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/**
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* Copyright (C) 2009 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.io.dwca.in;
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import java.util.ArrayList;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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import java.util.UUID;
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import org.apache.logging.log4j.LogManager;import org.apache.logging.log4j.Logger;
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import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;
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import eu.etaxonomy.cdm.io.stream.IPartitionableConverter;
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import eu.etaxonomy.cdm.io.stream.IReader;
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import eu.etaxonomy.cdm.io.stream.ListReader;
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import eu.etaxonomy.cdm.io.stream.MappedCdmBase;
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import eu.etaxonomy.cdm.io.stream.PartitionableConverterBase;
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import eu.etaxonomy.cdm.io.stream.StreamItem;
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import eu.etaxonomy.cdm.io.stream.terms.TermUri;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.description.TextData;
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import eu.etaxonomy.cdm.model.media.Rights;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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/**
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* @author a.mueller
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* @since 22.11.2011
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*/
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public class GbifDescriptionCsv2CdmConverter extends PartitionableConverterBase<DwcaDataImportConfiguratorBase, DwcaDataImportStateBase<DwcaDataImportConfiguratorBase>>
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implements IPartitionableConverter<StreamItem, IReader<CdmBase>, String>{
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@SuppressWarnings("unused")
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private static final Logger logger = LogManager.getLogger(GbifDescriptionCsv2CdmConverter.class);
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private static final String CORE_ID = "coreId";
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public GbifDescriptionCsv2CdmConverter(DwcaDataImportStateBase state) {
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super(state);
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}
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@Override
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public IReader<MappedCdmBase<? extends CdmBase>> map(StreamItem item ){
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List<MappedCdmBase<? extends CdmBase>> resultList = new ArrayList<>();
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Map<String, String> csv = item.map;
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Reference sourceReference = state.getTransactionalSourceReference();
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String sourceReferecenDetail = null;
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String id = getSourceId(item);
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Taxon taxon = getTaxonBase(id, item, Taxon.class, state);
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if (taxon != null){
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String description = item.get(TermUri.DC_DESCRIPTION);
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//String license = item.get(TermUri.DC_LICENSE);//lorna check - often empty in SP dwca
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Language language = getDcLanguage(item, resultList);
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if(language == null){
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language = Language.UNKNOWN_LANGUAGE();
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}
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if (isNotBlank(description)){
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Feature feature = getFeatureByDcType(item, resultList);
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TaxonDescription taxonDescription = getTaxonDescription(taxon, false);
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//deduplicate - if this taxonDescription already got these Rights attached
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boolean addRights = true;
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String rights = item.get(TermUri.DC_RIGHTS);
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Set<Rights> allRights = taxonDescription.getRights();
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for (Rights r : allRights) {
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if (r.getText() == rights) {
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addRights = false;
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}
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}
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if (addRights && (isNotBlank(rights))) {
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Rights copyright = Rights.NewInstance(rights, language);
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taxonDescription.addRights(copyright);
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}
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TextData descElement = TextData.NewInstance(feature);
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//Language language = getLanguage(item); //TODO
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descElement.putText(language,description);
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taxonDescription.addElement(descElement);
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}else{
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String message = "Description is empty. Description item will not be imported.";
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fireWarningEvent(message, item, 4);
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}
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MappedCdmBase<? extends CdmBase> mcb = new MappedCdmBase<>(item.term, csv.get(CORE_ID), taxon);
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resultList.add(mcb);
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}else{
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String message = "Taxon is not available for id '%s'";
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message = String.format(message, id);
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fireWarningEvent(message, item, 12);
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}
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return new ListReader<>(resultList);
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}
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/**
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* Determines the feature by the dc:type attribute. Tries to reuse existing
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* features.
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*
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* @param item
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* @param resultList
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* @return
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*/
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private Feature getFeatureByDcType(StreamItem item, List<MappedCdmBase<? extends CdmBase>> resultList) {
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String descriptionType = item.get(TermUri.DC_TYPE);
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item.remove(TermUri.DC_TYPE);
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try {
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Feature feature = state.getTransformer().getFeatureByKey(descriptionType);
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if (feature != null){
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return feature;
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}
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String namespace = Feature.class.getCanonicalName();
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List<Feature> features = state.get(namespace, descriptionType, Feature.class);
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if (features.size() > 1){
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String message = "There is more than 1 cdm entity matching given locationId '%s'. I take an arbitrary one.";
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fireWarningEvent(String.format(message, item), item, 4);
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return features.iterator().next();
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}
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UUID featureUuid = state.getTransformer().getFeatureUuid(descriptionType);
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feature = state.getCurrentIO().getFeature(state, featureUuid, descriptionType, descriptionType, null, null);
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if (feature == null){
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feature = Feature.NewInstance(descriptionType, descriptionType, null);
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feature.setSupportsTextData(true);
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// state.putMapping(namespace, type, feature);
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state.getCurrentIO().saveNewTerm(feature);
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MappedCdmBase<? extends CdmBase> mcb = new MappedCdmBase<>(namespace, descriptionType, feature);
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resultList.add(mcb);
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}
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return feature;
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} catch (UndefinedTransformerMethodException e) {
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String message = "GetFeature not yet supported by DwcA-Transformer. This should not have happend. Please contact your application developer.";
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fireWarningEvent(message, item, 8);
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return null;
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}
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}
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@Override
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public String getSourceId(StreamItem item) {
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String id = item.get(CORE_ID);
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return id;
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}
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//********************** PARTITIONABLE **************************************/
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@Override
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protected void makeForeignKeysForItem(StreamItem item, Map<String, Set<String>> fkMap) {
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String value;
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String key;
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if ( hasValue(value = item.get(CORE_ID))){
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key = TermUri.DWC_TAXON.toString();
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Set<String> keySet = getKeySet(key, fkMap);
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keySet.add(value);
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}
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}
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@Override
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public Set<String> requiredSourceNamespaces() {
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Set<String> result = new HashSet<>();
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result.add(TermUri.DWC_TAXON.toString());
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result.add(TermUri.DC_LANGUAGE.toString());
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return result;
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}
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//******************* TO STRING ******************************************/
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@Override
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public String toString(){
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return this.getClass().getName();
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}
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}
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