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

Example 1 with DatasetRegistryException

use of org.globalbioticinteractions.dataset.DatasetRegistryException 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 DatasetRegistryException

use of org.globalbioticinteractions.dataset.DatasetRegistryException 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 3 with DatasetRegistryException

use of org.globalbioticinteractions.dataset.DatasetRegistryException 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 4 with DatasetRegistryException

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

the class ProvenanceLog method parseProvenanceStream.

public static void parseProvenanceStream(InputStream is, ProvenanceEntryListener listener) throws DatasetRegistryException {
    try (InputStreamReader reader = new InputStreamReader(is, StandardCharsets.UTF_8)) {
        BufferedReader bufferedReader = IOUtils.toBufferedReader(reader);
        String line;
        while ((line = bufferedReader.readLine()) != null) {
            listener.onValues(CSVTSVUtil.splitTSV(line));
        }
    } catch (IOException e) {
        throw new DatasetRegistryException("failed to read ", e);
    }
}

Example 5 with DatasetRegistryException

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