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package eu.etaxonomy.cdm.io.csv.caryophyllales.out;
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import java.io.ByteArrayOutputStream;
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import java.io.FileOutputStream;
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import java.io.OutputStream;
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import java.io.OutputStreamWriter;
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import java.io.PrintWriter;
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import java.util.ArrayList;
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import java.util.Collections;
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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.Set;
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import java.util.TreeMap;
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import java.util.UUID;
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import org.apache.log4j.Logger;
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import org.springframework.beans.factory.annotation.Autowired;
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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.ext.geo.IEditGeoService;
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import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
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import eu.etaxonomy.cdm.model.common.DefinedTermBase;
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import eu.etaxonomy.cdm.model.common.Language;
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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.Feature;
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import eu.etaxonomy.cdm.model.description.TextData;
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import eu.etaxonomy.cdm.model.name.BotanicalName;
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import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
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import eu.etaxonomy.cdm.model.name.HomotypicalGroupComparator;
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import eu.etaxonomy.cdm.model.name.NameRelationship;
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import eu.etaxonomy.cdm.model.name.NameTypeDesignation;
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import eu.etaxonomy.cdm.model.name.NameTypeDesignationStatus;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.TaxonNameBase;
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import eu.etaxonomy.cdm.model.name.TypeDesignationBase;
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import eu.etaxonomy.cdm.model.taxon.Classification;
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import eu.etaxonomy.cdm.model.taxon.HomotypicGroupTaxonComparator;
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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import eu.etaxonomy.cdm.model.taxon.SynonymRelationship;
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import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
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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.TaxonComparator;
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import eu.etaxonomy.cdm.model.taxon.TaxonNode;
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import eu.etaxonomy.cdm.persistence.query.MatchMode;
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@Component
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public class CsvNameExport extends CsvNameExportBase {
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private static final Logger logger = Logger.getLogger(CsvNameExport.class);
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@Autowired
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IEditGeoService geoService;
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public CsvNameExport() {
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super();
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this.ioName = this.getClass().getSimpleName();
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}
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@Override
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protected void doInvoke(CsvNameExportState state) {
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CsvNameExportConfigurator config = state.getConfig();
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PrintWriter writer = null;
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try {
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switch(config.getTarget()) {
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case FILE :
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OutputStream os = new FileOutputStream(config.getDestination());
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os.write(239);
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os.write(187);
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os.write(191);
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writer = new PrintWriter(new OutputStreamWriter(os, "UTF-8"));
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break;
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case EXPORT_DATA :
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exportStream = new ByteArrayOutputStream();
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writer = new PrintWriter(exportStream);
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break;
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default:
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break;
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}
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List<HashMap<String, String>> result;
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if (config.isNamesOnly()){
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txStatus = startTransaction();
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result = getNameService().getNameRecords();
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} else {
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result = getRecordsForPrintPub(state);
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}
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NameRecord nameRecord;
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int count = 0;
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boolean isFirst = true;
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for (HashMap<String,String> record:result){
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if (count > 0){
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isFirst = false;
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}
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count++;
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nameRecord = new NameRecord(record, isFirst);
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nameRecord.print(writer, config);
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}
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writer.flush();
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writer.close();
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} catch (Exception e) {
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// TODO Auto-generated catch block
