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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.logging.log4j.LogManager;import org.apache.logging.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.dto.CondensedDistribution;
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import eu.etaxonomy.cdm.api.service.pager.Pager;
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import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;
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import eu.etaxonomy.cdm.compare.name.HomotypicalGroupComparator;
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import eu.etaxonomy.cdm.compare.taxon.HomotypicGroupTaxonComparator;
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import eu.etaxonomy.cdm.ext.geo.CondensedDistributionConfiguration;
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import eu.etaxonomy.cdm.ext.geo.IEditGeoService;
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import eu.etaxonomy.cdm.filter.TaxonNodeFilter;
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import eu.etaxonomy.cdm.io.common.TaxonNodeOutStreamPartitioner;
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import eu.etaxonomy.cdm.io.common.XmlExportState;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.description.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.location.NamedArea;
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import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
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import eu.etaxonomy.cdm.model.name.IBotanicalName;
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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.NameRelationshipType;
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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.NomenclaturalStatus;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.TypeDesignationBase;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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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.persistence.query.MatchMode;
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/**
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* @author k.luther
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* @since 2015-Apr
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*/
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@Component
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public class CsvNameExport extends CsvNameExportBase {
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private static final long serialVersionUID = 7289805663701807425L;
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private static final Logger logger = LogManager.getLogger(CsvNameExport.class);
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@Autowired
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private IEditGeoService geoService;
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private HashMap<UUID, HashMap<String,String>> familyMap = new HashMap<>();
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private HashMap<UUID, HashMap<String,String>> genusMap = new HashMap<>();
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private List<HashMap<String,String>> nameRecords = new ArrayList<>();
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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.getRank() == null){
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config.setRank(Rank.GENUS());
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}
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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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CsvRecord 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 CsvRecord(record, isFirst);
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nameRecord.print(writer, config);
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}
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if (exportStream != null){
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state.getResult().addExportData(getByteArray());
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//this.exportData.addExportData(exportStream.toByteArray());
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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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public long countSteps(CsvNameExportState state) {
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TaxonNodeFilter filter = state.getConfig().getTaxonNodeFilter();
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return getTaxonNodeService().count(filter);
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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;
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// if (classification != null){
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// rootNode = classification.getRootNode();
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// }else{
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// List<Classification> classifications = getClassificationService().list(Classification.class, 10, 0, null, null);
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// if (classifications.isEmpty()){
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// return null;
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// }
