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/**
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* Copyright (C) 2009 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.io.eflora;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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import java.util.UUID;
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import java.util.regex.Matcher;
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import java.util.regex.Pattern;
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import org.apache.commons.lang.CharUtils;
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import org.apache.commons.lang.StringUtils;
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import org.apache.log4j.Logger;
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import org.jdom.Attribute;
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import org.jdom.Element;
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import org.springframework.stereotype.Component;
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import org.springframework.transaction.TransactionStatus;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.common.ResultWrapper;
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import eu.etaxonomy.cdm.common.XmlHelp;
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import eu.etaxonomy.cdm.io.common.ICdmIO;
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import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;
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import eu.etaxonomy.cdm.io.eflora.UnmatchedLeads.UnmatchedLeadsKey;
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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.AnnotatableEntity;
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import eu.etaxonomy.cdm.model.common.Annotation;
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import eu.etaxonomy.cdm.model.common.AnnotationType;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.Credit;
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import eu.etaxonomy.cdm.model.common.ExtensionType;
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import eu.etaxonomy.cdm.model.common.ISourceable;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.common.Marker;
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import eu.etaxonomy.cdm.model.common.MarkerType;
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import eu.etaxonomy.cdm.model.common.OriginalSourceType;
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import eu.etaxonomy.cdm.model.common.TimePeriod;
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import eu.etaxonomy.cdm.model.description.CommonTaxonName;
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import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.KeyStatement;
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import eu.etaxonomy.cdm.model.description.PolytomousKey;
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import eu.etaxonomy.cdm.model.description.PolytomousKeyNode;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.description.TextData;
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import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
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import eu.etaxonomy.cdm.model.name.IBotanicalName;
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import eu.etaxonomy.cdm.model.name.INonViralName;
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import eu.etaxonomy.cdm.model.name.NameRelationshipType;
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import eu.etaxonomy.cdm.model.name.NameTypeDesignation;
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
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import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
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import eu.etaxonomy.cdm.model.name.TaxonNameBase;
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import eu.etaxonomy.cdm.model.name.TaxonNameFactory;
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import eu.etaxonomy.cdm.model.name.TypeDesignationBase;
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import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
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import eu.etaxonomy.cdm.model.reference.IBook;
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import eu.etaxonomy.cdm.model.reference.IJournal;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
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import eu.etaxonomy.cdm.model.reference.ReferenceType;
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import eu.etaxonomy.cdm.model.taxon.Classification;
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import eu.etaxonomy.cdm.model.taxon.SynonymType;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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import eu.etaxonomy.cdm.model.taxon.TaxonNode;
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import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
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import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
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import eu.etaxonomy.cdm.strategy.parser.TimePeriodParser;
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/**
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* @author a.mueller
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*
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*/
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@Component
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public class EfloraTaxonImport extends EfloraImportBase implements ICdmIO<EfloraImportState> {
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private static final Logger logger = Logger.getLogger(EfloraTaxonImport.class);
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private static int modCount = 30000;
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private final NonViralNameParserImpl parser = new NonViralNameParserImpl();
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public EfloraTaxonImport(){
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super();
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}
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@Override
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public boolean doCheck(EfloraImportState state){
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boolean result = true;
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return result;
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}
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//TODO make part of state, but state is renewed when invoking the import a second time
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private UnmatchedLeads unmatchedLeads;
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@Override
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public void doInvoke(EfloraImportState state){
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logger.info("start make Taxa ...");
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//FIXME reset state
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state.putTree(null, null);
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// UnmatchedLeads unmatchedLeads = state.getOpenKeys();
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if (unmatchedLeads == null){
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unmatchedLeads = UnmatchedLeads.NewInstance();
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}
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state.setUnmatchedLeads(unmatchedLeads);
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TransactionStatus tx = startTransaction();
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unmatchedLeads.saveToSession(getPolytomousKeyNodeService());
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//TODO generally do not store the reference object in the config
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Reference sourceReference = state.getConfig().getSourceReference();
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getReferenceService().saveOrUpdate(sourceReference);
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Set<TaxonBase> taxaToSave = new HashSet<TaxonBase>();
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ResultWrapper<Boolean> success = ResultWrapper.NewInstance(true);
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Element elbody= getBodyElement(state.getConfig());
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List<Element> elTaxonList = elbody.getChildren();
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int i = 0;
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Set<String> unhandledTitleClassess = new HashSet<String>();
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Set<String> unhandledNomeclatureChildren = new HashSet<String>();
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Set<String> unhandledDescriptionChildren = new HashSet<String>();
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Taxon lastTaxon = getLastTaxon(state);
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//for each taxon
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for (Element elTaxon : elTaxonList){
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try {
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if ((i++ % modCount) == 0 && i > 1){ logger.info("Taxa handled: " + (i-1));}
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if (! elTaxon.getName().equalsIgnoreCase("taxon")){
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logger.warn("body has element other than 'taxon'");
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}
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IBotanicalName botanicalName = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
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Taxon taxon = Taxon.NewInstance(botanicalName, state.getConfig().getSourceReference());
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handleTaxonAttributes(elTaxon, taxon, state);
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List<Element> children = elTaxon.getChildren();
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handleTaxonElement(state, unhandledTitleClassess, unhandledNomeclatureChildren, unhandledDescriptionChildren, taxon, children);
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handleTaxonRelation(state, taxon, lastTaxon);
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lastTaxon = taxon;
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taxaToSave.add(taxon);
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state.getConfig().setLastTaxonUuid(lastTaxon.getUuid());
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} catch (Exception e) {
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logger.warn("Exception occurred in Sapindacea taxon import: " + e);
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e.printStackTrace();
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}
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}
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System.out.println(state.getUnmatchedLeads().toString());
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logger.warn("There are taxa with attributes 'excluded' and 'dubious'");
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logger.info("Children for nomenclature are: " + unhandledNomeclatureChildren);
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logger.info("Children for description are: " + unhandledDescriptionChildren);
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logger.info("Children for homotypes are: " + unhandledHomotypeChildren);
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logger.info("Children for nom are: " + unhandledNomChildren);
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//invokeRelations(source, cdmApp, deleteAll, taxonMap, referenceMap);
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logger.info(i + " taxa handled. Saving ...");
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getTaxonService().saveOrUpdate(taxaToSave);
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getFeatureTreeService().saveOrUpdateFeatureNodesAll(state.getFeatureNodesToSave());
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state.getFeatureNodesToSave().clear();
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commitTransaction(tx);
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logger.info("end makeTaxa ...");
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logger.info("start makeKey ...");
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// invokeDoKey(state);
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logger.info("end makeKey ...");
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if (! success.getValue()){
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state.setUnsuccessfull();
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}