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e.printStackTrace();
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}
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if (txStatus != null ){
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commitTransaction(txStatus);
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}
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return;
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}
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@Override
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protected boolean doCheck(CsvNameExportState 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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protected boolean isIgnore(CsvNameExportState state) {
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return false;
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}
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public List<HashMap<String,String>> getRecordsForPrintPub(CsvNameExportState state){
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List<String> propertyPaths = new ArrayList<String>();
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propertyPaths.add("childNodes");
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txStatus = startTransaction();
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Classification classification = getClassificationService().load(state.getConfig().getClassificationUUID());
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TaxonNode rootNode = classification.getRootNode();
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rootNode = getTaxonNodeService().load(rootNode.getUuid(), propertyPaths);
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Set<UUID> childrenUuids = new HashSet<UUID>();
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rootNode = HibernateProxyHelper.deproxy(rootNode, TaxonNode.class);
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rootNode.removeNullValueFromChildren();
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for (TaxonNode child: rootNode.getChildNodes()){
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child = HibernateProxyHelper.deproxy(child, TaxonNode.class);
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childrenUuids.add(child.getUuid());
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}
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Set<UUID> parentsNodesUUID = new HashSet<UUID>(childrenUuids);
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childrenUuids.clear();
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List<TaxonNode> childrenNodes = new ArrayList<TaxonNode>();
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TaxonNameBase name;
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findChildren(state, childrenUuids, parentsNodesUUID);
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List<HashMap<String,String>> nameRecords = new ArrayList<HashMap<String,String>>();
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HashMap<String,String> nameRecord = new HashMap<String,String>();
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childrenNodes = getTaxonNodeService().find(childrenUuids);
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for(TaxonNode genusNode : childrenNodes) {
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if (!genusNode.isTopmostNode()){
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nameRecords.add(createNewRecord(genusNode, state));
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}
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refreshTransaction();
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}
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return nameRecords;
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}
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/**
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* @param state
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* @param childrenUuids
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* @param parentsNodesUUID
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* @param familyNode
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*/
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private void findChildren(CsvNameExportState state, Set<UUID> childrenUuids, Set<UUID> parentsNodesUUID) {
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TaxonNameBase name;
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List<TaxonNode> familyNodes = getTaxonNodeService().find(parentsNodesUUID);
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parentsNodesUUID =new HashSet<UUID>();
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for (TaxonNode familyNode: familyNodes){
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familyNode = HibernateProxyHelper.deproxy(familyNode, TaxonNode.class);
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familyNode.removeNullValueFromChildren();
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for (TaxonNode child: familyNode.getChildNodes()){
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child = HibernateProxyHelper.deproxy(child, TaxonNode.class);
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name = HibernateProxyHelper.deproxy(child.getTaxon().getName(), TaxonNameBase.class);
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if (name.isGenus()) {
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childrenUuids.add(child.getUuid());
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if (child.hasChildNodes()){
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parentsNodesUUID.add(child.getUuid());
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}
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}
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}
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//refreshTransaction();
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if (!parentsNodesUUID.isEmpty()){
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findChildren(state, childrenUuids, parentsNodesUUID);
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}
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}
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}
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private String createSynonymNameString(BotanicalName synonymName) {
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String synonymString = null;
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synonymString = synonymName.generateFullTitle();
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if (synonymName.getNameCache() != null){
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synonymString = synonymString.replaceAll(synonymName.getNameCache(), "<i>"+ synonymName.getNameCache() + "</i>");
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} else{
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if (synonymName.getGenusOrUninomial() != null){
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synonymString = synonymString.replaceAll(synonymName.getGenusOrUninomial(), "<i>"+ synonymName.getGenusOrUninomial() + "</i>");
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}
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if (synonymName.getInfraGenericEpithet() != null){
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synonymString = synonymString.replaceAll(synonymName.getInfraGenericEpithet(), "<i>"+ synonymName.getInfraGenericEpithet() + "</i>");
