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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.strategy.cache.name;
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import java.util.ArrayList;
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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.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 eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
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import eu.etaxonomy.cdm.model.agent.INomenclaturalAuthor;
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import eu.etaxonomy.cdm.model.agent.Team;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.common.Representation;
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import eu.etaxonomy.cdm.model.name.BotanicalName;
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import eu.etaxonomy.cdm.model.name.HybridRelationship;
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
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import eu.etaxonomy.cdm.model.name.NonViralName;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.reference.INomenclaturalReference;
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import eu.etaxonomy.cdm.strategy.TagEnum;
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import eu.etaxonomy.cdm.strategy.TaggedText;
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import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
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import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImplRegExBase;
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/**
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* This class is a default implementation for the INonViralNameCacheStrategy<T extends NonViralName>
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* interface.<BR>
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* The method implements a cache strategy for botanical names so no method has to be overwritten by
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* a subclass for botanic names.
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* Where differing from this default botanic name strategy other subclasses should overwrite the
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* existing methods, e.g. a CacheStrategy for zoological names should overwrite getAuthorAndExAuthor
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* @author a.mueller
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*/
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/**
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* @author AM
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*
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* @param <T>
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*/
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public class NonViralNameDefaultCacheStrategy<T extends NonViralName> extends NameCacheStrategyBase<T> implements INonViralNameCacheStrategy<T> {
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private static final Logger logger = Logger.getLogger(NonViralNameDefaultCacheStrategy.class);
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final static UUID uuid = UUID.fromString("1cdda0d1-d5bc-480f-bf08-40a510a2f223");
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protected String NameAuthorSeperator = " ";
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protected String BasionymStart = "(";
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protected String BasionymEnd = ")";
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protected String ExAuthorSeperator = " ex ";
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protected CharSequence BasionymAuthorCombinationAuthorSeperator = " ";
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@Override
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public UUID getUuid(){
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return uuid;
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}
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/**
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* Factory method
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* @return NonViralNameDefaultCacheStrategy A new instance of NonViralNameDefaultCacheStrategy
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*/
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public static NonViralNameDefaultCacheStrategy NewInstance(){
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return new NonViralNameDefaultCacheStrategy();
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}
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/**
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* Factory method
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* @return NonViralNameDefaultCacheStrategy A new instance of NonViralNameDefaultCacheStrategy
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*/
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public static <T extends NonViralName<?>> NonViralNameDefaultCacheStrategy<T> NewInstance(Class<T> clazz){
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return new NonViralNameDefaultCacheStrategy<T>();
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}
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/**
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* Constructor
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*/
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protected NonViralNameDefaultCacheStrategy(){
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super();
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}
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/* **************** GETTER / SETTER **************************************/
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/**
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* String that separates the NameCache part from the AuthorCache part
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* @return
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*/
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public String getNameAuthorSeperator() {
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return NameAuthorSeperator;
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}
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public void setNameAuthorSeperator(String nameAuthorSeperator) {
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NameAuthorSeperator = nameAuthorSeperator;
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}
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/**
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* String the basionym author part starts with e.g. '('.
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* This should correspond with the {@link NonViralNameDefaultCacheStrategy#getBasionymEnd() basionymEnd} attribute
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* @return
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*/
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public String getBasionymStart() {
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return BasionymStart;
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}
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public void setBasionymStart(String basionymStart) {
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BasionymStart = basionymStart;
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}
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/**
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* String the basionym author part ends with e.g. ')'.
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* This should correspond with the {@link NonViralNameDefaultCacheStrategy#getBasionymStart() basionymStart} attribute
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* @return
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*/
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public String getBasionymEnd() {
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return BasionymEnd;
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}
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public void setBasionymEnd(String basionymEnd) {
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BasionymEnd = basionymEnd;
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}
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/**
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* String to seperate ex author from author.
