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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.cyprus;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.Iterator;
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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.commons.lang.StringUtils;
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import org.apache.log4j.Logger;
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import org.springframework.stereotype.Component;
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import eu.etaxonomy.cdm.api.service.pager.Pager;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer;
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import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;
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import eu.etaxonomy.cdm.io.excel.common.ExcelImporterBase;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.OriginalSourceType;
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import eu.etaxonomy.cdm.model.common.TermType;
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import eu.etaxonomy.cdm.model.common.TermVocabulary;
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import eu.etaxonomy.cdm.model.description.DescriptionBase;
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import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
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import eu.etaxonomy.cdm.model.description.Distribution;
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import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.location.Country;
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import eu.etaxonomy.cdm.model.location.NamedArea;
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import eu.etaxonomy.cdm.model.location.NamedAreaLevel;
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import eu.etaxonomy.cdm.model.location.NamedAreaType;
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import eu.etaxonomy.cdm.model.name.BotanicalName;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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/**
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* @author a.babadshanjan
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* @created 08.01.2009
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* @version 1.0
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*/
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@Component
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public class CyprusDistributionImport extends ExcelImporterBase<CyprusImportState> {
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private static final Logger logger = Logger.getLogger(CyprusDistributionImport.class);
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IoStateBase)
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*/
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@Override
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protected boolean doCheck(CyprusImportState state) {
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logger.warn("DoCheck not yet implemented for CyprusExcelImport");
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return true;
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}
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// protected static final String ID_COLUMN = "Id";
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protected static final String SPECIES_COLUMN = "Taxon";
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protected static final String DISTRIBUTION_COLUMN = "Distribution";
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protected static final String REFERENCE_COLUMN = "source";
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private Reference<?> refMeikle1977 = ReferenceFactory.newGeneric();
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private Reference<?> refMeikle1985 = ReferenceFactory.newGeneric();
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private Map<String, Taxon> taxonWithAuthorStore = new HashMap<String, Taxon>();
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private Map<String, Taxon> taxonNameOnlyStore = new HashMap<String, Taxon>();
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private boolean areasCreated = false;
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private Map<String, NamedArea> divisions = new HashMap<String, NamedArea>();
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private void makeAreasAndReference(CyprusImportState state) {
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if (areasCreated == false){
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IInputTransformer transformer = state.getTransformer();
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try {
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//divisions
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makeNewDivisions(state, transformer);
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loadReferences();
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loadStatus();
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loadTaxa();
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areasCreated = true;
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return;
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} catch (Exception e) {
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e.printStackTrace();
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state.setUnsuccessfull();
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return;
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}
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}
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}
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/**
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* Stores taxa records in DB
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*/
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@Override
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protected void firstPass(CyprusImportState state) {
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makeAreasAndReference(state);
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CyprusDistributionRow taxonLight = state.getCyprusDistributionRow();
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//species name
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String taxonStr = taxonLight.getSpecies();
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if ("#entf�llt#".equalsIgnoreCase(taxonStr)){
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logger.warn("entf�llt");
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return;
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}
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Taxon taxon = getTaxon(state, taxonStr);
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Reference<?> ref = getReference(taxonLight.getReference());
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if (taxon != null){
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makeDistribution(state, taxon, taxonLight.getDistribution(), ref);
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getTaxonService().save(taxon);
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}
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return;
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}
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protected static final boolean CREATE = true;
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protected static final boolean CREATE_NOT = false;
