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

Example 26 with Dataset

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

the class DatasetImporterForRSS method datasetFor.

private static Dataset datasetFor(Dataset datasetOrig, SyndEntry entry, Map<String, String> foreignEntries) {
    Dataset dataset;
    String title = entry.getTitle();
    String citation = StringUtils.trim(title);
    dataset = embeddedDatasetFor(datasetOrig, citation, URI.create(foreignEntries.get("dwca")), parseForeignEntriesAndCategories(entry));
    return dataset;
}

Example 27 with Dataset

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

the class DatasetImporterForMetaTable method importStudy.

@Override
public void importStudy() throws StudyImporterException {
    try {
        for (JsonNode tableConfig : collectTables(dataset)) {
            Dataset datasetProxy = new DatasetProxy(dataset);
            datasetProxy.setConfig(tableConfig);
            InteractionListener interactionListener = getInteractionListener();
            final InteractionListener listener = new TableInteractionListenerProxy(datasetProxy, interactionListener);
            importTable(listener, new TableParserFactoryImpl(), tableConfig, datasetProxy, getLogger());
        }
    } catch (IOException | NodeFactoryException e) {
        String msg = "problem importing from [" + getBaseUrl() + "]";
        LogUtil.logError(getLogger(), msg, e);
        throw new StudyImporterException(msg, e);
    }
}

Example 28 with Dataset

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

the class DatasetImporterForTSVTest method assertTermValues.

public void assertTermValues(String firstFewLines, Map<String, String> expected) throws StudyImporterException {
    AtomicInteger atomicInteger = new AtomicInteger(0);
    Dataset dataset = getDataset(new TreeMap<URI, String>() {

        {
            put(URI.create("/interactions.tsv"), firstFewLines);
        }
    });
    DatasetImporterForTSV importer = new DatasetImporterForTSV(null, nodeFactory);
    importer.setDataset(dataset);
    importer.setInteractionListener(link -> {
        int i = atomicInteger.incrementAndGet();
        expected.values().forEach(termName -> {
            assertThat(link.get(termName), is(expected.get(termName)));
        });
    });
    importStudy(importer);
    assertThat(atomicInteger.get(), greaterThan(0));
}

Example 29 with Dataset

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

the class DatasetImporterForTSVTest method associatedTaxaNotSupported.

@Test
public void associatedTaxaNotSupported() throws StudyImporterException {
    AtomicInteger atomicInteger = new AtomicInteger(0);
    String firstFewLines = "sourceTaxonName\tassociatedTaxa\n" + "Homo sapiens\teats: Canis lupus | eats: Felis catus";
    Dataset dataset = getDataset(new TreeMap<URI, String>() {

        {
            put(URI.create("/interactions.tsv"), firstFewLines);
        }
    });
    DatasetImporterForTSV importer = new DatasetImporterForTSV(null, nodeFactory);
    importer.setDataset(dataset);
    importer.setInteractionListener(link -> {
        int i = atomicInteger.incrementAndGet();
        assertThat(link.get(INTERACTION_TYPE_ID), is(nullValue()));
        assertThat(link.get(INTERACTION_TYPE_NAME), is(nullValue()));
        assertThat(link.get(TARGET_TAXON_NAME), is(nullValue()));
        assertThat(link.get(ASSOCIATED_TAXA), is(notNullValue()));
    });
    importStudy(importer);
    assertThat(atomicInteger.get(), greaterThan(0));
}

Example 30 with Dataset

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

the class DatasetImporterForTSVTest method importFewLinesCSV.

@Test
public void importFewLinesCSV() throws StudyImporterException {
    Dataset dataset = getDataset(new TreeMap<URI, String>() {

        {
            put(URI.create("/interactions.csv"), firstFewLinesCSV);
        }
    });
    DatasetImporterForTSV importer = new DatasetImporterForTSV(null, nodeFactory);
    importer.setDataset(dataset);
    importStudy(importer);
    assertExists("TESTLeptoconchus incycloseris");
    assertExists("Sandalolitha dentata");
    assertStudyTitles("someRepodoi:10.1007/s13127-011-0039-1");
}