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

Example 6 with NodeFactory

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

the class DatasetImportUtil method importDataset.

public static void importDataset(StudyImporterConfigurator studyImporterConfigurator, Dataset dataset, NodeFactory nodeFactory, ImportLogger logger, GeoNamesService geoNamesService) throws StudyImporterException {
    nodeFactory.getOrCreateDataset(dataset);
    NodeFactory nodeFactoryForDataset = new NodeFactoryWithDatasetContext(nodeFactory, dataset);
    DatasetImporter datasetImporter = new StudyImporterFactoryImpl(nodeFactoryForDataset).createImporter(dataset);
    datasetImporter.setDataset(dataset);
    if (studyImporterConfigurator != null) {
        studyImporterConfigurator.configure(datasetImporter);
    }
    if (logger != null) {
        datasetImporter.setLogger(logger);
    }
    if (geoNamesService != null) {
        datasetImporter.setGeoNamesService(geoNamesService);
    }
    datasetImporter.importStudy();
}

Example 7 with NodeFactory

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

the class ExportUnmatchedTaxonNamesTest method exportOnePredatorNoPathButWithSameAs.

@Test
public void exportOnePredatorNoPathButWithSameAs() throws NodeFactoryException, IOException {
    taxonIndex = ExportTestUtil.taxonIndexWithEnricher(null, getGraphDb());
    String citation = "cite, study";
    NodeFactory nodeFactory = nodeFactoryWithDataset();
    StudyNode study = (StudyNode) nodeFactory.getOrCreateStudy(new StudyImpl("my, study", null, citation));
    Specimen predatorSpecimen = nodeFactory.createSpecimen(study, new TaxonImpl("Homo sapienz", null));
    Taxon humanz = taxonIndex.getOrCreateTaxon(new TaxonImpl("Homo sapienz", null));
    TaxonImpl taxon = new TaxonImpl("Homo sapiens", "TESTING:123");
    taxon.setPath("one | two | Homo sapiens");
    NodeUtil.connectTaxa(taxon, (TaxonNode) humanz, getGraphDb(), RelTypes.SIMILAR_TO);
    assertNotNull(humanz);
    Specimen preySpecimen = nodeFactory.createSpecimen(study, new TaxonImpl("Caniz", null));
    predatorSpecimen.interactsWith(preySpecimen, InteractType.ATE);
    predatorSpecimen = nodeFactory.createSpecimen(study, new TaxonImpl("Homo sapiens", null));
    Node synonymNode = ((NodeBacked) taxonIndex.getOrCreateTaxon(new TaxonImpl("Homo sapiens Synonym", null))).getUnderlyingNode();
    Node node = ((NodeBacked) taxonIndex.getOrCreateTaxon(new TaxonImpl("Homo sapiens", null))).getUnderlyingNode();
    node.createRelationshipTo(synonymNode, NodeUtil.asNeo4j(RelTypes.SAME_AS));
    preySpecimen = nodeFactory.createSpecimen(study, new TaxonImpl("Canis", null));
    predatorSpecimen.ate(preySpecimen);
    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("\nHomo sapienz\t\t\tHomo sapiens\tone | two | Homo sapiens\tTESTING:123\tcite, study\t<some:archive>"));
    assertThat(actual, containsString("\nCaniz\t\t\t\t\t\tcite, study\t<some:archive>"));
    assertThat(actual, containsString("\nCanis\t\t\t\t\t\tcite, study\t<some:archive>"));
}

Example 8 with NodeFactory

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

the class NodeFactoryTest method doSingleImportNeo4j2.

@Test
public void doSingleImportNeo4j2() throws StudyImporterException {
    GraphDatabaseService graphDb = getGraphDb();
    NodeFactory factory = createNeo4j2(graphDb);
    try (Transaction tx = getGraphDb().beginTx()) {
        importWithGraphDB(factory);
    }
}

Example 9 with NodeFactory

use of org.eol.globi.data.NodeFactory 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;
}