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return ;
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}
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private void handleTaxonAttributes(Element elTaxon, Taxon taxon, EfloraImportState state) {
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List<Attribute> attrList = elTaxon.getAttributes();
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for (Attribute attr : attrList){
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String attrName = attr.getName();
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String attrValue = attr.getValue();
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if ("class".equals(attrName)){
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if (attrValue.equalsIgnoreCase("dubious") || attrValue.equalsIgnoreCase("DUBIOUS GENUS") || attrValue.equalsIgnoreCase("DOUBTFUL SPECIES") ){
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taxon.setDoubtful(true);
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}else{
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MarkerType markerType = getMarkerType(state, attrValue);
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if (markerType == null){
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logger.warn("Class attribute value for taxon not yet supported: " + attrValue);
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}else{
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taxon.addMarker(Marker.NewInstance(markerType, true));
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}
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}
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}else if ("num".equals(attrName)){
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logger.warn("num not yet supported");
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}else{
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logger.warn("Attribute " + attrName + " not yet supported for element taxon");
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}
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}
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}
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private Taxon getLastTaxon(EfloraImportState state) {
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if (state.getConfig().getLastTaxonUuid() == null){
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return null;
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}else{
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return (Taxon)getTaxonService().find(state.getConfig().getLastTaxonUuid());
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}
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}
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// private void invokeDoKey(SapindaceaeImportState state) {
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// TransactionStatus tx = startTransaction();
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//
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// Set<FeatureNode> nodesToSave = new HashSet<FeatureNode>();
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// ITaxonService taxonService = getTaxonService();
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// ResultWrapper<Boolean> success = ResultWrapper.NewInstance(true);
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//
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// Element elbody= getBodyElement(state.getConfig());
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// List<Element> elTaxonList = elbody.getChildren();
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//
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// int i = 0;
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//
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// //for each taxon
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// for (Element elTaxon : elTaxonList){
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// if ((i++ % modCount) == 0 && i > 1){ logger.info("Taxa handled: " + (i-1));}
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// if (! elTaxon.getName().equalsIgnoreCase("taxon")){
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// continue;
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// }
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//
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// List<Element> children = elTaxon.getChildren("key");
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// for (Element element : children){
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// handleKeys(state, element, null);
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// }
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// nodesToSave.add(taxon);
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//
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// }
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//
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// }
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// body/taxon/*
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private void handleTaxonElement(EfloraImportState state, Set<String> unhandledTitleClassess, Set<String> unhandledNomeclatureChildren, Set<String> unhandledDescriptionChildren, Taxon taxon, List<Element> children) {
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AnnotatableEntity lastEntity = null;
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for (Element element : children){
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String elName = element.getName();
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if (elName.equalsIgnoreCase("title")){
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handleTitle(state, element, taxon, unhandledTitleClassess);
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lastEntity = null;
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}else if(elName.equalsIgnoreCase("nomenclature")){
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handleNomenclature(state, element, taxon, unhandledNomeclatureChildren);
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lastEntity = null;
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}else if(elName.equalsIgnoreCase("description")){
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handleDescription(state, element, taxon, unhandledDescriptionChildren);
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lastEntity = null;
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}else if(elName.equalsIgnoreCase("habitatecology")){
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lastEntity = handleEcology(state, element, taxon);
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}else if(elName.equalsIgnoreCase("distribution")){
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lastEntity = handleDistribution(state, element, taxon);
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}else if(elName.equalsIgnoreCase("uses")){
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lastEntity = handleUses(state, element, taxon);
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}else if(elName.equalsIgnoreCase("notes")){
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lastEntity = handleTaxonNotes(state, element, taxon);
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}else if(elName.equalsIgnoreCase("chromosomes")){
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lastEntity = handleChromosomes(state, element, taxon);
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}else if(elName.equalsIgnoreCase("vernacularnames")){
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handleVernaculars(state, element, taxon);
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}else if(elName.equalsIgnoreCase("key")){
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lastEntity = handleKeys(state, element, taxon);
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}else if(elName.equalsIgnoreCase("references")){
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handleReferences(state, element, taxon, lastEntity);
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lastEntity = null;
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}else if(elName.equalsIgnoreCase("taxon")){
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logger.warn("A taxon should not be part of a taxon");
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}else if(elName.equalsIgnoreCase("homotypes")){
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logger.warn("Homotypes should be included in the nomenclature flag but is child of taxon [XPath: body/taxon/homotypes]");
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}else{
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logger.warn("Unexpected child for taxon: " + elName);
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}
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}
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}
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private void handleVernaculars(EfloraImportState state, Element elVernacular, Taxon taxon) {
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verifyNoAttribute(elVernacular);
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verifyNoChildren(elVernacular, false);
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String value = elVernacular.getTextNormalize();
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Feature feature = Feature.COMMON_NAME();
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value = replaceStart(value, "Noms vernaculaires");
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String[] dialects = value.split(";");
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for (String singleDialect : dialects){
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handleSingleDialect(taxon, singleDialect, feature, state);
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}
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return;
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}
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private void handleSingleDialect(Taxon taxon, String singleDialect, Feature feature, EfloraImportState state) {
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singleDialect = singleDialect.trim();
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TaxonDescription description = getDescription(taxon);
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String reDialect = "\\(dial\\.\\s.*\\)";
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// String reDialect = "\\(.*\\)";
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Pattern patDialect = Pattern.compile(reDialect);
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Matcher matcher = patDialect.matcher(singleDialect);
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if (matcher.find()){
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String dialect = singleDialect.substring(matcher.start(), matcher.end());
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dialect = dialect.replace("(dial. ", "").replace(")", "");
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334
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Language language = null;
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try {
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language = this.getLanguage(state, state.getTransformer().getLanguageUuid(dialect), dialect, dialect, dialect);
|
|
338
|
} catch (UndefinedTransformerMethodException e) {
|
|
339
|
logger.error(e.getMessage());
|
|
340
|
}
|
|
341
|
|
|
342
|
String commonNames = singleDialect.substring(0, matcher.start());
|
|
343
|
String[] splitNames = commonNames.split(",");
|
|
344
|
for (String commonNameString : splitNames){
|
|
345
|
commonNameString = commonNameString.trim();
|
|
346
|
CommonTaxonName commonName = CommonTaxonName.NewInstance(commonNameString, language);
|
|
347
|
description.addElement(commonName);
|
|
348
|
}
|
|
349
|
}else{
|
|
350
|
logger.warn("No dialect match: " + singleDialect);
|
|
351
|
}
|
|
352
|
}
|
|
353
|
|
|
354
|
|
|
355
|
private void handleReferences(EfloraImportState state, Element elReferences, Taxon taxon, AnnotatableEntity lastEntity) {
|
|
356
|
verifyNoAttribute(elReferences);
|
|
357
|
verifyNoChildren(elReferences, true);
|
|
358
|
String refString = elReferences.getTextNormalize();
|
|
359
|
if (lastEntity == null){
|
|
360
|
logger.warn("No last entity defined: " + refString);
|
|
361
|
return;
|
|
362
|
}
|
|
363
|
|
|
364
|
Annotation annotation = Annotation.NewInstance(refString, AnnotationType.EDITORIAL(), Language.DEFAULT());
|
|
365
|
lastEntity.addAnnotation(annotation);
|
|
366
|
}
|
|
367
|
|
|
368
|
|
|
369
|
private PolytomousKey handleKeys(EfloraImportState state, Element elKey, Taxon taxon) {
|
|
370
|
UnmatchedLeads openKeys = state.getUnmatchedLeads();
|
|
371
|
|
|
372
|
//title
|
|
373
|
String title = makeKeyTitle(elKey);
|
|
374
|
|
|
375
|
//key
|
|
376
|
PolytomousKey key = PolytomousKey.NewTitledInstance(title);
|
|
377
|
|
|
378
|
//TODO add covered taxa etc.
