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/**
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*
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*/
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package eu.etaxonomy.cdm.strategy.parser;
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import java.util.regex.Matcher;
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import java.util.regex.Pattern;
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import org.apache.log4j.Logger;
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import org.joda.time.DateTimeFieldType;
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import org.joda.time.Partial;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.model.agent.Person;
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import eu.etaxonomy.cdm.model.agent.Team;
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import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
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import eu.etaxonomy.cdm.model.common.IParsable;
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import eu.etaxonomy.cdm.model.common.TimePeriod;
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import eu.etaxonomy.cdm.model.name.BacterialName;
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import eu.etaxonomy.cdm.model.name.BotanicalName;
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import eu.etaxonomy.cdm.model.name.CultivarPlantName;
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
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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.name.TaxonNameBase;
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import eu.etaxonomy.cdm.model.name.ZoologicalName;
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import eu.etaxonomy.cdm.model.reference.Article;
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import eu.etaxonomy.cdm.model.reference.BibtexReference;
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import eu.etaxonomy.cdm.model.reference.Book;
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import eu.etaxonomy.cdm.model.reference.BookSection;
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import eu.etaxonomy.cdm.model.reference.Generic;
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import eu.etaxonomy.cdm.model.reference.INomenclaturalReference;
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import eu.etaxonomy.cdm.model.reference.IVolumeReference;
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import eu.etaxonomy.cdm.model.reference.Journal;
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import eu.etaxonomy.cdm.model.reference.ReferenceBase;
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import eu.etaxonomy.cdm.model.reference.StrictReferenceBase;
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import eu.etaxonomy.cdm.strategy.exceptions.StringNotParsableException;
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import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
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/**
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* @author a.mueller
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*
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*/
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public class NonViralNameParserImpl extends NonViralNameParserImplRegExBase implements INonViralNameParser<NonViralName> {
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private static final Logger logger = Logger.getLogger(NonViralNameParserImpl.class);
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// good intro: http://java.sun.com/docs/books/tutorial/essential/regex/index.html
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final static boolean MAKE_EMPTY = true;
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final static boolean MAKE_NOT_EMPTY = false;
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public static NonViralNameParserImpl NewInstance(){
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return new NonViralNameParserImpl();
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.strategy.ITaxonNameParser#parseSimpleName(java.lang.String, eu.etaxonomy.cdm.model.name.Rank)
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*/
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public NonViralName parseSimpleName(String simpleName, Rank rank){
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//TODO
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logger.warn("parseSimpleName() not yet implemented. Uses parseFullName() instead");
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return parseFullName(simpleName, null, rank);
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.strategy.ITaxonNameParser#parseSubGenericSimpleName(java.lang.String)
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*/
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public NonViralName parseSimpleName(String simpleName){
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return parseSimpleName(simpleName, null);
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}
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public NonViralName getNonViralNameInstance(String fullString, NomenclaturalCode code){
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return getNonViralNameInstance(fullString, code, null);
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}
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public NonViralName getNonViralNameInstance(String fullString, NomenclaturalCode code, Rank rank){
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NonViralName result = null;
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if(code ==null) {
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boolean isBotanicalName = anyBotanicFullNamePattern.matcher(fullString).find();
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boolean isZoologicalName = anyZooFullNamePattern.matcher(fullString).find();;
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boolean isBacteriologicalName = false;
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boolean isCultivatedPlantName = false;
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if ( (isBotanicalName || isCultivatedPlantName) && ! isZoologicalName && !isBacteriologicalName){
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if (isBotanicalName){
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result = BotanicalName.NewInstance(rank);
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}else{
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result = CultivarPlantName.NewInstance(rank);
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}
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}else if ( isZoologicalName /*&& ! isBotanicalName*/ && !isBacteriologicalName && !isCultivatedPlantName){
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result = ZoologicalName.NewInstance(rank);
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}else if ( isZoologicalName && ! isBotanicalName && !isBacteriologicalName && !isCultivatedPlantName){
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result = BacterialName.NewInstance(rank);
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}else {
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result = NonViralName.NewInstance(rank);
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}
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} else {
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switch (code) {
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case ICBN:
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result = BotanicalName.NewInstance(rank);
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break;
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case ICZN:
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result = ZoologicalName.NewInstance(rank);
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break;
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case ICNCP:
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logger.warn("ICNCP parsing not yet implemented");
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result = CultivarPlantName.NewInstance(rank);
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break;
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case ICNB:
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logger.warn("ICNB not yet implemented");
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result = BacterialName.NewInstance(rank);
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break;
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case ICVCN:
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logger.error("Viral name is not a NonViralName !!");
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break;
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default:
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// FIXME Unreachable code
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logger.error("Unknown Nomenclatural Code !!");
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}
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}
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return result;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.strategy.parser.INonViralNameParser#parseFullReference(java.lang.String)
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*/
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public NonViralName parseReferencedName(String fullReferenceString) {
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return parseReferencedName(fullReferenceString, null, null);
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.strategy.ITaxonNameParser#parseFullReference(java.lang.String, eu.etaxonomy.cdm.model.name.Rank)
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*/
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public NonViralName parseReferencedName(String fullReferenceString, NomenclaturalCode nomCode, Rank rank) {
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if (fullReferenceString == null){
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return null;
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}else{
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NonViralName result = getNonViralNameInstance(fullReferenceString, nomCode, rank);
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parseReferencedName(result, fullReferenceString, rank, MAKE_EMPTY);
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return result;
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}
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}
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private String standardize(NonViralName nameToBeFilled, String fullReferenceString, boolean makeEmpty){
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//Check null and standardize
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if (fullReferenceString == null){
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//return null;
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return null;
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}
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if (makeEmpty){
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makeEmpty(nameToBeFilled);
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}
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fullReferenceString = fullReferenceString.replaceAll(oWs , " ");
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fullReferenceString = fullReferenceString.trim();
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if ("".equals(fullReferenceString)){
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fullReferenceString = null;
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}
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return fullReferenceString;
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}
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/**
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* Returns the regEx to be used for the full-name depending on the code
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* @param nameToBeFilled
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* @return
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*/
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private String getLocalFullName(NonViralName nameToBeFilled){
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if (nameToBeFilled instanceof ZoologicalName){
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return anyZooFullName;
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}else if (nameToBeFilled instanceof BotanicalName) {
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return anyBotanicFullName;
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}else if (nameToBeFilled instanceof NonViralName) {
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return anyBotanicFullName; //TODO ?
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}else{
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logger.warn("nameToBeFilled class not supported ("+nameToBeFilled.getClass()+")");
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return null;
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}
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}
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/**
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* Returns the regEx to be used for the fsimple-name depending on the code
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* @param nameToBeFilled
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* @return
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*/
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private String getLocalSimpleName(NonViralName nameToBeFilled){
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if (nameToBeFilled instanceof ZoologicalName){
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return anyZooName;
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}else if (nameToBeFilled instanceof NonViralName){
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return anyZooName; //TODO ?
