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

Example 16 with Dataset

use of org.globalbioticinteractions.dataset.Dataset 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 17 with Dataset

use of org.globalbioticinteractions.dataset.Dataset 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();
}

Example 18 with Dataset

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

the class DatasetImplTest method doiExpectedPrefix.

@Test
public void doiExpectedPrefix() throws IOException {
    Dataset dataset = new DatasetImpl("some/namespace", URI.create("some:uri"), inStream -> inStream);
    dataset.setConfig(new ObjectMapper().readTree("{\"doi\": \"doi:10.2980/1195-6860(2006)13[23:TDOFUB]2.0.CO;2\" }"));
    assertThat(dataset.getDOI(), is(new DOI("2980", "1195-6860(2006)13[23:TDOFUB]2.0.CO;2")));
}

Example 19 with Dataset

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

the class DatasetImplTest method doiExpected.

@Test
public void doiExpected() throws IOException {
    Dataset dataset = new DatasetImpl("some/namespace", URI.create("some:uri"), inStream -> inStream);
    dataset.setConfig(new ObjectMapper().readTree("{\"doi\": \"http://dx.doi.org/10.2980/1195-6860(2006)13[23:TDOFUB]2.0.CO;2\" }"));
    assertThat(dataset.getDOI(), is(new DOI("2980", "1195-6860(2006)13[23:TDOFUB]2.0.CO;2")));
}

Example 20 with Dataset

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

the class DatasetTest method resourceURL.

@Test
public void resourceURL() throws IOException, URISyntaxException {
    URL resource = getClass().getResource("archive.zip");
    File archive = new File(resource.toURI());
    assertThat(archive.exists(), is(true));
    URI parentDir = archive.getParentFile().toURI();
    Dataset dataset = new DatasetImpl("some/namespace", parentDir, inStream -> inStream);
    InputStream retrieve = dataset.retrieve(resource.toURI());
    assertArchiveHash(retrieve);
    assertArchiveHash(dataset.retrieve(URI.create("archive.zip")));
    assertArchiveHash(dataset.retrieve(URI.create("/archive.zip")));
}