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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.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.Set;
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import java.util.UUID;
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import org.apache.log4j.Logger;
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import eu.etaxonomy.cdm.io.common.CdmExportBase;
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import eu.etaxonomy.cdm.io.common.ICdmExport;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
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import eu.etaxonomy.cdm.model.location.NamedArea;
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import eu.etaxonomy.cdm.model.location.WaterbodyOrCountry;
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import eu.etaxonomy.cdm.model.taxon.Classification;
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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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/**
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* @author a.mueller
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* @date 18.04.2011
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*
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*/
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public abstract class DwcaExportBase extends CdmExportBase<DwcaTaxExportConfigurator, DwcaTaxExportState> implements ICdmExport<DwcaTaxExportConfigurator, DwcaTaxExportState>{
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private static final Logger logger = Logger.getLogger(DwcaExportBase.class);
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protected Set<Integer> existingRecordIds = new HashSet<Integer>();
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protected Set<UUID> existingRecordUuids = new HashSet<UUID>();
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/**
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* Returns the list of taxon nodes that are part in one of the given classifications
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* and do have a taxon attached (empty taxon nodes should not but do exist in CDM databases).
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* Preliminary implementation. Better implement API method for this.
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* @return
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*/
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protected List<TaxonNode> getAllNodes(Set<Classification> classificationList) {
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List<TaxonNode> allNodes = getClassificationService().getAllNodes();
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List<TaxonNode> result = new ArrayList<TaxonNode>();
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for (TaxonNode node : allNodes){
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if (node.getClassification() == null ){
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continue;
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}else if (classificationList != null && classificationList.contains(node.getClassification())){
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continue;
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}
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Taxon taxon = CdmBase.deproxy(node.getTaxon(), Taxon.class);
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if (taxon == null){
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String message = "There is a taxon node without taxon: " + node.getId();
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logger.warn(message);
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continue;
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}
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result.add(node);
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}
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return result;
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}
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/**
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* Creates the locationId, locality, countryCode triple
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* @param record
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* @param area
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*/
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protected void handleArea(IDwcaAreaRecord record, NamedArea area, TaxonBase<?> taxon, boolean required) {
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if (area != null){
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record.setLocationId(area.getId());
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record.setLocality(area.getLabel());
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if (area.isInstanceOf(WaterbodyOrCountry.class)){
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WaterbodyOrCountry country = CdmBase.deproxy(area, WaterbodyOrCountry.class);
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record.setCountryCode(country.getIso3166_A2());
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}
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}else{
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if (required){
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String message = "Description requires area but area does not exist for taxon " + getTaxonLogString(taxon);
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logger.warn(message);
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}
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}
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}
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protected String getTaxonLogString(TaxonBase<?> taxon) {
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return taxon.getTitleCache() + "(" + taxon.getId() + ")";
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}
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/**
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* @param el
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* @return
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*/
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protected boolean recordExists(CdmBase el) {
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return existingRecordIds.contains(el.getId());
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}
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/**
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* @param sec
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*/
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protected void addExistingRecord(CdmBase cdmBase) {
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existingRecordIds.add(cdmBase.getId());
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}
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/**
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* @param el
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* @return
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*/
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protected boolean recordExistsUuid(CdmBase el) {
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return existingRecordUuids.contains(el.getUuid());
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}
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/**
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* @param sec
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*/
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protected void addExistingRecordUuid(CdmBase cdmBase) {
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existingRecordUuids.add(cdmBase.getUuid());
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}
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}
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