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// classification = classifications.get(0);
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// rootNode = classification.getRootNode();
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// }
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// rootNode = getTaxonNodeService().load(rootNode.getUuid(), propertyPaths);
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// Set<UUID> childrenUuids = new HashSet<>();
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//
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//
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// rootNode = CdmBase.deproxy(rootNode);
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// rootNode.removeNullValueFromChildren();
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// for (TaxonNode child: rootNode.getChildNodes()){
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// child = CdmBase.deproxy(child);
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// childrenUuids.add(child.getUuid());
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// }
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// Set<UUID> parentsNodesUUID = new HashSet<>(childrenUuids);
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// childrenUuids.clear();
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// List<TaxonNode> childrenNodes = new ArrayList<>();
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//
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// findChildren(state, childrenUuids, parentsNodesUUID);
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IProgressMonitor monitor = state.getConfig().getProgressMonitor();
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@SuppressWarnings("unchecked")
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TaxonNodeOutStreamPartitioner<XmlExportState> partitioner
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= TaxonNodeOutStreamPartitioner.NewInstance(
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this, state, state.getConfig().getTaxonNodeFilter(),
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100, monitor, null);
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partitioner.setReadOnly(false);
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monitor.subTask("Start partitioning");
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// List<HashMap<String,String>> nameRecords = new ArrayList<>();
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TaxonNode node = partitioner.next();
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while (node != null){
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HashMap<String, String> nameRecord = createNewRecord(node, state);
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if (nameRecord != null){
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nameRecords.add(nameRecord);
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}
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node = partitioner.next();
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}
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// List<HashMap<String,String>> nameRecords = new ArrayList<>();
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//
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// childrenNodes = getTaxonNodeService().find(childrenUuids);
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// for(TaxonNode genusNode : childrenNodes) {
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// nameRecords.add(createNewRecord(genusNode, state));
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// refreshTransaction();
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229
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// }
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230
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231
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return nameRecords;
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232
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}
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234
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235
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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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239
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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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// TaxonName name;
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// List<TaxonNode> familyNodes = getTaxonNodeService().find(parentsNodesUUID);
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// parentsNodesUUID =new HashSet<>();
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245
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// for (TaxonNode familyNode: familyNodes){
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246
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// familyNode = CdmBase.deproxy(familyNode);
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247
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// familyNode.removeNullValueFromChildren();
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248
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// for (TaxonNode child: familyNode.getChildNodes()){
