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

Example 1 with Dataset

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

the class StudyImporterForMetaTable method importStudy.

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

Example 2 with Dataset

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

the class DatasetFinderWithCacheTest method cacheDatasetLocal.

@Test
public void cacheDatasetLocal() throws DatasetFinderException, IOException, URISyntaxException {
    Dataset datasetCached = datasetCached();
    assertNotNull(datasetCached.getArchiveURI());
    URI uri = datasetCached.getResourceURI("globi.json");
    assertThat(uri.isAbsolute(), is(true));
    assertThat(uri.toString(), startsWith("jar:file:"));
    InputStream is = datasetCached.getResource("globi.json");
    assertNotNull(is);
    JsonNode jsonNode = new ObjectMapper().readTree(is);
    assertThat(jsonNode.has("citation"), is(true));
    String[] list = new File(cachePath + "/some/namespace").list();
    assertThat(list.length, is(2));
    assertThat(Arrays.asList(list), hasItem("c9ecb3b0100c890bd00a5c201d06f0a78d92488591f726fbf4de5c88bda39147"));
    assertThat(Arrays.asList(list), hasItem("access.tsv"));
}

Example 3 with Dataset

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

the class DatasetFinderLocal method datasetFor.

@Override
public Dataset datasetFor(String namespace) throws DatasetFinderException {
    Dataset dataset;
    try {
        final URI sourceURI = findLastCachedDatasetURI(namespace);
        dataset = sourceURI == null ? null : DatasetFactory.datasetFor(namespace, new DatasetFinder() {

            @Override
            public Collection<String> findNamespaces() throws DatasetFinderException {
                return Collections.singletonList(namespace);
            }

            @Override
            public Dataset datasetFor(String s) throws DatasetFinderException {
                Dataset dataset = new DatasetImpl(namespace, sourceURI);
                return new DatasetWithCache(dataset, cacheFactory.cacheFor(dataset));
            }
        });
    } catch (IOException e) {
        throw new DatasetFinderException("failed to access [" + namespace + "]", e);
    }
    if (dataset == null) {
        throw new DatasetFinderException("failed to retrieve/cache dataset in namespace [" + namespace + "]");
    }
    return dataset;
}

Example 4 with Dataset

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

the class NodeFactoryWithDatasetContextTest method getOrCreateStudy.

@Test
public void getOrCreateStudy() throws NodeFactoryException {
    NodeFactory factory = Mockito.mock(NodeFactory.class);
    Dataset dataset = new DatasetImpl("some/namespace", URI.create("some:uri"));
    NodeFactoryWithDatasetContext factoryWithDS = new NodeFactoryWithDatasetContext(factory, dataset);
    factoryWithDS.getOrCreateStudy(new StudyImpl("some title"));
    ArgumentCaptor<Study> argument = ArgumentCaptor.forClass(Study.class);
    verify(factory).getOrCreateStudy(argument.capture());
    assertEquals("globi:some/namespace", argument.getValue().getSourceId());
    assertEquals("some title", argument.getValue().getTitle());
}

Example 5 with Dataset

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

the class StudyImporterForArthopodEasyCaptureTest method embeddedDataset.

@Test
public void embeddedDataset() throws IOException {
    Dataset embeddedDataset = StudyImporterForArthopodEasyCapture.embeddedDatasetFor(getDatasetGroup(), "some other citation", URI.create("http://example.com/archive.zip"));
    assertThat(embeddedDataset.getCitation(), is("some other citation"));
    assertThat(embeddedDataset.getOrDefault(DatasetConstant.SHOULD_RESOLVE_REFERENCES, "foo"), is("foo"));
    assertThat(DatasetUtil.getNamedResourceURI(embeddedDataset, "archive"), is("http://example.com/archive.zip"));
}