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}else if (nameToBeFilled instanceof BotanicalName) {
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return anyBotanicName;
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}else{
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logger.warn("nameToBeFilled class not supported ("+nameToBeFilled.getClass()+")");
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return null;
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}
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}
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private Matcher getMatcher(String regEx, String matchString){
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Pattern pattern = Pattern.compile(regEx);
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Matcher matcher = pattern.matcher(matchString);
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return matcher;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.strategy.ITaxonNameParser#parseFullReference(eu.etaxonomy.cdm.model.name.BotanicalName, java.lang.String, eu.etaxonomy.cdm.model.name.Rank, boolean)
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*/
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public void parseReferencedName(NonViralName nameToBeFilled, String fullReferenceString, Rank rank, boolean makeEmpty) {
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//standardize
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fullReferenceString = standardize(nameToBeFilled, fullReferenceString, makeEmpty);
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if (fullReferenceString == null){
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return;
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}
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makeProblemEmpty(nameToBeFilled);
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//make nomenclatural status and replace it by empty string
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fullReferenceString = parseNomStatus(fullReferenceString, nameToBeFilled);
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nameToBeFilled.setProblemEnds(fullReferenceString.length());
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//get full name reg
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String localFullName = getLocalFullName(nameToBeFilled);
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//get full name reg
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String localSimpleName = getLocalSimpleName(nameToBeFilled);
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//separate name and reference part
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String nameAndRefSeparator = "(^" + localFullName + ")("+ referenceSeperator + ")";
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Matcher nameAndRefSeparatorMatcher = getMatcher (nameAndRefSeparator, fullReferenceString);
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Matcher onlyNameMatcher = getMatcher (localFullName, fullReferenceString);
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Matcher onlySimpleNameMatcher = getMatcher (localSimpleName, fullReferenceString);
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if (nameAndRefSeparatorMatcher.find()){
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makeNameWithReference(nameToBeFilled, fullReferenceString, nameAndRefSeparatorMatcher, rank, makeEmpty);
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}else if (onlyNameMatcher.matches()){
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makeEmpty = false;
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parseFullName(nameToBeFilled, fullReferenceString, rank, makeEmpty);
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}else if (onlySimpleNameMatcher.matches()){
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makeEmpty = false;
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parseFullName(nameToBeFilled, fullReferenceString, rank, makeEmpty); //simpleName not yet implemented
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}else{
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makeNoFullRefMatch(nameToBeFilled, fullReferenceString, rank);
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}
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//problem handling. Start and end solved in subroutines
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if (nameToBeFilled.hasProblem()==0){
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248
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makeProblemEmpty(nameToBeFilled);
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249
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}
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250
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}
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251
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252
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private void makeProblemEmpty(IParsable parsable){
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253
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parsable.setHasProblem(0);
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254
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parsable.setProblemStarts(-1);
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255
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parsable.setProblemEnds(-1);
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256
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}
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257
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258
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private void makeNoFullRefMatch(NonViralName nameToBeFilled, String fullReferenceString, Rank rank){
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259
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//try to parse first part as name, but keep in mind full string is not parsable
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260
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int start = 0;
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261
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262
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String localFullName = getLocalFullName(nameToBeFilled);
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263
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Matcher fullNameMatcher = getMatcher (pStart + localFullName, fullReferenceString);
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264
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if (fullNameMatcher.find()){
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265
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String fullNameString = fullNameMatcher.group(0);
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266
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nameToBeFilled.setProtectedNameCache(false); //TODO why is is true?
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267
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parseFullName(nameToBeFilled, fullNameString, rank, false);
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268
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String sure = nameToBeFilled.getNameCache();
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269
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start = sure.length();
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270
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}
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271
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272
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// String localSimpleName = getLocalSimpleName(nameToBeFilled);
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273
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// Matcher simpleNameMatcher = getMatcher (start + localSimpleName, fullReferenceString);
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274
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// if (simpleNameMatcher.find()){
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275
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// String simpleNameString = simpleNameMatcher.group(0);
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276
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// parseFullName(nameToBeFilled, simpleNameString, rank, false);
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277
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// start = simpleNameString.length();
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278
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// }
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279
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280
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//don't parse if name can't be separated
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281
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nameToBeFilled.setHasProblem(1);
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282
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nameToBeFilled.setTitleCache(fullReferenceString);
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283
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nameToBeFilled.setFullTitleCache(fullReferenceString);
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284
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// FIXME Quick fix, otherwise search would not deilver results for unparsable names
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285
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nameToBeFilled.setNameCache(fullReferenceString);
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|
286
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// END
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|
287
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nameToBeFilled.setProblemStarts(start);
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288
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nameToBeFilled.setProblemEnds(fullReferenceString.length());
|
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289
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logger.info("no applicable parsing rule could be found for \"" + fullReferenceString + "\"");
|
|
290
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}
|
|
291
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|
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292
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private void makeNameWithReference(NonViralName nameToBeFilled,
|
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293
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String fullReferenceString,
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294
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Matcher nameAndRefSeparatorMatcher,
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295
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Rank rank,
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296
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boolean makeEmpty){
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|
297
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|
|
298
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String nameAndSeparator = nameAndRefSeparatorMatcher.group(0);
|
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299
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String name = nameAndRefSeparatorMatcher.group(1);
|
|
300
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String referenceString = fullReferenceString.substring(nameAndRefSeparatorMatcher.end());
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|
301
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|
|
302
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// is reference an in ref?
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|
303
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String separator = nameAndSeparator.substring(name.length());
|
|
304
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boolean isInReference = separator.matches(inReferenceSeparator);
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|
305
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|
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306
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//parse subparts
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307
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|
|
308
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int oldProblemEnds = nameToBeFilled.getProblemEnds();
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309
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parseFullName(nameToBeFilled, name, rank, makeEmpty);
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310
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nameToBeFilled.setProblemEnds(oldProblemEnds);
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311
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parseReference(nameToBeFilled, referenceString, isInReference);
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312
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INomenclaturalReference ref = (INomenclaturalReference)nameToBeFilled.getNomenclaturalReference();
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|
313
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|
|
314
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//problem start
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|
315
|
int start = nameToBeFilled.getProblemStarts();
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|
316
|
int nameLength = name.length();
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|
317
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int nameAndSeparatorLength = nameAndSeparator.length();
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318
|
int fullRefLength = nameToBeFilled.getFullTitleCache().length();
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319
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320
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if (nameToBeFilled.isProtectedTitleCache() || nameToBeFilled.getRank() == null ){
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321
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start = Math.max(0, start);
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322
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}else{
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323
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if (ref != null && ref.getHasProblem()!=0){
|
|
324
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start = Math.max(nameAndSeparatorLength, start);
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|
325
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//TODO search within ref
|
|
326
|
}
|
|
327
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}
|
|
328
|
|
|
329
|
//end
|
|
330
|
int end = nameToBeFilled.getProblemEnds();
|
|
331
|
|
|
332
|
if (ref != null && ref.getHasProblem()!=0){
|
|
333
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end = Math.min(nameAndSeparatorLength + ref.getProblemEnds(), end);
|
|
334
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}else{
|
|
335
|
if (nameToBeFilled.isProtectedTitleCache() ){
|
|
336
|
end = Math.min(end, nameAndSeparatorLength);
|
|
337
|
//TODO search within name
|
|
338
|
}
|
|
339
|
}
|
|
340
|
nameToBeFilled.setProblemStarts(start);
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|
341
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nameToBeFilled.setProblemEnds(end);
|
|
342
|
|
|
343
|
//delegate has problem to name
|
|
344
|
if (ref != null && ref.getHasProblem()!=0){
|
|
345
|
nameToBeFilled.setHasProblem(1);
|
|
346
|
}
|
|
347
|
|
|
348
|
ReferenceBase<?> nomRef;
|
|
349
|
if ( (nomRef = nameToBeFilled.getNomenclaturalReference()) != null ){
|
|
350
|
nomRef.setAuthorTeam((TeamOrPersonBase)nameToBeFilled.getCombinationAuthorTeam());
|
|
351
|
}
|
|
352
|
}
|
|
353
|
|
|
354
|
//TODO make it an Array of status
|
|
355
|
/**
|
|
356
|
* Extracts a {@link NomenclaturalStatus} from the reference String and adds it to the @link {@link TaxonNameBase}.
