Examples with DatasetFinder org.eol.globi.service.DatasetFinder used on opensource projects

Example 1 with DatasetFinder

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

the class DatasetFinderLocal method datasetFor.

@Override
public Dataset datasetFor(String namespace) throws DatasetFinderException {
    Dataset dataset;
    try {
        final URI sourceURI = findLastCachedDatasetURI(namespace);
        dataset = sourceURI == null ? null : DatasetFactory.datasetFor(namespace, new DatasetFinder() {

            @Override
            public Collection<String> findNamespaces() throws DatasetFinderException {
                return Collections.singletonList(namespace);
            }

            @Override
            public Dataset datasetFor(String s) throws DatasetFinderException {
                Dataset dataset = new DatasetImpl(namespace, sourceURI);
                return new DatasetWithCache(dataset, cacheFactory.cacheFor(dataset));
            }
        });
    } catch (IOException e) {
        throw new DatasetFinderException("failed to access [" + namespace + "]", e);
    }
    if (dataset == null) {
        throw new DatasetFinderException("failed to retrieve/cache dataset in namespace [" + namespace + "]");
    }
    return dataset;
}

Example 2 with DatasetFinder

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

the class DatasetFinderWithCacheIT method hafnerTest.

@Test
public void hafnerTest() throws DatasetFinderException, IOException {
    DatasetFinder finder = new DatasetFinderWithCache(new DatasetFinderGitHubArchive(), cachePath);
    Dataset dataset = DatasetFactory.datasetFor("globalbioticinteractions/hafner", finder);
    assertNotNull(dataset.getResource("hafner/gopher_lice_int.csv"));
}

Example 3 with DatasetFinder

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

the class DatasetFinderWithCacheIT method gitHubTest.

@Test
public void gitHubTest() throws DatasetFinderException {
    DatasetFinder finder = new DatasetFinderWithCache(new DatasetFinderGitHubArchive(), cachePath);
    Dataset dataset = DatasetFactory.datasetFor("globalbioticinteractions/Catalogue-of-Afrotropical-Bees", finder);
    assertThat(dataset.getArchiveURI().toString(), containsString("github.com"));
    assertThat(dataset.getResourceURI("globi.json").toString(), startsWith("jar:file:/"));
    assertThat(dataset.getCitation(), startsWith("Shan Kothari, Pers. Comm. 2014."));
}

Example 4 with DatasetFinder

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

the class DatasetFinderWithCacheIT method assertTemplateDataset.

private void assertTemplateDataset(String expectedURIFragment, DatasetFinder datasetFinder, String expectedCitation) throws DatasetFinderException, IOException {
    DatasetFinder finder = new DatasetFinderWithCache(datasetFinder, cachePath);
    Dataset dataset = DatasetFactory.datasetFor("globalbioticinteractions/template-dataset", finder);
    assertThat(dataset.getArchiveURI().toString(), containsString(expectedURIFragment));
    assertThat(dataset.getResourceURI("globi.json").toString(), startsWith("jar:file:/"));
    assertThat(dataset.getCitation(), startsWith(expectedCitation));
}

Example 5 with DatasetFinder

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

the class Normalizer method importData.

void importData(GraphDatabaseService graphService, String cacheDir) {
    NodeFactoryNeo4j factory = new NodeFactoryNeo4j(graphService);
    factory.setEcoregionFinder(getEcoregionFinder());
    factory.setDoiResolver(new DOIResolverImpl());
    try {
        CacheFactory cacheFactory = dataset -> new CacheLocalReadonly(dataset.getNamespace(), cacheDir);
        DatasetFinder finder = new DatasetFinderLocal(cacheDir, cacheFactory);
        StudyImporter importer = new StudyImporterForGitHubData(new ParserFactoryLocal(), factory, finder);
        importer.setDataset(new DatasetLocal());
        importer.setLogger(new StudyImportLogger());
        importer.importStudy();
    } catch (StudyImporterException e) {
        LOG.error("problem encountered while importing [" + StudyImporterForGitHubData.class.getName() + "]", e);
    }
    EcoregionFinder regionFinder = getEcoregionFinder();
    if (regionFinder != null) {
        regionFinder.shutdown();
    }
}