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protected static final boolean NO_IMAGE_GALLERY = false;
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protected static final boolean IMAGE_GALLERY = false;
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private void makeDistribution(CyprusImportState state, Taxon taxon, String distributionStr, Reference<?> ref) {
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// TaxonDescription description = getTaxonDescription(taxon, NO_IMAGE_GALLERY, CREATE);
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TaxonDescription description = getNewDescription(state, taxon);
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PresenceAbsenceTerm status = getStatus(taxon);
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status = removeDoubtfulStatus(status);
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removeDistributions(taxon);
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for (int i = 1; i <= 8; i++){
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if (distributionStr.contains(String.valueOf(i))){
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NamedArea area = this.divisions.get(String.valueOf(i));
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Distribution distribution = Distribution.NewInstance(area, status);
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distribution.addSource(OriginalSourceType.PrimaryTaxonomicSource, null, null, ref, null);
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description.addElement(distribution);
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}
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}
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}
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private TaxonDescription getNewDescription(CyprusImportState state, Taxon taxon) {
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Reference<?> excelRef = state.getConfig().getSourceReference();
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TaxonDescription desc = TaxonDescription.NewInstance(taxon, false);
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desc.setTitleCache(excelRef.getTitleCache() + " for " + taxon.getTitleCache(), true);
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desc.addSource(OriginalSourceType.Import, null, null, excelRef, null);
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return desc;
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}
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private PresenceAbsenceTerm indigenousStatus;
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private PresenceAbsenceTerm casualStatus;
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private PresenceAbsenceTerm nonInvasiveStatus;
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private PresenceAbsenceTerm invasiveStatus;
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private PresenceAbsenceTerm questionableStatus;
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private PresenceAbsenceTerm removeDoubtfulStatus(PresenceAbsenceTerm status) {
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if (status == null){
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return null;
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}
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if (status.getUuid().equals(CyprusTransformer.indigenousDoubtfulUuid)){
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status = indigenousStatus;
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}else if (status.getUuid().equals(CyprusTransformer.casualDoubtfulUuid)){
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status = casualStatus;
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}else if (status.getUuid().equals(CyprusTransformer.nonInvasiveDoubtfulUuid)){
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status = nonInvasiveStatus;
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}else if (status.getUuid().equals(CyprusTransformer.invasiveDoubtfulUuid)){
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status = invasiveStatus;
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}else if (status.getUuid().equals(CyprusTransformer.questionableDoubtfulUuid)){
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status = questionableStatus;
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}else if (status.getUuid().equals(CyprusTransformer.cultivatedDoubtfulUuid)){
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status = PresenceAbsenceTerm.CULTIVATED();
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}
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return status;
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}
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private PresenceAbsenceTerm getStatus(Taxon taxon) {
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Set<PresenceAbsenceTerm> statusSet = new HashSet<PresenceAbsenceTerm>();
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Set<Distribution> existingDistributions = getExistingDistributions(taxon);
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if (existingDistributions.size() > 1){
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logger.warn("There is more than 1 distribution: " + taxon.getTitleCache());
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}
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for (Distribution distribution: existingDistributions){
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PresenceAbsenceTerm status = distribution.getStatus();
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statusSet.add(status);
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}
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if (statusSet.size() == 0){
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logger.warn("No status found for: " + taxon.getTitleCache());
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return null;
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}else if (statusSet.size() == 1){
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return statusSet.iterator().next();
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}else{
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logger.warn("More than 1 status found. Return first: " + taxon.getTitleCache());
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return statusSet.iterator().next();
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}
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}
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/**
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* @param taxon
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* @param statusSet
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*/
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private void removeDistributions(Taxon taxon) {
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Set<Distribution> toRemove = new HashSet<Distribution>();
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for (TaxonDescription desc : taxon.getDescriptions()){
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if (desc.isImageGallery() == NO_IMAGE_GALLERY ){
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Iterator<DescriptionElementBase> iterator = desc.getElements().iterator();
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while (iterator.hasNext()){
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DescriptionElementBase element = iterator.next();
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if (element.isInstanceOf(Distribution.class)){