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* @return
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*/
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public String getExAuthorSeperator() {
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return ExAuthorSeperator;
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}
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public void setExAuthorSeperator(String exAuthorSeperator) {
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ExAuthorSeperator = exAuthorSeperator;
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}
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/**
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* String that seperates the basionym/original_combination author part from the combination author part
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* @return
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*/
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public CharSequence getBasionymAuthorCombinationAuthorSeperator() {
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return BasionymAuthorCombinationAuthorSeperator;
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}
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public void setBasionymAuthorCombinationAuthorSeperator( CharSequence basionymAuthorCombinationAuthorSeperator) {
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BasionymAuthorCombinationAuthorSeperator = basionymAuthorCombinationAuthorSeperator;
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}
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//** *****************************************************************************************/
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.strategy.cache.name.NameCacheStrategyBase#getTitleCache(eu.etaxonomy.cdm.model.name.TaxonNameBase)
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*/
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@Override
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public String getTitleCache(T nonViralName) {
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List<TaggedText> tags = getTaggedTitle(nonViralName);
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if (tags == null){
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return null;
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}else{
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String result = createString(tags);
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return result;
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}
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.strategy.cache.name.NameCacheStrategyBase#getFullTitleCache(eu.etaxonomy.cdm.model.name.TaxonNameBase)
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*/
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@Override
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public String getFullTitleCache(T nonViralName) {
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List<TaggedText> tags = getTaggedFullTitle(nonViralName);
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if (tags == null){
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return null;
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}else{
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String result = createString(tags);
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return result;
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}
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}
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/**
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* Generates and returns the "name cache" (only scientific name without author teams and year).
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* @see eu.etaxonomy.cdm.strategy.cache.name.INameCacheStrategy#getNameCache(eu.etaxonomy.cdm.model.name.TaxonNameBase)
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*/
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public String getNameCache(T nonViralName) {
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List<TaggedText> tags = getTaggedName(nonViralName);
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if (tags == null){
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return null;
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}else{
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String result = createString(tags);
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return result;
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}
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}
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/**
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* Creates a string from tagged text.
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* @param tags
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* @return
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*/
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protected String createString(List<TaggedText> tags) {
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StringBuffer result = new StringBuffer();
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boolean isSeparator;
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boolean wasSeparator = true; //true for start tag
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for (TaggedText tag: tags){
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isSeparator = tag.getType().equals(TagEnum.separator);
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if (! wasSeparator && ! isSeparator ){
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result.append(" ");
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}
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result.append(tag.getText());
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wasSeparator = isSeparator;
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}
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return result.toString();
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}
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// ******************* Authorship ******************************/
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.strategy.cache.INonViralNameCacheStrategy#getAuthorCache(eu.etaxonomy.cdm.model.name.NonViralName)
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*/
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public String getAuthorshipCache(T nonViralName) {
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if (nonViralName == null){
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return null;
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}
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//cache protected
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if (nonViralName.isProtectedAuthorshipCache() == true) {
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return nonViralName.getAuthorshipCache();
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}
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return getNonCacheAuthorshipCache(nonViralName);
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}
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/**
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* Returns the authorshipcache string for the atomized authorship fields. Does not use the authorshipfield.
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* @throws NullPointerException if nonViralName is null.
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* @param nonViralName
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* @return
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*/
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protected String getNonCacheAuthorshipCache(T nonViralName){
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String result = "";
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INomenclaturalAuthor combinationAuthor = nonViralName.getCombinationAuthorTeam();
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INomenclaturalAuthor exCombinationAuthor = nonViralName.getExCombinationAuthorTeam();
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INomenclaturalAuthor basionymAuthor = nonViralName.getBasionymAuthorTeam();
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INomenclaturalAuthor exBasionymAuthor = nonViralName.getExBasionymAuthorTeam();
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String basionymPart = "";
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String authorPart = "";
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//basionym
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if (basionymAuthor != null || exBasionymAuthor != null){
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basionymPart = BasionymStart + getAuthorAndExAuthor(basionymAuthor, exBasionymAuthor) + BasionymEnd;
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}
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if (combinationAuthor != null || exCombinationAuthor != null){
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authorPart = getAuthorAndExAuthor(combinationAuthor, exCombinationAuthor);
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}
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result = CdmUtils.concat(BasionymAuthorCombinationAuthorSeperator, basionymPart, authorPart);
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return result;
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}
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/**
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* Returns the AuthorCache part for a combination of an author and an ex author. This applies on combination authors
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* as well as on basionym/orginal combination authors.
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* @param author the author
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* @param exAuthor the ex-author
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* @return
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*/
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protected String getAuthorAndExAuthor(INomenclaturalAuthor author, INomenclaturalAuthor exAuthor){
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String result = "";
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String authorString = "";
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String exAuthorString = "";
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if (author != null){
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authorString = CdmUtils.Nz(author.getNomenclaturalTitle());
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}
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if (exAuthor != null){
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exAuthorString = CdmUtils.Nz(exAuthor.getNomenclaturalTitle());
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}
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if (exAuthorString.length() > 0 ){
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exAuthorString = exAuthorString + ExAuthorSeperator;
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}
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result = exAuthorString + authorString;
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return result;
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}
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/**
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* Checks if the given name should include the author in it's cached version.<BR>
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* This is usually the case but not for <i>species aggregates</i>.