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}
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if (synonymName.getSpecificEpithet() != null){
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synonymString = synonymString.replaceAll(synonymName.getSpecificEpithet(), "<i>"+ synonymName.getSpecificEpithet() + "</i>");
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}
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if (synonymName.getInfraSpecificEpithet() != null){
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synonymString = synonymString.replaceAll(synonymName.getInfraSpecificEpithet(), "<i>"+ synonymName.getInfraSpecificEpithet() + "</i>");
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}
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}
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return synonymString;
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}
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private List<TaxonNode> getGenusNodes (UUID classificationUUID){
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Classification classification = getClassificationService().load(classificationUUID);
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TaxonNode rootNode = classification.getRootNode();
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rootNode = getTaxonNodeService().load(rootNode.getUuid());
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Set<UUID> childrenUuids = new HashSet<UUID>();
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for (TaxonNode child: rootNode.getChildNodes()){
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child = HibernateProxyHelper.deproxy(child, TaxonNode.class);
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childrenUuids.add(child.getUuid());
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}
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List<TaxonNode> familyNodes = getTaxonNodeService().find(childrenUuids);
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childrenUuids.clear();
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List<TaxonNode> genusNodes = new ArrayList<TaxonNode>();
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for (TaxonNode familyNode: familyNodes){
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for (TaxonNode child: familyNode.getChildNodes()){
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child = HibernateProxyHelper.deproxy(child, TaxonNode.class);
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childrenUuids.add(child.getUuid());
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}
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genusNodes = getTaxonNodeService().find(childrenUuids);
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}
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return genusNodes;
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}
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private TaxonNode getHigherNode(TaxonNode node, Rank rank){
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node = HibernateProxyHelper.deproxy(node, TaxonNode.class);
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TaxonNameBase name = HibernateProxyHelper.deproxy( node.getTaxon().getName(), TaxonNameBase.class);
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Rank nodeRank = node.getTaxon().getName().getRank();
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if (nodeRank.equals(rank)){
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return node;
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}else if (nodeRank.isHigher(rank)){
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return null;
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} else {
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return node.getAncestorOfRank(rank);
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}
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}
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private void extractDescriptions(HashMap<String, String> nameRecord, Taxon taxon, Feature feature, String columnName, CsvNameExportState state){
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StringBuffer descriptionsString = new StringBuffer();
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TextData textElement;
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Set<Distribution> distributions = new HashSet<Distribution>();
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for (DescriptionBase<?> descriptionBase: taxon.getDescriptions()){
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Set<DescriptionElementBase> elements = descriptionBase.getElements();
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for (DescriptionElementBase element: elements){
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if (element.getFeature().equals(feature)){
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if (element instanceof TextData){
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textElement = HibernateProxyHelper.deproxy(element, TextData.class);
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descriptionsString.append(textElement.getText(Language.ENGLISH()));
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}else if (element instanceof Distribution ){
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Distribution distribution = HibernateProxyHelper.deproxy(element, Distribution.class);
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distributions.add(distribution);
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}
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}
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}
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}
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// Collections.sort(distributions, new DistributionNodeByAreaLabelComparator());
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312
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if (state.getConfig().isCondensedDistribution()){
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List<Language> langs = new ArrayList<Language>();
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langs.add(Language.ENGLISH());
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316
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// CondensedDistribution conDis = geoService.getCondensedDistribution(distributions, true, null,null,CondensedDistributionRecipe.FloraCuba, langs );
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//
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319
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// nameRecord.put(columnName, conDis.toString());
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320
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321
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} else{
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for (Distribution distribution:distributions){
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323
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324
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if (descriptionsString.length()> 0 ){
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descriptionsString.append(", ");
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326
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}
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descriptionsString.append(distribution.getArea().getIdInVocabulary());
