Examples with REFERENCE_URL org.eol.globi.data.DatasetImporterForTSV.REFERENCE_URL used on opensource projects

Example 1 with REFERENCE_URL

use of org.eol.globi.data.DatasetImporterForTSV.REFERENCE_URL 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 2 with REFERENCE_URL

use of org.eol.globi.data.DatasetImporterForTSV.REFERENCE_URL in project eol-globi-data by jhpoelen.

the class DatasetImporterForDwCATest method importRecordsFromArctosArchive.

@Test
public void importRecordsFromArctosArchive() throws StudyImporterException, URISyntaxException {
    URL resource = getClass().getResource("/org/globalbioticinteractions/dataset/arctos_mvz_bird_small.zip");
    DatasetImporterForDwCA studyImporterForDwCA = new DatasetImporterForDwCA(null, null);
    studyImporterForDwCA.setDataset(new DatasetImpl("some/namespace", resource.toURI(), inStream -> inStream));
    List<String> families = new ArrayList<>();
    AtomicBoolean someRecords = new AtomicBoolean(false);
    studyImporterForDwCA.setInteractionListener(new InteractionListener() {

        @Override
        public void on(Map<String, String> interaction) throws StudyImporterException {
            assertThat(interaction.get(REFERENCE_URL), startsWith("http://arctos.database.museum/guid/"));
            assertThat(interaction.get(SOURCE_OCCURRENCE_ID), anyOf(is("http://arctos.database.museum/guid/MVZ:Bird:180448?seid=587053"), is("http://arctos.database.museum/guid/MVZ:Bird:183644?seid=158590"), is("http://arctos.database.museum/guid/MVZ:Bird:58090?seid=657121")));
            if (interaction.containsKey(DatasetImporterForTSV.TARGET_OCCURRENCE_ID)) {
                assertThat(interaction.get(DatasetImporterForTSV.TARGET_OCCURRENCE_ID), anyOf(is("http://arctos.database.museum/guid/MVZ:Herp:241200"), is("http://arctos.database.museum/guid/MVZ:Bird:183643"), is("http://arctos.database.museum/guid/MVZ:Bird:58093")));
            }
            assertThat(interaction.get(SOURCE_TAXON_FAMILY), anyOf(is("Accipitridae"), is("Strigidae")));
            assertThat(interaction.get(DatasetImporterForTSV.RESOURCE_TYPES), is("http://rs.tdwg.org/dwc/terms/associatedOccurrences | http://rs.tdwg.org/dwc/terms/Occurrence"));
            someRecords.set(true);
        }
    });
    studyImporterForDwCA.importStudy();
    assertThat(someRecords.get(), is(true));
}

Example 3 with REFERENCE_URL

use of org.eol.globi.data.DatasetImporterForTSV.REFERENCE_URL in project eol-globi-data by jhpoelen.

the class DatasetImporterForDwCATest method importRecords.

@Test
public void importRecords() throws StudyImporterException, URISyntaxException, IOException {
    URL resource = getClass().getResource("/org/globalbioticinteractions/dataset/dwca.zip");
    DatasetImporterForDwCA studyImporterForDwCA = new DatasetImporterForDwCA(null, null);
    DatasetImpl dataset = new DatasetImpl("some/namespace", resource.toURI(), inStream -> inStream);
    dataset.setConfig(new ObjectMapper().readTree("{ \"citation\": \"some citation\" }"));
    studyImporterForDwCA.setDataset(dataset);
    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("some citation"));
            assertThat(interaction.get(DatasetImporterForTSV.DATASET_CITATION), containsString("Accessed at"));
            assertThat(interaction.get(DatasetImporterForTSV.DATASET_CITATION), containsString("dataset/dwca.zip"));
            assertThat(interaction.get(REFERENCE_ID), is(not(nullValue())));
            assertThat(interaction.get(DatasetImporterForTSV.REFERENCE_CITATION), is(not(nullValue())));
            assertThat(interaction.get(REFERENCE_URL), is(not(nullValue())));
            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 4 with REFERENCE_URL

use of org.eol.globi.data.DatasetImporterForTSV.REFERENCE_URL in project eol-globi-data by jhpoelen.

the class DatasetImporterForDwCA method mapReferenceInfo.

static void mapReferenceInfo(Record rec, Map<String, String> interactionProperties) {
    String value = StringUtils.trim(rec.value(DcTerm.references));
    if (StringUtils.isBlank(value)) {
        value = StringUtils.trim(rec.value(DwcTerm.occurrenceID));
    }
    if (StringUtils.isNotBlank(value)) {
        appendResourceType(interactionProperties, rec.rowType());
        interactionProperties.put(REFERENCE_CITATION, value);
        interactionProperties.put(REFERENCE_ID, value);
        try {
            URI referenceURI = new URI(value);
            URL url = referenceURI.toURL();
            interactionProperties.put(REFERENCE_URL, url.toString());
        } catch (MalformedURLException | URISyntaxException | IllegalArgumentException e) {
        // opportunistic extraction of url from references to take advantage of practice used in Symbiota)
        }
    }
}