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

Example 11 with DatasetImporter

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

the class DatasetImporterFactoryImplIT method defaultTSVImporterNotCached.

@Test
public void defaultTSVImporterNotCached() throws StudyImporterException, DatasetRegistryException, IOException {
    final DatasetRegistry datasetRegistry = new DatasetRegistryGitHubRemote(inStream -> inStream);
    DatasetImporter importer = getTemplateImporter(datasetRegistry, "globalbioticinteractions/template-dataset");
    assertThat(((DatasetImporterForTSV) importer).getBaseUrl(), startsWith("https://raw.githubusercontent.com/globalbioticinteractions/template-dataset/"));
    InputStream actual = ((DatasetImporterForTSV) importer).getDataset().retrieve(URI.create("globi.json"));
    assertThat(actual, is(notNullValue()));
}

Example 12 with DatasetImporter

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

the class DatasetImporterFactoryImplTest method createImporter.

@Test
public void createImporter() throws StudyImporterException {
    DatasetImporter someImporter = new StudyImporterFactoryImpl(null).createImporter(new DatasetImpl("namespace", URI.create("some:uri"), is -> is));
    assertThat(someImporter, instanceOf(DatasetImporterForTSV.class));
}

Example 13 with DatasetImporter

use of org.eol.globi.data.DatasetImporter 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 14 with DatasetImporter

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

the class DatasetImporterFactoryImplIT method createSIAD.

@Test
public void createSIAD() throws StudyImporterException, DatasetRegistryException {
    final DatasetRegistryGitHubRemote datasetFinderGitHubRemote = new DatasetRegistryGitHubRemote(inStream -> inStream);
    DatasetImporter importer = importerFor(datasetFinderGitHubRemote, "globalbioticinteractions/siad");
    assertThat(importer, is(notNullValue()));
    Dataset dataset = ((BaseDatasetImporter) importer).getDataset();
    final JsonNode config = dataset.getConfig();
    assertThat(config, is(notNullValue()));
    assertThat(dataset.getOrDefault(DatasetConstant.SHOULD_RESOLVE_REFERENCES, "donald"), is("false"));
}

Example 15 with DatasetImporter

use of org.eol.globi.data.DatasetImporter 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()));
}