|
|
379
|
verifyNoAttribute(elKey);
|
|
380
|
|
|
381
|
//notes
|
|
382
|
makeKeyNotes(elKey, key);
|
|
383
|
|
|
384
|
//keycouplets
|
|
385
|
List<Element> keychoices = new ArrayList<Element>();
|
|
386
|
keychoices.addAll(elKey.getChildren("keycouplet"));
|
|
387
|
keychoices.addAll(elKey.getChildren("keychoice"));
|
|
388
|
|
|
389
|
|
|
390
|
for (Element elKeychoice : keychoices){
|
|
391
|
handleKeyChoices(state, openKeys, key, elKeychoice, taxon);
|
|
392
|
elKey.removeContent(elKeychoice);
|
|
393
|
}
|
|
394
|
|
|
395
|
//
|
|
396
|
verifyNoChildren(elKey);
|
|
397
|
logger.info("Unmatched leads after key handling:" + openKeys.toString());
|
|
398
|
|
|
399
|
|
|
400
|
if (state.getConfig().isDoPrintKeys()){
|
|
401
|
key.print(System.err);
|
|
402
|
}
|
|
403
|
getPolytomousKeyService().save(key);
|
|
404
|
return key;
|
|
405
|
}
|
|
406
|
|
|
407
|
|
|
408
|
/**
|
|
409
|
* @param state
|
|
410
|
* @param elKey
|
|
411
|
* @param openKeys
|
|
412
|
* @param key
|
|
413
|
* @param elKeychoice
|
|
414
|
* @param taxon
|
|
415
|
*/
|
|
416
|
private void handleKeyChoices(EfloraImportState state, UnmatchedLeads openKeys, PolytomousKey key, Element elKeychoice, Taxon taxon) {
|
|
417
|
|
|
418
|
//char Attribute
|
|
419
|
//TODO it's still unclear if char is a feature and needs to be a new attribute
|
|
420
|
//or if it is handled as question. Therefore both cases are handled but feature
|
|
421
|
//is finally not yet set
|
|
422
|
KeyStatement question = handleKeychoiceChar(state, elKeychoice);
|
|
423
|
Feature feature = handleKeychoiceCharAsFeature(state, elKeychoice);
|
|
424
|
|
|
425
|
//lead
|
|
426
|
List<PolytomousKeyNode> childNodes = handleKeychoiceLeads(state, key, elKeychoice, taxon, question, feature);
|
|
427
|
|
|
428
|
//num -> match with unmatched leads
|
|
429
|
handleKeychoiceNum(openKeys, key, elKeychoice, childNodes);
|
|
430
|
|
|
431
|
//others
|
|
432
|
verifyNoAttribute(elKeychoice);
|
|
433
|
}
|
|
434
|
|
|
435
|
|
|
436
|
/**
|
|
437
|
* @param openKeys
|
|
438
|
* @param key
|
|
439
|
* @param elKeychoice
|
|
440
|
* @param childNodes
|
|
441
|
*/
|
|
442
|
private void handleKeychoiceNum(UnmatchedLeads openKeys, PolytomousKey key, Element elKeychoice, List<PolytomousKeyNode> childNodes) {
|
|
443
|
Attribute numAttr = elKeychoice.getAttribute("num");
|
|
444
|
String num = CdmUtils.removeTrailingDot(numAttr == null? "":numAttr.getValue());
|
|
445
|
UnmatchedLeadsKey okk = UnmatchedLeadsKey.NewInstance(key, num);
|
|
446
|
Set<PolytomousKeyNode> matchingNodes = openKeys.getNodes(okk);
|
|
447
|
for (PolytomousKeyNode matchingNode : matchingNodes){
|
|
448
|
for (PolytomousKeyNode childNode : childNodes){
|
|
449
|
matchingNode.addChild(childNode);
|
|
450
|
}
|
|
451
|
openKeys.removeNode(okk, matchingNode);
|
|
452
|
}
|
|
453
|
if (matchingNodes.isEmpty()){
|
|
454
|
for (PolytomousKeyNode childNode : childNodes){
|
|
455
|
key.getRoot().addChild(childNode);
|
|
456
|
}
|
|
457
|
}
|
|
458
|
|
|
459
|
elKeychoice.removeAttribute("num");
|
|
460
|
}
|
|
461
|
|
|
462
|
|
|
463
|
/**
|
|
464
|
* @param state
|
|
465
|
* @param key
|
|
466
|
* @param elKeychoice
|
|
467
|
* @param taxon
|
|
468
|
* @param feature
|
|
469
|
* @return
|
|
470
|
*/
|
|
471
|
private List<PolytomousKeyNode> handleKeychoiceLeads( EfloraImportState state, PolytomousKey key, Element elKeychoice, Taxon taxon, KeyStatement question, Feature feature) {
|
|
472
|
List<PolytomousKeyNode> childNodes = new ArrayList<PolytomousKeyNode>();
|
|
473
|
List<Element> leads = elKeychoice.getChildren("lead");
|
|
474
|
for(Element elLead : leads){
|
|
475
|
PolytomousKeyNode childNode = handleLead(state, key, elLead, taxon, question, feature);
|
|
476
|
childNodes.add(childNode);
|
|
477
|
}
|
|
478
|
return childNodes;
|
|
479
|
}
|
|
480
|
|
|
481
|
|
|
482
|
/**
|
|
483
|
* @param state
|
|
484
|
* @param elKeychoice
|
|
485
|
* @return
|
|
486
|
*/
|
|
487
|
private KeyStatement handleKeychoiceChar(EfloraImportState state, Element elKeychoice) {
|
|
488
|
KeyStatement statement = null;
|
|
489
|
Attribute charAttr = elKeychoice.getAttribute("char");
|
|
490
|
if (charAttr != null){
|
|
491
|
String charStr = charAttr.getValue();
|
|
492
|
if (StringUtils.isNotBlank(charStr)){
|
|
493
|
statement = KeyStatement.NewInstance(charStr);
|
|
494
|
}
|
|
495
|
elKeychoice.removeAttribute("char");
|
|
496
|
}
|
|
497
|
return statement;
|
|
498
|
}
|
|
499
|
|
|
500
|
/**
|
|
501
|
* @param state
|
|
502
|
* @param elKeychoice
|
|
503
|
* @return
|
|
504
|
*/
|
|
505
|
private Feature handleKeychoiceCharAsFeature(EfloraImportState state, Element elKeychoice) {
|
|
506
|
Feature feature = null;
|
|
507
|
Attribute charAttr = elKeychoice.getAttribute("char");
|
|
508
|
if (charAttr != null){
|
|
509
|
String charStr = charAttr.getValue();
|
|
510
|
feature = getFeature(charStr, state);
|
|
511
|
elKeychoice.removeAttribute("char");
|
|
512
|
}
|
|
513
|
return feature;
|
|
514
|
}
|
|
515
|
|
|
516
|
|
|
517
|
private PolytomousKeyNode handleLead(EfloraImportState state, PolytomousKey key, Element elLead, Taxon taxon, KeyStatement question, Feature feature) {
|
|
518
|
PolytomousKeyNode node = PolytomousKeyNode.NewInstance();
|
|
519
|
//TODO the char attribute in the keychoice is more a feature than a question
|
|
520
|
//needs to be discussed on model side
|
|
521
|
node.setQuestion(question);
|
|
522
|
// node.setFeature(feature);
|
|
523
|
|
|
524
|
//text
|
|
525
|
String text = handleLeadText(elLead, node);
|
|
526
|
|
|
527
|
//num
|
|
528
|
