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

Example 1 with DatasetImporter

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

the class StudyImporterFactoryImpl method createImporter.

public static DatasetImporter createImporter(Dataset dataset, final NodeFactory nodeFactory) throws StudyImporterException {
    Class<? extends DatasetImporter> anImporter = findImporterFor(dataset);
    try {
        Constructor<? extends DatasetImporter> constructor = anImporter.getConstructor(ParserFactory.class, NodeFactory.class);
        ParserFactoryForDataset parserFactory = new ParserFactoryForDataset(dataset);
        DatasetImporter datasetImporter = constructor.newInstance(parserFactory, new NodeFactoryWithDatasetContext(nodeFactory, dataset));
        datasetImporter.setDataset(dataset);
        return datasetImporter;
    } catch (NoSuchMethodException | IllegalAccessException | InvocationTargetException | InstantiationException e) {
        throw new StudyImporterException("failed to instantiate importer for [" + dataset.getNamespace() + "]", e);
    }
}

Example 2 with DatasetImporter

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

the class DatasetImporterFactoryImplIT method createHurlbert.

@Test
public void createHurlbert() throws StudyImporterException, DatasetRegistryException {
    final DatasetRegistryGitHubRemote datasetFinderGitHubRemote = new DatasetRegistryGitHubRemote(inStream -> inStream);
    DatasetImporter importer = importerFor(datasetFinderGitHubRemote, "hurlbertlab/dietdatabase");
    assertThat(importer, is(notNullValue()));
    assertThat(importer, is(instanceOf(DatasetImporterForHurlbert.class)));
    final JsonNode config = ((BaseDatasetImporter) importer).getDataset().getConfig();
    assertThat(config, is(notNullValue()));
}

Example 3 with DatasetImporter

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

the class DatasetImporterFactoryImplIT method createMetaTable.

@Test
public void createMetaTable() throws DatasetRegistryException, StudyImporterException {
    final DatasetRegistryGitHubRemote datasetFinderGitHubRemote = new DatasetRegistryGitHubRemote(inStream -> inStream);
    DatasetImporter importer = importerFor(datasetFinderGitHubRemote, "globalbioticinteractions/AfricaTreeDatabase");
    assertThat(importer, is(notNullValue()));
    assertThat(importer, is(instanceOf(DatasetImporterForMetaTable.class)));
    assertThat(((DatasetImporterForMetaTable) importer).getConfig(), is(notNullValue()));
    assertThat(((DatasetImporterForMetaTable) importer).getBaseUrl(), startsWith("https://raw.githubusercontent.com/globalbioticinteractions/AfricaTreeDatabase/"));
}

Example 4 with DatasetImporter

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

the class DatasetImporterFactoryImplIT method createPlanque.

@Test
public void createPlanque() throws StudyImporterException, DatasetRegistryException, IOException {
    final DatasetRegistryGitHubRemote datasetFinderGitHubRemote = new DatasetRegistryGitHubRemote(inStream -> inStream);
    DatasetImporter importer = importerFor(datasetFinderGitHubRemote, "globalbioticinteractions/planque2014");
    assertThat(importer, is(notNullValue()));
    assertThat(importer, is(instanceOf(DatasetImporterForPlanque.class)));
    DatasetImporterForPlanque importerz = (DatasetImporterForPlanque) importer;
    assertThat(importerz.getSourceCitation(), containsString("Planque"));
}

Example 5 with DatasetImporter

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