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249
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// child = CdmBase.deproxy(child);
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250
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// Taxon taxon = CdmBase.deproxy(child.getTaxon());
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251
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// if (taxon != null){
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252
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// name = CdmBase.deproxy(taxon.getName());
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253
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// if (child.getTaxon().getName().getRank().isLower(state.getConfig().getRank()) ) {
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254
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// childrenUuids.add(child.getUuid());
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255
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// if (child.hasChildNodes()){
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256
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// parentsNodesUUID.add(child.getUuid());
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257
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// }
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258
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// }else{
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259
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// parentsNodesUUID.add(child.getUuid());
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260
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// }
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261
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// }
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262
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// }
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263
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// //refreshTransaction();
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264
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// if (!parentsNodesUUID.isEmpty()){
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265
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// findChildren(state, childrenUuids, parentsNodesUUID);
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266
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// }
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267
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// }
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268
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//
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269
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// }
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270
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271
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272
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273
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274
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private String createSynonymNameString(IBotanicalName synonymName, boolean isInvalid) {
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275
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String synonymString = null;
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276
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277
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synonymString= createTaggedNameString(synonymName, isInvalid);
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278
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Set<NameRelationship> nameRelations = synonymName.getNameRelations();
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279
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280
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INonViralName relatedName = null;
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281
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String nameRelType = null;
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282
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boolean first = true;
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283
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boolean isInvalidRel = false;
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284
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for (NameRelationship nameRel: nameRelations){
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285
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// NameRelationship nameRel = nameRelations.iterator().next();
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286
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if (!nameRel.getType().equals(NameRelationshipType.BASIONYM())){
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287
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IBotanicalName fromName = CdmBase.deproxy(nameRel.getFromName());
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288
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289
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nameRel = CdmBase.deproxy(nameRel);
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290
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nameRelType = nameRel.getType().getTitleCache();