handleLeadNum(elLead, text);
|
|
529
|
|
|
530
|
//goto
|
|
531
|
handleLeadGoto(state, key, elLead, taxon, node);
|
|
532
|
|
|
533
|
//others
|
|
534
|
verifyNoAttribute(elLead);
|
|
535
|
|
|
536
|
return node;
|
|
537
|
}
|
|
538
|
|
|
539
|
|
|
540
|
/**
|
|
541
|
* @param elLead
|
|
542
|
* @param node
|
|
543
|
* @return
|
|
544
|
*/
|
|
545
|
private String handleLeadText(Element elLead, PolytomousKeyNode node) {
|
|
546
|
String text = elLead.getAttributeValue("text").trim();
|
|
547
|
if (StringUtils.isBlank(text)){
|
|
548
|
logger.warn("Empty text in lead");
|
|
549
|
}
|
|
550
|
elLead.removeAttribute("text");
|
|
551
|
KeyStatement statement = KeyStatement.NewInstance(text);
|
|
552
|
node.setStatement(statement);
|
|
553
|
return text;
|
|
554
|
}
|
|
555
|
|
|
556
|
|
|
557
|
/**
|
|
558
|
* @param state
|
|
559
|
* @param key
|
|
560
|
* @param elLead
|
|
561
|
* @param taxon
|
|
562
|
* @param node
|
|
563
|
*/
|
|
564
|
private void handleLeadGoto(EfloraImportState state, PolytomousKey key, Element elLead, Taxon taxon, PolytomousKeyNode node) {
|
|
565
|
Attribute gotoAttr = elLead.getAttribute("goto");
|
|
566
|
if (gotoAttr != null){
|
|
567
|
String strGoto = gotoAttr.getValue().trim();
|
|
568
|
//create key
|
|
569
|
UnmatchedLeadsKey gotoKey = null;
|
|
570
|
if (isInternalNode(strGoto)){
|
|
571
|
gotoKey = UnmatchedLeadsKey.NewInstance(key, strGoto);
|
|
572
|
}else{
|
|
573
|
String taxonKey = makeTaxonKey(strGoto, taxon);
|
|
574
|
gotoKey = UnmatchedLeadsKey.NewInstance(taxonKey);
|
|
575
|
}
|
|
576
|
//
|
|
577
|
UnmatchedLeads openKeys = state.getUnmatchedLeads();
|
|
578
|
if (gotoKey.isInnerLead()){
|
|
579
|
Set<PolytomousKeyNode> existingNodes = openKeys.getNodes(gotoKey);
|
|
580
|
for (PolytomousKeyNode existingNode : existingNodes){
|
|
581
|
node.addChild(existingNode);
|
|
582
|
}
|
|
583
|
}
|
|
584
|
openKeys.addKey(gotoKey, node);
|
|
585
|
//remove attribute (need for consistency check)
|
|
586
|
elLead.removeAttribute("goto");
|
|
587
|
}else{
|
|
588
|
logger.warn("lead has no goto attribute");
|
|
589
|
}
|
|
590
|
}
|
|
591
|
|
|
592
|
|
|
593
|
/**
|
|
594
|
* @param elLead
|
|
595
|
* @param text
|
|
596
|
*/
|
|
597
|
private void handleLeadNum(Element elLead, String text) {
|
|
598
|
Attribute numAttr = elLead.getAttribute("num");
|
|
599
|
if (numAttr != null){
|
|
600
|
//TODO num
|
|
601
|
String num = numAttr.getValue();
|
|
602
|
elLead.removeAttribute("num");
|
|
603
|
}else{
|
|
604
|
logger.info("Keychoice has no num attribute: " + text);
|
|
605
|
}
|
|
606
|
}
|
|
607
|
|
|
608
|
|
|
609
|
private String makeTaxonKey(String strGoto, Taxon taxon) {
|
|
610
|
String result = "";
|
|
611
|
if (strGoto == null){
|
|
612
|
return "";
|
|
613
|
}
|
|
614
|
String strGenusName = taxon.getName().getGenusOrUninomial();
|
|
615
|
strGoto = strGoto.replaceAll("\\([^\\(\\)]*\\)", ""); //replace all brackets
|
|
616
|
strGoto = strGoto.replaceAll("\\s+", " "); //replace multiple whitespaces by exactly one whitespace
|
|
617
|
|
|
618
|
strGoto = strGoto.trim();
|
|
619
|
String[] split = strGoto.split("\\s");
|
|
620
|
for (int i = 0; i<split.length; i++){
|
|
621
|
String single = split[i];
|
|
622
|
if (isGenusAbbrev(single, strGenusName)){
|
|
623
|
split[i] = strGenusName;
|
|
624
|
}
|
|
625
|
// if (isInfraSpecificMarker(single)){
|
|
626
|
// String strSpeciesName = taxon.getName().getSpecificEpithet();
|
|
627
|
// split[i] = strGenusName + " " + strSpeciesName + " ";
|
|
628
|
// }
|
|
629
|
result = (result + " " + split[i]).trim();
|
|
630
|
}
|
|
631
|
return result;
|
|
632
|
}
|
|
633
|
|
|
634
|
|
|
635
|
private boolean isInfraSpecificMarker(String single) {
|
|
636
|
try {
|
|
637
|
if (Rank.getRankByIdInVoc(single).isInfraSpecific()){
|
|
638
|
return true;
|
|
639
|
}
|
|
640
|
} catch (UnknownCdmTypeException e) {
|
|
641
|
return false;
|
|
642
|
}
|
|
643
|
return false;
|
|
644
|
}
|
|
645
|
|
|
646
|
|
|
647
|
private boolean isGenusAbbrev(String single, String strGenusName) {
|
|
648
|
if (! single.matches("[A-Z]\\.?")) {
|
|
649
|
return false;
|
|
650
|
}else if (single.length() == 0 || strGenusName == null || strGenusName.length() == 0){
|
|
651
|
return false;
|
|
652
|
}else{
|
|
653
|
return single.charAt(0) == strGenusName.charAt(0);
|
|
654
|
}
|
|
655
|
}
|
|
656
|
|
|
657
|
|
|
658
|
private boolean isInternalNode(String strGoto) {
|
|
659
|
return CdmUtils.isNumeric(strGoto);
|
|
660
|
}
|
|
661
|
|
|
662
|
|
|
663
|
private void makeKeyNotes(Element keyElement, PolytomousKey key) {
|
|
664
|
Element elNotes = keyElement.getChild("notes");
|
|
665
|
if (elNotes != null){
|
|
666
|
keyElement.removeContent(elNotes);
|
|
667
|
String notes = elNotes.getTextNormalize();
|
|
668
|
if (StringUtils.isNotBlank(notes)){
|
|
669
|
key.addAnnotation(Annotation.NewInstance(notes, AnnotationType.EDITORIAL(), Language.DEFAULT()));
|
|
670
|
}
|
|
671
|
}
|
|
672
|
}
|
|
673
|
|
|
674
|
|
|
675
|
private String makeKeyTitle(Element keyElement) {
|
|
676
|
String title = "- no title - ";
|
|
677
|
Attribute titleAttr = keyElement.getAttribute("title");
|
|
678
|
keyElement.removeAttribute(titleAttr);
|
|
679
|
if (titleAttr == null){
|
|
680
|
Element elTitle = keyElement.getChild("keytitle");
|
|
681
|
keyElement.removeContent(elTitle);
|
|
682
|
if (elTitle != null){
|
|
683
|
title = elTitle.getTextNormalize();
|
|
684
|
}
|
|
685
|
}else{
|
|
686
|
title = titleAttr.getValue();
|
|
687
|
}
|
|
688
|
return title;
|
|
689
|
}
|
|
690
|
|
|
691
|
|
|
692
|
/**
|
|
693
|
* @param state