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toRemove.add(CdmBase.deproxy(element, Distribution.class));
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// iterator.remove();
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}
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}
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}
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}
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for (Distribution distribution : toRemove){
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DescriptionBase<?> desc = distribution.getInDescription();
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desc.removeElement(distribution);
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getDescriptionService().saveOrUpdate(desc);
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}
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return;
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}
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/**
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* @param taxon
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* @param statusSet
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*/
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private Set<Distribution> getExistingDistributions(Taxon taxon) {
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Set<Distribution> result = new HashSet<Distribution>();
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for (TaxonDescription desc : taxon.getDescriptions()){
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if (desc.isImageGallery() == NO_IMAGE_GALLERY ){
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for (DescriptionElementBase element : desc.getElements()){
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if (element.isInstanceOf(Distribution.class)){
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Distribution distribution = CdmBase.deproxy(element, Distribution.class);
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result.add(distribution);
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}
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}
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}
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}
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return result;
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}
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private Reference<?> getReference(String referenceStr) {
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Reference<?> result;
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if ("Meikle 1977".equals(referenceStr)){
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result = refMeikle1977;
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}else if("Meikle 1985".equals(referenceStr)){
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result = refMeikle1985;
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}else{
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logger.warn("Reference not recognized: " + referenceStr);
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result = null;
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}
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return result;
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}
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private Taxon getTaxon(CyprusImportState state, String taxonStr) {
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Taxon result;
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if (taxonWithAuthorStore.get(taxonStr) != null){
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result = taxonWithAuthorStore.get(taxonStr);
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}else if(taxonNameOnlyStore.get(taxonStr) != null){
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result = taxonNameOnlyStore.get(taxonStr);
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}else {
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// result = getTaxonService().findBestMatchingTaxon(taxonStr);
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// TaxonNameBase name = BotanicalName.NewInstance(Rank.SPECIES());
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// name.setTitleCache(taxonStr, true);
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//
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// result = Taxon.NewInstance(name, null);
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// if (result == null){
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logger.warn("Taxon not found: " + taxonStr);
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// }else{
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// taxonStore.put(taxonStr, result);
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// }
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result = null;
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}
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return result;
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}
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/**
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*
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*/
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private void loadTaxa() {
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List<String> propertyPaths = new ArrayList<String>();
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propertyPaths.add("*.name");
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List<Taxon> taxonList = (List)getTaxonService().list(Taxon.class, null, null, null, propertyPaths);
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for (Taxon taxon: taxonList){
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if (taxon.getTaxonNodes().size() == 0){
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continue;
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}
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String nameTitle = taxon.getName().getTitleCache();
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String nameCache = CdmBase.deproxy(taxon.getName(), BotanicalName.class).getNameCache();
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Taxon returnValue = taxonWithAuthorStore.put(nameTitle, taxon);
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if (returnValue != null){
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logger.warn("Duplicate titleCache entry for taxon: " + nameTitle);
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}
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returnValue = taxonNameOnlyStore.put(nameCache, taxon);
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if (returnValue != null){
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logger.warn("Duplicate nameCache entry for taxon: " + nameCache);
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}
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}
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}
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/**
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* @param meikle1977List
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*/
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private void loadReferences() {
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Pager<Reference> meikle1977List = getReferenceService().findByTitle(Reference.class, "R. D. Meikle, Flora of Cyprus 1. 1977", null, null, null, null, null, null);
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if (meikle1977List.getCount() != 1){
