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

Example 1 with DatasetFactory

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

the class DatasetImporterFactoryImplIT method jsonldImporterCached.

@Test
public void jsonldImporterCached() throws StudyImporterException, DatasetRegistryException {
    final DatasetRegistry datasetRegistry = new DatasetRegistryWithCache(new DatasetRegistryGitHubArchive(inStream -> inStream), dataset -> CacheUtil.cacheFor(dataset.getNamespace(), "target/datasets", inStream -> inStream));
    Dataset dataset = new DatasetFactory(datasetRegistry).datasetFor("globalbioticinteractions/jsonld-template-dataset");
    DatasetImporter importer = new StudyImporterFactoryImpl(null).createImporter(dataset);
    assertThat(importer, is(notNullValue()));
    assertThat(importer, is(instanceOf(DatasetImporterForJSONLD.class)));
}

Example 2 with DatasetFactory

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

the class DatasetImporterFactoryImplIT method createHafner.

@Test
public void createHafner() throws StudyImporterException, DatasetRegistryException, IOException {
    final DatasetRegistry datasetRegistryGitHubRemote = new DatasetRegistryGitHubRemote(inStream -> inStream);
    Dataset dataset = new DatasetFactory(datasetRegistryGitHubRemote).datasetFor("globalbioticinteractions/hafner");
    DatasetImporter importer = new StudyImporterFactoryImpl(null).createImporter(dataset);
    assertThat(importer, is(notNullValue()));
    DatasetImporterForHafner haftnerImporter = (DatasetImporterForHafner) importer;
    assertThat(haftnerImporter.getDataset().retrieve(URI.create("hafner/gopher_lice_int.csv")), is(notNullValue()));
}

Example 3 with DatasetFactory

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

the class DatasetImporterFactoryImplIT method getTemplateImporter.

DatasetImporter getTemplateImporter(DatasetRegistry datasetRegistry, String repo) throws DatasetRegistryException, StudyImporterException {
    Dataset dataset = new DatasetFactory(datasetRegistry).datasetFor(repo);
    DatasetImporter importer = new StudyImporterFactoryImpl(null).createImporter(dataset);
    assertThat(importer, is(notNullValue()));
    assertThat(importer, is(instanceOf(DatasetImporterForTSV.class)));
    return importer;
}

Example 4 with DatasetFactory

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

the class DatasetImporterForRegistry method importData.

private void importData(String namespace) throws StudyImporterException {
    try {
        LOG.info("[" + namespace + "] checking status...");
        Dataset dataset = new DatasetFactory(getRegistry()).datasetFor(namespace);
        if (datasetFilter.test(dataset)) {
            StopWatch stopWatch = new StopWatch();
            stopWatch.start();
            LOG.info("[" + namespace + "] is active, importing...");
            getNodeFactory().getOrCreateDataset(dataset);
            importData(dataset);
            stopWatch.stop();
            LOG.info("[" + namespace + "] imported in " + stopWatch.getTime(TimeUnit.SECONDS) + "s");
        } else {
            LOG.info("[" + namespace + "] is deprecated, not importing.");
        }
    } catch (StudyImporterException | DatasetRegistryException ex) {
        String msg = "failed to import data from repo [" + namespace + "]";
        LOG.error(msg, ex);
        throw new StudyImporterException(msg, ex);
    }
}