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

Example 1 with DatasetImpl

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

the class DatasetImporterForMetaTableIT method importAll.

public static void importAll(InteractionListener interactionListener, DatasetImporterForMetaTable.TableParserFactory tableFactory, String baseUrl, String resource) throws IOException, StudyImporterException {
    final InputStream inputStream = ResourceUtil.asInputStream(resource, inStream -> inStream);
    final JsonNode config = new ObjectMapper().readTree(inputStream);
    final Dataset dataset = new DatasetImpl("some/namespace", URI.create("http://example.com"), inStream -> inStream);
    dataset.setConfig(config);
    for (JsonNode table : DatasetImporterForMetaTable.collectTables(dataset)) {
        DatasetImporterForMetaTable.importTable(interactionListener, tableFactory, table, new DatasetImpl(null, URI.create(baseUrl), inStream -> inStream), null);
    }
}

Example 2 with DatasetImpl

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

the class DatasetImporterForPensoftIT method importStudy.

@Test
public void importStudy() throws StudyImporterException, URISyntaxException {
    final DatasetImporterForPensoft importer = new DatasetImporterForPensoft(new ParserFactoryLocal(), null);
    final Dataset dataset = new DatasetImpl("some/name", URI.create("some:uri"), in -> in);
    final ObjectNode objectNode = new ObjectMapper().createObjectNode();
    final URL resource = getClass().getResource("pensoft/annotated-tables-first-two.json");
    objectNode.put("url", resource.toURI().toString());
    objectNode.put("citation", "some dataset citation");
    dataset.setConfig(objectNode);
    List<Map<String, String>> links = new ArrayList<>();
    importer.setDataset(dataset);
    importer.setInteractionListener(new InteractionListener() {

        @Override
        public void on(Map<String, String> interaction) throws StudyImporterException {
            links.add(interaction);
        }
    });
    importer.importStudy();
    assertThat(links.size(), is(121));
    assertThat(links.get(0), hasEntry("Family Name", "Acanthaceae"));
    assertThat(links.get(0), hasEntry("Family Name_expanded_taxon_name", "Acanthaceae"));
    assertThat(links.get(0), hasEntry("Family Name_expanded_taxon_id", "http://openbiodiv.net/4B689A17-2541-4F5F-A896-6F0C2EEA3FB4"));
    assertThat(links.get(0), hasEntry("referenceUrl", "https://doi.org/10.3897/zookeys.306.5455"));
    assertThat(links.get(0), hasEntry("referenceDoi", "10.3897/zookeys.306.5455"));
    assertThat(links.get(0), hasEntry("referenceCitation", "Dewi Sartiami, Laurence A. Mound. 2013. Identification of the terebrantian thrips (Insecta, Thysanoptera) associated with cultivated plants in Java, Indonesia. ZooKeys. https://doi.org/10.3897/zookeys.306.5455"));
}

Example 3 with DatasetImpl

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

the class DatasetImporterForRSSTest method useUrlOnly.

@Test
public void useUrlOnly() throws IOException {
    DatasetImpl dataset = datasetFor("{ \"url\": \"bar\" }");
    assertThat(DatasetImporterForRSS.getRSSEndpoint(dataset), is("bar"));
}

Example 4 with DatasetImpl

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

the class DatasetImporterForRSSTest method useUrl.

@Test
public void useUrl() throws IOException {
    DatasetImpl dataset = datasetFor("{ \"url\": \"bar\", " + "\"resources\": { \"rss\": \"foo\" } " + "}");
    assertThat(DatasetImporterForRSS.getRSSEndpoint(dataset), is("bar"));
}

Example 5 with DatasetImpl

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

the class DatasetImporterForRSSTest method useRssNamedProperty.

@Test
public void useRssNamedProperty() throws IOException {
    DatasetImpl dataset = datasetFor("{ \"url\": \"bar\", " + "\"resources\": { \"rss\": \"foo\" } " + "}");
    assertThat(DatasetImporterForRSS.getRSSEndpoint(dataset), is("bar"));
}