Examples with TARGET_TAXON_NAME org.eol.globi.service.TaxonUtil.TARGET_TAXON_NAME used on opensource projects

Example 6 with TARGET_TAXON_NAME

use of org.eol.globi.service.TaxonUtil.TARGET_TAXON_NAME in project eol-globi-data by jhpoelen.

the class InteractionImporterTest method assertSymbiotaDateString.

public void assertSymbiotaDateString(String symbiotaTime, String expectedUTC) throws StudyImporterException {
    final InteractionListener listener = getAssertingInteractionImporter();
    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(DatasetImporterForMetaTable.EVENT_DATE, symbiotaTime);
    link.put(REFERENCE_ID, "123");
    link.put(DATASET_CITATION, "some source ref");
    link.put(REFERENCE_CITATION, "");
    listener.on(link);
    AtomicBoolean foundSpecimen = new AtomicBoolean(false);
    RelationshipListener someListener = relationship -> {
        final SpecimenNode someSpecimen = new SpecimenNode(relationship.getEndNode());
        assertTrue(someSpecimen.getUnderlyingNode().hasRelationship(Direction.INCOMING, NodeUtil.asNeo4j(RelTypes.COLLECTED)));
        try {
            Date eventDate = nodeFactory.getUnixEpochProperty(someSpecimen);
            assertThat(DateUtil.printDate(eventDate), is(expectedUTC));
        } catch (NodeFactoryException e) {
            fail(e.getMessage());
        }
        foundSpecimen.set(true);
    };
    handleRelations(someListener, RelTypes.COLLECTED);
    assertThat(foundSpecimen.get(), is(true));
}

Example 7 with TARGET_TAXON_NAME

use of org.eol.globi.service.TaxonUtil.TARGET_TAXON_NAME in project eol-globi-data by jhpoelen.

the class InteractionImporterTest method importBlankCitation.

@Test
public void importBlankCitation() throws StudyImporterException {
    final InteractionListener listener = new InteractionImporter(nodeFactory, (GeoNamesService) null, null);
    final TreeMap<String, String> link = new TreeMap<String, String>();
    link.put(SOURCE_OCCURRENCE_ID, "123");
    link.put(SOURCE_CATALOG_NUMBER, "catalogNumber123");
    link.put(SOURCE_COLLECTION_CODE, "collectionCode123");
    link.put(SOURCE_COLLECTION_ID, "collectionId123");
    link.put(SOURCE_INSTITUTION_CODE, "institutionCode123");
    link.put(TARGET_OCCURRENCE_ID, "456");
    link.put(TARGET_CATALOG_NUMBER, "targetCatalogNumber123");
    link.put(TARGET_COLLECTION_CODE, "targetCollectionCode123");
    link.put(TARGET_COLLECTION_ID, "targetCollectionId123");
    link.put(TARGET_INSTITUTION_CODE, "targetInstitutionCode123");
    link.put(SOURCE_TAXON_NAME, "donald");
    link.put(SOURCE_TAXON_ID, "duck");
    link.put(SOURCE_BODY_PART_ID, "bla:123");
    link.put(SOURCE_BODY_PART_NAME, "snout");
    link.put(SOURCE_LIFE_STAGE_ID, "some:stage");
    link.put(SOURCE_LIFE_STAGE_NAME, "stage");
    link.put(TARGET_TAXON_NAME, "mini");
    link.put(TARGET_TAXON_ID, "mouse");
    link.put(TARGET_BODY_PART_ID, "bla:345");
    link.put(TARGET_BODY_PART_NAME, "tail");
    link.put(DatasetImporterForMetaTable.EVENT_DATE, "20160404T21:31:40Z");
    link.put(DatasetImporterForMetaTable.LATITUDE, "12.1");
    link.put(DatasetImporterForMetaTable.LONGITUDE, "13.2");
    link.put(DatasetImporterForTSV.INTERACTION_TYPE_ID, "http://purl.obolibrary.org/obo/RO_0002470");
    link.put(REFERENCE_ID, "123");
    link.put(DATASET_CITATION, "some source ref");
    link.put(REFERENCE_CITATION, "");
    link.put(REFERENCE_DOI, "doi:1234");
    listener.on(link);
    final AtomicBoolean foundPair = new AtomicBoolean(false);
    RelationshipListener relationshipListener = relationship -> {
        final SpecimenNode predator = new SpecimenNode(relationship.getEndNode());
        for (Relationship stomachRel : NodeUtil.getStomachContents(predator)) {
            final SpecimenNode prey = new SpecimenNode(stomachRel.getEndNode());
            final TaxonNode preyTaxon = getOrigTaxon(prey);
            final TaxonNode predTaxon = getOrigTaxon(predator);
            assertThat(preyTaxon.getName(), is("mini"));
            assertThat(preyTaxon.getExternalId(), is("mouse"));
            assertThat(predTaxon.getName(), is("donald"));
            assertThat(predTaxon.getExternalId(), is("duck"));
            assertLocation(predator.getSampleLocation());
            assertLocation(prey.getSampleLocation());
            assertThat(predator.getExternalId(), is("123"));
            assertThat(prey.getExternalId(), is("456"));
            assertThat(predator.getLifeStage().getId(), is("some:stage"));
            assertThat(predator.getLifeStage().getName(), is("stage"));
            assertThat(predator.getProperty(OCCURRENCE_ID), is("123"));
            assertThat(predator.getProperty(CATALOG_NUMBER), is("catalogNumber123"));
            assertThat(predator.getProperty(COLLECTION_CODE), is("collectionCode123"));
            assertThat(predator.getProperty(COLLECTION_ID), is("collectionId123"));
            assertThat(predator.getProperty(INSTITUTION_CODE), is("institutionCode123"));
            assertThat(prey.getProperty(OCCURRENCE_ID), is("456"));
            assertThat(prey.getProperty(CATALOG_NUMBER), is("targetCatalogNumber123"));
            assertThat(prey.getProperty(COLLECTION_CODE), is("targetCollectionCode123"));
            assertThat(prey.getProperty(COLLECTION_ID), is("targetCollectionId123"));
            assertThat(prey.getProperty(INSTITUTION_CODE), is("targetInstitutionCode123"));
            foundPair.set(true);
            assertThat(relationship.getProperty(SpecimenConstant.EVENT_DATE), is(notNullValue()));
            List<SpecimenNode> specimens = Arrays.asList(predator, prey);
            for (SpecimenNode specimen : specimens) {
                assertThat(specimen.getBodyPart().getId(), is(notNullValue()));
                assertThat(specimen.getBodyPart().getName(), is(notNullValue()));
            }
        }
    };
    handleRelations(relationshipListener, RelTypes.COLLECTED);
    assertThat(foundPair.get(), is(true));
}

