Examples with Dataset org.globalbioticinteractions.dataset.Dataset used on opensource projects

Example 31 with Dataset

use of org.globalbioticinteractions.dataset.Dataset in project eol-globi-data by jhpoelen.

the class DatasetImporterForTSVTest method importFewLines.

@Test
public void importFewLines() throws StudyImporterException {
    Dataset dataset = getDataset(new TreeMap<URI, String>() {

        {
            put(URI.create("/interactions.tsv"), firstFewLinesTSV);
        }
    });
    DatasetImporterForTSV importer = new DatasetImporterForTSV(null, nodeFactory);
    importer.setDataset(dataset);
    importStudy(importer);
    assertExists("Leptoconchus incycloseris");
    assertExists("Sandalolitha dentata");
    assertStudyTitles("someRepodoi:10.1007/s13127-011-0039-1");
}

Example 32 with Dataset

use of org.globalbioticinteractions.dataset.Dataset in project eol-globi-data by jhpoelen.

the class DatasetImporterForTSVTest method importFewLinesTSV.

@Test
public void importFewLinesTSV() throws StudyImporterException {
    Dataset dataset = getDataset(new TreeMap<URI, String>() {

        {
            put(URI.create("/interactions.tsv"), firstFewLinesTSV);
        }
    });
    DatasetImporterForTSV importer = new DatasetImporterForTSV(null, nodeFactory);
    importer.setDataset(dataset);
    importStudy(importer);
    assertExists("Leptoconchus incycloseris");
    assertExists("Sandalolitha dentata");
    assertStudyTitles("someRepodoi:10.1007/s13127-011-0039-1");
}

Example 33 with Dataset

use of org.globalbioticinteractions.dataset.Dataset in project eol-globi-data by jhpoelen.

the class DatasetImporterForINaturalistTest method setup.

@Before
public void setup() throws DatasetRegistryException {
    Dataset dataset = datasetFor("globalbioticinteractions/inaturalist");
    ParserFactory parserFactory = new ParserFactoryForDataset(dataset);
    importer = new DatasetImporterForINaturalist(parserFactory, nodeFactory);
    importer.setDataset(dataset);
}

Example 34 with Dataset

use of org.globalbioticinteractions.dataset.Dataset 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 35 with Dataset

use of org.globalbioticinteractions.dataset.Dataset in project eol-globi-data by jhpoelen.

the class DatasetImporterForHurlbertTest method doImport.

public DatasetImporter doImport(final String namespace) throws StudyImporterException {
    DatasetImporter importer = new DatasetImporterForHurlbert(null, nodeFactory);
    Dataset dataset = new DatasetImpl(namespace, URI.create("some:uri"), inStream -> inStream) {

        @Override
        public InputStream retrieve(URI name) {
            return DatasetImporterForHurlbertTest.getResource();
        }
    };
    importer.setDataset(dataset);
    importStudy(importer);
    return importer;
}