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* @param nonViralName
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* @return
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*/
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protected boolean nameIncludesAuthorship(NonViralName<?> nonViralName){
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Rank rank = nonViralName.getRank();
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if (rank != null && rank.isSpeciesAggregate()){
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return false;
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}else{
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return true;
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}
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}
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// ************* TAGGED NAME ***************************************/
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.strategy.cache.name.NameCacheStrategyBase#getTaggedFullTitle(eu.etaxonomy.cdm.model.name.TaxonNameBase)
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*/
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@Override
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public List<TaggedText> getTaggedFullTitle(T nonViralName) {
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List<TaggedText> tags = new ArrayList<TaggedText>();
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//null
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if (nonViralName == null){
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return null;
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}
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//protected full title cache
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if (nonViralName.isProtectedFullTitleCache()){
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tags.add(new TaggedText(TagEnum.fullName, nonViralName.getFullTitleCache()));
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return tags;
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}
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//title cache
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// String titleCache = nonViralName.getTitleCache();
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List<TaggedText> titleTags = getTaggedTitle(nonViralName);
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tags.addAll(titleTags);
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//reference
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String microReference = nonViralName.getNomenclaturalMicroReference();
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INomenclaturalReference ref = nonViralName.getNomenclaturalReference();
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String referenceBaseCache = null;
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if (ref != null){
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INomenclaturalReference nomenclaturalReference = HibernateProxyHelper.deproxy(ref, INomenclaturalReference.class);
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nomenclaturalReference.setCacheStrategy(nomenclaturalReference.getType().getCacheStrategy());
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referenceBaseCache = nomenclaturalReference.getNomenclaturalCitation(microReference);
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}
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//add to tags
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if (StringUtils.isNotBlank(referenceBaseCache)){
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if (! referenceBaseCache.trim().startsWith("in ")){
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String refConcat = ", ";
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tags.add(new TaggedText(TagEnum.separator, refConcat));
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}
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tags.add(new TaggedText(TagEnum.reference, referenceBaseCache));
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}
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//nomenclatural status
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Set<NomenclaturalStatus> ncStati = nonViralName.getStatus();
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Iterator<NomenclaturalStatus> iterator = ncStati.iterator();
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List<TaggedText> nomStatusTags = new ArrayList<TaggedText>();
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while (iterator.hasNext()) {
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NomenclaturalStatus ncStatus = (NomenclaturalStatus)iterator.next();
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// since the NewInstance method of nomencatural status allows null as parameter
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// we have to check for null values here
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String suffix = "not defined";
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if(ncStatus.getType() != null){
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NomenclaturalStatusType statusType = ncStatus.getType();
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Language lang = Language.LATIN();
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Representation repr = statusType.getRepresentation(lang);
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if (repr != null){
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suffix = repr.getAbbreviatedLabel();
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}else{
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String message = "No latin representation available for nom. status. " + statusType.getTitleCache();
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logger.warn(message);
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throw new IllegalStateException(message);
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}
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}else if(ncStatus.getRuleConsidered() != null && ! ncStatus.getRuleConsidered().equals("")){
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suffix = ncStatus.getRuleConsidered();
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}
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String statusSeparator = ", ";
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nomStatusTags.add(new TaggedText(TagEnum.separator, statusSeparator));
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nomStatusTags.add(new TaggedText(TagEnum.nomStatus, suffix));
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}
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tags.addAll(nomStatusTags);
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return tags;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.strategy.cache.name.NameCacheStrategyBase#getTaggedTitle(eu.etaxonomy.cdm.model.name.TaxonNameBase)
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*/
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public List<TaggedText> getTaggedTitle(T nonViralName) {
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if (nonViralName == null){
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return null;
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}
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List<TaggedText> tags = new ArrayList<TaggedText>();
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//TODO how to handle protected fullTitleCache here?
