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

Example 1 with GraphServiceFactory

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

the class NameResolverTest method iNaturalistTaxon.

@Test
public void iNaturalistTaxon() throws NodeFactoryException {
    Specimen someOtherOrganism = nodeFactory.createSpecimen(nodeFactory.createStudy(new StudyImpl("bla", null, null)), new TaxonImpl("Blaus bla", "INAT_TAXON:58831"));
    Specimen someOtherOrganism2 = nodeFactory.createSpecimen(nodeFactory.createStudy(new StudyImpl("bla", null, null)), new TaxonImpl("Redus rha", "INAT_TAXON:126777"));
    someOtherOrganism.ate(someOtherOrganism2);
    GraphServiceFactory graphServiceFactory = new GraphServiceFactoryProxy(getGraphDb());
    final NameResolver nameResolver = new NameResolver(graphServiceFactory, new NonResolvingTaxonIndex(getGraphDb()));
    nameResolver.setBatchSize(1L);
    nameResolver.index();
    Taxon resolvedTaxon = taxonIndex.findTaxonById("INAT_TAXON:58831");
    assertThat(resolvedTaxon, is(notNullValue()));
    assertThat(resolvedTaxon.getExternalId(), is("INAT_TAXON:58831"));
    assertThat(resolvedTaxon.getName(), is("Blaus bla"));
    Taxon resolvedTaxon2 = taxonIndex.findTaxonByName("Blaus bla");
    assertThat(resolvedTaxon2, is(notNullValue()));
    assertThat(resolvedTaxon2.getExternalId(), is("INAT_TAXON:58831"));
}

Example 2 with GraphServiceFactory

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

the class Elton4N method importWithVersion.

private void importWithVersion(CommandLine cmdLine, String neo4jVersion) throws StudyImporterException {
    final String graphDbDirPath = cmdLine.getOptionValue(CmdOptionConstants.OPTION_GRAPHDB_DIR, "graph.db");
    Factories factoriesNeo4j = new Factories() {

        final GraphServiceFactory factory = new GraphServiceFactoryImpl(new File(graphDbDirPath));

        final NodeFactoryFactory nodeFactoryFactory = StringUtils.equals("2", neo4jVersion) ? new NodeFactoryFactoryTransactingOnDatasetNeo4j2(factory) : new NodeFactoryFactoryTransactingOnDatasetNeo4j3(factory);

        @Override
        public GraphServiceFactory getGraphServiceFactory() {
            return factory;
        }

        @Override
        public NodeFactoryFactory getNodeFactoryFactory() {
            return nodeFactoryFactory;
        }
    };
    try {
        String datasetDir = CmdUtil.getDatasetDir(cmdLine);
        GraphServiceFactory graphServiceFactory = factoriesNeo4j.getGraphServiceFactory();
        List<Cmd> steps = new ArrayList<>();
        LOG.info("processing steps: [" + StringUtils.join(cmdLine.getArgList(), ", ") + "]");
        if (cmdLine.getArgList().isEmpty() || cmdLine.getArgList().contains(ELTON_STEP_COMPILE)) {
            steps.add(new CmdImportDatasets(factoriesNeo4j.getNodeFactoryFactory(), graphServiceFactory, datasetDir));
        }
        String exportDir = cmdLine.getOptionValue(CmdOptionConstants.OPTION_EXPORT_DIR, ".");
        CmdInterpretTaxa interpretTaxa = createInterpretTaxaCmd(cmdLine, graphServiceFactory, exportDir);
        if (cmdLine.getArgList().isEmpty() || cmdLine.getArgList().contains(ELTON_STEP_LINK_NAMES)) {
            steps.add(interpretTaxa);
        }
        if (cmdLine.getArgList().isEmpty() || cmdLine.getArgList().contains(ELTON_STEP_LINK)) {
            if (!steps.contains(interpretTaxa)) {
                steps.add(interpretTaxa);
            }
            steps.addAll(Arrays.asList(new CmdIndexTaxa(graphServiceFactory), new CmdIndexTaxonStrings(graphServiceFactory), new CmdGenerateReport(graphServiceFactory.getGraphService())));
        }
        CmdExportInteractionsTSV interactionsTSVExporter = new CmdExportInteractionsTSV(graphServiceFactory, new File(exportDir));
        if (cmdLine.getArgList().isEmpty() || cmdLine.getArgList().contains(ELTON_STEP_PACKAGE_INTERACTIONS_TSV)) {
            steps.add(interactionsTSVExporter);
        }
        if (cmdLine.getArgList().isEmpty() || cmdLine.getArgList().contains(ELTON_STEP_PACKAGE)) {
            if (!steps.contains(interactionsTSVExporter)) {
                steps.add(interactionsTSVExporter);
            }
            steps.add(new CmdExport(graphServiceFactory, new File(exportDir)));
        }
        for (Cmd step : steps) {
            step.run();
        }
    } finally {
        HttpUtil.shutdown();
    }
}

Example 3 with GraphServiceFactory

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

the class GraphDBTestCaseAbstract method getGraphFactory.

protected GraphServiceFactory getGraphFactory() {
    return new GraphServiceFactory() {

        private GraphDatabaseService graphDb = null;

        @Override
        public GraphDatabaseService getGraphService() {
            GraphDatabaseService graphDb = this.graphDb;
            GraphServiceUtil.verifyState(graphDb);
            if (this.graphDb == null) {
                this.graphDb = new TestGraphDatabaseFactory().newImpermanentDatabase();
            }
            return this.graphDb;
        }

        @Override
        public void close() {
            if (graphDb != null) {
                graphDb.shutdown();
                graphDb = null;
            }
        }
    };
}

Example 4 with GraphServiceFactory

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

the class NameResolverTest method assertResolveNames.

private void assertResolveNames(RelTypes relTypes, final GraphDatabaseService graphDb) throws NodeFactoryException {
    Specimen human = nodeFactory.createSpecimen(nodeFactory.createStudy(new StudyImpl("bla", null, null)), new TaxonImpl("Homo sapiens", "NCBI:9606"), relTypes);
    Specimen animal = nodeFactory.createSpecimen(nodeFactory.createStudy(new StudyImpl("bla", null, null)), new TaxonImpl("Animalia", "WORMS:2"), relTypes);
    human.ate(animal);
    Specimen fish = nodeFactory.createSpecimen(nodeFactory.createStudy(new StudyImpl("bla", null, null)), new TaxonImpl("Arius felis", "WORMS:158711"), relTypes);
    human.ate(fish);
    assertNull(taxonIndex.findTaxonById("NCBI:9606"));
    assertNull(taxonIndex.findTaxonByName("Homo sapiens"));
    final GraphServiceFactory factory = new GraphServiceFactory() {

        @Override
        public GraphDatabaseService getGraphService() {
            return getGraphDb();
        }

        @Override
        public void close() {
        }
    };
    final NameResolver nameResolver = new NameResolver(factory, new NonResolvingTaxonIndex(graphDb));
    nameResolver.setBatchSize(1L);
    nameResolver.index();
    assertAnimalia(taxonIndex.findTaxonById("WORMS:2"));
    assertThat(taxonIndex.findTaxonByName("Arius felis"), is(notNullValue()));
    Taxon homoSapiens = taxonIndex.findTaxonByName("Homo sapiens");
    assertNotNull(homoSapiens);
    assertThat(homoSapiens.getExternalId(), is("NCBI:9606"));
}