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/**
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* Copyright (C) 2007 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.out;
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import java.io.FileNotFoundException;
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import java.io.IOException;
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import java.io.PrintWriter;
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import java.io.UnsupportedEncodingException;
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import java.util.Map;
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import java.util.Set;
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import org.apache.log4j.Logger;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.common.LanguageString;
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import eu.etaxonomy.cdm.model.common.RelationshipBase;
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import eu.etaxonomy.cdm.model.common.RelationshipTermBase;
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import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.description.TaxonInteraction;
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import eu.etaxonomy.cdm.model.name.INonViralName;
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import eu.etaxonomy.cdm.model.name.NameRelationship;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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import eu.etaxonomy.cdm.model.taxon.TaxonNode;
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
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/**
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* Mapps taxon concept relationships, taxon name relationships and taxon interactions
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* @author a.mueller
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* @created 20.04.2011
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*/
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public class DwcaResourceRelationExport extends DwcaDataExportBase {
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private static final long serialVersionUID = 33810773244068812L;
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private static final Logger logger = Logger.getLogger(DwcaResourceRelationExport.class);
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private static final String ROW_TYPE = "http://rs.tdwg.org/dwc/terms/ResourceRelationship";
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protected static final String fileName = "resourceRelationship.txt";
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private DwcaMetaDataRecord metaRecord;
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/**
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* Constructor
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*/
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public DwcaResourceRelationExport(DwcaTaxExportState state) {
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super();
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this.ioName = this.getClass().getSimpleName();
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metaRecord = new DwcaMetaDataRecord(! IS_CORE, fileName, ROW_TYPE);
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state.addMetaRecord(metaRecord);
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file = DwcaTaxExportFile.RESOURCE_RELATION;
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}
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@Override
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protected void doInvoke(DwcaTaxExportState state){}
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@Override
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protected void handleTaxonNode(DwcaTaxExportState state, TaxonNode node) throws FileNotFoundException, UnsupportedEncodingException, IOException{
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try {
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DwcaTaxExportConfigurator config = state.getConfig();
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Taxon taxon = CdmBase.deproxy(node.getTaxon());
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//taxon interactions
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Set<TaxonDescription> descriptions = taxon.getDescriptions();
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for (TaxonDescription description : descriptions){
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for (DescriptionElementBase el : description.getElements()){
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if (el.isInstanceOf(TaxonInteraction.class)){
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DwcaResourceRelationRecord record = new DwcaResourceRelationRecord(metaRecord, config);
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TaxonInteraction taxonInteraction = CdmBase.deproxy(el,TaxonInteraction.class);
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if (! state.recordExistsUuid(taxonInteraction)){
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handleInteraction(state, record, taxon, taxonInteraction);
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PrintWriter writer = createPrintWriter(state, file);
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record.write(state, writer);
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state.addExistingRecordUuid(taxonInteraction);
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}
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}
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}
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}
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//concept relationships
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for (TaxonRelationship rel : taxon.getTaxonRelations()){
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DwcaResourceRelationRecord record = new DwcaResourceRelationRecord(metaRecord, config);
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IdentifiableEntity<?> subject = rel.getFromTaxon();
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IdentifiableEntity<?> object = rel.getToTaxon();
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if (rel.getType().equals(TaxonRelationshipType.MISAPPLIED_NAME_FOR()) ){
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//misapplied names are handled in core (tax)
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continue;
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}
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if (! state.recordExistsUuid(rel)){
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handleRelationship(record, subject, object, rel, false);
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PrintWriter writer = createPrintWriter(state, file);
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record.write(state, writer);
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state.addExistingRecordUuid(rel);
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}
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}
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//Name relationship
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//TODO
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INonViralName name = taxon.getName();
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if (name == null){
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String message = "There is a taxon node without name: " + node.getId();
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state.getResult().addError(message, "DwcaResourceRelationExport.makeSingleTaxonNode");
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return;
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}
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Set<NameRelationship> rels = name.getNameRelations();
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for (NameRelationship rel : rels){
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DwcaResourceRelationRecord record = new DwcaResourceRelationRecord(metaRecord, config);
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IdentifiableEntity<?> subject = CdmBase.deproxy(rel.getFromName());
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IdentifiableEntity<?> object = CdmBase.deproxy(rel.getToName());
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name = CdmBase.deproxy(name);
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boolean isInverse = false;
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if(subject == name){
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subject = taxon;
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}else if(object == name){
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object = subject;
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subject = taxon;
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isInverse = true;
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}else{
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String message = "Both, subject and object, are not part of the relationship for " + name.getTitleCache();
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state.getResult().addWarning(message);
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}
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if (! state.recordExistsUuid(rel)){
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//????