|
|
357
|
* The nomenclatural status part ist deleted from the reference String.
|
|
358
|
* @return String the new (shortend) reference String
|
|
359
|
*/
|
|
360
|
private String parseNomStatus(String fullString, NonViralName nameToBeFilled) {
|
|
361
|
String statusString;
|
|
362
|
Pattern hasStatusPattern = Pattern.compile("(" + pNomStatusPhrase + ")");
|
|
363
|
Matcher hasStatusMatcher = hasStatusPattern.matcher(fullString);
|
|
364
|
|
|
365
|
if (hasStatusMatcher.find()) {
|
|
366
|
String statusPhrase = hasStatusMatcher.group(0);
|
|
367
|
|
|
368
|
Pattern statusPattern = Pattern.compile(pNomStatus);
|
|
369
|
Matcher statusMatcher = statusPattern.matcher(statusPhrase);
|
|
370
|
statusMatcher.find();
|
|
371
|
statusString = statusMatcher.group(0);
|
|
372
|
try {
|
|
373
|
NomenclaturalStatusType nomStatusType = NomenclaturalStatusType.getNomenclaturalStatusTypeByAbbreviation(statusString);
|
|
374
|
NomenclaturalStatus nomStatus = NomenclaturalStatus.NewInstance(nomStatusType);
|
|
375
|
nameToBeFilled.addStatus(nomStatus);
|
|
376
|
|
|
377
|
fullString = fullString.replace(statusPhrase, "");
|
|
378
|
} catch (UnknownCdmTypeException e) {
|
|
379
|
//Do nothing
|
|
380
|
}
|
|
381
|
}
|
|
382
|
return fullString;
|
|
383
|
}
|
|
384
|
|
|
385
|
|
|
386
|
private void parseReference(NonViralName nameToBeFilled, String strReference, boolean isInReference){
|
|
387
|
INomenclaturalReference ref;
|
|
388
|
String originalStrReference = strReference;
|
|
389
|
|
|
390
|
//End (just delete end (e.g. '.', may be ambigous for yearPhrase, but no real information gets lost
|
|
391
|
Matcher endMatcher = getMatcher(referenceEnd + end, strReference);
|
|
392
|
if (endMatcher.find()){
|
|
393
|
String endPart = endMatcher.group(0);
|
|
394
|
strReference = strReference.substring(0, strReference.length() - endPart.length());
|
|
395
|
}
|
|
396
|
|
|
397
|
String pDetailYear = ".*" + detailSeparator + detail + fWs + yearSeperator + fWs + yearPhrase + fWs + end;
|
|
398
|
Matcher detailYearMatcher = getMatcher(pDetailYear, strReference);
|
|
399
|
|
|
400
|
//if (referencePattern.matcher(reference).matches() ){
|
|
401
|
if (detailYearMatcher.matches() ){
|
|
402
|
|
|
403
|
//year
|
|
404
|
String yearPart = null;
|
|
405
|
String pYearPhrase = yearSeperator + fWs + yearPhrase + fWs + end;
|
|
406
|
Matcher yearPhraseMatcher = getMatcher(pYearPhrase, strReference);
|
|
407
|
if (yearPhraseMatcher.find()){
|
|
408
|
yearPart = yearPhraseMatcher.group(0);
|
|
409
|
strReference = strReference.substring(0, strReference.length() - yearPart.length());
|
|
410
|
yearPart = yearPart.replaceFirst(pStart + yearSeperator, "").trim();
|
|
411
|
}
|
|
412
|
|
|
413
|
//detail
|
|
414
|
String pDetailPhrase = detailSeparator + fWs + detail + fWs + end;
|
|
415
|
Matcher detailPhraseMatcher = getMatcher(pDetailPhrase, strReference);
|
|
416
|
if (detailPhraseMatcher.find()){
|
|
417
|
String detailPart = detailPhraseMatcher.group(0);
|
|
418
|
strReference = strReference.substring(0, strReference.length() - detailPart.length());
|
|
419
|
detailPart = detailPart.replaceFirst(pStart + detailSeparator, "").trim();
|
|
420
|
nameToBeFilled.setNomenclaturalMicroReference(detailPart);
|
|
421
|
}
|
|
422
|
//parse title and author
|
|
423
|
ref = parseReferenceTitle(strReference, yearPart, isInReference);
|
|
424
|
if (ref.hasProblem()!=0){
|
|
425
|
ref.setTitleCache( (isInReference?"in ":"") + originalStrReference);
|
|
426
|
}
|
|
427
|
nameToBeFilled.setNomenclaturalReference((ReferenceBase)ref);
|
|
428
|
int end = Math.min(strReference.length(), ref.getProblemEnds());
|
|
429
|
ref.setProblemEnds(end);
|
|
430
|
}else{ //detail and year not parsable
|
|
431
|
ref = Generic.NewInstance();
|
|
432
|
ref.setTitleCache(strReference);
|
|
433
|
ref.setProblemEnds(strReference.length());
|
|
434
|
ref.setHasProblem(1);
|
|
435
|
nameToBeFilled.setHasProblem(1);
|
|
436
|
nameToBeFilled.setNomenclaturalReference((ReferenceBase)ref);
|
|
437
|
}
|
|
438
|
}
|
|
439
|
|
|
440
|
/**
|
|
441
|
* Parses the referenceTitlePart, including the author volume and edition.
|
|
442
|
* @param reference
|
|
443
|
* @param year
|
|
444
|
* @return
|
|
445
|
*/
|
|
446
|
private INomenclaturalReference parseReferenceTitle(String strReference, String year, boolean isInReference){
|
|
447
|
INomenclaturalReference result = null;
|
|
448
|
|
|
449
|
Matcher refSineDetailMatcher = referenceSineDetailPattern.matcher(strReference);
|
|
450
|
if (! refSineDetailMatcher.matches()){
|
|
451
|
//TODO ?