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329
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}
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331
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}
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332
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nameRecord.put(columnName, descriptionsString.toString());
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333
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334
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}
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335
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336
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private Feature getNotesFeature(CsvNameExportState state){
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337
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if (state.getNotesFeature() != null){
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338
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return state.getNotesFeature();
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339
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} else{
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340
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Pager<DefinedTermBase> notesFeature = getTermService().findByTitle(Feature.class, "Notes" ,MatchMode.EXACT, null, null, null, null, null);
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if (notesFeature.getRecords().size() == 0){
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return null;
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}else{
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344
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DefinedTermBase feature= notesFeature.getRecords().iterator().next();
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345
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if (feature instanceof Feature){
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346
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state.setNotesFeature((Feature)feature);
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347
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return (Feature) feature;
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348
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} else{
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349
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return null;
|
350
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}
|
351
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}
|
352
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}
|
353
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|
354
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}
|
355
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|
356
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private HashMap<String, String> createNewRecord(TaxonNode childNode, CsvNameExportState state){
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357
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HashMap<String, String> nameRecord = new HashMap<String,String>();
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358
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nameRecord.put("classification", childNode.getClassification().getTitleCache());
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359
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TaxonNode familyNode = getHigherNode(childNode, Rank.FAMILY());
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360
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Taxon taxon;
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361
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BotanicalName name;
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362
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if (familyNode != null){
|
363
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familyNode = HibernateProxyHelper.deproxy(familyNode, TaxonNode.class);
|
364
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familyNode.getTaxon().setProtectedTitleCache(true);
|
365
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366
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nameRecord.put("familyTaxon", familyNode.getTaxon().getTitleCache());
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367
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|
368
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|
369
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|
370
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|
371
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taxon = (Taxon)getTaxonService().load(familyNode.getTaxon().getUuid());
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372
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taxon = HibernateProxyHelper.deproxy(taxon, Taxon.class);
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373
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//if publish flag is set
|
374
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|
375
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// if (taxon.isPublish()){
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376
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name = HibernateProxyHelper.deproxy(taxon.getName(), BotanicalName.class);
|
377
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nameRecord.put("familyName", name.getNameCache());
|
378
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extractDescriptions(nameRecord, taxon, Feature.INTRODUCTION(), "descriptionsFam", state);
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379
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} else{
|
380
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nameRecord.put("familyTaxon", null);
|
381
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nameRecord.put("familyName", null);
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382
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nameRecord.put("descriptionsFam", null);
|
383
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}
|
384
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TaxonNode genusNode = getHigherNode(childNode, Rank.GENUS());
|
385
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if (genusNode!= null){
|
386
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genusNode = HibernateProxyHelper.deproxy(genusNode, TaxonNode.class);
|
387
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genusNode.getTaxon().setProtectedTitleCache(true);
|
388
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nameRecord.put("genusTaxon", genusNode.getTaxon().getTitleCache());
|
389
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|
390
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taxon = (Taxon)getTaxonService().load(genusNode.getTaxon().getUuid());
|
391
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taxon = HibernateProxyHelper.deproxy(taxon, Taxon.class);
|
392
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//if publish flag is set
|
393
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|
394
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// if (taxon.isPublish()){
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395
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name = HibernateProxyHelper.deproxy(taxon.getName(), BotanicalName.class);