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if (nonViralName.isProtectedTitleCache()){
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//protected title cache
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tags.add(new TaggedText(TagEnum.name, nonViralName.getTitleCache()));
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return tags;
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}else if (nonViralName.isHybridFormula()){
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//hybrid formula
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String hybridSeparator = NonViralNameParserImplRegExBase.hybridSign;
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boolean isFirst = true;
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List<HybridRelationship> rels = nonViralName.getOrderedChildRelationships();
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for (HybridRelationship rel: rels){
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if (! isFirst){
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tags.add(new TaggedText(TagEnum.hybridSign, hybridSeparator));
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}
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isFirst = false;
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tags.addAll(getTaggedTitle((T)rel.getParentName()));
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}
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return tags;
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}else if (nonViralName.isAutonym()){
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//Autonym
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tags.addAll(handleTaggedAutonym(nonViralName));
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}else{ //not Autonym
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// String nameCache = nonViralName.getNameCache(); //OLD: CdmUtils.Nz(getNameCache(nonViralName));
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List<TaggedText> nameTags = getTaggedName(nonViralName);
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tags.addAll(nameTags);
|
429
|
if (nameIncludesAuthorship(nonViralName)){
|
430
|
String authorCache = getAuthorshipCache(nonViralName);
|
431
|
if (StringUtils.isNotBlank(authorCache)){
|
432
|
tags.add(new TaggedText(TagEnum.authors, authorCache));
|
433
|
}
|
434
|
}
|
435
|
}
|
436
|
return tags;
|
437
|
|
438
|
}
|
439
|
|
440
|
|
441
|
/**
|
442
|
* Returns the tag list of the name part (without author and reference).
|
443
|
* @param nonViralName
|
444
|
* @return
|
445
|
*/
|
446
|
public List<TaggedText> getTaggedName(T nonViralName) {
|
447
|
if (nonViralName == null){
|
448
|
return null;
|
449
|
}
|
450
|
List<TaggedText> tags = new ArrayList<TaggedText>();
|
451
|
Rank rank = nonViralName.getRank();
|
452
|
|
453
|
if (nonViralName.isProtectedNameCache()){
|
454
|
tags.add(new TaggedText(TagEnum.name, nonViralName.getNameCache()));
|
455
|
}else if (rank == null){
|
456
|
tags = getRanklessTaggedNameCache(nonViralName);
|
457
|
// }else if (nonViralName.isInfragenericUnranked()){
|
458
|
// result = getUnrankedInfragenericNameCache(nonViralName);
|
459
|
}else if (rank.isInfraSpecific()){
|
460
|
tags = getInfraSpeciesTaggedNameCache(nonViralName);
|
461
|
}else if (rank.isSpecies()){
|
462
|
tags = getSpeciesTaggedNameCache(nonViralName);
|
463
|
}else if (rank.isInfraGeneric()){
|
464
|
tags = getInfraGenusTaggedNameCache(nonViralName);
|
465
|
}else if (rank.isGenus()){
|
466
|
tags = getGenusOrUninomialTaggedNameCache(nonViralName);
|
467
|
}else if (rank.isSupraGeneric()){
|
468
|
tags = getGenusOrUninomialTaggedNameCache(nonViralName);
|
469
|
}else{
|
470
|
logger.warn("Name Strategy for Name (UUID: " + nonViralName.getUuid() + ") not yet implemented");
|
471
|
}
|
472
|
//TODO handle appended phrase here instead of different places, check first if this is true for all
|
473
|
//cases
|
474
|
|
475
|
return tags;
|
476
|
|
477
|
}
|
478
|
|
479
|
|
480
|
|
481
|
|
482
|
//***************************** PRIVATES ***************************************/
|
483
|
|
484
|
|
485
|
/**
|
486
|
* Returns the tag list for an autonym taxon.
|
487
|
*
|
488
|
* @see NonViralName#isAutonym()
|
489
|
* @see BotanicalName#isAutonym()
|
490
|
* @param nonViralName
|
491
|
* @return
|
492
|
*/
|
493
|
private List<TaggedText> handleTaggedAutonym(T nonViralName) {
|
494
|
|
495
|
//species part
|
496
|
List<TaggedText> tags = getSpeciesTaggedNameCache(nonViralName);
|
497
|
|
498
|
//author
|
499
|
//TODO should this include basionym authors and ex authors
|
500
|
INomenclaturalAuthor author = nonViralName.getCombinationAuthorTeam();
|
501
|
String authorPart = "";
|
502
|
if (author != null){
|
503
|
authorPart = CdmUtils.Nz(author.getNomenclaturalTitle());
|
504
|
}
|
505
|
INomenclaturalAuthor basAuthor = nonViralName.getBasionymAuthorTeam();
|
506
|
String basAuthorPart = "";
|
507
|
if (basAuthor != null){
|
508
|
basAuthorPart = CdmUtils.Nz(basAuthor.getNomenclaturalTitle());
|
509
|
}
|
510
|
if (! "".equals(basAuthorPart)){
|
511
|
authorPart = "("+ basAuthorPart +") " + authorPart;
|
512
|
}
|
513
|
if (StringUtils.isNotBlank(authorPart)){
|
514
|
tags.add(new TaggedText(TagEnum.authors, authorPart));
|
515
|
}
|
516
|
|
517
|
|
518
|
//infra species marker
|
519
|
if (nonViralName.getRank() == null || !nonViralName.getRank().isInfraSpecific()){
|
520
|
//TODO handle exception
|
521
|
logger.warn("Rank for autonym does not exist or is not lower than species !!");
|
522
|
}else{
|
523
|
String infraSpeciesMarker = nonViralName.getRank().getAbbreviation();
|
524
|
if (StringUtils.isNotBlank(infraSpeciesMarker)){
|
525
|
tags.add(new TaggedText(TagEnum.rank, infraSpeciesMarker));
|
526
|
}
|
527
|
}
|
528
|
|
529
|
//infra species
|
530
|
String infraSpeciesPart = CdmUtils.Nz(nonViralName.getInfraSpecificEpithet()).trim().replace("null", "");
|
531
|
if (StringUtils.isNotBlank(infraSpeciesPart)){
|
532
|
tags.add(new TaggedText(TagEnum.name, infraSpeciesPart));
|
533
|
}
|
534
|
|
535
|
return tags;
|
536
|
}
|
537
|
|
538
|
|
539
|
|
540
|
/**
|
541
|
* Returns the tag list for rankless taxa.