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handleRelationship(record, subject, object, rel, isInverse);
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PrintWriter writer = createPrintWriter(state, file);
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record.write(state, writer);
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state.addExistingRecordUuid(rel);
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}
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}
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} catch (Exception e) {
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String message = "Unexpected exception: " + e.getMessage();
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state.getResult().addException(e, message);
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}finally{
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flushWriter(state, file);
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}
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return;
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}
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private void handleRelationship(DwcaResourceRelationRecord record, IdentifiableEntity<?> subject, IdentifiableEntity<?> object,
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RelationshipBase<?,?,?> rel, boolean isInverse) {
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RelationshipTermBase<?> type = rel.getType();
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record.setId(subject.getId());
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record.setUuid(subject.getUuid());
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record.setResourceRelationshipId(rel.getId());
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record.setResourceRelationshipId(rel.getUuid());
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//TODO id / uuid / names ??
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if (object.isInstanceOf(TaxonBase.class)){
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record.setRelatedResourceId(object.getUuid());
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}
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//TODO transform to controlled voc
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String relTypeLabel;
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if (isInverse){
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relTypeLabel = type.getInverseLabel();
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}else{
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relTypeLabel = type.getLabel();
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}
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record.setRelationshipOfResource(relTypeLabel);
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record.setRelationshipAccordingTo(rel.getCitation()== null? null : rel.getCitation().getTitleCache());
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//TODO missing
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record.setRelatioshipEstablishedDate(null);
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record.setRelationshipRemarks(rel.getAnnotations());
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if (object.isInstanceOf(TaxonName.class)){
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record.setScientificName(object.getTitleCache());
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}
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}
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private void handleInteraction(DwcaTaxExportState state, DwcaResourceRelationRecord record, IdentifiableEntity<?> subject, TaxonInteraction interaction) {
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Taxon object = interaction.getTaxon2();
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if (object == null){
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state.getResult().addWarning("Taxon interaction has no target object.");
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}
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Map<Language, LanguageString> description = interaction.getDescription();
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record.setId(subject.getId());
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record.setUuid(subject.getUuid());
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record.setRelatedResourceId(object == null ? null : object.getUuid());
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//TODO transform to controlled voc
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if (description != null && description.get(Language.DEFAULT()) != null){
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record.setRelationshipOfResource(description.get(Language.DEFAULT()).getText());
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}else{
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record.setRelationshipOfResource(interaction.getFeature().getLabel());
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}
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//TODO uuid
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record.setResourceRelationshipId(interaction.getId());
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record.setResourceRelationshipId(interaction.getUuid());
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//FIXME multiple sources
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record.setRelationshipAccordingTo(null);
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//TODO missing
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record.setRelatioshipEstablishedDate(null);
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record.setRelationshipRemarks(interaction.getAnnotations());
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//TODO does this need to be filled?
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record.setScientificName(null);
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}
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@Override
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protected boolean doCheck(DwcaTaxExportState state) {
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boolean result = true;
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logger.warn("No check implemented for " + this.ioName);
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return result;
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}
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@Override
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public boolean isIgnore(DwcaTaxExportState state) {
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return ! state.getConfig().isDoResourceRelation();
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}
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}
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