Examples with Term org.gbif.dwc.terms.Term used on opensource projects

Example 1 with Term

use of org.gbif.dwc.terms.Term in project eol-globi-data by jhpoelen.

the class DatasetImporterForDwCA method termsToMap.

private static void termsToMap(Record record, Map<String, String> props) {
    for (Term term : record.terms()) {
        String value = record.value(term);
        if (StringUtils.isNotBlank(value)) {
            props.put(term.qualifiedName(), value);
        }
        appendResourceType(props, record.rowType());
    }
}

Example 2 with Term

use of org.gbif.dwc.terms.Term in project eol-globi-data by jhpoelen.

the class DatasetImporterForDwCA method handleRecord.

private void handleRecord(InteractionListener interactionListener, Record rec) throws StudyImporterException {
    List<Map<String, String>> interactionCandidates = new ArrayList<>();
    appendInteractionCandidatesIfAvailable(rec, interactionCandidates, DwcTerm.associatedTaxa, "");
    appendInteractionCandidatesIfAvailable(rec, interactionCandidates, DwcTerm.habitat, null);
    appendAssociatedOccurrencesIfAvailable(rec, interactionCandidates);
    // see https://github.com/globalbioticinteractions/globalbioticinteractions/issues/755#issuecomment-1029509362
    appendAssociatedSequencesIfAvailable(rec, interactionCandidates);
    String occurrenceRemarks = rec.value(DwcTerm.occurrenceRemarks);
    try {
        addCandidatesFromRemarks(interactionCandidates, occurrenceRemarks);
    } catch (IOException e) {
        if (getLogger() != null) {
            Map<String, String> interactionProperties = new HashMap<>();
            mapCoreProperties(rec, interactionProperties);
            getLogger().warn(LogUtil.contextFor(interactionProperties), e.getMessage());
        }
    }
    String dynamicProperties = rec.value(DwcTerm.dynamicProperties);
    if (StringUtils.isNotBlank(dynamicProperties)) {
        Map<String, String> parsedDynamicProperties = parseDynamicPropertiesForInteractionsOnly(dynamicProperties);
        if (!parsedDynamicProperties.isEmpty()) {
            interactionCandidates.add(parsedDynamicProperties);
        }
    }
    Map<String, String> interaction = new HashMap<>(rec.terms().size());
    for (Term term : rec.terms()) {
        interaction.put(term.qualifiedName(), rec.value(term));
    }
    if (interactionCandidates.isEmpty() && isDependency()) {
        // If no candidates are found,
        // add empty candidate to allow interaction listeners to do indexing/enriching
        interactionCandidates.add(new TreeMap<>());
    }
    for (Map<String, String> interactionProperties : interactionCandidates) {
        interactionProperties.putAll(interaction);
        interactionProperties.put(DWC_COREID, rec.id());
        mapIfAvailable(rec, interactionProperties, BASIS_OF_RECORD_NAME, DwcTerm.basisOfRecord);
        mapCoreProperties(rec, interactionProperties);
        appendResourceType(interactionProperties, rec.rowType());
        interactionListener.on(interactionProperties);
    }
}

Example 3 with Term

use of org.gbif.dwc.terms.Term 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) {
            // 
            }
        }
    }
}