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

Example 11 with NullImportLogger

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

the class DatasetImporterForDwCATest method nonInteractionRecordMessage.

@Test
public void nonInteractionRecordMessage() throws StudyImporterException, URISyntaxException {
    List<String> msgs = new ArrayList<>();
    URL resource = getClass().getResource("/org/globalbioticinteractions/dataset/mcz-adjusted/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 info(LogContext ctx, String message) {
            msgs.add(message);
        }
    });
    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"));
            recordCounter.incrementAndGet();
        }
    });
    studyImporterForDwCA.importStudy();
    assertThat(recordCounter.get(), is(0));
    String joinedMsgs = StringUtils.join(msgs, "\n");
    assertThat(joinedMsgs, containsString("]: indexing interaction records"));
    assertThat(joinedMsgs, containsString("]: scanned [1] record(s)"));
}

Example 12 with NullImportLogger

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

the class InteractionListenerWithInteractionTypeMappingTest method withVerbatimInteractionType.

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

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

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

        {
            put(INTERACTION_TYPE_NAME, "Donald");
            put(INTERACTION_TYPE_ID, "duck");
        }
    });
    assertThat(links.size(), is(1));
    assertThat(links.get(0).get(INTERACTION_TYPE_ID_VERBATIM), is("duck"));
    assertThat(links.get(0).get(INTERACTION_TYPE_NAME_VERBATIM), is("Donald"));
    assertThat(links.get(0).get(INTERACTION_TYPE_ID), is("http://purl.obolibrary.org/obo/RO_0002470"));
    assertThat(links.get(0).get(INTERACTION_TYPE_NAME), is("eats"));
}

Example 13 with NullImportLogger

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

the class InteractionListenerWithInteractionTypeMappingTest method withBlankInteractionType.

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

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

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

        {
            put(INTERACTION_TYPE_NAME, "");
            put(INTERACTION_TYPE_ID, "");
        }
    });
    assertThat(links.size(), is(1));
    assertThat(links.get(0).get(INTERACTION_TYPE_ID), is("http://purl.obolibrary.org/obo/RO_0002470"));
    assertThat(links.get(0).get(INTERACTION_TYPE_NAME), is("eats"));
    assertThat(links.get(0).get(INTERACTION_TYPE_ID_VERBATIM), is(""));
    assertThat(links.get(0).get(INTERACTION_TYPE_NAME_VERBATIM), is(""));
}

Example 14 with NullImportLogger

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

the class InteractionListenerWithInteractionTypeMappingTest method withNullInteractionType.

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

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

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

        {
            put(INTERACTION_TYPE_NAME, null);
            put(INTERACTION_TYPE_ID, null);
        }
    });
    assertThat(links.size(), is(1));
    assertThat(links.get(0).get(INTERACTION_TYPE_ID), is(nullValue()));
    assertThat(links.get(0).get(INTERACTION_TYPE_NAME), is(nullValue()));
    assertThat(links.get(0).get(INTERACTION_TYPE_ID_VERBATIM), is(nullValue()));
    assertThat(links.get(0).get(INTERACTION_TYPE_NAME_VERBATIM), is(nullValue()));
}

Example 15 with NullImportLogger

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

the class TaxonNameEnricherTest method importWithMissingTargetTaxonButAvailableInstitutionCollectionCatalogTriple.

@Test
public void importWithMissingTargetTaxonButAvailableInstitutionCollectionCatalogTriple() 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(SOURCE_TAXON_NAME, "Donald duck");
    link.put(SOURCE_TAXON_PATH, "Aves | Donald | Donald duck");
    link.put(SOURCE_TAXON_PATH_NAMES, "class | genus | species");
    link.put(SOURCE_TAXON_SPECIFIC_EPITHET, "duck");
    link.put(DatasetImporterForTSV.INTERACTION_TYPE_ID, InteractType.ATE.getIRI());
    link.put(TARGET_OCCURRENCE_ID, "occurrenceId123");
    link.put(TARGET_INSTITUTION_CODE, "institutionCode123");
    link.put(TARGET_COLLECTION_CODE, "collectionCode123");
    link.put(TARGET_COLLECTION_ID, "collectionId123");
    link.put(TARGET_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("target taxon name missing: using institutionCode/collectionCode/collectionId/catalogNumber/occurrenceId as placeholder"));
    assertThat(received.size(), is(1));
    Map<String, String> receivedInteraction = received.get(0);
    assertThat(receivedInteraction.get(TARGET_TAXON_NAME), is("institutionCode123 | collectionCode123 | collectionId123 | catalogNumber123 | occurrenceId123"));
}