|
542
|
* @param nonViralName
|
543
|
* @return
|
544
|
*/
|
545
|
protected List<TaggedText> getRanklessTaggedNameCache(NonViralName<?> nonViralName){
|
546
|
List<TaggedText> tags = getUninomialTaggedPart(nonViralName);
|
547
|
String speciesEpi = CdmUtils.Nz(nonViralName.getSpecificEpithet()).trim().replace("null", "");
|
548
|
if (StringUtils.isNotBlank(speciesEpi)){
|
549
|
tags.add(new TaggedText(TagEnum.name, speciesEpi));
|
550
|
}
|
551
|
|
552
|
String infraSpeciesEpi = CdmUtils.Nz(nonViralName.getInfraSpecificEpithet()).trim().replace("null", "");
|
553
|
if (StringUtils.isNotBlank(infraSpeciesEpi)){
|
554
|
tags.add(new TaggedText(TagEnum.name, infraSpeciesEpi));
|
555
|
}
|
556
|
|
557
|
//result += " (rankless)";
|
558
|
addAppendedTaggedPhrase(tags, nonViralName);
|
559
|
return tags;
|
560
|
}
|
561
|
|
562
|
/**
|
563
|
* Returns the tag list for the first epithet (including a hybrid sign if required).
|
564
|
* @param nonViralName
|
565
|
* @return
|
566
|
*/
|
567
|
private List<TaggedText> getUninomialTaggedPart(NonViralName<?> nonViralName) {
|
568
|
List<TaggedText> tags = new ArrayList<TaggedText>();
|
569
|
|
570
|
if (nonViralName.isMonomHybrid()){
|
571
|
addHybridPrefix(tags);
|
572
|
}
|
573
|
|
574
|
String uninomial = CdmUtils.Nz(nonViralName.getGenusOrUninomial()).trim().replace("null", "");
|
575
|
if (StringUtils.isNotBlank(uninomial)){
|
576
|
tags.add(new TaggedText(TagEnum.name, uninomial));
|
577
|
}
|
578
|
|
579
|
return tags;
|
580
|
}
|
581
|
|
582
|
/**
|
583
|
* Returns the tag list for an genus or higher taxon.
|
584
|
*
|
585
|
* @param nonViralName
|
586
|
* @return
|
587
|
*/
|
588
|
protected List<TaggedText> getGenusOrUninomialTaggedNameCache(NonViralName<?> nonViralName){
|
589
|
List<TaggedText> tags = getUninomialTaggedPart(nonViralName);
|
590
|
addAppendedTaggedPhrase(tags, nonViralName);
|
591
|
return tags;
|
592
|
}
|
593
|
|
594
|
/**
|
595
|
* Returns the tag list for an infrageneric taxon (including species aggregates).