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291
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String relatedNameString = "";
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292
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if (fromName.equals(synonymName)){
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293
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relatedName = nameRel.getToName();
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294
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}else{
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295
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relatedName = nameRel.getFromName();
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296
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}
|
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297
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|
298
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isInvalidRel = getStatus(relatedName);
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299
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relatedNameString = createTaggedNameString(relatedName, isInvalidRel&&isInvalid);
|
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300
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|
|
301
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if (nameRel.getType().equals(NameRelationshipType.LATER_HOMONYM())){
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302
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if (synonymName.equals(nameRel.getFromName())){
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303
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if (first){
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304
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synonymString = synonymString + " [non " + relatedNameString ;
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305
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first = false;
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306
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} else{
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307
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synonymString = synonymString + " nec " + relatedNameString ;
|
|
308
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}
|
|
309
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}
|
|
310
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} else if (nameRel.getType().equals(NameRelationshipType.REPLACED_SYNONYM())){
|
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311
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//synonymString = synonymString + " [non " + relatedNameString + "]";
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312
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} else if (nameRel.getType().equals(NameRelationshipType.BLOCKING_NAME_FOR())){
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313
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if (synonymName.equals(nameRel.getToName())){
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314
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if (first){
|
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315
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synonymString = synonymString + " [non " + relatedNameString ;
|
|
316
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first = false;
|
|
317
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} else{
|
|
318
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synonymString = synonymString + " nec " + relatedNameString ;
|
|
319
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}
|
|
320
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|
|
321
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}
|
|
322
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} else if (nameRel.getType().equals(NameRelationshipType.TREATED_AS_LATER_HOMONYM())){
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323
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if (first){
|
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324
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synonymString = synonymString + " [non " + relatedNameString ;
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|
325
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first = false;
|
|
326
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} else{
|
|
327
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synonymString = synonymString + " nec " + relatedNameString ;
|
|
328
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}
|
|
329
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} else if (nameRel.getType().equals(NameRelationshipType.ALTERNATIVE_NAME())){
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330
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if (first){
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331
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synonymString = synonymString + " [non " + relatedNameString ;
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332
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first = false;
|
|
333
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} else{
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334