|
|
452
|
}
|
|
453
|
|
|
454
|
Matcher articleMatcher = getMatcher(pArticleReference, strReference);
|
|
455
|
|
|
456
|
Matcher softArticleMatcher = getMatcher(pSoftArticleReference, strReference);
|
|
457
|
Matcher bookMatcher = getMatcher(pBookReference, strReference);
|
|
458
|
Matcher bookSectionMatcher = getMatcher(pBookSectionReference, strReference);
|
|
459
|
|
|
460
|
|
|
461
|
if(isInReference == false){
|
|
462
|
if (bookMatcher.matches() ){
|
|
463
|
result = parseBook(strReference);
|
|
464
|
}else{
|
|
465
|
logger.warn("Non-InRef must be book but does not match book");
|
|
466
|
result = Book.NewInstance();
|
|
467
|
makeUnparsableRefTitle(result, strReference);
|
|
468
|
}
|
|
469
|
}else{ //inRef
|
|
470
|
if (articleMatcher.matches()){
|
|
471
|
//article without separators like ","
|
|
472
|
result = parseArticle(strReference);
|
|
473
|
}else if (softArticleMatcher.matches()){
|
|
474
|
result = parseArticle(strReference);
|
|
475
|
}else if (bookSectionMatcher.matches()){
|
|
476
|
result = parseBookSection(strReference);
|
|
477
|
}else{
|
|
478
|
result = Generic.NewInstance();
|
|
479
|
makeUnparsableRefTitle(result, "in " + strReference);
|
|
480
|
}
|
|
481
|
}
|
|
482
|
//make year
|
|
483
|
if (makeYear(result, year) == false){
|
|
484
|
//TODO
|
|
485
|
logger.warn("Year could not be parsed");
|
|
486
|
}
|
|
487
|
result.setProblemStarts(0);
|
|
488
|
result.setProblemEnds(strReference.length());
|
|
489
|
return result;
|
|
490
|
}
|
|
491
|
|
|
492
|
private void makeUnparsableRefTitle(INomenclaturalReference result, String reference){
|
|
493
|
result.setTitleCache(reference);
|
|
494
|
result.setHasProblem(1);
|
|
495
|
}
|
|
496
|
|
|
497
|
/**
|
|
498
|
* Parses a single date string. If the string is not parsable a StringNotParsableException is thrown
|
|
499
|
* @param singleDateString
|
|
500
|
* @return
|
|
501
|
* @throws StringNotParsableException
|
|
502
|
*/
|
|
503
|
private static Partial parseSingleDate(String singleDateString)
|
|
504
|
throws StringNotParsableException{
|
|
505
|
Partial dt = new Partial();
|
|
506
|
if (CdmUtils.isNumeric(singleDateString)){
|
|
507
|
try {
|
|
508
|
Integer year = Integer.valueOf(singleDateString.trim());
|
|
509
|
if (year > 1750 && year < 2050){
|
|
510
|
dt = dt.with(DateTimeFieldType.year(), year);
|
|
511
|
}else{
|
|
512
|
dt = null;
|
|
513
|
}
|
|
514
|
} catch (NumberFormatException e) {
|
|
515
|
logger.debug("Not a Integer format in getCalendar()");
|
|
516
|
throw new StringNotParsableException(singleDateString + "is not parsable as a single Date");
|
|
517
|
}
|
|
518
|
}
|
|
519
|
return dt;
|
|
520
|
}
|
|
521
|
|
|
522
|
|
|
523
|
/**
|
|
524
|
* Parses the publication date part.
|
|
525
|
* @param nomRef
|
|
526
|
* @param year
|
|
527
|
* @return If the string is not parsable <code>false</code>
|
|
528
|
* is returned. <code>True</code> otherwise
|
|
529
|
*/
|
|
530
|
private boolean makeYear(INomenclaturalReference nomRef, String year){
|
|
531
|
boolean result = true;
|
|
532
|
if (year == null){
|
|
533
|
return false;
|
|
534
|
}
|
|
535
|
if ("".equals(year.trim())){
|
|
536
|
return true;
|
|
537
|
}
|
|
538
|
String[] years = year.split("-");
|
|
539
|
Partial startDate = null;
|
|
540
|
Partial endDate = null;
|
|
541
|
try{
|
|
542
|
if (years.length < 1){
|
|
543
|
throw new StringNotParsableException();
|
|
544
|
}else {
|
|
545
|
startDate = parseSingleDate(years[0]);
|
|
546
|
if (years.length > 1){
|
|
547
|
endDate = parseSingleDate(years[1]);
|
|
548
|
if (years.length > 2){
|
|
549
|
throw new StringNotParsableException();
|
|
550
|
}
|
|
551
|
}
|
|
552
|
}
|
|
553
|
}catch(StringNotParsableException npe){
|
|
554
|
result = false;
|
|
555
|
}
|
|
556
|
TimePeriod datePublished = TimePeriod.NewInstance(startDate, endDate);
|
|
557
|
|
|
558
|
if (nomRef instanceof BookSection){
|
|
559
|
handleBookSectionYear((BookSection)nomRef, datePublished);
|
|
560
|
}else if (nomRef instanceof StrictReferenceBase){
|
|
561
|
((StrictReferenceBase)nomRef).setDatePublished(datePublished);
|
|
562
|
}else if (nomRef instanceof BibtexReference){
|
|
563
|
((BibtexReference)nomRef).setDatePublished(datePublished);
|
|
564
|
((BibtexReference)nomRef).setYear(year);
|
|
565
|
}else{
|
|
566
|
throw new ClassCastException("nom Ref is not of type StrictReferenceBase but " + (nomRef == null? "(null)" : nomRef.getClass()));
|
|
567
|
}
|
|
568
|
return result;
|
|
569
|
}
|
|
570
|
|
|
571
|
private String makeVolume(IVolumeReference nomRef, String strReference){
|
|
572
|
//volume
|
|
573
|
String volPart = null;
|
|
574
|
String pVolPhrase = volumeSeparator + volume + end;
|
|
575
|
Matcher volPhraseMatcher = getMatcher(pVolPhrase, strReference);
|
|
576
|
if (volPhraseMatcher.find()){
|
|
577
|
volPart = volPhraseMatcher.group(0);
|
|
578
|
strReference = strReference.substring(0, strReference.length() - volPart.length());
|
|
579
|
volPart = volPart.replaceFirst(pStart + volumeSeparator, "").trim();
|
|
580
|
nomRef.setVolume(volPart);
|
|
581
|
}
|
|
582
|
return strReference;
|
|
583
|
}
|
|
584
|
|
|
585
|
private String makeEdition(Book book, String strReference){
|
|
586
|
//volume
|
|
587
|
String editionPart = null;
|
|
588
|
Matcher editionPhraseMatcher = getMatcher(pEditionPart, strReference);
|
|
589
|
|
|
590
|
Matcher editionVolumeMatcher = getMatcher(pEditionVolPart, strReference);
|
|
591
|
boolean isEditionAndVol = editionVolumeMatcher.find();
|
|
592
|
|
|
593
|
if (editionPhraseMatcher.find()){
|
|
594
|
editionPart = editionPhraseMatcher.group(0);
|
|
595
|
int pos = strReference.indexOf(editionPart);
|
|
596
|
int posEnd = pos + editionPart.length();
|
|
597
|
if (isEditionAndVol){
|
|
598
|
posEnd++; //delete also comma
|
|
599
|
}
|
|
600
|
strReference = strReference.substring(0, pos) + strReference.substring(posEnd);
|
|
601
|
editionPart = editionPart.replaceFirst(pStart + editionSeparator, "").trim();
|
|
602
|
book.setEdition(editionPart);
|
|
603
|
}
|
|
604
|
return strReference;
|
|
605
|
}
|
|
606
|
|
|
607
|
private Book parseBook(String reference){
|
|
608
|
Book result = Book.NewInstance();
|
|
609
|
reference = makeEdition(result, reference);
|
|
610
|
reference = makeVolume(result, reference);
|
|
611
|
result.setTitle(reference);
|
|
612
|
return result;
|
|
613
|
}
|
|
614
|
|
|
615
|
|
|
616
|
private Article parseArticle(String reference){
|
|
617
|
//if (articlePatter)
|
|
618
|
//(type, author, title, volume, editor, series;
|
|
619
|
Article result = Article.NewInstance();
|
|
620
|
reference = makeVolume(result, reference);
|
|
621
|
Journal inJournal = Journal.NewInstance();
|
|
622
|
inJournal.setTitle(reference);
|
|
623
|
result.setInJournal(inJournal);
|
|
624
|
return result;
|
|
625
|
}
|
|
626
|
|
|
627
|
private BookSection parseBookSection(String reference){
|
|
628
|
BookSection result = BookSection.NewInstance();
|
|
629
|
String[] parts = reference.split(referenceAuthorSeparator, 2);
|
|
630
|
if (parts.length != 2){
|
|
631
|
logger.warn("Unexpected number of parts");
|
|
632
|
result.setTitleCache(reference);
|
|
633
|
}else{
|
|
634
|
String authorString = parts[0];
|
|
635
|
String bookString = parts[1];
|
|
636
|
|
|
637
|
TeamOrPersonBase<?> authorTeam = author(authorString);
|
|
638
|
Book inBook = parseBook(bookString);
|
|
639
|
inBook.setAuthorTeam(authorTeam);
|
|
640
|
result.setInBook(inBook);
|
|
641
|
}
|
|
642
|
return result;
|
|
643
|
}
|
|
644
|
|
|
645
|
/**
|
|
646
|
* If the publication date of a book section and it's inBook do differ this is usually
|
|
647
|
* caused by the fact that a book has been published during a period, because originally
|
|
648
|
* it consisted of several parts that only later where put together to one book.