|
|
694
|
* @param element
|
|
695
|
* @param taxon
|
|
696
|
*/
|
|
697
|
private TextData handleChromosomes(EfloraImportState state, Element element, Taxon taxon) {
|
|
698
|
Feature chromosomeFeature = getFeature("chromosomes", state);
|
|
699
|
verifyNoAttribute(element);
|
|
700
|
verifyNoChildren(element);
|
|
701
|
String value = element.getTextNormalize();
|
|
702
|
value = replaceStart(value, "Chromosomes");
|
|
703
|
String chromosomesPart = getChromosomesPart(value);
|
|
704
|
String references = value.replace(chromosomesPart, "").trim();
|
|
705
|
chromosomesPart = chromosomesPart.replace(":", "").trim();
|
|
706
|
return addDescriptionElement(state, taxon, chromosomesPart, chromosomeFeature, references);
|
|
707
|
}
|
|
708
|
|
|
709
|
|
|
710
|
/**
|
|
711
|
* @param ref
|
|
712
|
* @param string
|
|
713
|
* @return
|
|
714
|
*/
|
|
715
|
private void makeOriginalSourceReferences(ISourceable sourcable, String splitter, String refAll) {
|
|
716
|
String[] splits = refAll.split(splitter);
|
|
717
|
for (String strRef: splits){
|
|
718
|
Reference ref = ReferenceFactory.newGeneric();
|
|
719
|
ref.setTitleCache(strRef, true);
|
|
720
|
String refDetail = parseReferenceYearAndDetail(ref);
|
|
721
|
sourcable.addSource(OriginalSourceType.PrimaryTaxonomicSource, null, null, ref, refDetail);
|
|
722
|
}
|
|
723
|
|
|
724
|
|
|
725
|
//TODO use regex instead
|
|
726
|
/* String detailResult = null;
|
|
727
|
String titleToParse = ref.getTitleCache();
|
|
728
|
String reReference = "^\\.{1,}";
|
|
729
|
// String reYear = "\\([1-2]{1}[0-9]{3}\\)";
|
|
730
|
String reYear = "\\([1-2]{1}[0-9]{3}\\)";
|
|
731
|
String reYearPeriod = reYear + "(-" + reYear + ")+";
|
|
732
|
String reDetail = "\\.{1,10}$";
|
|
733
|
*/
|
|
734
|
}
|
|
735
|
|
|
736
|
|
|
737
|
/**
|
|
738
|
* @param value
|
|
739
|
* @return
|
|
740
|
*/
|
|
741
|
private String getChromosomesPart(String str) {
|
|
742
|
Pattern pattern = Pattern.compile("2n\\s*=\\s*\\d{1,2}:");
|
|
743
|
Matcher matcher = pattern.matcher(str);
|
|
744
|
if (matcher.find()){
|
|
745
|
return matcher.group(0);
|
|
746
|
}else{
|
|
747
|
logger.warn("Chromosomes could not be parsed: " + str);
|
|
748
|
}
|
|
749
|
return str;
|
|
750
|
}
|
|
751
|
|
|
752
|
|
|
753
|
/**
|
|
754
|
* @param state
|
|
755
|
* @param element
|
|
756
|
* @param taxon
|
|
757
|
*/
|
|
758
|
private TextData handleTaxonNotes(EfloraImportState state, Element element, Taxon taxon) {
|
|
759
|
TextData result = null;
|
|
760
|
verifyNoChildren(element, true);
|
|
761
|
//verifyNoAttribute(element);
|
|
762
|
List<Attribute> attributes = element.getAttributes();
|
|
763
|
for (Attribute attribute : attributes){
|
|
764
|
if (! attribute.getName().equalsIgnoreCase("class")){
|
|
765
|
logger.warn("Char has unhandled attribute " + attribute.getName());
|
|
766
|
}else{
|
|
767
|
String classValue = attribute.getValue();
|
|
768
|
result = handleDescriptiveElement(state, element, taxon, classValue);
|
|
769
|
}
|
|
770
|
}
|
|
771
|
//if no class attribute exists, handle as note
|
|
772
|
if (attributes.isEmpty()){
|
|
773
|
result = handleDescriptiveElement(state, element, taxon, "Note");
|
|
774
|
}
|
|
775
|
|
|
776
|
//Annotation annotation = Annotation.NewInstance(value, AnnotationType.EDITORIAL(), Language.ENGLISH());
|
|
777
|
//taxon.addAnnotation(annotation);
|
|
778
|
return result; //annotation;
|
|
779
|
}
|
|
780
|
|
|
781
|
|
|
782
|
/**
|
|
783
|
* @param state
|
|
784
|
* @param element
|
|
785
|
* @param taxon
|
|
786
|
* @param result
|
|
787
|
* @param attribute
|
|
788
|
* @return
|
|
789
|
*/
|
|
790
|
private TextData handleDescriptiveElement(EfloraImportState state, Element element, Taxon taxon, String classValue) {
|
|
791
|
TextData result = null;
|
|
792
|
Feature feature = getFeature(classValue, state);
|
|
793
|
if (feature == null){
|
|
794
|
logger.warn("Unhandled feature: " + classValue);
|
|
795
|
}else{
|
|
796
|
String value = element.getValue();
|
|
797
|
value = replaceStart(value, "Notes");
|
|
798
|
value = replaceStart(value, "Note");
|
|
799
|
result = addDescriptionElement(state, taxon, value, feature, null);
|
|
800
|
}
|
|
801
|
return result;
|
|
802
|
}
|
|
803
|
|
|
804
|
|
|
805
|
private void removeBr(Element element) {
|
|
806
|
element.removeChildren("Br");
|
|
807
|
element.removeChildren("br");
|
|
808
|
element.removeChildren("BR");
|
|
809
|
}
|
|
810
|
|
|
811
|
|
|
812
|
/**
|
|
813
|
* @param state
|
|
814
|
* @param element
|
|
815
|
* @param taxon
|
|
816
|
*/
|
|
817
|
private TextData handleUses(EfloraImportState state, Element element, Taxon taxon) {
|
|
818
|
verifyNoAttribute(element);
|
|
819
|
verifyNoChildren(element, true);
|
|
820
|
String value = element.getTextNormalize();
|
|
821
|
value = replaceStart(value, "Uses");
|
|
822
|
Feature feature = Feature.USES();
|
|
823
|
return addDescriptionElement(state, taxon, value, feature, null);
|
|
824
|
|
|
825
|
}
|
|
826
|
|
|
827
|
|
|
828
|
/**
|
|
829
|
* @param state
|
|
830
|
* @param element
|
|
831
|
* @param taxon
|
|
832
|
* @param unhandledDescriptionChildren
|
|
833
|
*/
|
|
834
|
private DescriptionElementBase handleDistribution(EfloraImportState state, Element element, Taxon taxon) {
|
|
835
|
verifyNoAttribute(element);
|
|
836
|
verifyNoChildren(element, true);
|
|
837
|
String value = element.getTextNormalize();
|
|
838
|
value = replaceStart(value, "Distribution");
|
|
839
|
Feature feature = Feature.DISTRIBUTION();
|
|
840
|
//distribution parsing almost impossible as there is lots of freetext in the distribution tag