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synonymString = synonymString + " nec " + relatedNameString ;
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|
335
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}
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336
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} else if (nameRel.getType().equals(NameRelationshipType.CONSERVED_AGAINST())) {
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337
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|
338
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}else if (nameRel.getType().equals(NameRelationshipType.ORTHOGRAPHIC_VARIANT())){
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339
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|
340
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}
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|
341
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}
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|
342
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}
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|
343
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if (!first){
|
|
344
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synonymString = synonymString + "]";
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|
345
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}
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|
346
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|
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347
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return synonymString;
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|
348
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}
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|
349
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|
|
350
|
/**
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|
351
|
* @param relatedName
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|
352
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* @return
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|
353
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*/
|
|
354
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private boolean getStatus(INonViralName relatedName) {
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355
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boolean result;
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|
356
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if (!relatedName.getStatus().isEmpty()){
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357
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NomenclaturalStatus status = CdmBase.deproxy(relatedName.getStatus().iterator().next());
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358
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if (status.getType().isInvalid()){
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359
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result = true;
|
|
360
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}else{
|
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361
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result = false;
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|
362
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}
|
|
363
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}else{
|
|
364
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result = false;
|
|
365
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}
|
|
366
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return result;
|
|
367
|
}
|
|
368
|
|
|
369
|
private String createTaggedNameString(INonViralName name, boolean isInvalid){
|
|
370
|
String nameString = null;
|
|
371
|
if (name == null){
|
|
372
|
return nameString;
|
|
373
|
}
|
|
374
|
|
|
375
|
nameString = name.generateFullTitle();
|
|
376
|
if (isInvalid){
|
|
377
|
nameString = nameString.replace(name.getTitleCache(), "\""+name.getTitleCache()+"\"");
|
|
378
|
}
|
|
379
|
if (name.getGenusOrUninomial() != null){
|
|
380
|
nameString = nameString.replaceAll(name.getGenusOrUninomial(), "<i>"+ name.getGenusOrUninomial() + "</i>");
|
|
381
|
}
|
|
382
|
if (name.getInfraGenericEpithet() != null){
|
|
383
|
nameString = nameString.replaceAll(name.getInfraGenericEpithet(), "<i>"+ name.getInfraGenericEpithet() + "</i>");
|
|
384
|
}
|
|
385
|
if (name.getSpecificEpithet() != null){
|
|
386
|
nameString = nameString.replaceAll(name.getSpecificEpithet(), "<i>"+ name.getSpecificEpithet() + "</i>");
|
|
387
|
}
|
|
388
|
if (name.getInfraSpecificEpithet() != null && !name.isAutonym()){
|
|
389
|
nameString = nameString.replaceAll(name.getInfraSpecificEpithet(), "<i>"+ name.getInfraSpecificEpithet() + "</i>");
|
|
390
|
}
|
|
391
|
|
|
392
|
return nameString;
|
|
393
|
}
|
|
394
|
|
|
395
|
|
|
396
|
|
|
397
|
// private List<TaxonNode> getGenusNodes (UUID classificationUUID){
|
|
398
|
// Classification classification = getClassificationService().load(classificationUUID);
|
|
399
|
// TaxonNode rootNode = classification.getRootNode();
|
|
400
|
// rootNode = getTaxonNodeService().load(rootNode.getUuid());
|
|
401
|
// Set<UUID> childrenUuids = new HashSet<>();
|
|
402
|
//
|
|
403
|
// for (TaxonNode child: rootNode.getChildNodes()){
|
|
404
|
// child = CdmBase.deproxy(child);
|
|
405
|
// childrenUuids.add(child.getUuid());
