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

Example 1 with DatasetRegistry

use of org.globalbioticinteractions.dataset.DatasetRegistry 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 DatasetRegistry

use of org.globalbioticinteractions.dataset.DatasetRegistry 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 DatasetRegistry

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

the class DatasetImporterFactoryImplIT method defaultTSVImporterCachedZenodo.

@Test
public void defaultTSVImporterCachedZenodo() throws StudyImporterException, DatasetRegistryException {
    final DatasetRegistry datasetRegistry = new DatasetRegistryWithCache(new DatasetRegistryZenodo(inStream -> inStream), dataset -> CacheUtil.cacheFor(dataset.getNamespace(), "target/datasets", inStream -> inStream));
    DatasetImporter importer = getTemplateImporter(datasetRegistry, "globalbioticinteractions/template-dataset");
    DatasetImporterForTSV importerTSV = (DatasetImporterForTSV) importer;
    assertThat(importerTSV.getSourceCitation(), containsString("doi.org"));
}

Example 4 with DatasetRegistry

use of org.globalbioticinteractions.dataset.DatasetRegistry 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 5 with DatasetRegistry

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

the class DatasetImporterForRegistryTest method filteredDatasets.

@Test
public void filteredDatasets() throws StudyImporterException {
    DatasetImporterForRegistry importer = new DatasetImporterForRegistry(null, null, new DatasetRegistry() {

        @Override
        public Collection<String> findNamespaces() throws DatasetRegistryException {
            return Collections.singletonList("some/namespace");
        }

        @Override
        public Dataset datasetFor(String namespace) throws DatasetRegistryException {
            DatasetImpl dataset = new DatasetImpl("some/namespace", URI.create("some:uri"), in -> in) {

                @Override
                public InputStream retrieve(URI resource) throws IOException {
                    if (!StringUtils.endsWith(resource.toString(), "globi.json")) {
                        throw new IOException();
                    }
                    return IOUtils.toInputStream("{\"some\":\"thing\"}", StandardCharsets.UTF_8);
                }
            };
            return dataset;
        }
    });
    importer.setDatasetFilter(x -> false);
    importer.importStudy();
}