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

Example 46 with DatasetImpl

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

the class DatasetImporterForJSONLDTest method importStatic.

@Test
public void importStatic() throws StudyImporterException, URISyntaxException {
    DatasetImporter importer = new DatasetImporterForJSONLD(null, nodeFactory);
    DatasetImpl dataset = new DatasetImpl("some/namespace", URI.create("http://example.com"), inStream -> inStream);
    dataset.setConfigURI(URI.create("classpath:/org/eol/globi/data/globi-jsonld/globi-dataset.jsonld"));
    importer.setDataset(dataset);
    importStudy(importer);
    List<StudyNode> allStudies = NodeUtil.findAllStudies(getGraphDb());
    for (Study study : allStudies) {
        assertThat(study.getExternalId(), is("http://arctos.database.museum/guid/CUMV:Bird:25225"));
        assertThat(study.getCitation(), is("http://arctos.database.museum/guid/CUMV:Bird:25225"));
    }
    assertThat(taxonIndex.findTaxonById("NCBI:8782"), not(is(nullValue())));
}

Example 47 with DatasetImpl

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

the class DatasetImporterForCoetzerTest method importSome.

@Test
public void importSome() throws StudyImporterException, IOException {
    DatasetImporterForCoetzer importer = new DatasetImporterForCoetzer(null, nodeFactory);
    DatasetImpl dataset = new DatasetLocal(inStream -> inStream);
    JsonNode config = new ObjectMapper().readTree("{\"citation\": \"source citation\", \"resources\": {\"archive\": \"coetzer/CatalogOfAfrotropicalBees.zip\"}}");
    dataset.setConfig(config);
    importer.setDataset(dataset);
    importStudy(importer);
    List<StudyNode> allStudies = NodeUtil.findAllStudies(getGraphDb());
    for (Study allStudy : allStudies) {
        assertThat(allStudy.getCitation(), is(notNullValue()));
    }
    assertThat(taxonIndex.findTaxonByName("Agrostis tremula"), is(notNullValue()));
    assertThat(taxonIndex.findTaxonByName("Coelioxys erythrura"), is(notNullValue()));
    assertThat(taxonIndex.findTaxonByName("Patellapis namaquensis"), is(notNullValue()));
}

Example 48 with DatasetImpl

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

the class DatasetImporterForHurlbertTest method doImport.

public DatasetImporter doImport(final String namespace) throws StudyImporterException {
    DatasetImporter importer = new DatasetImporterForHurlbert(null, nodeFactory);
    Dataset dataset = new DatasetImpl(namespace, URI.create("some:uri"), inStream -> inStream) {

        @Override
        public InputStream retrieve(URI name) {
            return DatasetImporterForHurlbertTest.getResource();
        }
    };
    importer.setDataset(dataset);
    importStudy(importer);
    return importer;
}

Example 49 with DatasetImpl

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

the class DatasetImporterForDunneIT method importStudy.

@Test
public void importStudy() throws StudyImporterException, IOException {
    String configJson = "{ \"citation\": \"blabla\",\n" + "  \"format\": \"dunne\",\n" + "  \"resources\": {\n" + "    \"nodes\": \"https://raw.githubusercontent.com/globalbioticinteractions/dunne2016SanakIntertidal/main/nodes.tsv\",\n" + "    \"links\": \"https://raw.githubusercontent.com/globalbioticinteractions/dunne2016SanakIntertidal/main/links.tsv\"\n" + "  },\n" + "  \"location\": {\n" + "    \"locality\": {\n" + "      \"id\": \"GEONAMES:5873327\",\n" + "      \"name\": \"Sanak Island, Alaska, USA\"\n" + "    },\n" + "    \"latitude\": 60,\n" + "    \"longitude\": 60\n" + "  }\n" + "}";
    JsonNode jsonNode = new ObjectMapper().readTree(configJson);
    DatasetImpl dunne2016 = new DatasetImpl("dunne2016", URI.create("http://example.com"), inStream -> inStream);
    dunne2016.setConfig(jsonNode);
    ParserFactory parserFactory = new ParserFactoryForDataset(dunne2016);
    DatasetImporterForDunne importer = new DatasetImporterForDunne(parserFactory, nodeFactory);
    importer.setDataset(dunne2016);
    importStudy(importer);
    StudyNode study = getStudySingleton(getGraphDb());
    assertThat(study, is(notNullValue()));
    assertThat(getSpecimenCount(study), is(1804 * 2));
}

Example 50 with DatasetImpl

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

the class DatasetImporterForGrayTest method createImporter.

static DatasetImporterForGray createImporter(NodeFactory nodeFactory) throws IOException {
    DatasetImporterForGray gray = new DatasetImporterForGray(new ParserFactoryLocal(), nodeFactory);
    JsonNode config = new ObjectMapper().readTree("{ \"citation\": \"Gray C, Ma A, Perkins D, Hudson L, Figueroa D, Woodward G (2015). Database of trophic interactions. Zenodo. https://doi.org/10.5281/zenodo.13751\",\n" + "  \"doi\": \"https://doi.org/10.5281/zenodo.13751\",\n" + "  \"format\": \"gray\",\n" + "  \"resources\": {\n" + "    \"links\": \"https://zenodo.org/record/13751/files/trophic.links.2014-11-10.csv\"  \n" + "  }\n" + "}");
    DatasetImpl dataset = new DatasetImpl("some/namespace", URI.create("http://example.com"), inStream -> inStream);
    dataset.setConfig(config);
    gray.setDataset(dataset);
    return gray;
}