|
|
406
|
// }
|
|
407
|
//
|
|
408
|
// List<TaxonNode> familyNodes = getTaxonNodeService().find(childrenUuids);
|
|
409
|
// childrenUuids.clear();
|
|
410
|
// List<TaxonNode> genusNodes = new ArrayList<>();
|
|
411
|
// for (TaxonNode familyNode: familyNodes){
|
|
412
|
// for (TaxonNode child: familyNode.getChildNodes()){
|
|
413
|
// child = CdmBase.deproxy(child);
|
|
414
|
// childrenUuids.add(child.getUuid());
|
|
415
|
// }
|
|
416
|
//
|
|
417
|
// genusNodes = getTaxonNodeService().find(childrenUuids);
|
|
418
|
// }
|
|
419
|
// return genusNodes;
|
|
420
|
// }
|
|
421
|
|
|
422
|
private TaxonNode getHigherNode(TaxonNode node, Rank rank){
|
|
423
|
|
|
424
|
Rank nodeRank = node.getTaxon().getName().getRank();
|
|
425
|
if (nodeRank.isKindOf(rank)){
|
|
426
|
return null;
|
|
427
|
|
|
428
|
}else if (nodeRank.isHigher(rank)){
|
|
429
|
return null;
|
|
430
|
} else {
|
|
431
|
return node.getAncestorOfRank(rank);
|
|
432
|
}
|
|
433
|
}
|
|
434
|
|
|
435
|
private void extractDescriptions(HashMap<String, String> nameRecord, Taxon taxon, Feature feature,
|
|
436
|
String columnName, CsvNameExportState state){
|
|
437
|
|
|
438
|
StringBuffer descriptionsString = new StringBuffer();
|
|
439
|
TextData textElement;
|
|
440
|
Set<Distribution> distributions = new HashSet<>();
|
|
441
|
if (taxon.getDescriptions().isEmpty()){
|
|
442
|
nameRecord.put(columnName, null);
|
|
443
|
return;
|
|
444
|
}
|
|
445
|
for (DescriptionBase<?> descriptionBase: taxon.getDescriptions()){
|
|
446
|
if (!descriptionBase.isImageGallery()){
|
|
447
|
Set<DescriptionElementBase> elements = descriptionBase.getElements();
|
|
448
|
for (DescriptionElementBase element: elements){
|
|
449
|
if (element.getFeature().equals(feature)){
|
|
450
|
if (element instanceof TextData){
|
|
451
|
textElement = CdmBase.deproxy(element, TextData.class);
|
|
452
|
descriptionsString.append(textElement.getText(Language.ENGLISH()));
|
|
453
|
}else if (element instanceof Distribution ){
|
|
454
|
Distribution distribution = CdmBase.deproxy(element, Distribution.class);
|
|
455
|
distributions.add(distribution);
|
|
456
|
}
|
|
457
|
}
|
|
458
|
}
|
|
459
|
}
|
|
460
|
}
|
|
461
|
if (state.getConfig().isCondensedDistribution()){
|
|
462
|
List<Language> langs = new ArrayList<>();
|
|
463
|
langs.add(Language.ENGLISH());
|
|
464
|
|
|
465
|
//TODO add condensed distribution configuration to export configuration
|
|
466
|
CondensedDistribution conDis = geoService.getCondensedDistribution(
|
|
467
|
distributions, true, null, CondensedDistributionConfiguration.NewCubaInstance(), langs );
|
|
468
|
|
|
469
|
nameRecord.put(columnName, conDis.toString());
|
|
470
|
|
|
471
|
} else{
|
|
472
|
NamedArea area ;
|
|
473
|
for (Distribution distribution:distributions){
|
|
474
|
|
|
475
|
if (descriptionsString.length()> 0 ){
|
|
476
|
descriptionsString.append(", ");
|
|
477
|
}
|
|
478
|
area = CdmBase.deproxy(distribution.getArea());
|
|
479
|
if (area.getIdInVocabulary() != null){
|
|
480
|
descriptionsString.append(area.getIdInVocabulary());
|
|
481
|
}else if (area.getSymbol() != null){
|
|
482
|
descriptionsString.append(area.getSymbol());
|
|
483
|
}else{
|
|
484
|
descriptionsString.append(area.getLabel());
|
|
485
|
}
|
|
486
|
|
|
487
|
}
|
|
488
|
nameRecord.put(columnName, descriptionsString.toString());
|
|
489
|
}
|
|
490
|
|
|
491
|
}
|
|
492
|
|
|
493
|
private Feature getNotesFeature(CsvNameExportState state){
|
|
494
|
if (state.getNotesFeature() != null){
|
|
495
|
return state.getNotesFeature();
|
|
496
|
} else{
|
|
497
|
Pager<Feature> notesFeature = getTermService().findByTitleWithRestrictions(Feature.class, "Notes" ,MatchMode.EXACT, null, null, null, null, null);
|
|
498
|
if (notesFeature.getRecords().size() == 0){
|
|
499
|
return null;
|
|
500
|
}else{
|
|
501
|
Feature feature= notesFeature.getRecords().iterator().next();
|
|
502
|
state.setNotesFeature(feature);
|
|
503
|
return feature;
|
|
504
|
}
|
|
505
|
}
|
|
506
|
|
|
507
|
}
|
|
508
|
|
|
509
|
private HashMap<String, String> createNewRecord(TaxonNode childNode, CsvNameExportState state){
|
|
510
|
HashMap<String, String> nameRecord = new HashMap<>();
|
|
511
|
nameRecord.put("classification", childNode.getClassification().getTitleCache());
|
|
512
|
if (!childNode.getTaxon().getName().getRank().isLower(Rank.GENUS())){
|
|
513
|
return null;
|
|
514
|
}
|
|
515
|
TaxonNode familyNode = getHigherNode(childNode, Rank.FAMILY());
|
|
516
|
Taxon taxon;
|
|
517
|
String nameString;
|
|
518
|
IBotanicalName name;
|
|
519
|
if (familyNode == null){
|
|
520
|
nameRecord.put("familyTaxon", null);
|
|
521
|
nameRecord.put("familyName", null);
|
|
522
|
nameRecord.put("descriptionsFam", null);
|
|
523
|
}else{
|
|
524
|
familyNode = CdmBase.deproxy(familyNode);
|
|
525
|
familyNode.getTaxon().setProtectedTitleCache(true);
|
|
526
|
nameRecord.put("familyTaxon", familyNode.getTaxon().getTitleCache());
|
|
527
|
if (familyMap.get(familyNode.getTaxon().getUuid()) != null){
|
|
528
|
nameRecord.putAll(familyMap.get(familyNode.getTaxon().getUuid()));
|
|
529
|
}else{
|
|
530
|
taxon = (Taxon)getTaxonService().load(familyNode.getTaxon().getUuid());
|
|
531
|
taxon = CdmBase.deproxy(taxon);
|
|
532
|
name = CdmBase.deproxy(taxon.getName());
|
|
533
|
nameRecord.put("familyName", name.getNameCache());
|
|
534
|
extractDescriptions(nameRecord, taxon, Feature.INTRODUCTION(), "descriptionsFam", state);
|
|