|
|
841
|
return addDescriptionElement(state, taxon, value, feature, null);
|
|
842
|
}
|
|
843
|
|
|
844
|
|
|
845
|
/**
|
|
846
|
* @param state
|
|
847
|
* @param element
|
|
848
|
* @param taxon
|
|
849
|
* @param unhandledDescriptionChildren
|
|
850
|
*/
|
|
851
|
private TextData handleEcology(EfloraImportState state, Element elEcology, Taxon taxon) {
|
|
852
|
verifyNoAttribute(elEcology);
|
|
853
|
verifyNoChildren(elEcology, true);
|
|
854
|
String value = elEcology.getTextNormalize();
|
|
855
|
Feature feature = Feature.ECOLOGY();
|
|
856
|
if (value.startsWith("Habitat & Ecology")){
|
|
857
|
feature = getFeature("Habitat & Ecology", state);
|
|
858
|
value = replaceStart(value, "Habitat & Ecology");
|
|
859
|
}else if (value.startsWith("Habitat")){
|
|
860
|
value = replaceStart(value, "Habitat");
|
|
861
|
feature = getFeature("Habitat", state);
|
|
862
|
}
|
|
863
|
return addDescriptionElement(state, taxon, value, feature, null);
|
|
864
|
}
|
|
865
|
|
|
866
|
|
|
867
|
|
|
868
|
/**
|
|
869
|
* @param value
|
|
870
|
* @param replacementString
|
|
871
|
*/
|
|
872
|
private String replaceStart(String value, String replacementString) {
|
|
873
|
if (value.startsWith(replacementString) ){
|
|
874
|
value = value.substring(replacementString.length()).trim();
|
|
875
|
}
|
|
876
|
while (value.startsWith("-") || value.startsWith("–") ){
|
|
877
|
value = value.substring("-".length()).trim();
|
|
878
|
}
|
|
879
|
return value;
|
|
880
|
}
|
|
881
|
|
|
882
|
|
|
883
|
/**
|
|
884
|
* @param value
|
|
885
|
* @param replacementString
|
|
886
|
*/
|
|
887
|
protected String removeTrailing(String value, String replacementString) {
|
|
888
|
if (value == null){
|
|
889
|
return null;
|
|
890
|
}
|
|
891
|
if (value.endsWith(replacementString) ){
|
|
892
|
value = value.substring(0, value.length() - replacementString.length()).trim();
|
|
893
|
}
|
|
894
|
return value;
|
|
895
|
}
|
|
896
|
|
|
897
|
/**
|
|
898
|
* @param state
|
|
899
|
* @param element
|
|
900
|
* @param taxon
|
|
901
|
* @param unhandledNomeclatureChildren
|
|
902
|
*/
|
|
903
|
private void handleNomenclature(EfloraImportState state, Element elNomenclature, Taxon taxon, Set<String> unhandledChildren) {
|
|
904
|
verifyNoAttribute(elNomenclature);
|
|
905
|
|
|
906
|
List<Element> elements = elNomenclature.getChildren();
|
|
907
|
for (Element element : elements){
|
|
908
|
if (element.getName().equals("homotypes")){
|
|
909
|
handleHomotypes(state, element, taxon);
|
|
910
|
}else if (element.getName().equals("notes")){
|
|
911
|
handleNomenclatureNotes(state, element, taxon);
|
|
912
|
}else{
|
|
913
|
unhandledChildren.add(element.getName());
|
|
914
|
}
|
|
915
|
}
|
|
916
|
|
|
917
|
}
|
|
918
|
|
|
919
|
|
|
920
|
|
|
921
|
private void handleNomenclatureNotes(EfloraImportState state, Element elNotes, Taxon taxon) {
|
|
922
|
verifyNoAttribute(elNotes);
|
|
923
|
verifyNoChildren(elNotes);
|
|
924
|
String notesText = elNotes.getTextNormalize();
|
|
925
|
Annotation annotation = Annotation.NewInstance(notesText, AnnotationType.EDITORIAL(), Language.DEFAULT());
|
|
926
|
taxon.addAnnotation(annotation);
|
|
927
|
}
|
|
928
|
|
|
929
|
|
|
930
|
|
|
931
|
private static Set<String> unhandledHomotypeChildren = new HashSet<String>();
|
|
932
|
/**
|
|
933
|
* @param state
|
|
934
|
* @param element
|
|
935
|
* @param taxon
|
|
936
|
*/
|
|
937
|
private void handleHomotypes(EfloraImportState state, Element elHomotypes, Taxon taxon) {
|
|
938
|
verifyNoAttribute(elHomotypes);
|
|
939
|
|
|
940
|
List<Element> elements = elHomotypes.getChildren();
|
|
941
|
HomotypicalGroup homotypicalGroup = null;
|
|
942
|
for (Element element : elements){
|
|
943
|
if (element.getName().equals("nom")){
|
|
944
|
homotypicalGroup = handleNom(state, element, taxon, homotypicalGroup);
|
|
945
|
}else{
|
|
946
|
unhandledHomotypeChildren.add(element.getName());
|
|
947
|
}
|
|
948
|
}
|
|
949
|
|
|
950
|
}
|
|
951
|
|
|
952
|
private static Set<String> unhandledNomChildren = new HashSet<String>();
|
|
953
|
|
|
954
|
/**
|
|
955
|
* @param state
|
|
956
|
* @param element
|
|
957
|
* @param taxon
|
|
958
|
*/
|
|
959
|
private HomotypicalGroup handleNom(EfloraImportState state, Element elNom, Taxon taxon, HomotypicalGroup homotypicalGroup) {
|
|
960
|
List<Attribute> attributes = elNom.getAttributes();
|
|
961
|
|
|
962
|
boolean taxonBaseClassType = false;
|
|
963
|
for (Attribute attribute : attributes){
|
|
964
|
if (! attribute.getName().equalsIgnoreCase("class")){
|
|
965
|
logger.warn("Nom has unhandled attribute " + attribute.getName());
|
|
966
|
}else{
|
|
967
|
String classValue = attribute.getValue();
|
|
968
|
if (classValue.equalsIgnoreCase("acceptedname")){
|
|
969
|
homotypicalGroup = handleNomTaxon(state, elNom, taxon,homotypicalGroup, false);
|
|
970
|
taxonBaseClassType = true;
|
|
971
|
}else if (classValue.equalsIgnoreCase("synonym")){
|
|
972
|
homotypicalGroup = handleNomTaxon(state, elNom, taxon, homotypicalGroup, true);
|
|
973
|
taxonBaseClassType = true;
|
|
974
|
}else if (classValue.equalsIgnoreCase("typeref")){
|
|
975
|
handleTypeRef(state, elNom, taxon, homotypicalGroup);
|
|
976
|
}else{
|
|
977
|
logger.warn("Unhandled class value for nom: " + classValue);
|
|
978
|
}
|
|
979
|
|
|
980
|
}
|
|
981
|
}
|
|
982
|
|
|
983
|
List<Element> elements = elNom.getChildren();
|
|
984
|
for (Element element : elements){
|
|
985
|
if (element.getName().equals("name") || element.getName().equals("homonym") ){
|
|
986
|
if (taxonBaseClassType == false){
