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

Example 1 with NodeFactory

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

the class IndexerDataset method index.

@Override
public void index() throws StudyImporterException {
    GraphDatabaseService graphService = graphServiceFactory.getGraphService();
    NodeFactory nodeFactory;
    try (Transaction tx = graphService.beginTx()) {
        nodeFactory = nodeFactoryFactory.create(graphService);
        tx.success();
    }
    try {
        indexDatasets(this.registry, nodeFactory);
    } finally {
        if (nodeFactory != null) {
            try {
                nodeFactory.close();
            } catch (Exception e) {
                throw new StudyImporterException("failed to gracefully end index process", e);
            }
        }
    }
}

Example 2 with NodeFactory

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

the class ExportUnmatchedTaxonNamesTest method exportOnePredatorTwoPrey.

@Test
public void exportOnePredatorTwoPrey() throws NodeFactoryException, IOException {
    taxonIndex = ExportTestUtil.taxonIndexWithEnricher(null, getGraphDb());
    String title = "my study\"";
    String citation = "citation my study";
    NodeFactory nodeFactory = nodeFactoryWithDataset();
    StudyNode study = (StudyNode) nodeFactory.getOrCreateStudy(new StudyImpl(title, null, citation));
    taxonIndex.getOrCreateTaxon(new TaxonImpl("Homo sapiens", null));
    Specimen predatorSpecimen = nodeFactory.createSpecimen(study, human());
    taxonIndex.getOrCreateTaxon(new TaxonImpl("Canis lupus", null));
    Specimen preySpecimen6 = nodeFactory.createSpecimen(study, dog());
    predatorSpecimen.interactsWith(preySpecimen6, InteractType.ATE);
    Specimen preySpecimen5 = nodeFactory.createSpecimen(study, dog());
    predatorSpecimen.interactsWith(preySpecimen5, InteractType.ATE);
    Specimen preySpecimen = nodeFactory.createSpecimen(study, new TaxonImpl("Caniz", null));
    predatorSpecimen.ate(preySpecimen);
    Specimen predatorSpecimen23 = nodeFactory.createSpecimen(study, new TaxonImpl("Homo sapiens2", null));
    Specimen preySpecimen4 = nodeFactory.createSpecimen(study, dog());
    predatorSpecimen23.interactsWith(preySpecimen4, InteractType.ATE);
    Specimen predatorSpecimen22 = nodeFactory.createSpecimen(study, new TaxonImpl("Homo sapiens2", null));
    Specimen preySpecimen3 = nodeFactory.createSpecimen(study, dog());
    predatorSpecimen22.interactsWith(preySpecimen3, InteractType.ATE);
    Study study2 = nodeFactory.getOrCreateStudy(new StudyImpl("my study2", null, "citation study2"));
    Specimen predatorSpecimen21 = nodeFactory.createSpecimen(study2, new TaxonImpl("Homo sapiens2", null));
    Specimen preySpecimen2 = nodeFactory.createSpecimen(study2, dog());
    predatorSpecimen21.interactsWith(preySpecimen2, InteractType.ATE);
    Specimen predatorSpecimen2 = nodeFactory.createSpecimen(study, new TaxonImpl("Homo sapiens3", PropertyAndValueDictionary.NO_MATCH));
    Specimen preySpecimen1 = nodeFactory.createSpecimen(study, dog());
    predatorSpecimen2.interactsWith(preySpecimen1, InteractType.ATE);
    resolveNames();
    StringWriter writer = new StringWriter();
    new ExportUnmatchedTaxonNames().exportStudy(study, ExportUtil.AppenderWriter.of(writer), true);
    String actual = writer.toString();
    assertThat(actual, startsWith("unmatched taxon name\tunmatched taxon id\tname status\tsimilar to taxon name\tsimilar to taxon path\tsimilar to taxon id\tstudy\tsource"));
    assertThat(actual, containsString("\nCaniz\t\t\t\t\t\tcitation my study\t<some:archive>"));
    assertThat(actual, containsString("\nHomo sapiens2\t\t\t\t\t\tcitation my study\t<some:archive>"));
    assertThat(actual, containsString("\nHomo sapiens3\tno:match\t\t\t\t\tcitation my study\t<some:archive>"));
}

Example 3 with NodeFactory

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

the class NodeFactoryFactoryTransactingOnDatasetNeo4j3 method create.

@Override
public NodeFactory create(GraphDatabaseService service) {
    GraphDatabaseService graphService = graphServiceFactory.getGraphService();
    try (Transaction tx = graphService.beginTx()) {
        NodeFactory nodeFactory = new NodeFactoryNeo4j3(graphService) {

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

            final AtomicBoolean closing = new AtomicBoolean(false);

            @Override
            public Dataset getOrCreateDataset(Dataset dataset) {
                if (closing.get()) {
                    throw new IllegalStateException("cannot create a dataset on closing node factory");
                } else {
                    Transaction transaction = tx.get();
                    if (transaction != null) {
                        transaction.success();
                        transaction.close();
                    }
                    tx.set(graphServiceFactory.getGraphService().beginTx());
                }
                return super.getOrCreateDataset(dataset);
            }

            @Override
            public void close() {
                closing.set(true);
                Transaction lastTx = tx.getAndSet(null);
                if (lastTx != null) {
                    lastTx.success();
                    lastTx.close();
                }
            }
        };
        tx.success();
        return nodeFactory;
    }
}

Example 4 with NodeFactory

use of org.eol.globi.data.NodeFactory 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 5 with NodeFactory

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

the class IndexerDataset method indexDatasets.

private static void indexDatasets(DatasetRegistry registry, NodeFactory nodeFactory) {
    try {
        final Collection<String> namespaces = registry.findNamespaces();
        String namespacelist = StringUtils.join(namespaces, CharsetConstant.SEPARATOR);
        LOG.info("found dataset namespaces: {" + namespacelist + "}");
        DatasetImporterForRegistry importer = new DatasetImporterForRegistry(new ParserFactoryLocal(), nodeFactory, registry);
        importer.setDatasetFilter(x -> !DatasetUtil.isDeprecated(x));
        importer.setDataset(new DatasetLocal(inStream -> inStream));
        importer.setLogger(new NullImportLogger());
        importer.importStudy();
    } catch (DatasetRegistryException | StudyImporterException e) {
        LOG.error("problem encountered while importing [" + DatasetImporterForRegistry.class.getName() + "]", e);
    }
}