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

Example 11 with Dataset

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

the class DatasetImportUtil method importDatasets.

public static void importDatasets(Map<Pair<String, String>, Map<String, String>> interactionsWithUnresolvedOccurrenceIds, List<Dataset> datasets, ImportLogger logger, NodeFactory nodeFactory) throws StudyImporterException {
    for (Dataset dataset : datasets) {
        try {
            importDataset(studyImporter -> {
                if (studyImporter instanceof DatasetImporterWithListener) {
                    final InteractionListenerResolving interactionListener = new InteractionListenerResolving(interactionsWithUnresolvedOccurrenceIds, ((DatasetImporterWithListener) studyImporter).getInteractionListener());
                    ((DatasetImporterWithListener) studyImporter).setInteractionListener(interactionListener);
                }
            }, dataset, nodeFactory, logger);
        } catch (StudyImporterException | IllegalStateException ex) {
            LogUtil.logError(logger, ex);
        }
    }
}

Example 12 with Dataset

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

the class NodeFactoryNeo4j2 method getOrCreateDatasetNoTx.

@Override
protected Dataset getOrCreateDatasetNoTx(Dataset originatingDataset) {
    Dataset datasetCreated = null;
    if (originatingDataset != null && StringUtils.isNotBlank(originatingDataset.getNamespace())) {
        IndexHits<Node> datasetHits = datasets.get(DatasetConstant.NAMESPACE, originatingDataset.getNamespace());
        Node datasetNode = datasetHits.hasNext() ? datasetHits.next() : createDatasetNode(originatingDataset);
        datasetCreated = new DatasetNode(datasetNode);
    }
    return datasetCreated;
}

Example 13 with Dataset

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

the class InteractionListenerImplTest method processMessageWithOIgnoredInteractionType.

@Test
public void processMessageWithOIgnoredInteractionType() throws StudyImporterException, IOException {
    ResourceService resourceService = Mockito.mock(ResourceService.class);
    when(resourceService.retrieve(URI.create("interaction_types_ignored.csv"))).thenReturn(IOUtils.toInputStream("provided_interaction_type_id\nshouldBeIgnored", StandardCharsets.UTF_8)).thenReturn(IOUtils.toInputStream("provided_interaction_type_id\nshouldBeIgnored", StandardCharsets.UTF_8));
    when(resourceService.retrieve(URI.create("interaction_types_mapping.csv"))).thenReturn(IOUtils.toInputStream(getTestMap(), StandardCharsets.UTF_8));
    Dataset dataset = new DatasetImpl("bla", resourceService, URI.create("foo:bar"));
    InteractionListenerImpl interactionListener = new InteractionListenerImpl(nodeFactory, null, null, dataset);
    HashMap<String, String> interaction = new HashMap<>();
    interaction.put(SOURCE_TAXON_NAME, "sourceName");
    interaction.put(DatasetImporterForTSV.INTERACTION_TYPE_NAME, "shouldBeIgnored");
    interaction.put(TARGET_TAXON_NAME, "targetName");
    interaction.put(REFERENCE_ID, "citation");
    assertStudyCount(0L);
    interactionListener.on(interaction);
    assertStudyCount(0L);
}

Example 14 with Dataset

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

the class DatasetImporterFactoryImplIT method jsonldImporterCached.

@Test
public void jsonldImporterCached() throws StudyImporterException, DatasetRegistryException {
    final DatasetRegistry datasetRegistry = new DatasetRegistryWithCache(new DatasetRegistryGitHubArchive(inStream -> inStream), dataset -> CacheUtil.cacheFor(dataset.getNamespace(), "target/datasets", inStream -> inStream));
    Dataset dataset = new DatasetFactory(datasetRegistry).datasetFor("globalbioticinteractions/jsonld-template-dataset");
    DatasetImporter importer = new StudyImporterFactoryImpl(null).createImporter(dataset);
    assertThat(importer, is(notNullValue()));
    assertThat(importer, is(instanceOf(DatasetImporterForJSONLD.class)));
}

Example 15 with Dataset

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

the class DatasetImporterFactoryImplIT method createHafner.

@Test
public void createHafner() throws StudyImporterException, DatasetRegistryException, IOException {
    final DatasetRegistry datasetRegistryGitHubRemote = new DatasetRegistryGitHubRemote(inStream -> inStream);
    Dataset dataset = new DatasetFactory(datasetRegistryGitHubRemote).datasetFor("globalbioticinteractions/hafner");
    DatasetImporter importer = new StudyImporterFactoryImpl(null).createImporter(dataset);
    assertThat(importer, is(notNullValue()));
    DatasetImporterForHafner haftnerImporter = (DatasetImporterForHafner) importer;
    assertThat(haftnerImporter.getDataset().retrieve(URI.create("hafner/gopher_lice_int.csv")), is(notNullValue()));
}