|
|
987
|
logger.warn("Name or homonym tag not allowed in non taxon nom tag");
|
|
988
|
}
|
|
989
|
}else{
|
|
990
|
unhandledNomChildren.add(element.getName());
|
|
991
|
}
|
|
992
|
}
|
|
993
|
|
|
994
|
return homotypicalGroup;
|
|
995
|
|
|
996
|
}
|
|
997
|
|
|
998
|
/**
|
|
999
|
* @param state
|
|
1000
|
* @param elNom
|
|
1001
|
* @param taxon
|
|
1002
|
* @param homotypicalGroup
|
|
1003
|
*/
|
|
1004
|
protected void handleTypeRef(EfloraImportState state, Element elNom, Taxon taxon, HomotypicalGroup homotypicalGroup) {
|
|
1005
|
verifyNoChildren(elNom);
|
|
1006
|
String typeRef = elNom.getTextNormalize();
|
|
1007
|
typeRef = removeStartingTypeRefMinus(typeRef);
|
|
1008
|
|
|
1009
|
String[] split = typeRef.split(":");
|
|
1010
|
if (split.length < 2){
|
|
1011
|
logger.warn("typeRef has no ':' : " + typeRef);
|
|
1012
|
}else if (split.length > 2){
|
|
1013
|
logger.warn("typeRef has more than 1 ':' : " + typeRef);
|
|
1014
|
}else{
|
|
1015
|
StringBuffer typeType = new StringBuffer(split[0]);
|
|
1016
|
String typeText = split[1].trim();
|
|
1017
|
TypeDesignationBase typeDesignation = getTypeDesignationAndReference(typeType);
|
|
1018
|
|
|
1019
|
//Name Type Desitnations
|
|
1020
|
if (typeDesignation instanceof NameTypeDesignation){
|
|
1021
|
makeNameTypeDesignations(typeType, typeText, typeDesignation);
|
|
1022
|
}
|
|
1023
|
//SpecimenTypeDesignations
|
|
1024
|
else if (typeDesignation instanceof SpecimenTypeDesignation){
|
|
1025
|
makeSpecimenTypeDesignation(typeType, typeText, typeDesignation);
|
|
1026
|
}else{
|
|
1027
|
logger.error("Unhandled type designation class" + typeDesignation.getClass().getName());
|
|
1028
|
}
|
|
1029
|
for (TaxonNameBase name : homotypicalGroup.getTypifiedNames()){
|
|
1030
|
name.addTypeDesignation(typeDesignation, true);
|
|
1031
|
}
|
|
1032
|
}
|
|
1033
|
}
|
|
1034
|
|
|
1035
|
|
|
1036
|
/**
|
|
1037
|
* @param typeRef
|
|
1038
|
* @return
|
|
1039
|
*/
|
|
1040
|
protected String removeStartingTypeRefMinus(String typeRef) {
|
|
1041
|
typeRef = replaceStart(typeRef, "-");
|
|
1042
|
typeRef = replaceStart(typeRef, "—");
|
|
1043
|
typeRef = replaceStart(typeRef, "\u002d");
|
|
1044
|
typeRef = replaceStart(typeRef, "\u2013");
|
|
1045
|
typeRef = replaceStart(typeRef, "--");
|
|
1046
|
return typeRef;
|
|
1047
|
}
|
|
1048
|
|
|
1049
|
/**
|
|
1050
|
* @param typeType
|
|
1051
|
* @param typeText
|
|
1052
|
* @param typeDesignation
|
|
1053
|
*/
|
|
1054
|
private void makeNameTypeDesignations(StringBuffer typeType, String typeText, TypeDesignationBase typeDesignation) {
|
|
1055
|
if (typeType.toString().trim().equalsIgnoreCase("Type")){
|
|
1056
|
//do nothing
|
|
1057
|
}else if (typeType.toString().trim().equalsIgnoreCase("Lectotype")){
|
|
1058
|
typeDesignation.setTypeStatus(SpecimenTypeDesignationStatus.LECTOTYPE());
|
|
1059
|
}else if (typeType.toString().trim().equalsIgnoreCase("Syntype")){
|
|
1060
|
typeDesignation.setTypeStatus(SpecimenTypeDesignationStatus.SYNTYPE());
|
|
1061
|
}else{
|
|
1062
|
logger.warn("Unhandled type string: " + typeType + "(" + CharUtils.unicodeEscaped(typeType.charAt(0)) + ")");
|
|
1063
|
}
|
|
1064
|
//clean
|
|
1065
|
typeText = cleanNameType(typeText);
|
|
1066
|
//create name
|
|
1067
|
TaxonNameBase<?,?> nameType = (TaxonNameBase<?,?>)parser.parseFullName(typeText, NomenclaturalCode.ICNAFP, Rank.SPECIES());
|
|
1068
|
((NameTypeDesignation) typeDesignation).setTypeName(nameType);
|
|
1069
|
//TODO wie können NameTypes den Namen zugeordnet werden? - wird aber vom Portal via NameCache matching gemacht
|
|
1070
|
}
|
|
1071
|
|
|
1072
|
|
|
1073
|
private String cleanNameType(String typeText) {
|
|
1074
|
String result;
|
|
1075
|
String[] split = typeText.split("\\[.*\\].?");
|
|
1076
|
result = split[0];
|
|
1077
|
return result;
|
|
1078
|
}
|
|
1079
|
|
|
1080
|
|
|
1081
|
/**
|
|
1082
|
* @param typeType
|
|
1083
|
* @param typeText
|
|
1084
|
* @param typeDesignation
|
|
1085
|
*/
|
|
1086
|
protected void makeSpecimenTypeDesignation(StringBuffer typeType, String typeText, TypeDesignationBase typeDesignation) {
|
|
1087
|
if (typeType.toString().trim().equalsIgnoreCase("Type")){
|
|
1088
|
//do nothing
|
|
1089
|
}else if (typeType.toString().trim().equalsIgnoreCase("Neotype") || typeType.toString().trim().equalsIgnoreCase("Neotypes")){
|
|
1090
|
typeDesignation.setTypeStatus(SpecimenTypeDesignationStatus.NEOTYPE());
|
|
1091
|
}else if (typeType.toString().trim().equalsIgnoreCase("Syntype") || typeType.toString().trim().equalsIgnoreCase("Syntypes")){
|
|
1092
|
typeDesignation.setTypeStatus(SpecimenTypeDesignationStatus.SYNTYPE());
|
|
1093
|
}else if (typeType.toString().trim().equalsIgnoreCase("Lectotype")){
|
|
1094
|
typeDesignation.setTypeStatus(SpecimenTypeDesignationStatus.LECTOTYPE());
|
|
1095
|
}else if (typeType.toString().trim().equalsIgnoreCase("Paratype")){
|
|
1096
|
typeDesignation.setTypeStatus(SpecimenTypeDesignationStatus.PARATYPE());
|
|
1097
|
}else{
|
|
1098
|
logger.warn("Unhandled type string: " + typeType);
|
|
1099
|
}
|
|
1100
|
DerivedUnit specimen = DerivedUnit.NewPreservedSpecimenInstance();
|
|
1101
|
if (typeText.length() > 255){
|
|
1102
|
specimen.setTitleCache(typeText.substring(0, 252) + "...", true);
|
|
1103
|
}else{
|
|
1104
|
specimen.setTitleCache(typeText, true);
|
|
1105
|
}
|
|
1106
|
specimen.putDefinition(Language.ENGLISH(), typeText);
|
|
1107
|
((SpecimenTypeDesignation) typeDesignation).setTypeSpecimen(specimen);
|
|
1108
|
}
|
|
1109
|
|
|
1110
|
