Examples with Record org.gbif.dwc.record.Record used on opensource projects

Example 6 with Record

use of org.gbif.dwc.record.Record in project eol-globi-data by jhpoelen.

the class DwCAUtilTest method assertHasRecords.

private void assertHasRecords(Archive dwcArchive) {
    // Loop over core core records and display id, basis of record and scientific name
    boolean hasRecords = false;
    for (Record rec : dwcArchive.getCore()) {
        hasRecords = true;
        break;
    }
    assertThat(hasRecords, is(true));
}

Example 7 with Record

use of org.gbif.dwc.record.Record in project eol-globi-data by jhpoelen.

the class DatasetImporterForDwCA method importTaxaExtension.

private static void importTaxaExtension(InteractionListener interactionListener, ArchiveFile extension, ArchiveFile core, BTreeMap<String, Map<String, String>> associationsMap) {
    for (Record record : extension) {
        Map<String, String> props = new TreeMap<>();
        termsToMap(record, props);
        associationsMap.put(record.id(), props);
    }
    for (Record coreRecord : core) {
        String id = coreRecord.id();
        if (contains(associationsMap, id)) {
            try {
                Map<String, String> targetProperties = associationsMap.get(id);
                TreeMap<String, String> interaction = new TreeMap<>();
                mapAssociationProperties(targetProperties, interaction);
                mapCoreProperties(coreRecord, interaction);
                interaction.put(RESOURCE_TYPES, StringUtils.join(Arrays.asList(core.getRowType().qualifiedName(), extension.getRowType().qualifiedName()), CharsetConstant.SEPARATOR));
                interactionListener.on(interaction);
            } catch (StudyImporterException e) {
            // 
            }
        }
    }
}

Example 8 with Record

use of org.gbif.dwc.record.Record in project eol-globi-data by jhpoelen.

the class DatasetImporterForDwCA method importCore.

private int importCore(Archive archive, InteractionListener interactionListener) throws StudyImporterException {
    AtomicInteger recordCounter = new AtomicInteger(0);
    ClosableIterator<Record> iterator = archive.getCore().iterator();
    while (true) {
        try {
            if (!iterator.hasNext()) {
                break;
            }
            Record rec = iterator.next();
            handleRecord(interactionListener, rec);
            recordCounter.incrementAndGet();
        } catch (IllegalStateException ex) {
            LogUtil.logError(getLogger(), "failed to handle dwc record", ex);
        }
    }
    return recordCounter.get();
}

Example 9 with Record

use of org.gbif.dwc.record.Record in project eol-globi-data by jhpoelen.

the class DatasetImporterForDwCA method collectRelatedResourceIds.

private static void collectRelatedResourceIds(ArchiveFile resourceExtension, Set<String> referencedSourceIds, Set<String> referencedTargetIds) {
    for (Record record : resourceExtension) {
        String targetId = record.value(DwcTerm.relatedResourceID);
        String sourceId = record.value(DwcTerm.resourceID);
        String relationshipRemarks = record.value(DwcTerm.relationshipRemarks);
        if (StringUtils.isNotBlank(sourceId)) {
            if (StringUtils.isNotBlank(targetId)) {
                referencedSourceIds.add(sourceId);
                referencedTargetIds.add(targetId);
            } else if (StringUtils.contains(relationshipRemarks, "scientificName:")) {
                referencedSourceIds.add(sourceId);
            }
        }
    }
}

Example 10 with Record

use of org.gbif.dwc.record.Record 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) {
            // 
            }
        }
    }
}