Examples with NodeFactoryNeo4j2 org.eol.globi.data.NodeFactoryNeo4j2 used on opensource projects

Example 1 with NodeFactoryNeo4j2

use of org.eol.globi.data.NodeFactoryNeo4j2 in project eol-globi-data by jhpoelen.

the class IndexInteractionsTest method indexInteractions.

@Test
public void indexInteractions() throws NodeFactoryException {
    TaxonIndex taxonIndex = getOrCreateTaxonIndex();
    // see https://github.com/globalbioticinteractions/globalbioticinteractions/wiki/Nanopubs
    StudyImpl study = new StudyImpl("some study", new DOI("123.23", "222"), "some study citation");
    NodeFactoryWithDatasetContext factory = new NodeFactoryWithDatasetContext(nodeFactory, new DatasetImpl("some/namespace", URI.create("https://some.uri"), inStream -> inStream));
    Study interaction = factory.getOrCreateStudy(study);
    TaxonImpl donaldTaxon = new TaxonImpl("donald duck", "NCBI:1234");
    Specimen donald = factory.createSpecimen(interaction, donaldTaxon);
    donald.classifyAs(taxonIndex.getOrCreateTaxon(donaldTaxon));
    TaxonImpl mickeyTaxon = new TaxonImpl("mickey mouse", "NCBI:4444");
    Taxon mickeyTaxonNCBI = taxonIndex.getOrCreateTaxon(new TaxonImpl("mickey mouse", "EOL:567"));
    NodeUtil.connectTaxa(mickeyTaxon, (TaxonNode) mickeyTaxonNCBI, getGraphDb(), RelTypes.SAME_AS);
    Specimen mickey = factory.createSpecimen(interaction, mickeyTaxon);
    mickey.classifyAs(taxonIndex.getOrCreateTaxon(mickeyTaxon));
    donald.ate(mickey);
    new IndexInteractions(new GraphServiceFactoryProxy(getGraphDb())).index();
    NodeFactoryNeo4j nodeFactoryNeo4j = new NodeFactoryNeo4j2(getGraphDb());
    StudyImpl study1 = new StudyImpl("some study", new DOI("123.23", "222"), "come citation");
    study1.setOriginatingDataset(new DatasetImpl("some/namespace", URI.create("some:uri"), inStream -> inStream));
    StudyNode someStudy = nodeFactoryNeo4j.getOrCreateStudy(study1);
    assertThat(interaction.getOriginatingDataset().getNamespace(), is(someStudy.getOriginatingDataset().getNamespace()));
    assertThat(interaction.getTitle(), is(someStudy.getTitle()));
    RelationshipType hasParticipant = NodeUtil.asNeo4j(RelTypes.HAS_PARTICIPANT);
    Set<Long> ids = new HashSet<>();
    List<Long> idList = new ArrayList<>();
    NodeUtil.handleCollectedRelationships(new NodeTypeDirection(someStudy.getUnderlyingNode()), new RelationshipListener() {

        @Override
        public void on(Relationship specimen) {
            assertThat(specimen.getEndNode().hasRelationship(Direction.INCOMING, hasParticipant), Is.is(true));
            Iterable<Relationship> relationships = specimen.getEndNode().getRelationships(hasParticipant, Direction.INCOMING);
            for (Relationship relationship : relationships) {
                long id = relationship.getStartNode().getId();
                ids.add(id);
                idList.add(id);
            }
        }
    });
    assertThat(ids.size(), Is.is(1));
    assertThat(idList.size(), Is.is(2));
    Node interactionNode = getGraphDb().getNodeById(idList.get(0));
    assertTrue(interactionNode.hasRelationship(Direction.OUTGOING, NodeUtil.asNeo4j(RelTypes.DERIVED_FROM)));
    assertTrue(interactionNode.hasRelationship(Direction.OUTGOING, NodeUtil.asNeo4j(RelTypes.ACCESSED_AT)));
}

Example 2 with NodeFactoryNeo4j2

use of org.eol.globi.data.NodeFactoryNeo4j2 in project eol-globi-data by jhpoelen.

the class NodeFactoryFactoryTransactingOnDatasetNeo4j2 method create.

@Override
public NodeFactory create(GraphDatabaseService service) {
    GraphDatabaseService graphService = graphServiceFactory.getGraphService();
    try (Transaction tx = graphService.beginTx()) {
        NodeFactory nodeFactory = new NodeFactoryNeo4j2(graphService) {

            final AtomicReference<Transaction> tx = new AtomicReference<>();

            final AtomicBoolean closing = new AtomicBoolean(false);

            final AtomicLong counter = new AtomicLong(0);

            @Override
            public Dataset getOrCreateDataset(Dataset dataset) {
                if (closing.get()) {
                    throw new IllegalStateException("cannot create a dataset on closing node factory");
                } else {
                    startBatchTransactionIfNeeded();
                }
                return super.getOrCreateDataset(dataset);
            }

            void startBatchTransactionIfNeeded() {
                tx.getAndUpdate(transaction -> {
                    if (counter.getAndIncrement() % TRANSACTION_BATCH_SIZE_DEFAULT == 0) {
                        if (transaction != null) {
                            transaction.success();
                            transaction.close();
                            transaction = null;
                        }
                    }
                    return transaction == null ? beginTx() : transaction;
                });
            }

            private Transaction beginTx() {
                return graphServiceFactory.getGraphService().beginTx();
            }

            @Override
            public SpecimenNode createSpecimen(Study study, Taxon taxon, RelTypes... types) throws NodeFactoryException {
                startBatchTransactionIfNeeded();
                return super.createSpecimen(study, taxon, types);
            }

            @Override
            public void close() {
                tx.getAndUpdate(tx -> {
                    closing.set(true);
                    if (tx != null) {
                        tx.success();
                        tx.close();
                    }
                    return null;
                });
            }
        };
        tx.success();
        return nodeFactory;
    }
}

Example 3 with NodeFactoryNeo4j2

use of org.eol.globi.data.NodeFactoryNeo4j2 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 4 with NodeFactoryNeo4j2

use of org.eol.globi.data.NodeFactoryNeo4j2 in project eol-globi-data by jhpoelen.

the class NodeFactoryTest method createNeo4j2.

private NodeFactory createNeo4j2(GraphDatabaseService graphDb) {
    NodeFactory factory;
    try (Transaction tx = getGraphDb().beginTx()) {
        factory = new NodeFactoryNeo4j2(graphDb);
        tx.success();
    }
    return factory;
}