Examples with NullImportLogger org.eol.globi.tool.NullImportLogger used on opensource projects

Example 1 with NullImportLogger

use of org.eol.globi.tool.NullImportLogger in project eol-globi-data by jhpoelen.

the class DatasetImporterForPensoftTest method parseRowsAndEnrich.

public static void parseRowsAndEnrich(JsonNode biodivTable, InteractionListener listener, ResourceService resourceService) throws StudyImporterException {
    DatasetImporterForPensoft datasetImporterForPensoft = new DatasetImporterForPensoft(null, null);
    datasetImporterForPensoft.parseRowsAndEnrich(biodivTable, listener, new NullImportLogger(), new OpenBiodivClientImpl(resourceService));
}

Example 2 with NullImportLogger

use of org.eol.globi.tool.NullImportLogger in project eol-globi-data by jhpoelen.

the class DatasetImporterForDwCATest method importRecordsFromMCZ.

@Test
public void importRecordsFromMCZ() throws StudyImporterException, URISyntaxException {
    StringBuilder actualMessage = new StringBuilder();
    URL resource = getClass().getResource("/org/globalbioticinteractions/dataset/mcz/meta.xml");
    URI archiveRoot = new File(resource.toURI()).getParentFile().toURI();
    AtomicInteger recordCounter = new AtomicInteger(0);
    DatasetImporterForDwCA studyImporterForDwCA = new DatasetImporterForDwCA(null, null);
    studyImporterForDwCA.setLogger(new NullImportLogger() {

        @Override
        public void severe(LogContext ctx, String message) {
            actualMessage.append(message);
        }
    });
    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 : new String[] {}) {
                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(DatasetImporterForTSV.RESOURCE_TYPES), is("http://rs.tdwg.org/dwc/terms/ResourceRelationship | http://rs.tdwg.org/dwc/terms/Occurrence"));
            recordCounter.incrementAndGet();
        }
    });
    studyImporterForDwCA.importStudy();
    assertThat(recordCounter.get(), is(0));
    assertThat(actualMessage.toString(), startsWith("[failed to handle dwc record]"));
}

Example 3 with NullImportLogger

use of org.eol.globi.tool.NullImportLogger in project eol-globi-data by jhpoelen.

the class InteractionListenerWithInteractionTypeMappingTest method withTaxonHierarchy.

@Test
public void withTaxonHierarchy() throws StudyImporterException {
    final List<Map<String, String>> links = new ArrayList<Map<String, String>>();
    InteractionListener listener = new InteractionListenerWithInteractionTypeMapping(links::add, new InteractTypeMapper() {

        @Override
        public boolean shouldIgnoreInteractionType(String nameOrId) {
            return false;
        }

        @Override
        public InteractType getInteractType(String nameOrId) {
            return null;
        }
    }, new NullImportLogger());
    listener.on(new HashMap<String, String>() {

        {
            put(INTERACTION_TYPE_NAME, "eats");
            put(TaxonUtil.TARGET_TAXON_GENUS, "Donald");
            put(TaxonUtil.TARGET_TAXON_SPECIFIC_EPITHET, "duck");
        }
    });
    assertThat(links.size(), is(1));
    assertThat(links.get(0).get(TaxonUtil.TARGET_TAXON_NAME), is("Donald duck"));
    assertThat(links.get(0).get(TaxonUtil.TARGET_TAXON_PATH_NAMES), is("genus | species"));
    assertThat(links.get(0).get(TaxonUtil.TARGET_TAXON_PATH), is("Donald | Donald duck"));
}

Example 4 with NullImportLogger

use of org.eol.globi.tool.NullImportLogger in project eol-globi-data by jhpoelen.

the class TaxonNameEnricherTest method importWithMissingSourceTaxonButAvailableInstitutionCollectionCatalogTriple.

@Test
public void importWithMissingSourceTaxonButAvailableInstitutionCollectionCatalogTriple() throws StudyImporterException {
    List<String> msgs = new ArrayList<>();
    List<Map<String, String>> received = new ArrayList<>();
    final InteractionListener listener = new TaxonNameEnricher(interaction -> received.add(interaction), new NullImportLogger() {

        @Override
        public void info(LogContext ctx, String message) {
            msgs.add(message);
        }

        @Override
        public void warn(LogContext ctx, String message) {
            msgs.add(message);
        }

        @Override
        public void severe(LogContext ctx, String message) {
            msgs.add(message);
        }
    });
    final TreeMap<String, String> link = new TreeMap<>();
    link.put(TARGET_TAXON_NAME, "Donald duck");
    link.put(DatasetImporterForTSV.INTERACTION_TYPE_ID, InteractType.ATE.getIRI());
    link.put(SOURCE_OCCURRENCE_ID, "occurrenceId123");
    link.put(SOURCE_INSTITUTION_CODE, "institutionCode123");
    link.put(SOURCE_COLLECTION_CODE, "collectionCode123");
    link.put(SOURCE_COLLECTION_ID, "collectionId123");
    link.put(SOURCE_CATALOG_NUMBER, "catalogNumber123");
    link.put(DATASET_CITATION, "some source ref");
    link.put(REFERENCE_ID, "123");
    link.put(REFERENCE_CITATION, "");
    listener.on(link);
    assertThat(msgs, hasItem("source taxon name missing: using institutionCode/collectionCode/collectionId/catalogNumber/occurrenceId as placeholder"));
    assertThat(received.size(), is(1));
    String expectedPlaceholder = "institutionCode123 | collectionCode123 | collectionId123 | catalogNumber123 | occurrenceId123";
    assertThat(received.get(0).get(SOURCE_TAXON_NAME), is(expectedPlaceholder));
}

Example 5 with NullImportLogger

use of org.eol.globi.tool.NullImportLogger in project eol-globi-data by jhpoelen.

the class InteractionImporterTest method malformedDOI.

@Test
public void malformedDOI() {
    final List<String> msgs = new ArrayList<>();
    InteractionListener interactionListener = new InteractionImporter(nodeFactory, new GeoNamesService() {

        @Override
        public boolean hasTermForLocale(String locality) {
            return true;
        }

        @Override
        public LatLng findLatLng(String locality) throws IOException {
            throw new IOException("kaboom!");
        }
    }, new NullImportLogger() {

        @Override
        public void warn(LogContext ctx, String message) {
            msgs.add(message);
        }
    });
    final TreeMap<String, String> link = new TreeMap<>();
    link.put(SOURCE_TAXON_NAME, "donald");
    link.put(DatasetImporterForTSV.INTERACTION_TYPE_ID, "http://purl.obolibrary.org/obo/RO_0002470");
    link.put(TARGET_TAXON_NAME, "mini");
    link.put(REFERENCE_ID, "123");
    link.put(DATASET_CITATION, "some source ref");
    link.put(REFERENCE_CITATION, "");
    link.put(REFERENCE_DOI, "bla:XXX");
    try {
        interactionListener.on(link);
        assertThat(msgs.size(), is(1));
        assertThat(msgs.get(0), startsWith("found malformed doi [bla:XXX]"));
    } catch (StudyImporterException ex) {
        fail("should not throw on failing geoname lookup");
    }
}