Examples with LinkerTaxonIndex org.eol.globi.tool.LinkerTaxonIndex used on opensource projects

Example 1 with LinkerTaxonIndex

use of org.eol.globi.tool.LinkerTaxonIndex in project eol-globi-data by jhpoelen.

the class ResolvingTaxonIndexTest method ensureThatEnrichedPropertiesAreLinked.

@Test
public void ensureThatEnrichedPropertiesAreLinked() throws NodeFactoryException {
    this.taxonService = 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 {
            Taxon taxon1 = enrichTaxonWithSuffix(properties, "1");
            Taxon taxon2 = enrichTaxonWithSuffix(properties, "2");
            return Arrays.asList(TaxonUtil.taxonToMap(taxon1), TaxonUtil.taxonToMap(taxon2));
        }

        Taxon enrichTaxonWithSuffix(Map<String, String> properties, String suffix) {
            Taxon taxon = TaxonUtil.mapToTaxon(properties);
            taxon.setPathNames("kingdom" + suffix + CharsetConstant.SEPARATOR + "phylum" + CharsetConstant.SEPARATOR + "etc" + CharsetConstant.SEPARATOR);
            taxon.setPath("a kingdom name" + suffix + CharsetConstant.SEPARATOR + "a phylum name" + CharsetConstant.SEPARATOR + "a etc name" + CharsetConstant.SEPARATOR);
            taxon.setPathIds("a kingdom id" + suffix + CharsetConstant.SEPARATOR + "a phylum id" + CharsetConstant.SEPARATOR + "a etc id" + CharsetConstant.SEPARATOR);
            taxon.setExternalId("anExternalId" + suffix);
            taxon.setCommonNames(EXPECTED_COMMON_NAMES);
            return taxon;
        }

        @Override
        public void shutdown() {
        }
    }, getGraphDb());
    assertThat(getGraphDb().index().existsForNodes("taxons"), is(false));
    assertThat(getGraphDb().index().existsForNodes("thisDoesnoTExist"), is(false));
    TaxonNode indexedTaxonNode = taxonService.getOrCreateTaxon(new TaxonImpl("some name1"));
    assertThat(getGraphDb().index().existsForNodes("taxons"), is(true));
    assertEnrichedPropertiesSet(indexedTaxonNode, "1");
    TaxonNode someFoundTaxonNode = taxonService.findTaxonByName("some name1");
    assertThat(someFoundTaxonNode.getNodeID(), is(indexedTaxonNode.getNodeID()));
    assertEnrichedPropertiesSet(someFoundTaxonNode, "1");
    {
        Index<Node> ids = getGraphDb().index().forNodes(INDEX_TAXON_NAMES_AND_IDS, MapUtil.stringMap(IndexManager.PROVIDER, "lucene", "type", "fulltext"));
        assertThat(ids.query("path:\"some name2\"").size(), is(0));
    }
    LinkerTaxonIndex linkerTaxonIndex = new LinkerTaxonIndex(new GraphServiceFactoryProxy(getGraphDb()));
    linkerTaxonIndex.index();
    {
        Index<Node> ids = getGraphDb().index().forNodes(INDEX_TAXON_NAMES_AND_IDS, MapUtil.stringMap(IndexManager.PROVIDER, "lucene", "type", "fulltext"));
        IndexHits<Node> hits = ids.query("path:\"a kingdom name2\"");
        assertThat(hits.size(), is(1));
        for (Node hit : hits) {
            TaxonNode taxonHit = new TaxonNode(hit);
            assertNotNull(taxonHit);
            assertThat(taxonHit.getNodeID(), is(indexedTaxonNode.getNodeID()));
        }
    }
    TaxonNode someOtherFoundTaxonNodeTake2 = taxonService.findTaxonByName("some name2");
    assertNull(someOtherFoundTaxonNodeTake2);
}

Example 2 with LinkerTaxonIndex

use of org.eol.globi.tool.LinkerTaxonIndex in project eol-globi-data by jhpoelen.

the class CypherTestUtil method validate.

public static void validate(CypherQuery cypherQuery, GraphDatabaseService graphDatabaseService) {
    try (Transaction tx = graphDatabaseService.beginTx()) {
        new NodeFactoryNeo4j2(graphDatabaseService);
        new NonResolvingTaxonIndex(graphDatabaseService);
        new LinkerTaxonIndex(new GraphServiceFactoryProxy(graphDatabaseService)).index();
        CacheService cacheService = new CacheService();
        File cacheDir = new File("target/reportGeneration" + UUID.randomUUID());
        cacheService.setCacheDir(cacheDir);
        CmdGenerateReport reportGenerator = new CmdGenerateReport(graphDatabaseService, cacheService);
        reportGenerator.run(NOPLogger.NOP_LOGGER);
        Map<String, Object> params = cypherQuery.getParams() == null ? Collections.emptyMap() : new HashMap<>(cypherQuery.getParams());
        try {
            graphDatabaseService.execute(cypherQuery.getVersionedQuery(), params);
        } catch (NullPointerException ex) {
            // encountered nullpointer exceptions were caused by initialization of graph database
            throw ex;
        } catch (RuntimeException ex) {
            // work fine in cypher query, but cause parse exception when running programatically
            if (!ex.getMessage().contains("Encountered \" \":\" \": \"\"")) {
                throw ex;
            }
        } finally {
            FileUtils.deleteQuietly(cacheDir);
        }
    }
}