|
|
649
|
* If so, the book section's publication date may be a point in time (year or month of year)
|
|
650
|
* whereas the books publication date may be a period of several years.
|
|
651
|
* Therefore a valid nomenclatural reference string should use the book sections
|
|
652
|
* publication date rather then the book's publication date.<BR>
|
|
653
|
* This method in general adds the publication date to the book section.
|
|
654
|
* An exception exists if the publication date is a period. Then the parser
|
|
655
|
* assumes that the nomenclatural reference string does not follow the above rule but
|
|
656
|
* the books publication date is set.
|
|
657
|
* @param bookSection
|
|
658
|
* @param datePublished
|
|
659
|
*/
|
|
660
|
private void handleBookSectionYear(BookSection bookSection, TimePeriod datePublished){
|
|
661
|
if (datePublished == null || datePublished.getStart() == null || bookSection == null){
|
|
662
|
return;
|
|
663
|
}
|
|
664
|
if (datePublished.isPeriod() && bookSection.getInBook() != null){
|
|
665
|
bookSection.getInBook().setDatePublished(datePublished);
|
|
666
|
}else{
|
|
667
|
bookSection.setDatePublished(datePublished);
|
|
668
|
}
|
|
669
|
}
|
|
670
|
|
|
671
|
|
|
672
|
/* (non-Javadoc)
|
|
673
|
* @see eu.etaxonomy.cdm.strategy.parser.INonViralNameParser#parseFullName(java.lang.String)
|
|
674
|
*/
|
|
675
|
public NonViralName parseFullName(String fullNameString){
|
|
676
|
return parseFullName(fullNameString, null, null);
|
|
677
|
}
|
|
678
|
|
|
679
|
|
|
680
|
/* (non-Javadoc)
|
|
681
|
* @see eu.etaxonomy.cdm.strategy.ITaxonNameParser#parseFullName(java.lang.String, eu.etaxonomy.cdm.model.name.Rank)
|
|
682
|
*/
|
|
683
|
public NonViralName parseFullName(String fullNameString, NomenclaturalCode nomCode, Rank rank) {
|
|
684
|
if (fullNameString == null){
|
|
685
|
return null;
|
|
686
|
}else{
|
|
687
|
NonViralName result = getNonViralNameInstance(fullNameString, nomCode, rank);
|
|
688
|
parseFullName(result, fullNameString, rank, false);
|
|
689
|
return result;
|
|
690
|
}
|
|
691
|
}
|
|
692
|
|
|
693
|
|
|
694
|
public void parseFullName(NonViralName nameToBeFilled, String fullNameString, Rank rank, boolean makeEmpty) {
|
|
695
|
//TODO prol. etc.
|
|
696
|
|
|
697
|
if (nameToBeFilled == null){
|
|
698
|
logger.warn("name is null!");
|
|
699
|
}
|
|
700
|
String authorString = null;
|
|
701
|
|
|
702
|
if (fullNameString == null){
|
|
703
|
return;
|
|
704
|
}
|
|
705
|
if (makeEmpty){
|
|
706
|
makeEmpty(nameToBeFilled);
|
|
707
|
}
|
|
708
|
fullNameString.replaceAll(oWs , " ");
|
|
709
|
//TODO
|
|
710
|
// OLD: fullName = oWsRE.subst(fullName, " "); //substitute multiple whitespaces
|
|
711
|
fullNameString = fullNameString.trim();
|
|
712
|
|
|
713
|
String[] epi = pattern.split(fullNameString);
|
|
714
|
try {
|
|
715
|
//cultivars //TODO 2 implement cultivars
|
|
716
|
// if ( cultivarMarkerRE.match(fullName) ){ funktioniert noch nicht, da es z.B. auch Namen gibt, wie 't Hart
|
|
717
|
// result = parseCultivar(fullName);
|
|
718
|
// }
|
|
719
|
//hybrids //TODO 2 implement hybrids
|
|
720
|
//else
|
|
721
|
if (hybridPattern.matcher(fullNameString).matches() ){
|
|
722
|
nameToBeFilled = parseHybrid(fullNameString);
|
|
723
|
}
|
|
724
|
else if (genusOrSupraGenusPattern.matcher(fullNameString).matches()){
|
|
725
|
//supraGeneric
|
|
726
|
if (rank != null && (rank.isSupraGeneric()|| rank.isGenus())){
|
|
727
|
nameToBeFilled.setRank(rank);
|
|
728
|
nameToBeFilled.setGenusOrUninomial(epi[0]);
|
|
729
|
}
|
|
730
|
//genus
|
|
731
|
else {
|
|
732
|
rank = null;
|
|
733
|
nameToBeFilled.setRank(rank);
|
|
734
|
nameToBeFilled.setGenusOrUninomial(epi[0]);
|
|
735
|
nameToBeFilled.setHasProblem(1);
|
|
736
|
nameToBeFilled.setProblemStarts(0);
|
|
737
|
nameToBeFilled.setProblemEnds(epi[0].length());
|
|
738
|
}
|
|
739
|
authorString = fullNameString.substring(epi[0].length());
|
|
740
|
}
|
|
741
|
//infra genus
|
|
742
|
else if (infraGenusPattern.matcher(fullNameString).matches()){
|
|
743
|
nameToBeFilled.setRank(Rank.getRankByAbbreviation(epi[1]));
|
|
744
|
nameToBeFilled.setGenusOrUninomial(epi[0]);
|
|
745
|
nameToBeFilled.setInfraGenericEpithet(epi[2]);
|
|
746
|
authorString = fullNameString.substring(epi[0].length() + 1 + epi[1].length()+ 1 + epi[2].length());
|
|
747
|
}
|
|
748
|
//aggr. or group
|
|
749
|
else if (aggrOrGroupPattern.matcher(fullNameString).matches()){
|
|
750
|
nameToBeFilled.setRank(Rank.getRankByAbbreviation(epi[2]));
|
|
751
|
nameToBeFilled.setGenusOrUninomial(epi[0]);
|
|
752
|
nameToBeFilled.setSpecificEpithet(epi[1]);
|
|
753
|
}
|
|
754
|
//species
|
|
755
|
else if (speciesPattern.matcher(fullNameString).matches()){
|
|
756
|
nameToBeFilled.setRank(Rank.SPECIES());
|
|
757
|
nameToBeFilled.setGenusOrUninomial(epi[0]);
|
|
758
|
nameToBeFilled.setSpecificEpithet(epi[1]);
|
|
759
|
authorString = fullNameString.substring(epi[0].length() + 1 + epi[1].length());
|
|
760
|
}
|
|
761
|
//autonym
|
|
762
|
else if (autonymPattern.matcher(fullNameString).matches()){
|
|
763
|
nameToBeFilled.setRank(Rank.getRankByAbbreviation(epi[epi.length - 2]));
|
|
764
|
nameToBeFilled.setGenusOrUninomial(epi[0]);
|
|
765
|
nameToBeFilled.setSpecificEpithet(epi[1]);
|
|
766
|
