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

Example 16 with StudyImporter

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

the class GitHubImporterFactoryIT method defaultTSVImporterCachedZenodo.

@Test
public void defaultTSVImporterCachedZenodo() throws StudyImporterException, DatasetFinderException {
    final DatasetFinder datasetFinder = new DatasetFinderWithCache(new DatasetFinderZenodo());
    StudyImporter importer = getTemplateImporter(datasetFinder, "globalbioticinteractions/template-dataset");
    StudyImporterForTSV importerTSV = (StudyImporterForTSV) importer;
    assertThat(importerTSV.getSourceCitation(), containsString("doi.org"));
}

Example 17 with StudyImporter

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

the class GitHubImporterFactoryIT method createHurlbert.

@Test
public void createHurlbert() throws StudyImporterException, DatasetFinderException {
    final DatasetFinderGitHubRemote datasetFinderGitHubRemote = new DatasetFinderGitHubRemote();
    StudyImporter importer = importerFor(datasetFinderGitHubRemote, "hurlbertlab/dietdatabase");
    assertThat(importer, is(notNullValue()));
    assertThat(importer, is(instanceOf(StudyImporterForHurlbert.class)));
    final JsonNode config = ((BaseStudyImporter) importer).getDataset().getConfig();
    assertThat(config, is(notNullValue()));
}

Example 18 with StudyImporter

use of org.eol.globi.data.StudyImporter 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();
    }
}

Example 19 with StudyImporter

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

the class NormalizerTest method createStudyImporter.

private static StudyImporter createStudyImporter(Class<? extends StudyImporter> studyImporter, NodeFactoryNeo4j factory) throws StudyImporterException {
    StudyImporter importer = new StudyImporterTestFactory(factory).instantiateImporter(studyImporter);
    importer.setLogger(new StudyImportLogger());
    return importer;
}

Example 20 with StudyImporter

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

the class GitHubImporterFactory method createImporter.

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