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logger.error("There is not exactly 1 Meikle 1977 reference");
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}else{
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refMeikle1977 = meikle1977List.getRecords().iterator().next();
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}
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328
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Pager<Reference> meikle1985List = getReferenceService().findByTitle(Reference.class, "R. D. Meikle, Flora of Cyprus 2. 1985", null, null, null, null, null, null);
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330
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if (meikle1985List.getCount() != 1){
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logger.error("There is not exactly 1 Meikle 1985 reference");
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}else{
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refMeikle1985 = meikle1977List.getRecords().iterator().next();
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}
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}
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337
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/**
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338
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*
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339
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*/
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340
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private void loadStatus() {
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indigenousStatus = (PresenceAbsenceTerm)getTermService().find(CyprusTransformer.indigenousUuid);
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casualStatus = (PresenceAbsenceTerm)getTermService().find(CyprusTransformer.casualUuid);
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nonInvasiveStatus = (PresenceAbsenceTerm)getTermService().find(CyprusTransformer.nonInvasiveUuid);
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invasiveStatus = (PresenceAbsenceTerm)getTermService().find(CyprusTransformer.invasiveUuid);
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questionableStatus = (PresenceAbsenceTerm)getTermService().find(CyprusTransformer.questionableUuid);
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346
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}
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347
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348
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/**
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349
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* @param state
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350
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* @param transformer
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351
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* @throws UndefinedTransformerMethodException
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352
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*/
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353
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private void makeNewDivisions(CyprusImportState state,
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354
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IInputTransformer transformer)
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355
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throws UndefinedTransformerMethodException {
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356
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NamedAreaType areaType = NamedAreaType.NATURAL_AREA();
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357
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NamedAreaLevel areaLevel = (NamedAreaLevel)getTermService().find(CyprusTransformer.uuidCyprusDivisionsAreaLevel);
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358
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if (areaLevel == null){
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359
|
areaLevel = NamedAreaLevel.NewInstance("Cyprus Division", "Cyprus Division", null);
|
|
360
|
getTermService().save(areaLevel);
|
|
361
|
}
|
|
362
|
|
|
363
|
TermVocabulary<NamedArea> areaVocabulary = getVocabulary(TermType.NamedArea, CyprusTransformer.uuidCyprusDivisionsVocabulary, "Cyprus devisions", "Cyprus divisions", null, null, true, NamedArea.NewInstance());
|
|
364
|
NamedArea tdwg4Cyprus = (NamedArea)getTermService().find(UUID.fromString("9d447b51-e363-4dde-ae40-84c55679983c"));
|
|
365
|
Country isoCountryCyprus = (Country)getTermService().find(UUID.fromString("4b13d6b8-7eca-4d42-8172-f2018051ca19"));
|
|
366
|
|
|
367
|
for(int i = 1; i <= 8; i++){
|
|
368
|
UUID divisionUuid = transformer.getNamedAreaUuid(String.valueOf(i));
|
|
369
|
NamedArea division = this.getNamedArea(state, divisionUuid, "Division " + i, "Cyprus: Division " + i, String.valueOf(i), areaType, areaLevel, areaVocabulary, null);
|
|
370
|
divisions.put(String.valueOf(i), division);
|
|
371
|
tdwg4Cyprus.addIncludes(division);
|
|
372
|
isoCountryCyprus.addIncludes(division);
|
|
373
|
getTermService().save(division);
|
|
374
|
}
|
|
375
|
}
|
|
376
|
|
|
377
|
|
|
378
|
/* (non-Javadoc)
|
|
379
|
* @see eu.etaxonomy.cdm.io.excel.common.ExcelImporterBase#analyzeRecord(java.util.HashMap, eu.etaxonomy.cdm.io.excel.common.ExcelImportState)
|
|
380
|
*/
|
|
381
|
@Override
|
|
382
|
protected void analyzeRecord(HashMap<String, String> record, CyprusImportState state) {
|
|
383
|
|
|
384
|
Set<String> keys = record.keySet();
|
|
385
|
CyprusDistributionRow cyprusDistributionRow = new CyprusDistributionRow();
|
|
386
|
state.setCyprusDistributionRow(cyprusDistributionRow);
|
|
387
|
|
|
388
|
for (String originalKey: keys) {
|
|
389
|
String indexedKey = CdmUtils.removeDuplicateWhitespace(originalKey.trim()).toString();
|
|
390
|
String[] split = indexedKey.split("_");
|
|
391
|
String key = split[0];
|
|
392
|
if (split.length > 1){
|
|
393
|
String indexString = split[1];
|
|
394
|
try {
|
|
395
|
Integer.valueOf(indexString);
|
|
396
|
} catch (NumberFormatException e) {
|
|
397
|
String message = "Index must be integer";
|
|
398
|
logger.error(message);
|
|
399
|
continue;
|
|
400
|
}
|
|
401
|
}
|
|
402
|
|
|
403
|
String value = (String) record.get(indexedKey);
|
|
404
|
if (! StringUtils.isBlank(value)) {
|
|
405
|
if (logger.isDebugEnabled()) { logger.debug(key + ": " + value); }
|
|
406
|
value = CdmUtils.removeDuplicateWhitespace(value.trim()).toString();
|
|
407
|
}else{
|
|
408
|
continue;
|
|
409
|
}
|
|
410
|
|
|
411
|
|
|
412
|
if (key.equalsIgnoreCase(SPECIES_COLUMN)) {
|
|
413
|
cyprusDistributionRow.setSpecies(value);
|
|
414
|
|
|
415
|
} else if(key.equalsIgnoreCase(DISTRIBUTION_COLUMN)) {
|
|
416
|
cyprusDistributionRow.setDistribution(value);
|
|
417
|
|
|
418
|
} else if(key.equalsIgnoreCase(REFERENCE_COLUMN)) {
|
|
419
|
cyprusDistributionRow.setReference(value);
|
|
420
|
|
|
421
|
} else {
|
|
422
|
state.setUnsuccessfull();
|
|
423
|
logger.error("Unexpected column header " + key);
|
|
424
|
}
|
|
425
|
}
|
|
426
|
return;
|
|
427
|
}
|
|
428
|
|
|
429
|
|
|
430
|
/**
|
|
431
|
*
|
|
432
|
*/
|
|
433
|
@Override
|
|
434
|
protected void secondPass(CyprusImportState state) {
|
|
435
|
//no second pass for this import
|
|
436
|
return;
|
|
437
|
}
|
|
438
|
|
|
439
|
@Override
|
|
440
|
protected boolean isIgnore(CyprusImportState state) {
|
|
441
|
return ! state.getConfig().isDoDistribution();
|
|
442
|
}
|
|
443
|
|
|
444
|
}
|