|
596
|
*
|
597
|
* @see #getSpeciesAggregateTaggedCache(NonViralName)
|
598
|
* @param nonViralName
|
599
|
* @return
|
600
|
*/
|
601
|
protected List<TaggedText> getInfraGenusTaggedNameCache(NonViralName<?> nonViralName){
|
602
|
Rank rank = nonViralName.getRank();
|
603
|
if (rank.isSpeciesAggregate()){
|
604
|
return getSpeciesAggregateTaggedCache(nonViralName);
|
605
|
}
|
606
|
|
607
|
//genus
|
608
|
List<TaggedText> tags = getUninomialTaggedPart(nonViralName);
|
609
|
|
610
|
//marker
|
611
|
String infraGenericMarker = "'unhandled infrageneric rank'";
|
612
|
if (rank != null){
|
613
|
try {
|
614
|
infraGenericMarker = rank.getInfraGenericMarker();
|
615
|
} catch (UnknownCdmTypeException e) {
|
616
|
infraGenericMarker = "'unhandled infrageneric rank'";
|
617
|
}
|
618
|
}
|
619
|
tags.add(new TaggedText(TagEnum.rank, infraGenericMarker));
|
620
|
|
621
|
|
622
|
String infraGenEpi = CdmUtils.Nz(nonViralName.getInfraGenericEpithet()).trim().replace("null", "");
|
623
|
if (StringUtils.isNotBlank(infraGenEpi)){
|
624
|
tags.add(new TaggedText(TagEnum.name, infraGenEpi));
|
625
|
}
|
626
|
|
627
|
addAppendedTaggedPhrase(tags, nonViralName);
|
628
|
return tags;
|
629
|
}
|
630
|
|
631
|
/**
|
632
|
* Returns the tag list for a species aggregate (or similar) taxon.<BR>
|
633
|
* Possible ranks for a <i>species aggregate</i> are "aggr.", "species group", ...
|
634
|
* @param nonViralName
|
635
|
* @return
|
636
|
*/
|
637
|
protected List<TaggedText> getSpeciesAggregateTaggedCache(NonViralName<?> nonViralName){
|
638
|
List<TaggedText> tags = getGenusAndSpeciesTaggedPart(nonViralName);
|
639
|
|
640
|
addSpeciesAggregateTaggedEpithet(tags, nonViralName);
|
641
|
addAppendedTaggedPhrase(tags, nonViralName);
|
642
|
return tags;
|
643
|
}
|
644
|
|
645
|
/**
|
646
|
* Adds the aggregate tag to the tag list.
|
647
|
* @param tags
|
648
|
* @param nonViralName
|
649
|
*/
|
650
|
private void addSpeciesAggregateTaggedEpithet(List<TaggedText> tags, NonViralName<?> nonViralName) {
|
651
|
String marker;
|
652
|
try {
|
653
|
marker = nonViralName.getRank().getInfraGenericMarker();
|
654
|
} catch (UnknownCdmTypeException e) {
|
655
|
marker = "'unknown aggregat type'";
|
656
|
}
|
657
|
if (StringUtils.isNotBlank(marker)){
|
658
|
tags.add(new TaggedText(TagEnum.rank, marker));
|
659
|
}
|
660
|
}
|
661
|
|
662
|
|
663
|
/**
|
664
|
* Returns the tag list for a species taxon.
|
665
|
* @param nonViralName
|
666
|
* @return
|
667
|
*/
|
668
|
protected List<TaggedText> getSpeciesTaggedNameCache(NonViralName<?> nonViralName){
|
669
|
List<TaggedText> tags = getGenusAndSpeciesTaggedPart(nonViralName);
|
670
|
addAppendedTaggedPhrase(tags, nonViralName);
|
671
|
return tags;
|
672
|
}
|
673
|
|
674
|
/**
|
675
|
* Creates the tag list for an infraspecific taxon. In include is true the result will contain
|
676
|
* @param nonViralName
|
677
|
* @return
|
678
|
*/
|
679
|
protected List<TaggedText> getInfraSpeciesTaggedNameCache(NonViralName<?> nonViralName){
|
680
|
return getInfraSpeciesTaggedNameCache(nonViralName, true);
|
681
|
}
|
682
|
|
683
|
/**
|
684
|
* Creates the tag list for an infraspecific taxon. In include is true the result will contain
|
685
|
* the infraspecific marker (e.g. "var.")
