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

Example 6 with DatasetRegistry

use of org.globalbioticinteractions.dataset.DatasetRegistry 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);
    }
}

Example 7 with DatasetRegistry

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

the class DatasetImporterFactoryImplIT method defaultTSVImporterCached.

@Test
public void defaultTSVImporterCached() throws StudyImporterException, DatasetRegistryException, IOException {
    final DatasetRegistry datasetRegistry = new DatasetRegistryWithCache(new DatasetRegistryGitHubArchive(inStream -> inStream), dataset -> CacheUtil.cacheFor(dataset.getNamespace(), "target/datasets", inStream -> inStream));
    DatasetImporter importer = getTemplateImporter(datasetRegistry, "globalbioticinteractions/template-dataset");
    DatasetImporterForTSV importerTSV = (DatasetImporterForTSV) importer;
    assertThat(importerTSV.getBaseUrl(), startsWith("https://github.com/globalbioticinteractions/template-dataset/"));
    assertThat(importerTSV.getDataset().retrieve(URI.create("globi.json")), is(notNullValue()));
}

Example 8 with DatasetRegistry

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

the class CmdImportDatasets method run.

@Override
public void run() throws StudyImporterException {
    DatasetRegistry registry = DatasetRegistryUtil.getDatasetRegistry(datasetDir);
    new IndexerDataset(registry, nodeFactoryFactory, graphServiceFactory).index();
}