nameToBeFilled.setInfraSpecificEpithet(epi[epi.length - 1]);
|
|
767
|
int lenSpecies = 2 + epi[0].length()+epi[1].length();
|
|
768
|
int lenInfraSpecies = 2 + epi[epi.length - 2].length() + epi[epi.length - 1].length();
|
|
769
|
authorString = fullNameString.substring(lenSpecies, fullNameString.length() - lenInfraSpecies);
|
|
770
|
}
|
|
771
|
//infraSpecies
|
|
772
|
else if (infraSpeciesPattern.matcher(fullNameString).matches()){
|
|
773
|
String infraSpecRankEpi = epi[2];
|
|
774
|
String infraSpecEpi = epi[3];
|
|
775
|
if ("tax.".equals(infraSpecRankEpi)){
|
|
776
|
infraSpecRankEpi += " " + epi[3];
|
|
777
|
infraSpecEpi = epi[4];
|
|
778
|
}
|
|
779
|
nameToBeFilled.setRank(Rank.getRankByAbbreviation(infraSpecRankEpi));
|
|
780
|
nameToBeFilled.setGenusOrUninomial(epi[0]);
|
|
781
|
nameToBeFilled.setSpecificEpithet(epi[1]);
|
|
782
|
nameToBeFilled.setInfraSpecificEpithet(infraSpecEpi);
|
|
783
|
authorString = fullNameString.substring(epi[0].length()+ 1 + epi[1].length() +1 + infraSpecRankEpi.length() + 1 + infraSpecEpi.length());
|
|
784
|
}//old infraSpecies
|
|
785
|
else if (oldInfraSpeciesPattern.matcher(fullNameString).matches()){
|
|
786
|
boolean implemented = false;
|
|
787
|
if (implemented){
|
|
788
|
nameToBeFilled.setRank(Rank.getRankByNameOrAbbreviation(epi[2]));
|
|
789
|
nameToBeFilled.setGenusOrUninomial(epi[0]);
|
|
790
|
nameToBeFilled.setSpecificEpithet(epi[1]);
|
|
791
|
//TODO result.setUnnamedNamePhrase(epi[2] + " " + epi[3]);
|
|
792
|
authorString = fullNameString.substring(epi[0].length()+ 1 + epi[1].length() +1 + epi[2].length() + 1 + epi[3].length());
|
|
793
|
}else{
|
|
794
|
nameToBeFilled.setHasProblem(1);
|
|
795
|
nameToBeFilled.setTitleCache(fullNameString);
|
|
796
|
// FIXME Quick fix, otherwise search would not deilver results for unparsable names
|
|
797
|
nameToBeFilled.setNameCache(fullNameString);
|
|
798
|
// END
|
|
799
|
logger.info("Name string " + fullNameString + " could not be parsed because UnnnamedNamePhrase is not yet implemented!");
|
|
800
|
}
|
|
801
|
}
|
|
802
|
//none
|
|
803
|
else{
|
|
804
|
nameToBeFilled.setHasProblem(1);
|
|
805
|
nameToBeFilled.setTitleCache(fullNameString);
|
|
806
|
// FIXME Quick fix, otherwise search would not deilver results for unparsable names
|
|
807
|
nameToBeFilled.setNameCache(fullNameString);
|
|
808
|
// END
|
|
809
|
logger.info("no applicable parsing rule could be found for \"" + fullNameString + "\"");
|
|
810
|
}
|
|
811
|
//authors
|
|
812
|
if (nameToBeFilled != null && authorString != null && authorString.trim().length() > 0 ){
|
|
813
|
TeamOrPersonBase<?>[] authors = new TeamOrPersonBase[4];
|
|
814
|
Integer[] years = new Integer[4];
|
|
815
|
try {
|
|
816
|
Class<? extends NonViralName> clazz = nameToBeFilled.getClass();
|
|
817
|
fullAuthors(authorString, authors, years, clazz);
|
|
818
|
} catch (StringNotParsableException e) {
|
|
819
|
nameToBeFilled.setHasProblem(1);
|
|
820
|
nameToBeFilled.setTitleCache(fullNameString);
|
|
821
|
// FIXME Quick fix, otherwise search would not deilver results for unparsable names
|
|
822
|
nameToBeFilled.setNameCache(fullNameString);
|
|
823
|
// END
|
|
824
|
logger.info("no applicable parsing rule could be found for \"" + fullNameString + "\"");;
|
|
825
|
}
|
|
826
|
nameToBeFilled.setCombinationAuthorTeam(authors[0]);
|
|
827
|
nameToBeFilled.setExCombinationAuthorTeam(authors[1]);
|
|
828
|
nameToBeFilled.setBasionymAuthorTeam(authors[2]);
|
|
829
|
nameToBeFilled.setExBasionymAuthorTeam(authors[3]);
|
|
830
|
if (nameToBeFilled instanceof ZoologicalName){
|
|
831
|
ZoologicalName zooName = (ZoologicalName)nameToBeFilled;
|
|
832
|
zooName.setPublicationYear(years[0]);
|
|
833
|
zooName.setOriginalPublicationYear(years[2]);
|
|
834
|
}
|
|
835
|
}
|
|
836
|
//return
|
|
837
|
if (nameToBeFilled != null){
|
|
838
|
//return(BotanicalName)result;
|
|
839
|
return;
|
|
840
|
}
|
|
841
|
} catch (UnknownCdmTypeException e) {
|
|
842
|
nameToBeFilled.setHasProblem(1);
|
|
843
|
nameToBeFilled.setTitleCache(fullNameString);
|
|
844
|
// FIXME Quick fix, otherwise search would not deilver results for unparsable names
|
|
845
|
nameToBeFilled.setNameCache(fullNameString);
|
|
846
|
// END
|
|
847
|
logger.info("unknown rank (" + (rank == null? "null":rank) + ") or abbreviation in string " + fullNameString);
|
|
848
|
//return result;
|
|
849
|
return;
|
|
850
|
}
|
|
851
|
}
|
|
852
|
|
|
853
|
|
|
854
|
|
|
855
|
/**
|
|
856
|
* Parses the fullAuthorString
|
|
857
|
* @param fullAuthorString
|
|
858
|
* @return array of Teams containing the Team[0],
|
|
859
|
* ExTeam[1], BasionymTeam[2], ExBasionymTeam[3]
|
|
860
|
*/
|
|
861
|
protected void fullAuthors (String fullAuthorString, TeamOrPersonBase<?>[] authors, Integer[] years, Class<? extends NonViralName> clazz)
|
|
862
|
throws StringNotParsableException{
|
|
863
|
fullAuthorString = fullAuthorString.trim();
|
|
864
|
if (fullAuthorString == null || clazz == null){
|
|
865
|
return;
|
|
866
|
}
|
|
867
|
//Botanic
|
|
868
|
if ( BotanicalName.class.isAssignableFrom(clazz) ){
|
|
869
|
if (! fullBotanicAuthorStringPattern.matcher(fullAuthorString).matches() ){
|
|
870
|
throw new StringNotParsableException("fullAuthorString (" +fullAuthorString+") not parsable: ");