|
396
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if (name.getNameCache() != null){
|
397
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nameRecord.put("genusName", name.getNameCache());
|
398
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}else{
|
399
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nameRecord.put("genusName", name.getGenusOrUninomial());
|
400
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}
|
401
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extractDescriptions(nameRecord, taxon, getNotesFeature(state), "descriptionsGen", state);
|
402
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}
|
403
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taxon = (Taxon) getTaxonService().load(childNode.getTaxon().getUuid());
|
404
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taxon = HibernateProxyHelper.deproxy(taxon, Taxon.class);
|
405
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// if (taxon.isPublish()){
|
406
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nameRecord.put("childTaxon", taxon.getTitleCache());
|
407
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if (taxon.getSec()!= null){
|
408
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nameRecord.put("secRef", taxon.getSec().getTitleCache());
|
409
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}else{
|
410
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nameRecord.put("secRef", null);
|
411
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}
|
412
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|
413
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name = HibernateProxyHelper.deproxy(getNameService().load(taxon.getName().getUuid()), BotanicalName.class);
|
414
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nameRecord.put("childName",name.getTitleCache());
|
415
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nameRecord.put("nameId", String.valueOf(name.getId()));
|
416
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nameRecord.put("nameCache", name.getNameCache());
|
417
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nameRecord.put("titleName", name.getTitleCache());
|
418
|
if (name.getNomenclaturalReference() != null){
|
419
|
nameRecord.put("NomRefTitleCache", name.getNomenclaturalReference().getTitleCache());
|
420
|
} else{
|
421
|
nameRecord.put("NomRefTitleCache",null);
|
422
|
}
|
423
|
nameRecord.put("fullName", name.getNameCache());
|
424
|
nameRecord.put("fullTitleCache", name.getFullTitleCache());
|
425
|
Set<TypeDesignationBase> typeDesSet = name.getTypeDesignations();
|
426
|
Iterator<TypeDesignationBase> it = typeDesSet.iterator();
|
427
|
String typeNameString = NOT_DESIGNATED;
|
428
|
String statusString = null;
|
429
|
if (it.hasNext()){
|
430
|
NameTypeDesignation typeDes = HibernateProxyHelper.deproxy(it.next(), NameTypeDesignation.class);
|
431
|
|
432
|
|
433
|
BotanicalName typeName = HibernateProxyHelper.deproxy(typeDes.getTypeName(), BotanicalName.class);
|
434
|
if (typeName != null){
|
435
|
|
436
|
typeNameString = "<i>" + typeName.getNameCache() +"</i> " + typeName.getAuthorshipCache();
|
437
|
if (typeDes.getTypeStatus() != null){
|
438
|
NameTypeDesignationStatus status = HibernateProxyHelper.deproxy(typeDes.getTypeStatus(), NameTypeDesignationStatus.class);
|
439
|
statusString = status.getTitleCache();
|
440
|
}
|
441
|
}
|
442
|
|
443
|
}
|
444
|
nameRecord.put("typeName", typeNameString);
|
445
|
StringBuffer homotypicalSynonyms = new StringBuffer();
|
446
|
TreeMap<HomotypicalGroup,List<Synonym>> heterotypicSynonymsList = new TreeMap<HomotypicalGroup,List<Synonym>>(new HomotypicalGroupComparator());
|
447
|
List<Synonym> homotypicSynonymsList = new ArrayList<Synonym>();
|
448
|
StringBuffer heterotypicalSynonyms = new StringBuffer();
|
449
|
List<Synonym> homotypicSynonyms;
|
450
|
|
451
|
HomotypicalGroup group;
|
452
|
BotanicalName synonymName;
|
453
|
String doubtfulTitleCache;
|
454
|
for (SynonymRelationship synRel: taxon.getSynonymRelations()){
|
455
|
synonymName = HibernateProxyHelper.deproxy(synRel.getSynonym().getName(), BotanicalName.class);
|
456
|
if (synRel.getType().equals(SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF())){
|
457
|
group = HibernateProxyHelper.deproxy(synonymName.getHomotypicalGroup(), HomotypicalGroup.class);
|
458
|
synonymName.generateFullTitle();
|
459
|
if (synRel.getSynonym().isDoubtful()){
|
460
|
doubtfulTitleCache = "?" + synonymName.getFullTitleCache();
|
461
|
synonymName.setFullTitleCache(doubtfulTitleCache, true);
|
462
|
}
|
463
|
if (heterotypicSynonymsList.containsKey(group)){
|
464
|
heterotypicSynonymsList.get(group).add(synRel.getSynonym());
|
465
|
}else{
|
466
|
homotypicSynonyms = new ArrayList<Synonym>();
|
467
|
homotypicSynonyms.add(synRel.getSynonym());
|
468
|
heterotypicSynonymsList.put(group, homotypicSynonyms);
|
469
|
homotypicSynonyms= null;
|
470
|
}
|
471
|
} else{
|
472
|
synonymName.generateFullTitle();
|
473
|
homotypicSynonymsList.add(synRel.getSynonym());
|
474
|
}
|
475
|
}
|
476
|
|
477
|
|
478
|
|
479
|
String synonymString;
|
480
|
boolean first = true;
|
481
|
|
482
|
for (List<Synonym> list: heterotypicSynonymsList.values()){
|
483
|
Collections.sort(list, new HomotypicGroupTaxonComparator(null));
|
484
|
first = true;
|
485
|
for (TaxonBase<?> synonym : list){
|
486
|
if (first){
|
487
|
heterotypicalSynonyms.append(" <heterotypic> ");
|
488
|
}else{
|
489
|
heterotypicalSynonyms.append(" <homonym> ");
|
490
|
}
|
491
|
first = false;
|
492
|
synonymName = HibernateProxyHelper.deproxy(synonym.getName(), BotanicalName.class);
|
493
|
synonymString = createSynonymNameString(synonymName);
|
494
|
heterotypicalSynonyms.append(synonymString);
|
495
|
}
|
496
|
}
|
497
|
|
498
|
first = true;
|
499
|
Collections.sort(homotypicSynonymsList, new TaxonComparator());
|
500
|
for (TaxonBase<?> synonym : homotypicSynonymsList){
|
501
|
if (!first){
|
502
|
homotypicalSynonyms.append(" <homonym> ");
|
503
|
}
|
504
|
first = false;
|
505
|
synonymName = HibernateProxyHelper.deproxy(synonym.getName(), BotanicalName.class);
|
506
|
synonymString = createSynonymNameString(synonymName);
|
507
|
|
508
|
homotypicalSynonyms.append(synonymString);
|
509
|
|
510
|
}
|
511
|
|
512
|
nameRecord.put("synonyms_homotypic", homotypicalSynonyms.toString());
|
513
|
nameRecord.put("synonyms_heterotypic", heterotypicalSynonyms.toString());
|
514
|
nameRecord.put("status", statusString);
|
515
|
|
516
|
Set<NameRelationship> nameRelations = name.getNameRelations();
|
517
|
|
518
|
String relatedName = null;
|
519
|
String nameRelType = null;
|
520
|
if (nameRelations.size()>0){
|
521
|
NameRelationship nameRel = nameRelations.iterator().next();
|
522
|
BotanicalName fromName = HibernateProxyHelper.deproxy(nameRel.getFromName(), BotanicalName.class);
|
523
|
if (fromName.equals(taxon.getName())){
|
524
|
relatedName = nameRel.getToName().getTitleCache();
|
525
|
|
526
|
}else{
|
527
|
relatedName = nameRel.getFromName().getTitleCache();
|
528
|
}
|
529
|
nameRel = HibernateProxyHelper.deproxy(nameRel, NameRelationship.class);
|
530
|
nameRelType = nameRel.getType().getTitleCache();
|
531
|
}
|
532
|
|
533
|
|
534
|
nameRecord.put("relatedName", relatedName);
|
535
|
nameRecord.put("nameRelType", nameRelType);
|
536
|
|
537
|
extractDescriptions(nameRecord, taxon, Feature.DISTRIBUTION(), "description", state);
|
538
|
return nameRecord;
|
539
|
}
|
540
|
|
541
|
|
542
|
}
|
543
|
|