Example 8 with TARGET_TAXON_NAME

use of org.eol.globi.service.TaxonUtil.TARGET_TAXON_NAME in project eol-globi-data by jhpoelen.

the class InteractionImporterTest method importWithTaxonHierarchy.

@Test
public void importWithTaxonHierarchy() throws StudyImporterException {
    final InteractionListener listener = getAssertingInteractionImporter();
    final TreeMap<String, String> link = new TreeMap<>();
    link.put(SOURCE_TAXON_NAME, "Donald duck");
    link.put(SOURCE_TAXON_RANK, "species");
    link.put(SOURCE_TAXON_PATH, "Aves | Donald | Donald duck");
    link.put(SOURCE_TAXON_PATH_IDS, "AvesId | DonaldId | DonaldId duckId");
    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_TAXON_NAME, "mini");
    link.put(TARGET_TAXON_RANK, "species");
    link.put(TARGET_TAXON_PATH_IDS, "miniId");
    link.put(DATASET_CITATION, "some source ref");
    link.put(REFERENCE_ID, "123");
    link.put(REFERENCE_CITATION, "");
    listener.on(link);
    AtomicInteger foundSpecimen = new AtomicInteger(0);
    RelationshipListener someListener = relationship -> {
        final SpecimenNode someSpecimen = new SpecimenNode(relationship.getEndNode());
        assertTrue(someSpecimen.getUnderlyingNode().hasRelationship(Direction.INCOMING, NodeUtil.asNeo4j(RelTypes.COLLECTED)));
        assertTrue(someSpecimen.getUnderlyingNode().hasRelationship(NodeUtil.asNeo4j(RelTypes.ORIGINALLY_DESCRIBED_AS)));
        Node taxonNode = someSpecimen.getUnderlyingNode().getSingleRelationship(NodeUtil.asNeo4j(RelTypes.ORIGINALLY_DESCRIBED_AS), Direction.OUTGOING).getEndNode();
        TaxonNode taxon = new TaxonNode(taxonNode);
        if (someSpecimen.getUnderlyingNode().hasRelationship(Direction.OUTGOING, NodeUtil.asNeo4j(InteractType.ATE))) {
            assertThat(taxon.getPath(), is("Aves | Donald | Donald duck"));
            assertThat(taxon.getPathNames(), is("class | genus | species"));
            assertThat(taxon.getRank(), is("species"));
            assertThat(taxon.getPathIds(), is("AvesId | DonaldId | DonaldId duckId"));
            foundSpecimen.incrementAndGet();
        }
    };
    handleRelations(someListener, RelTypes.COLLECTED);
    assertThat(foundSpecimen.get(), is(1));
}

Example 9 with TARGET_TAXON_NAME

use of org.eol.globi.service.TaxonUtil.TARGET_TAXON_NAME in project eol-globi-data by jhpoelen.

the class DatasetImporterForDwCATest method importRecordsFromUnresolvedResourceRelationshipArchive.