|
|
871
|
}
|
|
872
|
}
|
|
873
|
//Zoo
|
|
874
|
else if ( ZoologicalName.class.isAssignableFrom(clazz) ){
|
|
875
|
if (! fullZooAuthorStringPattern.matcher(fullAuthorString).matches() ){
|
|
876
|
throw new StringNotParsableException("fullAuthorString (" +fullAuthorString+") not parsable: ");
|
|
877
|
}
|
|
878
|
}else {
|
|
879
|
//TODO
|
|
880
|
logger.warn ("not yet implemented");
|
|
881
|
throw new StringNotParsableException("fullAuthorString (" +fullAuthorString+") not parsable: ");
|
|
882
|
}
|
|
883
|
fullAuthorsChecked(fullAuthorString, authors, years);
|
|
884
|
}
|
|
885
|
|
|
886
|
/*
|
|
887
|
* like fullTeams but without trim and match check
|
|
888
|
*/
|
|
889
|
protected void fullAuthorsChecked (String fullAuthorString, TeamOrPersonBase<?>[] authors, Integer[] years){
|
|
890
|
int authorTeamStart = 0;
|
|
891
|
Matcher basionymMatcher = basionymPattern.matcher(fullAuthorString);
|
|
892
|
|
|
893
|
if (basionymMatcher.find(0)){
|
|
894
|
|
|
895
|
String basString = basionymMatcher.group();
|
|
896
|
basString = basString.replaceFirst(basStart, "");
|
|
897
|
basString = basString.replaceAll(basEnd, "").trim();
|
|
898
|
authorTeamStart = basionymMatcher.end(1) + 1;
|
|
899
|
|
|
900
|
TeamOrPersonBase<?>[] basAuthors = new TeamOrPersonBase[2];
|
|
901
|
Integer[] basYears = new Integer[2];
|
|
902
|
authorsAndEx(basString, basAuthors, basYears);
|
|
903
|
authors[2]= basAuthors[0];
|
|
904
|
years[2] = basYears[0];
|
|
905
|
authors[3]= basAuthors[1];
|
|
906
|
years[3] = basYears[1];
|
|
907
|
}
|
|
908
|
if (fullAuthorString.length() >= authorTeamStart){
|
|
909
|
TeamOrPersonBase<?>[] combinationAuthors = new TeamOrPersonBase[2];;
|
|
910
|
Integer[] combinationYears = new Integer[2];
|
|
911
|
authorsAndEx(fullAuthorString.substring(authorTeamStart), combinationAuthors, combinationYears);
|
|
912
|
authors[0]= combinationAuthors[0] ;
|
|
913
|
years[0] = combinationYears[0];
|
|
914
|
authors[1]= combinationAuthors[1];
|
|
915
|
years[1] = combinationYears[1];
|
|
916
|
}
|
|
917
|
}
|
|
918
|
|
|
919
|
|
|
920
|
/**
|
|
921
|
* Parses the author and ex-author String
|
|
922
|
* @param authorTeamString String representing the author and the ex-author team
|
|
923
|
* @return array of Teams containing the Team[0] and the ExTeam[1]
|
|
924
|
*/
|
|
925
|
protected void authorsAndEx (String authorTeamString, TeamOrPersonBase<?>[] authors, Integer[] years){
|
|
926
|
//TODO noch allgemeiner am anfang durch Replace etc.
|
|
927
|
authorTeamString = authorTeamString.trim();
|
|
928
|
authorTeamString = authorTeamString.replaceFirst(oWs + "ex" + oWs, " ex. " );
|
|
929
|
int authorEnd = authorTeamString.length();
|
|
930
|
|
|
931
|
Matcher exAuthorMatcher = exAuthorPattern.matcher(authorTeamString);
|
|
932
|
if (exAuthorMatcher.find(0)){
|
|
933
|
int exAuthorBegin = exAuthorMatcher.end(0);
|
|
934
|
String exString = authorTeamString.substring(exAuthorBegin).trim();
|
|
935
|
authorEnd = exAuthorMatcher.start(0);
|
|
936
|
authors [1] = author(exString);
|
|
937
|
}
|
|
938
|
zooOrBotanicAuthor(authorTeamString.substring(0, authorEnd), authors, years );
|
|
939
|
}
|
|
940
|
|
|
941
|
/**
|
|
942
|
* Parses the authorString and if it matches an botanical or zoological authorTeam it fills
|
|
943
|
* the computes the AuthorTeam and fills it into the first field of the team array. Same applies
|
|
944
|
* to the year in case of an zoological name.
|
|
945
|
* @param authorString
|
|
946
|
* @param team
|
|
947
|
* @param year
|
|
948
|
*/
|
|
949
|
protected void zooOrBotanicAuthor(String authorString, TeamOrPersonBase<?>[] team, Integer[] year){
|
|
950
|
if (authorString == null){
|
|
951
|
return;
|
|
952
|
}else if ((authorString = authorString.trim()).length() == 0){
|
|
953
|
return;
|
|
954
|
}
|
|
955
|
Matcher zooAuthorAddidtionMatcher = zooAuthorAddidtionPattern.matcher(authorString);
|
|
956
|
if (zooAuthorAddidtionMatcher.find()){
|
|
957
|
int index = zooAuthorAddidtionMatcher.start(0);
|
|
958
|
String strYear = authorString.substring(index);
|
|
959
|
strYear = strYear.replaceAll(zooAuthorYearSeperator, "").trim();
|
|
960
|
year[0] = Integer.valueOf(strYear);
|
|
961
|
authorString = authorString.substring(0, index).trim();
|
|
962
|
}
|
|
963
|
team[0] = author(authorString);
|
|
964
|
}
|
|
965
|
|
|
966
|
|
|
967
|
/**
|
|
968
|
* Parses an authorTeam String and returns the Team
|
|
969
|
* !!! TODO (atomization not yet implemented)
|
|
970
|
* @param authorTeamString String representing the author team
|
|
971
|
* @return an Team
|
|
972
|
*/
|
|
973
|
protected TeamOrPersonBase<?> author (String authorString){
|
|
974
|
if (authorString == null){
|
|
975
|
return null;
|
|
976
|
}else if ((authorString = authorString.trim()).length() == 0){
|
|
977
|
return null;
|
|
978
|
}else if (! teamSplitterPattern.matcher(authorString).find()){
|
|
979
|
//1 Person
|
|
980
|
Person result = Person.NewInstance();
|
|
981
|
result.setNomenclaturalTitle(authorString);
|
|
982
|
return result;
|
|
983
|
}else{
|
|
984
|
return parsedTeam(authorString);
|
|
985
|
}
|
|
986
|
|
|
987
|
}
|
|
988
|
|
|
989
|
/**
|
|
990
|
* Parses an authorString (reprsenting a team into the single authors and add
|
|
991
|
* them to the return Team.
