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

Example 61 with DatasetImpl

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

the class ExportFlatInteractionsTest method init.

@Before
public void init() throws IOException {
    super.startGraphDb();
    DatasetImpl dataset = new DatasetImpl("some/namespace", URI.create("http://example.com"), inStream -> inStream);
    factory = new NodeFactoryWithDatasetContext(nodeFactory, dataset);
}

Example 62 with DatasetImpl

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

the class DatasetImporterForWoodTest method createImporter.

static DatasetImporterForWood createImporter(NodeFactory nodeFactory) throws IOException {
    JsonNode config = new ObjectMapper().readTree("{ \"citation\": \"Wood SA, Russell R, Hanson D, Williams RJ, Dunne JA (2015) Data from: Effects of spatial scale of sampling on food web structure. Dryad Digital Repository. https://doi.org/10.5061/dryad.g1qr6\",\n" + "  \"doi\": \"https://doi.org/10.5061/dryad.g1qr6\",\n" + "  \"format\": \"wood\",\n" + "  \"resources\": {\n" + "    \"links\": \"http://datadryad.org/bitstream/handle/10255/dryad.93018/WoodEtal_Append1_v2.csv\"  \n" + "  },\n" + "  \"location\": {\n" + "    \"locality\": {\n" + "      \"id\": \"GEONAMES:5873327\",\n" + "      \"name\": \"Sanak Island, Alaska, USA\"\n" + "    },\n" + "    \"latitude\": 54.42972,\n" + "    \"longitude\": -162.70889\n" + "  }\n" + "}");
    DatasetImpl dataset = new DatasetImpl("some/namespace", URI.create("http://example.com"), inStream -> inStream);
    dataset.setConfig(config);
    DatasetImporterForWood wood = new DatasetImporterForWood(new ParserFactoryForDataset(dataset), nodeFactory);
    wood.setDataset(dataset);
    return wood;
}

Example 63 with DatasetImpl

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

the class InteractionListenerImplTest method processMessageWithTranslatedInteractionType.

@Test
public void processMessageWithTranslatedInteractionType() 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, "shouldBeMapped");
    interaction.put(TARGET_TAXON_NAME, "targetName");
    interaction.put(REFERENCE_ID, "citation");
    assertStudyCount(0L);
    interactionListener.on(interaction);
    assertStudyCount(1L);
}

Example 64 with DatasetImpl

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

the class LinkerDOITest method createStudyDOIlookupCitationEnabled.

@Test
public void createStudyDOIlookupCitationEnabled() throws NodeFactoryException {
    StudyImpl title = new StudyImpl("title", null, "some citation");
    DatasetImpl originatingDataset = new DatasetImpl("some/namespace", URI.create("some:uri"), inStream -> inStream);
    ObjectNode objectNode = new ObjectMapper().createObjectNode();
    objectNode.put(DatasetConstant.SHOULD_RESOLVE_REFERENCES, true);
    originatingDataset.setConfig(objectNode);
    title.setOriginatingDataset(originatingDataset);
    StudyNode study = getNodeFactory().getOrCreateStudy(title);
    LinkerDOI.linkStudy(new TestDOIResolver(), study);
    assertThat(study.getDOI().toString(), is("10.some/some citation"));
    assertThat(study.getExternalId(), is("https://doi.org/10.some/some%20citation"));
    assertThat(study.getCitation(), is("some citation"));
    assertThat(study.getTitle(), is("title"));
}

Example 65 with DatasetImpl

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

the class DatasetImporterForDwCATest method assertImportsSomethingOfType.

private void assertImportsSomethingOfType(URI archiveRoot, AtomicInteger recordCounter, String defaultResourceType, String... expectedProperties) throws StudyImporterException {
    final Set<String> resourceTypes = new TreeSet<>();
    DatasetImporterForDwCA studyImporterForDwCA = new DatasetImporterForDwCA(null, null);
    studyImporterForDwCA.setDataset(new DatasetImpl("some/namespace", archiveRoot, inStream -> inStream));
    studyImporterForDwCA.setInteractionListener(new InteractionListener() {

        @Override
        public void on(Map<String, String> interaction) throws StudyImporterException {
            for (String expectedProperty : expectedProperties) {
                assertThat("no [" + expectedProperty + "] found in " + interaction, interaction.containsKey(expectedProperty), is(true));
                assertThat("no value of [" + expectedProperty + "] found in " + interaction, interaction.get(expectedProperty), is(notNullValue()));
            }
            assertThat(interaction.get(RESOURCE_TYPES), is(notNullValue()));
            String[] types = splitByPipes(interaction.get(RESOURCE_TYPES));
            resourceTypes.addAll(Arrays.asList(types));
            recordCounter.incrementAndGet();
        }
    });
    studyImporterForDwCA.importStudy();
    assertThat(recordCounter.get(), greaterThan(0));
    String[] items = splitByPipes(defaultResourceType);
    assertThat(resourceTypes, containsInAnyOrder(items));
    assertThat(recordCounter.get(), greaterThan(0));
}