535
|
familyMap.put(familyNode.getTaxon().getUuid(), nameRecord);
|
|
536
|
}
|
|
537
|
|
|
538
|
}
|
|
539
|
TaxonNode genusNode = getHigherNode(childNode, Rank.GENUS());
|
|
540
|
if (genusNode!= null){
|
|
541
|
genusNode = CdmBase.deproxy(genusNode);
|
|
542
|
genusNode.getTaxon().setProtectedTitleCache(true);
|
|
543
|
nameRecord.put("genusTaxon", genusNode.getTaxon().getTitleCache());
|
|
544
|
if (genusMap.get(genusNode.getTaxon().getUuid()) != null){
|
|
545
|
nameRecord.putAll(genusMap.get(genusNode.getTaxon().getUuid()));
|
|
546
|
}else{
|
|
547
|
taxon = (Taxon)getTaxonService().load(genusNode.getTaxon().getUuid());
|
|
548
|
taxon = CdmBase.deproxy(taxon);
|
|
549
|
name = CdmBase.deproxy(taxon.getName());
|
|
550
|
if (name.getNameCache() != null){
|
|
551
|
nameRecord.put("genusName", name.getNameCache());
|
|
552
|
}else{
|
|
553
|
nameRecord.put("genusName", name.getGenusOrUninomial());
|
|
554
|
}
|
|
555
|
extractDescriptions(nameRecord, taxon,getNotesFeature(state), "descriptionsGen", state);
|
|
556
|
genusMap.put(genusNode.getTaxon().getUuid(), nameRecord);
|
|
557
|
}
|
|
558
|
|
|
559
|
|
|
560
|
}else{
|
|
561
|
nameRecord.put("genusTaxon", null);
|
|
562
|
nameRecord.put("genusName", null);
|
|
563
|
nameRecord.put("descriptionsGen", null);
|
|
564
|
}
|
|
565
|
|
|
566
|
// taxon = (Taxon) getTaxonService().load(childNode.getTaxon().getUuid());
|
|
567
|
taxon = CdmBase.deproxy(childNode.getTaxon());
|
|
568
|
// if (taxon.isPublish()){
|
|
569
|
|
|
570
|
INonViralName nonViralName = taxon.getName();
|
|
571
|
|
|
572
|
nameString = createTaggedNameString(nonViralName, false);
|
|
573
|
nameRecord.put("childTaxon", taxon.getTitleCache());
|
|
574
|
if (taxon.getSec()!= null){
|
|
575
|
nameRecord.put("secRef", taxon.getSec().getTitleCache());
|
|
576
|
}else{
|
|
577
|
nameRecord.put("secRef", null);
|
|
578
|
}
|
|
579
|
|
|
580
|
getTaxonRelations(nameRecord, taxon);
|
|
581
|
|
|
582
|
name = CdmBase.deproxy(taxon.getName());
|
|
583
|
nameRecord.put("childName",nameString);
|
|
584
|
nameRecord.put("nameId", String.valueOf(name.getId()));
|
|
585
|
nameRecord.put("nameCache", name.getNameCache());
|
|
586
|
nameRecord.put("titleName", name.getTitleCache());
|
|
587
|
if (name.getNomenclaturalReference() != null){
|
|
588
|
nameRecord.put("NomRefTitleCache", name.getNomenclaturalReference().getTitleCache());
|
|
589
|
} else{
|
|
590
|
nameRecord.put("NomRefTitleCache",null);
|
|
591
|
}
|
|
592
|
nameRecord.put("fullName", name.getNameCache());
|
|
593
|
nameRecord.put("fullTitleCache", name.getFullTitleCache());
|
|
594
|
Set<TypeDesignationBase> typeDesSet = name.getTypeDesignations();
|
|
595
|
Iterator<TypeDesignationBase> it = typeDesSet.iterator();
|
|
596
|
String typeNameString = NOT_DESIGNATED;
|
|
597
|
String statusString = null;
|
|
598
|
if (it.hasNext()){
|
|
599
|
|
|
600
|
TypeDesignationBase<?> typeDes = CdmBase.deproxy(it.next());
|
|
601
|
|
|
602
|
if (typeDes instanceof NameTypeDesignation){
|
|
603
|
NameTypeDesignation nameTypeDes = CdmBase.deproxy(typeDes, NameTypeDesignation.class);
|
|
604
|
|
|
605
|
IBotanicalName typeName = CdmBase.deproxy(nameTypeDes.getTypeName());
|
|
606
|
if (typeName != null){
|
|
607
|
|
|
608
|
typeNameString = "<i>" + typeName.getNameCache() +"</i> " + typeName.getAuthorshipCache();
|
|
609
|
if (nameTypeDes.getTypeStatus() != null){
|
|
610
|
NameTypeDesignationStatus status = CdmBase.deproxy(nameTypeDes.getTypeStatus());
|
|
611
|
statusString = status.getTitleCache();
|
|
612
|
}
|
|
613
|
}
|
|
614
|
}
|
|
615
|
}
|
|
616
|
nameRecord.put("typeName", typeNameString);
|
|
617
|
StringBuffer homotypicalSynonyms = new StringBuffer();
|
|
618
|
TreeMap<HomotypicalGroup,List<Synonym>> heterotypicSynonymsList = new TreeMap<>(new HomotypicalGroupComparator());
|
|
619
|
|
|
620
|
List<Synonym> homotypicSynonymsList = new ArrayList<>();
|
|
621
|
StringBuffer heterotypicalSynonyms = new StringBuffer();
|
|
622
|
List<Synonym> homotypicSynonyms;
|
|
623
|
|
|
624
|
HomotypicalGroup group;
|
|
625
|
IBotanicalName synonymName;
|
|
626
|
String doubtfulTitleCache;
|
|
627
|
for (Synonym synonym: taxon.getSynonyms()){
|
|
628
|
synonymName = CdmBase.deproxy(synonym.getName());
|
|
629
|
group = CdmBase.deproxy(synonymName.getHomotypicalGroup());
|
|
630
|
synonymName.generateFullTitle();
|
|
631
|
if (synonym.isDoubtful()){
|
|
632
|
if (!synonymName.getFullTitleCache().startsWith("?")){
|
|
633
|
doubtfulTitleCache = "?" + synonymName.getFullTitleCache();
|
|
634
|
synonymName = synonymName.clone();
|
|
635
|
synonymName.setFullTitleCache(doubtfulTitleCache, true);
|
|
636
|
}
|
|
637
|
}
|
|
638
|
if (!group.equals(name.getHomotypicalGroup())){
|
|
639
|
if (heterotypicSynonymsList.containsKey(group)){
|
|
640
|
heterotypicSynonymsList.get(group).add(synonym);
|
|
641
|
}else{
|
|
642
|
homotypicSynonyms = new ArrayList<>();
|
|
643
|
homotypicSynonyms.add(synonym);
|
|
644
|
heterotypicSynonymsList.put(group, homotypicSynonyms);
|
|
645
|
homotypicSynonyms= null;
|
|
646
|
}
|
|
647
|
} else{
|
|
648
|
synonymName.generateFullTitle();
|
|
649
|
homotypicSynonymsList.add(synonym);
|
|
650
|
}
|
|
651
|
}
|
|
652
|
|
|
653
|
|
|
654
|
|
|
655
|
String synonymString;
|
|
656
|
boolean first = true;
|
|
657
|
|
|
658
|
for (List<Synonym> list: heterotypicSynonymsList.values()){
|
|
659
|
Collections.sort(list, new HomotypicGroupTaxonComparator(null));
|
|
660