|
|
992
|
* @param authorString
|
|
993
|
* @return Team
|
|
994
|
*/
|
|
995
|
protected Team parsedTeam(String authorString){
|
|
996
|
Team result = Team.NewInstance();
|
|
997
|
String[] authors = authorString.split(teamSplitter);
|
|
998
|
for (String author : authors){
|
|
999
|
Person person = Person.NewInstance();
|
|
1000
|
person.setNomenclaturalTitle(author);
|
|
1001
|
result.addTeamMember(person);
|
|
1002
|
}
|
|
1003
|
return result;
|
|
1004
|
}
|
|
1005
|
|
|
1006
|
|
|
1007
|
//Parsing of the given full name that has been identified as hybrid already somewhere else.
|
|
1008
|
private BotanicalName parseHybrid(String fullName){
|
|
1009
|
logger.warn("parseHybrid --> function not yet implemented");
|
|
1010
|
BotanicalName result = BotanicalName.NewInstance(null);
|
|
1011
|
result.setTitleCache(fullName);
|
|
1012
|
return result;
|
|
1013
|
}
|
|
1014
|
|
|
1015
|
// // Parsing of the given full name that has been identified as a cultivar already somwhere else.
|
|
1016
|
// // The ... cv. ... syntax is not covered here as it is not according the rules for naming cultivars.
|
|
1017
|
public BotanicalName parseCultivar(String fullName) throws StringNotParsableException{
|
|
1018
|
CultivarPlantName result = null;
|
|
1019
|
String[] words = oWsPattern.split(fullName);
|
|
1020
|
|
|
1021
|
/* ---------------------------------------------------------------------------------
|
|
1022
|
* cultivar
|
|
1023
|
* ---------------------------------------------------------------------------------*/
|
|
1024
|
if (fullName.indexOf(" '") != 0){
|
|
1025
|
//TODO location of 'xx' is probably not arbitrary
|
|
1026
|
Matcher cultivarMatcher = cultivarPattern.matcher(fullName);
|
|
1027
|
if (cultivarMatcher.find()){
|
|
1028
|
String namePart = fullName.replaceFirst(cultivar, "");
|
|
1029
|
|
|
1030
|
String cultivarPart = cultivarMatcher.group(0).replace("'","").trim();
|
|
1031
|
//OLD: String cultivarPart = cultivarRE.getParen(0).replace("'","").trim();
|
|
1032
|
|
|
1033
|
result = (CultivarPlantName)parseFullName(namePart);
|
|
1034
|
result.setCultivarName(cultivarPart);
|
|
1035
|
}
|
|
1036
|
}else if (fullName.indexOf(" cv.") != 0){
|
|
1037
|
// cv. is old form (not official)
|
|
1038
|
throw new StringNotParsableException("Cultivars with only cv. not yet implemented in name parser!");
|
|
1039
|
}
|
|
1040
|
|
|
1041
|
/* ---------------------------------------------------------------------------------
|
|
1042
|
* cultivar group
|
|
1043
|
* ---------------------------------------------------------------------------------
|
|
1044
|
*/
|
|
1045
|
// TODO in work
|
|
1046
|
//Ann. this is not the official way of noting cultivar groups
|
|
1047
|
String group = oWs + "Group" + oWs + capitalEpiWord + end;
|
|
1048
|
Pattern groupRE = Pattern.compile(group);
|
|
1049
|
Matcher groupMatcher = groupRE.matcher(fullName);
|
|
1050
|
if (groupMatcher.find()){
|
|
1051
|
if (! words[words.length - 2].equals("group")){
|
|
1052
|
throw new StringNotParsableException ("fct ParseHybrid --> term before cultivar group name in " + fullName + " should be 'group'");
|
|
1053
|
}else{
|
|
1054
|
|
|
1055
|
String namePart = fullName.substring(0, groupMatcher.start(0) - 0);
|
|
1056
|
//OLD: String namePart = fullName.substring(0, groupRE.getParenStart(0) - 0);
|
|
1057
|
|
|
1058
|
String cultivarPart = words[words.length -1];
|
|
1059
|
result = (CultivarPlantName)parseFullName(namePart);
|
|
1060
|
if (result != null){
|
|
1061
|
result.setCultivarName(cultivarPart);
|
|
1062
|
|
|
1063
|
//OLD: result.setCultivarGroupName(cultivarPart);
|
|
1064
|
}
|
|
1065
|
}
|
|
1066
|
|
|
1067
|
}
|
|
1068
|
// // ---------------------------------------------------------------------------------
|
|
1069
|
// if ( result = "" ){
|
|
1070
|
// return "I: fct ParseCultivar: --> could not parse cultivar " + fullName;
|
|
1071
|
// }else{
|
|
1072
|
// return result;
|
|
1073
|
// }
|
|
1074
|
return result; //TODO
|
|
1075
|
}
|
|
1076
|
|
|
1077
|
|
|
1078
|
private void makeEmpty(NonViralName nameToBeFilled){
|
|
1079
|
nameToBeFilled.setRank(null);
|
|
1080
|
nameToBeFilled.setTitleCache(null, false);
|
|
1081
|
nameToBeFilled.setFullTitleCache(null, false);
|
|
1082
|
nameToBeFilled.setNameCache(null, false);
|
|
1083
|
|
|
1084
|
nameToBeFilled.setAppendedPhrase(null);
|
|
1085
|
//TODO ??
|
|
1086
|
//nameToBeFilled.setBasionym(basionym);
|
|
1087
|
nameToBeFilled.setBasionymAuthorTeam(null);
|
|
1088
|
nameToBeFilled.setCombinationAuthorTeam(null);
|
|
1089
|
nameToBeFilled.setExBasionymAuthorTeam(null);
|
|
1090
|
nameToBeFilled.setExCombinationAuthorTeam(null);
|
|
1091
|
nameToBeFilled.setAuthorshipCache(null, false);
|
|
1092
|
|
|
1093
|
|
|
1094
|
nameToBeFilled.setHasProblem(0);
|
|
1095
|
// TODO ?
|
|
1096
|
//nameToBeFilled.setHomotypicalGroup(newHomotypicalGroup);
|
|
1097
|
|
|
1098
|
|
|
1099
|
nameToBeFilled.setGenusOrUninomial(null);
|
|
1100
|
nameToBeFilled.setInfraGenericEpithet(null);
|
|
1101
|
nameToBeFilled.setSpecificEpithet(null);
|
|
1102
|
nameToBeFilled.setInfraSpecificEpithet(null);
|
|
1103
|
|
|
1104
|
nameToBeFilled.setNomenclaturalMicroReference(null);
|
|
1105
|
nameToBeFilled.setNomenclaturalReference(null);
|
|
1106
|
|
|
1107
|
if (nameToBeFilled instanceof BotanicalName){
|
|
1108
|
BotanicalName botanicalName = (BotanicalName)nameToBeFilled;
|
|
1109
|
botanicalName.setAnamorphic(false);
|
|
1110
|
botanicalName.setHybridFormula(false);
|
|
1111
|
botanicalName.setMonomHybrid(false);
|
|
1112
|
botanicalName.setBinomHybrid(false);
|
|
1113
|
botanicalName.setTrinomHybrid(false);
|
|
1114
|
}
|
|
1115
|
|
|
1116
|
if (nameToBeFilled instanceof ZoologicalName){
|
|
1117
|
ZoologicalName zoologicalName = (ZoologicalName)nameToBeFilled;
|
|
1118
|
zoologicalName.setBreed(null);
|
|
1119
|
zoologicalName.setOriginalPublicationYear(null);
|
|
1120
|
}
|
|
1121
|
}
|
|
1122
|
|
|
1123
|
|
|
1124
|
|
|
1125
|
}
|