@Test
public void importRecordsFromUnresolvedResourceRelationshipArchive() throws StudyImporterException, URISyntaxException {
    URL resource = getClass().getResource("fmnh-rr-unresolved-targetid-test.zip");
    AtomicInteger recordCounter = new AtomicInteger(0);
    DatasetImporterForDwCA studyImporterForDwCA = new DatasetImporterForDwCA(null, null);
    studyImporterForDwCA.setDataset(new DatasetImpl("some/namespace", resource.toURI(), inStream -> inStream));
    studyImporterForDwCA.setInteractionListener(interaction -> {
        if (interaction.get(TARGET_OCCURRENCE_ID) != null) {
            assertNull(interaction.get(TARGET_TAXON_NAME));
            assertThat(interaction.get(TARGET_OCCURRENCE_ID), is("http://n2t.net/ark:/65665/37d63a454-d948-4b1d-89db-89809887ef41"));
            recordCounter.incrementAndGet();
        }
        assertThat(interaction.get(DatasetImporterForTSV.RESOURCE_TYPES), is("http://rs.tdwg.org/dwc/terms/ResourceRelationship | http://rs.tdwg.org/dwc/terms/Occurrence"));
    });
    studyImporterForDwCA.importStudy();
    assertThat(recordCounter.get(), greaterThan(0));
}

Example 10 with TARGET_TAXON_NAME

use of org.eol.globi.service.TaxonUtil.TARGET_TAXON_NAME in project eol-globi-data by jhpoelen.

the class DatasetImporterForDwCA method importInteractionsFromResourceRelationships.

private static void importInteractionsFromResourceRelationships(InteractionListener interactionListener, ArchiveFile resourceExtension, Map<String, Map<String, Map<String, String>>> termTypeIdPropMap, List<DwcTerm> termTypes) {
    for (Record record : resourceExtension) {
        Map<String, String> props = new TreeMap<>();
        appendResourceType(props, resourceExtension.getRowType());
        String sourceId = record.value(DwcTerm.resourceID);
        String relationship = record.value(DwcTerm.relationshipOfResource);
        Optional<Term> relationshipOfResourceIDTerm = record.terms().stream().filter(x -> StringUtils.equals(x.simpleName(), "relationshipOfResourceID")).findFirst();
        String relationshipTypeIdValue = relationshipOfResourceIDTerm.map(record::value).orElse(null);
        String targetId = record.value(DwcTerm.relatedResourceID);
        if (StringUtils.isNotBlank(sourceId)) {
            appendVerbatimResourceRelationsValues(record, props);
            String relationshipAccordingTo = record.value(DwcTerm.relationshipAccordingTo);
            if (StringUtils.isNotBlank(relationshipAccordingTo)) {
                props.putIfAbsent(REFERENCE_CITATION, relationshipAccordingTo);
            }
            putIfAbsentAndNotBlank(props, INTERACTION_TYPE_NAME, relationship);
            putIfAbsentAndNotBlank(props, INTERACTION_TYPE_ID, relationshipTypeIdValue);
            putIfAbsentAndNotBlank(props, DatasetImporterForMetaTable.EVENT_DATE, record.value(DwcTerm.relationshipEstablishedDate));
            for (DwcTerm termType : termTypes) {
                String key = termType.qualifiedName();
                if (StringUtils.isNoneBlank(key) && termTypeIdPropMap.containsKey(key)) {
                    Map<String, Map<String, String>> propMap = termTypeIdPropMap.get(termType.qualifiedName());
                    populatePropertiesAssociatedWithId(props, sourceId, true, propMap.get(sourceId), labelPairFor(termType));
                    extractNameFromRelationshipRemarks(record).ifPresent(name -> props.put(TARGET_TAXON_NAME, name));
                    populatePropertiesAssociatedWithId(props, targetId, false, propMap.get(targetId), labelPairFor(termType));
                }
            }
            try {
                interactionListener.on(props);
            } catch (StudyImporterException e) {
            // 
            }
        }
    }
}