|
first = true;
|
|
661
|
for (TaxonBase<?> synonym : list){
|
|
662
|
NomenclaturalStatus status = null;
|
|
663
|
if (!synonym.getName().getStatus().isEmpty()){
|
|
664
|
status = CdmBase.deproxy(synonym.getName().getStatus().iterator().next());
|
|
665
|
if (status.getType().isInvalid()){
|
|
666
|
heterotypicalSynonyms.append(" <invalid> ");
|
|
667
|
synonymName = CdmBase.deproxy(synonym.getName());
|
|
668
|
|
|
669
|
synonymString = createSynonymNameString(synonymName, state.getConfig().isInvalidNamesQuoted()) ;
|
|
670
|
heterotypicalSynonyms.append(synonymString);
|
|
671
|
continue;
|
|
672
|
}
|
|
673
|
}
|
|
674
|
if (first){
|
|
675
|
heterotypicalSynonyms.append(" <heterotypic> ");
|
|
676
|
}else{
|
|
677
|
heterotypicalSynonyms.append(" <homonym> ");
|
|
678
|
}
|
|
679
|
first = false;
|
|
680
|
synonymName = CdmBase.deproxy(synonym.getName());
|
|
681
|
synonymString = createSynonymNameString(synonymName, false);
|
|
682
|
heterotypicalSynonyms.append(synonymString);
|
|
683
|
}
|
|
684
|
}
|
|
685
|
|
|
686
|
first = true;
|
|
687
|
Collections.sort(homotypicSynonymsList, new HomotypicGroupTaxonComparator(null) );
|
|
688
|
NomenclaturalStatus status = null;
|
|
689
|
for (TaxonBase<?> synonym : homotypicSynonymsList){
|
|
690
|
|
|
691
|
if (!synonym.getName().getStatus().isEmpty()){
|
|
692
|
status = CdmBase.deproxy(synonym.getName().getStatus().iterator().next());
|
|
693
|
if (status.getType().isInvalid()){
|
|
694
|
homotypicalSynonyms.append(" <invalid> ");
|
|
695
|
synonymName = CdmBase.deproxy(synonym.getName());
|
|
696
|
synonymString = createSynonymNameString(synonymName, true);
|
|
697
|
homotypicalSynonyms.append(synonymString);
|
|
698
|
continue;
|
|
699
|
}else if (!first){
|
|
700
|
homotypicalSynonyms.append(" <homonym> ");
|
|
701
|
}
|
|
702
|
|
|
703
|
}else if (!first){
|
|
704
|
homotypicalSynonyms.append(" <homonym> ");
|
|
705
|
}
|
|
706
|
first = false;
|
|
707
|
synonymName = CdmBase.deproxy(synonym.getName());
|
|
708
|
|
|
709
|
synonymString = createSynonymNameString(synonymName, false);
|
|
710
|
|
|
711
|
homotypicalSynonyms.append(synonymString);
|
|
712
|
|
|
713
|
}
|
|
714
|
|
|
715
|
nameRecord.put("synonyms_homotypic", homotypicalSynonyms.toString());
|
|
716
|
nameRecord.put("synonyms_heterotypic", heterotypicalSynonyms.toString());
|
|
717
|
nameRecord.put("status", statusString);
|
|
718
|
|
|
719
|
Set<NameRelationship> nameRelations = name.getNameRelations();
|
|
720
|
|
|
721
|
INonViralName relatedName = null;
|
|
722
|
String nameRelType = null;
|
|
723
|
String relNameString = null;
|
|
724
|
if (nameRelations.size()>0){
|
|
725
|
NameRelationship nameRel = nameRelations.iterator().next();
|
|
726
|
IBotanicalName fromName = CdmBase.deproxy(nameRel.getFromName());
|
|
727
|
if (fromName.equals(taxon.getName())){
|
|
728
|
relatedName = nameRel.getToName();
|
|
729
|
|
|
730
|
}else{
|
|
731
|
relatedName = nameRel.getFromName();
|
|
732
|
}
|
|
733
|
nameRel = CdmBase.deproxy(nameRel);
|
|
734
|
nameRelType = nameRel.getType().getTitleCache();
|
|
735
|
relNameString = createTaggedNameString(relatedName, getStatus(relatedName));
|
|
736
|
}
|
|
737
|
|
|
738
|
|
|
739
|
nameRecord.put("relatedName", relNameString);
|
|
740
|
nameRecord.put("nameRelType", nameRelType);
|
|
741
|
|
|
742
|
extractDescriptions(nameRecord, taxon, Feature.DISTRIBUTION(), "descriptions", state);
|
|
743
|
return nameRecord;
|
|
744
|
}
|
|
745
|
|
|
746
|
/**
|
|
747
|
* @param nameRecord
|
|
748
|
* @param taxon
|
|
749
|
*/
|
|
750
|
private void getTaxonRelations(HashMap<String, String> nameRecord, Taxon taxon) {
|
|
751
|
Set<TaxonRelationship> relations = new HashSet<>();
|
|
752
|
relations =taxon.getTaxonRelations();
|
|
753
|
if (relations.isEmpty()){
|
|
754
|
nameRecord.put("missappliedNames", null);
|
|
755
|
}else{
|
|
756
|
Taxon relatedTaxon = null;
|
|
757
|
StringBuffer nameString = new StringBuffer();
|
|
758
|
for (TaxonRelationship rel : relations){
|
|
759
|
if (rel.getType().isAnyMisappliedName()){
|
|
760
|
relatedTaxon = rel.getFromTaxon();
|
|
761
|
Reference secRef = relatedTaxon.getSec();
|
|
762
|
String appendedPhrase = "";
|
|
763
|
if (relatedTaxon.getAppendedPhrase() != null){
|
|
764
|
appendedPhrase = relatedTaxon.getAppendedPhrase();
|
|
765
|
}
|
|
766
|
if (appendedPhrase.equals("sphalm.")){
|
|
767
|
String relNameString = createTaggedNameString(relatedTaxon.getName(), getStatus(relatedTaxon.getName()));
|
|
768
|
|
|
769
|
nameRecord.put("relatedName", relNameString);
|
|
770
|
nameRecord.put("nameRelType", NameRelationshipType.ORTHOGRAPHIC_VARIANT().getTitleCache());
|
|
771
|
return;
|
|
772
|
}
|
|
773
|
if (secRef == null){
|
|
774
|
nameString.append("<misapplied>" +"\u201C" + createTaggedNameString(relatedTaxon.getName(), false) + "\u201D " + appendedPhrase);
|
|
775
|
} else if (secRef.getAuthorship() == null){
|
|
776
|
nameString.append("<misapplied>"+"\u201C" + createTaggedNameString(relatedTaxon.getName(), false) + "\u201D " + appendedPhrase + " sensu " + secRef.getTitleCache());
|
|
777
|
} else {
|
|
778
|
nameString.append("<misapplied>\"" + createTaggedNameString(relatedTaxon.getName(), false) + "\" " + appendedPhrase + " sensu " + secRef.getAuthorship().getFullTitle());
|
|
779
|
}
|
|
780
|
|
|
781
|
}
|
|
782
|
}
|
|
783
|
nameRecord.put("missappliedNames", nameString.toString());
|
|
784
|
}
|
|
785
|
}
|
|
786
|
|
|
787
|
}
|
|
788
|
|