|
686
|
* @param nonViralName
|
687
|
* @param includeMarker
|
688
|
* @return
|
689
|
*/
|
690
|
protected List<TaggedText> getInfraSpeciesTaggedNameCache(NonViralName<?> nonViralName, boolean includeMarker){
|
691
|
List<TaggedText> tags = getGenusAndSpeciesTaggedPart(nonViralName);
|
692
|
if (includeMarker){
|
693
|
String marker = (nonViralName.getRank().getAbbreviation()).trim().replace("null", "");
|
694
|
if (StringUtils.isNotBlank(marker)){
|
695
|
tags.add(new TaggedText(TagEnum.rank, marker));
|
696
|
}
|
697
|
}
|
698
|
String infrSpecEpi = CdmUtils.Nz(nonViralName.getInfraSpecificEpithet());
|
699
|
if (nonViralName.isTrinomHybrid()){
|
700
|
addHybridPrefix(tags);
|
701
|
}
|
702
|
|
703
|
infrSpecEpi = infrSpecEpi.trim().replace("null", "");
|
704
|
if (StringUtils.isNotBlank(infrSpecEpi)){
|
705
|
tags.add(new TaggedText(TagEnum.name, infrSpecEpi));
|
706
|
}
|
707
|
|
708
|
addAppendedTaggedPhrase(tags, nonViralName);
|
709
|
return tags;
|
710
|
}
|
711
|
|
712
|
|
713
|
/**
|
714
|
* Adds a tag for the hybrid sign and an empty separator to avoid trailing whitespaces.
|
715
|
* @param tags
|
716
|
*/
|
717
|
private void addHybridPrefix(List<TaggedText> tags) {
|
718
|
tags.add(new TaggedText(TagEnum.hybridSign, NonViralNameParserImplRegExBase.hybridSign));
|
719
|
tags.add(new TaggedText(TagEnum.separator, "")); //no whitespace separator
|
720
|
}
|
721
|
|
722
|
/**
|
723
|
* Creates the tag list for the genus and species part.
|
724
|
* @param nonViralName
|
725
|
* @return
|
726
|
*/
|
727
|
private List<TaggedText> getGenusAndSpeciesTaggedPart(NonViralName<?> nonViralName) {
|
728
|
//Uninomial
|
729
|
List<TaggedText> tags = getUninomialTaggedPart(nonViralName);
|
730
|
|
731
|
//InfraGenericEpi
|
732
|
boolean hasInfraGenericEpi = StringUtils.isNotBlank(nonViralName.getInfraGenericEpithet());
|
733
|
if (hasInfraGenericEpi){
|
734
|
String infrGenEpi = nonViralName.getInfraGenericEpithet().trim();
|
735
|
if (nonViralName.isBinomHybrid()){
|
736
|
// addHybridPrefix(tags); FIXME hybridSign should be tag, but then we need to handle "(" ")" differently.
|
737
|
infrGenEpi = NonViralNameParserImplRegExBase.hybridSign + infrGenEpi;
|
738
|
}
|
739
|
infrGenEpi = "(" + infrGenEpi + ")";
|
740
|
tags.add(new TaggedText(TagEnum.name, infrGenEpi));
|
741
|
}
|
742
|
|
743
|
//Species Epi
|
744
|
String specEpi = CdmUtils.Nz(nonViralName.getSpecificEpithet()).trim().replace("null", "");
|
745
|
if (! hasInfraGenericEpi && nonViralName.isBinomHybrid() ||
|
746
|
hasInfraGenericEpi && nonViralName.isTrinomHybrid()){
|
747
|
addHybridPrefix(tags);
|
748
|
}
|
749
|
if (StringUtils.isNotBlank(specEpi)){
|
750
|
tags.add(new TaggedText(TagEnum.name, specEpi));
|
751
|
}
|
752
|
return tags;
|
753
|
}
|
754
|
|
755
|
/**
|
756
|
* Adds the tag for the appended phrase if an appended phrase exists
|
757
|
* @param tags
|
758
|
* @param nonViralName
|
759
|
*/
|
760
|
protected void addAppendedTaggedPhrase(List<TaggedText> tags, NonViralName<?> nonViralName){
|
761
|
String appendedPhrase = nonViralName ==null ? null : nonViralName.getAppendedPhrase();
|
762
|
if (StringUtils.isNotEmpty(appendedPhrase)){
|
763
|
tags.add(new TaggedText(TagEnum.name, appendedPhrase));
|
764
|
}
|
765
|
}
|
766
|
|
767
|
public String getLastEpithet(T taxonNameBase) {
|
768
|
Rank rank = taxonNameBase.getRank();
|
769
|
if(rank.isGenus() || rank.isSupraGeneric()) {
|
770
|
return taxonNameBase.getGenusOrUninomial();
|
771
|
} else if(rank.isInfraGeneric()) {
|
772
|
return taxonNameBase.getInfraGenericEpithet();
|
773
|
} else if(rank.isSpecies()) {
|
774
|
return taxonNameBase.getSpecificEpithet();
|
775
|
} else {
|
776
|
return taxonNameBase.getInfraSpecificEpithet();
|
777
|
}
|
778
|
}
|
779
|
|
780
|
// *************************** DEPRECATED ***************************************************/
|
781
|
|
782
|
|
783
|
//Old: may be replaced once getTagged(Full)Title is fully tested
|
784
|
/* (non-Javadoc)
|
785
|
* @see eu.etaxonomy.cdm.strategy.INameCacheStrategy#getTaggedName(eu.etaxonomy.cdm.model.common.CdmBase)
|
786
|
*/
|
787
|
@Override
|
788
|
@Deprecated
|
789
|
public List<Object> getTaggedNameDeprecated(T nonViralName) {
|
790
|
List<Object> tags = new ArrayList<Object>();
|
791
|
|
792
|
if (nonViralName.isProtectedNameCache() ||
|
793
|
nonViralName.isProtectedAuthorshipCache() ||
|
794
|
nonViralName.isProtectedFullTitleCache() ||
|
795
|
nonViralName.isProtectedTitleCache()){
|
796
|
tags.add(nonViralName.getTitleCache());
|
797
|
return tags;
|
798
|
}
|
799
|
|
800
|
// Why does it make sense to add the nameCache in case of non existing genusOrUninomial?
