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

Example 6 with DatasetLocal

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

the class StudyImporterForSPIRETest method createImporter.

private StudyImporterForSPIRE createImporter() {
    StudyImporterForSPIRE studyImporterForSPIRE = new StudyImporterForSPIRE(null, nodeFactory);
    studyImporterForSPIRE.setDataset(new DatasetLocal());
    studyImporterForSPIRE.setGeoNamesService(new GeoNamesService() {

        @Override
        public boolean hasTermForLocale(String locality) {
            return "something".equals(locality);
        }

        @Override
        public LatLng findLatLng(String locality) throws IOException {
            return hasTermForLocale(locality) ? new LatLng(1.0, 2.0) : null;
        }
    });
    return studyImporterForSPIRE;
}

Example 7 with DatasetLocal

use of org.eol.globi.service.DatasetLocal 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 8 with DatasetLocal

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

the class StudyImporterTestFactory method instantiateImporter.

public StudyImporter instantiateImporter(Class<? extends StudyImporter> clazz) throws StudyImporterException {
    try {
        Constructor<? extends StudyImporter> aConstructor = clazz.getConstructor(ParserFactory.class, NodeFactory.class);
        StudyImporter studyImporter = aConstructor.newInstance(parserFactory, nodeFactory);
        studyImporter.setDataset(new DatasetLocal());
        return studyImporter;
    } catch (Exception ex) {
        throw new StudyImporterException("failed to create study importer for [" + clazz.toString() + "]", ex);
    }
}

Example 9 with DatasetLocal

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

the class StudyImporterForSzoboszlaiTest method getTestDataset.

private Dataset getTestDataset() throws IOException {
    JsonNode config = new ObjectMapper().readTree("{ \"citation\": \"Szoboszlai AI, Thayer JA, Wood SA, Sydeman WJ, Koehn LE (2015) Data from: Forage species in predator diets: synthesis of data from the California Current. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.nv5d2\",\n" + "  \"doi\": \"http://dx.doi.org/10.5061/dryad.nv5d2\",\n" + "  \"format\": \"szoboszlai\",\n" + "  \"resources\": {\n" + "    \"links\": \"szoboszlai/CCPDDlinkdata_v2.csv\",\n" + "    \"shapes\": \"szoboszlai/CCPDDlocationdata_test.zip\"\n" + "  }\n" + "}");
    Dataset dataset = new DatasetLocal();
    dataset.setConfig(config);
    return dataset;
}

Example 10 with DatasetLocal

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

the class StudyImporterForWebOfLifeTest method importSome.

@Test
public void importSome() throws StudyImporterException, IOException {
    StudyImporterForWebOfLife importer = new StudyImporterForWebOfLife(null, nodeFactory);
    importer.setDataset(new DatasetLocal());
    importer.importNetworks("weboflife/web-of-life_2016-01-15_192434.zip", "Web of Life. " + CitationUtil.createLastAccessedString("http://www.web-of-life.es/"));
    resolveNames();
    List<Study> allStudies = NodeUtil.findAllStudies(getGraphDb());
    List<String> references = new ArrayList<>();
    for (Study allStudy : allStudies) {
        assertThat(allStudy.getSource(), startsWith("Web of Life. Accessed at <http://www.web-of-life.es/>"));
        references.add(allStudy.getCitation());
    }
    assertThat(references, hasItem("Arroyo, M.T.K., R. Primack & J.J. Armesto. 1982. Community studies in pollination ecology in the high temperate Andes of central Chile. I. Pollination mechanisms and altitudinal variation. Amer. J. Bot. 69:82-97."));
    assertThat(taxonIndex.findTaxonByName("Diplopterys pubipetala"), is(notNullValue()));
    assertThat(taxonIndex.findTaxonByName("Juniperus communis"), is(notNullValue()));
    assertThat(taxonIndex.findTaxonByName("Turdus torquatus"), is(notNullValue()));
}