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

Example 11 with DatasetImpl

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

the class LinkerDOITest method createStudyDOIlookupCitationDisabled.

@Test
public void createStudyDOIlookupCitationDisabled() throws NodeFactoryException {
    StudyImpl study1 = new StudyImpl("title", null, "some citation");
    study1.setExternalId("some:id");
    DatasetImpl originatingDataset = new DatasetImpl("some/namespace", URI.create("some:uri"), inStream -> inStream);
    ObjectNode objectNode = new ObjectMapper().createObjectNode();
    objectNode.put(DatasetConstant.SHOULD_RESOLVE_REFERENCES, false);
    originatingDataset.setConfig(objectNode);
    study1.setOriginatingDataset(originatingDataset);
    Study study = getNodeFactory().getOrCreateStudy(study1);
    assertThat(study.getDOI(), is(nullValue()));
    assertThat(study.getCitation(), is("some citation"));
    assertThat(study.getTitle(), is("title"));
    assertThat(study.getExternalId(), is("some:id"));
}

Example 12 with DatasetImpl

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

the class DatasetImporterForMetaTableTest method assertExpectedColumnCount.

public void assertExpectedColumnCount(String metaTableDef) throws IOException {
    final Class<DatasetImporterForMetaTable> clazz = DatasetImporterForMetaTable.class;
    final URL resource = clazz.getResource(metaTableDef);
    assertNotNull(resource);
    final InputStream inputStream = clazz.getResourceAsStream(metaTableDef);
    final JsonNode config = new ObjectMapper().readTree(inputStream);
    String baseUrl = resource.toExternalForm().replaceFirst(metaTableDef + "$", "");
    List<DatasetImporterForMetaTable.Column> columnNames = DatasetImporterForMetaTable.columnsFromExternalSchema(config.get("tableSchema"), new DatasetImpl(null, URI.create(baseUrl), inStream -> inStream));
    assertThat(columnNames.size(), is(40));
}

Example 13 with DatasetImpl

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

the class DatasetImporterForDwCATest method importTaxonDescriptionsFromDirUnsupportedDescriptionType.

@Test
public void importTaxonDescriptionsFromDirUnsupportedDescriptionType() throws StudyImporterException, URISyntaxException {
    URL resource = getClass().getResource("/org/globalbioticinteractions/dataset/coetzer-unsupported-description-type/meta.xml");
    URI archiveRoot = new File(resource.toURI()).getParentFile().toURI();
    List<Map<String, String>> links = new ArrayList<>();
    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 {
            assertThat(interaction.get(DatasetImporterForTSV.RESOURCE_TYPES), is("http://rs.tdwg.org/dwc/terms/ResourceRelationship | http://rs.tdwg.org/dwc/terms/Occurrence"));
            links.add(interaction);
        }
    });
    studyImporterForDwCA.importStudy();
    assertThat(links.size(), is(0));
}

Example 14 with DatasetImpl

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

the class DatasetImporterForDwCATest method importRecordsFromZip.

@Test
public void importRecordsFromZip() throws StudyImporterException, IOException {
    URL resource = getClass().getResource("/org/globalbioticinteractions/dataset/dwca.zip");
    DatasetImporterForDwCA studyImporterForDwCA = new DatasetImporterForDwCA(null, null);
    DatasetImpl dataset = new DatasetImpl("some/namespace", URI.create("file:///some/path/data.zip"), inStream -> inStream);
    JsonNode jsonNode = new ObjectMapper().readTree("{ " + "\"interactionTypeId\": \"http://purl.obolibrary.org/obo/RO_0002437\"," + "\"url\": \"" + resource.toExternalForm() + "\"" + "}");
    dataset.setConfig(jsonNode);
    studyImporterForDwCA.setDataset(dataset);
    String expectedCitation = dataset.getCitation();
    AtomicBoolean someRecords = new AtomicBoolean(false);
    Set<String> resourceTypes = new TreeSet<>();
    studyImporterForDwCA.setInteractionListener(new InteractionListener() {

        @Override
        public void on(Map<String, String> interaction) throws StudyImporterException {
            String associatedTaxa = interaction.get("http://rs.tdwg.org/dwc/terms/associatedTaxa");
            String dynamicProperties = interaction.get("http://rs.tdwg.org/dwc/terms/dynamicProperties");
            assertThat(StringUtils.isNotBlank(associatedTaxa) || StringUtils.isNotBlank(dynamicProperties), is(true));
            assertThat(interaction.get(SOURCE_TAXON_NAME), is(not(nullValue())));
            assertThat(interaction.get(TaxonUtil.TARGET_TAXON_NAME), is(not(nullValue())));
            assertThat(interaction.get(INTERACTION_TYPE_NAME), is(not(nullValue())));
            assertThat(interaction.get(DatasetImporterForTSV.DATASET_CITATION), containsString(expectedCitation));
            assertThat(interaction.get(REFERENCE_ID), startsWith("https://symbiota.ccber.ucsb.edu:443/collections/individual/index.php?occid"));
            assertThat(interaction.get(DatasetImporterForTSV.REFERENCE_CITATION), startsWith("https://symbiota.ccber.ucsb.edu:443/collections/individual/index.php?occid"));
            assertThat(interaction.get(REFERENCE_URL), startsWith("https://symbiota.ccber.ucsb.edu:443/collections/individual/index.php?occid"));
            resourceTypes.addAll(Arrays.asList(splitByPipes(interaction.get(RESOURCE_TYPES))));
            someRecords.set(true);
        }
    });
    studyImporterForDwCA.importStudy();
    assertThat(someRecords.get(), is(true));
    assertThat(resourceTypes, containsInAnyOrder("http://rs.tdwg.org/dwc/terms/dynamicProperties", "http://rs.tdwg.org/dwc/terms/Occurrence", "http://rs.tdwg.org/dwc/terms/associatedTaxa"));
}

Example 15 with DatasetImpl

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

the class DatasetImporterForDwCATest method importTaxonDescriptionsFromDir.

@Test
public void importTaxonDescriptionsFromDir() throws StudyImporterException, URISyntaxException {
    URL resource = getClass().getResource("/org/globalbioticinteractions/dataset/coetzer/meta.xml");
    URI archiveRoot = new File(resource.toURI()).getParentFile().toURI();
    List<Map<String, String>> links = new ArrayList<>();
    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 {
            links.add(interaction);
        }
    });
    studyImporterForDwCA.importStudy();
    assertThat(links.size() > 0, is(true));
    assertThat(links.get(0).get(DATASET_CITATION), containsString("org/globalbioticinteractions/dataset/coetzer/"));
    assertThat(links.get(0).get(REFERENCE_CITATION), is("Cockerell, T.D.A. 1937. African bees of the genera Ceratina, Halictus and Megachile. 254 pp. William Clowes and Sons, London"));
    assertThat(links.get(0).get(TARGET_TAXON_NAME), is("Chaetodactylus leleupi"));
    assertThat(links.get(0).get(SOURCE_TAXON_NAME), is("Ceratina ruwenzorica Cockerell, 1937"));
    assertThat(links.get(0).get(INTERACTION_TYPE_NAME), is("Parasite"));
    assertThat(links.get(0).get(RESOURCE_TYPES), is("http://rs.gbif.org/terms/1.0/Reference"));
}