|
801
|
// if (nonViralName.getGenusOrUninomial() == null){
|
802
|
// tags.add(nonViralName.getNameCache());
|
803
|
// }else{
|
804
|
|
805
|
if (nonViralName.getGenusOrUninomial() != null) {
|
806
|
tags.add(nonViralName.getGenusOrUninomial());
|
807
|
}
|
808
|
if (nonViralName.isSpecies() || nonViralName.isInfraSpecific()){
|
809
|
tags.add(nonViralName.getSpecificEpithet());
|
810
|
}
|
811
|
|
812
|
// No autonym
|
813
|
if (nonViralName.isInfraSpecific() && ! nonViralName.getSpecificEpithet().equals(nonViralName.getInfraSpecificEpithet())){
|
814
|
tags.add(nonViralName.getRank());
|
815
|
tags.add(nonViralName.getInfraSpecificEpithet());
|
816
|
}
|
817
|
|
818
|
if (nonViralName.isInfraGeneric()){
|
819
|
//TODO choose right strategy or generic approach?
|
820
|
// --- strategy 1 ---
|
821
|
|
822
|
if (nonViralName.getRank().isSpeciesAggregate()){
|
823
|
tags.add(nonViralName.getSpecificEpithet());
|
824
|
tags.add(getSpeciesAggregateEpithet(nonViralName));
|
825
|
}else{
|
826
|
tags.add(nonViralName.getRank());
|
827
|
tags.add(nonViralName.getInfraGenericEpithet());
|
828
|
}
|
829
|
// --- strategy 2 ---
|
830
|
// tags.add('('+nvn.getInfraGenericEpithet()+')');
|
831
|
}
|
832
|
Team authorTeam = Team.NewInstance();
|
833
|
authorTeam.setProtectedTitleCache(true);
|
834
|
authorTeam.setTitleCache(nonViralName.getAuthorshipCache(), true);
|
835
|
tags.add(authorTeam);
|
836
|
|
837
|
// Name is an autonym. Rank and infraspecific epitheton follow the author
|
838
|
if (nonViralName.isInfraSpecific() && nonViralName.getSpecificEpithet().equals(nonViralName.getInfraSpecificEpithet())){
|
839
|
tags.add(nonViralName.getRank());
|
840
|
tags.add(nonViralName.getInfraSpecificEpithet());
|
841
|
}
|
842
|
|
843
|
if(! "".equals(nonViralName.getAppendedPhrase())&& (nonViralName.getAppendedPhrase() != null)){
|
844
|
tags.add(nonViralName.getAppendedPhrase());
|
845
|
}
|
846
|
|
847
|
return tags;
|
848
|
}
|
849
|
|
850
|
|
851
|
/**
|
852
|
* @deprecated use only for {@link #getTaggedNameDeprecated(NonViralName)}. Delete when the later
|
853
|
* is deleted.
|
854
|
*/
|
855
|
@Deprecated
|
856
|
private String getSpeciesAggregateEpithet(NonViralName<?> nonViralName) {
|
857
|
String marker;
|
858
|
try {
|
859
|
marker = nonViralName.getRank().getInfraGenericMarker();
|
860
|
} catch (UnknownCdmTypeException e) {
|
861
|
marker = "'unknown aggregat type'";
|
862
|
}
|
863
|
return marker;
|
864
|
}
|
865
|
|
866
|
|
867
|
}
|