOL:1234");
    taxon1.setPath(null);
    TaxonNode taxon = taxonService.getOrCreateTaxon(taxon1);
    assertThat(taxon, is(notNullValue()));
    assertEquals("no name", taxon.getName());
}

Example 19 with TaxonNode

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

the class ResolvingTaxonIndex method resolveAndIndex.

private TaxonNode resolveAndIndex(Taxon origTaxon, Taxon taxon) throws NodeFactoryException {
    TaxonNode indexedTaxon = findTaxon(taxon);
    while (indexedTaxon == null) {
        try {
            taxon = TaxonUtil.enrich(enricher, taxon);
        } catch (PropertyEnricherException e) {
            throw new NodeFactoryException("failed to enrich taxon with name [" + taxon.getName() + "]", e);
        }
        indexedTaxon = findTaxon(taxon);
        if (indexedTaxon == null) {
            if (TaxonUtil.isResolved(taxon)) {
                indexedTaxon = createAndIndexTaxon(origTaxon, taxon);
            } else {
                String truncatedName = NodeUtil.truncateTaxonName(taxon.getName());
                if (StringUtils.equals(truncatedName, taxon.getName())) {
                    if (isIndexResolvedOnly()) {
                        break;
                    } else {
                        indexedTaxon = addNoMatchTaxon(origTaxon);
                    }
                } else {
                    taxon = new TaxonImpl();
                    taxon.setName(truncatedName);
                    indexedTaxon = findTaxonByName(taxon.getName());
                }
            }
        }
    }
    return indexedTaxon;
}

Example 20 with TaxonNode

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

the class LinkerOpenTreeOfLife method link.

protected boolean link(GraphDatabaseService graphDb, OpenTreeTaxonIndex index, Map<String, Long> ottIds, Relationship rel) {
    boolean hasPrexistingLink = false;
    TaxonNode taxonNode = new TaxonNode(rel.getEndNode());
    String externalId = taxonNode.getExternalId();
    if (StringUtils.contains(externalId, TaxonomyProvider.OPEN_TREE_OF_LIFE.getIdPrefix())) {
        ottIds.clear();
        hasPrexistingLink = true;
    } else {
        externalId = StringUtils.replace(externalId, TaxonomyProvider.INTERIM_REGISTER_OF_MARINE_AND_NONMARINE_GENERA.getIdPrefix(), "irmng:");
        externalId = StringUtils.replace(externalId, TaxonomyProvider.INDEX_FUNGORUM.getIdPrefix(), "if:");
        externalId = StringUtils.replace(externalId, TaxonomyProvider.GBIF.getIdPrefix(), "gbif:");
        externalId = StringUtils.replace(externalId, TaxonomyProvider.NCBI.getIdPrefix(), "ncbi:");
        Long ottId = index.findOpenTreeTaxonIdFor(externalId);
        if (ottId != null) {
            if (ottIds.size() == 0) {
                Taxon taxonCopy = copyAndLinkToOpenTreeTaxon(taxonNode, ottId);
                NodeUtil.connectTaxa(taxonCopy, new TaxonNode(rel.getStartNode()), graphDb, RelTypes.SAME_AS);
            }
            ottIds.put(externalId, ottId);
        }
    }
    return hasPrexistingLink;
}