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

Example 11 with GraphServiceFactoryProxy

use of org.eol.globi.db.GraphServiceFactoryProxy 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);
        }
    }
}

Example 12 with GraphServiceFactoryProxy

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

the class LinkerOpenTreeOfLifeTest method assertOTTLink.

protected void assertOTTLink(int expectedCount, String ottId, Taxon taxon) throws NodeFactoryException, PropertyEnricherException {
    OpenTreeTaxonIndex index = null;
    try {
        index = new OpenTreeTaxonIndex(getClass().getResource("taxonomy-small.tsv"));
        Taxon createdTaxon = taxonIndex.getOrCreateTaxon(taxon);
        long nodeID = ((NodeBacked) createdTaxon).getNodeID();
        new LinkerTermMatcher((terms, termMatchListener) -> {
            for (Term term : terms) {
                termMatchListener.foundTaxonForTerm(nodeID, term, NameType.SAME_AS, taxon);
            }
        }, new GraphServiceFactoryProxy(getGraphDb())).index();
        new LinkerOpenTreeOfLife(index, new GraphServiceFactoryProxy(getGraphDb())).index();
        Collection<String> externalIds = LinkerTestUtil.assertHasOther(taxon.getName(), expectedCount, taxonIndex, RelTypes.SAME_AS);
        assertThat(externalIds, hasItem(TaxonomyProvider.OPEN_TREE_OF_LIFE.getIdPrefix() + ottId));
    } finally {
        if (index != null) {
            index.destroy();
        }
    }
}

Example 13 with GraphServiceFactoryProxy

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

the class LinkerTermMatcherTest method assertTaxonMapping.

private void assertTaxonMapping(String classifiedId) throws NodeFactoryException {
    Taxon taxon2 = new TaxonImpl("Holorchis castex", classifiedId);
    Taxon createdTaxon = taxonIndex.getOrCreateTaxon(taxon2);
    Node specimenDummy = getGraphDb().createNode();
    Node originalTaxonDummy = getGraphDb().createNode();
    originalTaxonDummy.setProperty("name", "holorchis castex");
    originalTaxonDummy.setProperty("externalId", "EOL:11987314");
    specimenDummy.createRelationshipTo(originalTaxonDummy, NodeUtil.asNeo4j(RelTypes.ORIGINALLY_DESCRIBED_AS));
    specimenDummy.createRelationshipTo(((TaxonNode) createdTaxon).getUnderlyingNode(), NodeUtil.asNeo4j(RelTypes.CLASSIFIED_AS));
    TaxonCacheService taxonCacheService = new TaxonCacheService("/org/eol/globi/taxon/taxonCacheHolorchis.tsv", "/org/eol/globi/taxon/taxonMapHolorchis.tsv");
    new LinkerTermMatcher(taxonCacheService, new GraphServiceFactoryProxy(getGraphDb())).index();
    Collection<String> externalIds = LinkerTestUtil.sameAsCountForNode(RelTypes.SAME_AS, (TaxonNode) createdTaxon);
    assertThat(externalIds, hasItem("EOL_V2:11987314"));
    assertThat(externalIds, hasItem("GBIF:5890922"));
}

Example 14 with GraphServiceFactoryProxy

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

the class TaxonInteractionIndexerTest method indexNoNameNoMatch.

@Test
public void indexNoNameNoMatch() throws NodeFactoryException {
    Specimen human = nodeFactory.createSpecimen(nodeFactory.createStudy(new StudyImpl("bla", null, null)), new TaxonImpl("Homo sapiens", PropertyAndValueDictionary.NO_MATCH));
    Specimen animal = nodeFactory.createSpecimen(nodeFactory.createStudy(new StudyImpl("bla", null, null)), new TaxonImpl("Canis lupus", PropertyAndValueDictionary.NO_MATCH));
    human.ate(animal);
    for (int i = 0; i < 10; i++) {
        Specimen fish = nodeFactory.createSpecimen(nodeFactory.createStudy(new StudyImpl("bla", null, null)), new TaxonImpl("Arius felis", null));
        human.ate(fish);
    }
    assertNull(taxonIndex.findTaxonById(PropertyAndValueDictionary.NO_MATCH));
    assertNull(taxonIndex.findTaxonByName("Homo sapiens"));
    new NameResolver(new GraphServiceFactoryProxy(getGraphDb()), new NonResolvingTaxonIndex(getGraphDb())).index();
    assertNotNull(taxonIndex.findTaxonByName("Homo sapiens"));
    assertNull(taxonIndex.findTaxonById(PropertyAndValueDictionary.NO_MATCH));
    assertNull(taxonIndex.findTaxonByName(PropertyAndValueDictionary.NO_NAME));
}

Example 15 with GraphServiceFactoryProxy

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

the class TaxonInteractionIndexerTest method buildTaxonInterIndex.

@Test
public void buildTaxonInterIndex() throws NodeFactoryException {
    Specimen human = nodeFactory.createSpecimen(nodeFactory.createStudy(new StudyImpl("bla", null, null)), new TaxonImpl("Homo sapiens", "NCBI:9606"));
    Specimen animal = nodeFactory.createSpecimen(nodeFactory.createStudy(new StudyImpl("bla", null, null)), new TaxonImpl("Canis lupus", "WORMS:2"));
    human.ate(animal);
    for (int i = 0; i < 10; i++) {
        Specimen fish = nodeFactory.createSpecimen(nodeFactory.createStudy(new StudyImpl("bla", null, null)), new TaxonImpl("Arius felis", "WORMS:158711"));
        human.ate(fish);
    }
    assertNull(taxonIndex.findTaxonById("WORMS:2"));
    assertNull(taxonIndex.findTaxonByName("Homo sapiens"));
    new NameResolver(new GraphServiceFactoryProxy(getGraphDb()), new NonResolvingTaxonIndex(getGraphDb())).index();
    new TaxonInteractionIndexer(new GraphServiceFactoryProxy(getGraphDb())).index();
    Taxon homoSapiens = taxonIndex.findTaxonByName("Homo sapiens");
    assertNotNull(homoSapiens);
    Iterable<Relationship> rels = ((NodeBacked) homoSapiens).getUnderlyingNode().getRelationships(Direction.OUTGOING, NodeUtil.asNeo4j(InteractType.ATE));
    List<String> humanFood = new ArrayList<String>();
    List<Long> counts = new ArrayList<Long>();
    List<String> labels = new ArrayList<>();
    for (Relationship rel : rels) {
        humanFood.add((String) rel.getEndNode().getProperty("name"));
        counts.add((Long) rel.getProperty("count"));
        labels.add((String) rel.getProperty("label"));
    }
    assertThat(humanFood.size(), is(4));
    assertThat(humanFood, hasItems("Arius felis", "Canis lupus"));
    assertThat(counts, hasItems(10L, 1L));
    assertThat(labels, hasItems("eats"));
}