private TypeDesignationBase getTypeDesignationAndReference(StringBuffer typeType) {
|
|
1111
|
TypeDesignationBase result;
|
|
1112
|
Reference ref = parseTypeDesignationReference(typeType);
|
|
1113
|
if (typeType.indexOf(" species")>-1 || typeType.indexOf("genus")>-1){
|
|
1114
|
if (typeType.indexOf(" species")>-1 ){
|
|
1115
|
result = NameTypeDesignation.NewInstance();
|
|
1116
|
int start = typeType.indexOf(" species");
|
|
1117
|
typeType.replace(start, start + " species".length(), "");
|
|
1118
|
}else {
|
|
1119
|
result = NameTypeDesignation.NewInstance();
|
|
1120
|
int start = typeType.indexOf(" genus");
|
|
1121
|
typeType.replace(start, start + " genus".length(), "");
|
|
1122
|
}
|
|
1123
|
}else{
|
|
1124
|
result = SpecimenTypeDesignation.NewInstance();
|
|
1125
|
}
|
|
1126
|
result.setCitation(ref);
|
|
1127
|
return result;
|
|
1128
|
}
|
|
1129
|
|
|
1130
|
|
|
1131
|
private Reference parseTypeDesignationReference(StringBuffer typeType) {
|
|
1132
|
Reference result = null;
|
|
1133
|
String reBracketReference = "\\(.*\\)";
|
|
1134
|
Pattern patBracketReference = Pattern.compile(reBracketReference);
|
|
1135
|
Matcher matcher = patBracketReference.matcher(typeType);
|
|
1136
|
if (matcher.find()){
|
|
1137
|
String refString = matcher.group();
|
|
1138
|
int start = typeType.indexOf(refString);
|
|
1139
|
typeType.replace(start, start + refString.length(), "");
|
|
1140
|
refString = refString.replace("(", "").replace(")", "").trim();
|
|
1141
|
Reference ref = ReferenceFactory.newGeneric();
|
|
1142
|
ref.setTitleCache(refString, true);
|
|
1143
|
result = ref;
|
|
1144
|
}
|
|
1145
|
return result;
|
|
1146
|
}
|
|
1147
|
|
|
1148
|
|
|
1149
|
/**
|
|
1150
|
* @param state
|
|
1151
|
* @param elNom
|
|
1152
|
* @param taxon
|
|
1153
|
*/
|
|
1154
|
//body/taxon/
|
|
1155
|
private HomotypicalGroup handleNomTaxon(EfloraImportState state, Element elNom, Taxon taxon, HomotypicalGroup homotypicalGroup, boolean isSynonym) {
|
|
1156
|
INonViralName nvn = makeName(taxon, homotypicalGroup, isSynonym);
|
|
1157
|
TaxonNameBase<?,?> name = TaxonNameBase.castAndDeproxy(nvn);
|
|
1158
|
String num = null;
|
|
1159
|
|
|
1160
|
boolean hasGenusInfo = false;
|
|
1161
|
TeamOrPersonBase<?> lastTeam = null;
|
|
1162
|
|
|
1163
|
//genus
|
|
1164
|
List<Element> elGenus = XmlHelp.getAttributedChildListWithValue(elNom, "name", "class", "genus");
|
|
1165
|
if (elGenus.size() > 0){
|
|
1166
|
hasGenusInfo = true;
|
|
1167
|
}else{
|
|
1168
|
logger.debug ("No Synonym Genus");
|
|
1169
|
}
|
|
1170
|
//infra rank -> needed to handle authors correctly
|
|
1171
|
List<Element> elInfraRank = XmlHelp.getAttributedChildListWithValue(elNom, "name", "class", "infrank");
|
|
1172
|
Rank infraRank = null;
|
|
1173
|
infraRank = handleInfRank(name, elInfraRank, infraRank);
|
|
1174
|
|
|
1175
|
//get left over elements
|
|
1176
|
List<Element> elements = elNom.getChildren();
|
|
1177
|
elements.removeAll(elInfraRank);
|
|
1178
|
|
|
1179
|
for (Element element : elements){
|
|
1180
|
if (element.getName().equals("name")){
|
|
1181
|
String classValue = element.getAttributeValue("class");
|
|
1182
|
String value = element.getValue().trim();
|
|
1183
|
if (classValue.equalsIgnoreCase("genus") || classValue.equalsIgnoreCase("family") ){
|
|
1184
|
name.setGenusOrUninomial(value);
|
|
1185
|
}else if (classValue.equalsIgnoreCase("family") ){
|
|
1186
|
name.setGenusOrUninomial(value);
|
|
1187
|
name.setRank(Rank.FAMILY());
|
|
1188
|
}else if (classValue.equalsIgnoreCase("subgenus")){
|
|
1189
|
//name.setInfraGenericEpithet(value);
|
|
1190
|
name.setNameCache(value.replace(":", "").trim());
|
|
1191
|
name.setRank(Rank.SUBGENUS());
|
|
1192
|
}else if (classValue.equalsIgnoreCase("epithet") ){
|
|
1193
|
if (hasGenusInfo == true){
|
|
1194
|
name.setSpecificEpithet(value);
|
|
1195
|
}else{
|
|
1196
|
handleInfraspecificEpithet(element, classValue, name);
|
|
1197
|
}
|
|
1198
|
}else if (classValue.equalsIgnoreCase("author")){
|
|
1199
|
handleNameAuthors(element, name);
|
|
1200
|
}else if (classValue.equalsIgnoreCase("paraut")){
|
|
1201
|
handleBasionymAuthor(state, element, name, false);
|
|
1202
|
}else if (classValue.equalsIgnoreCase("infrauthor") || classValue.equalsIgnoreCase("infraut")){
|
|
1203
|
handleInfrAuthor(state, element, name, true);
|
|
1204
|
}else if (classValue.equalsIgnoreCase("infrapar") || classValue.equalsIgnoreCase("infrpar") || classValue.equalsIgnoreCase("parauthor") ){
|
|
1205
|
handleBasionymAuthor(state, element, name, true);
|
|
1206
|
}else if (classValue.equalsIgnoreCase("infrepi")){
|
|
1207
|
handleInfrEpi(name, infraRank, value);
|
|
1208
|
}else if (classValue.equalsIgnoreCase("pub")){
|
|
1209
|
lastTeam = handleNomenclaturalReference(name, value);
|
|
1210
|
}else if (classValue.equalsIgnoreCase("usage")){
|
|
1211
|
lastTeam = handleNameUsage(taxon, name, value, lastTeam);
|
|
1212
|
}else if (classValue.equalsIgnoreCase("note")){
|
|
1213
|
handleNameNote(name, value);
|
|
1214
|
}else if (classValue.equalsIgnoreCase("num")){
|
|
1215
|
if (num != null){
|
|
1216
|
logger.warn("Duplicate num: " + value);
|
|
1217
|
}else{
|
|
1218
|
num = value;
|
|
1219
|
}
|
|
1220
|
if (isSynonym == true){
|
|
1221
|
logger.warn("Synonym should not have a num");
|
|
1222
|
}
|
|
1223
|
}else if (classValue.equalsIgnoreCase("typification")){
|
|
1224
|
logger.warn("Typification should not be a nom class");
|
|
1225
|
}else{
|
|
1226
|
logger.warn("Unhandled name class: " + classValue);
|
|
1227
|
}
|
|
1228
|
}else if(element.getName().equals("homonym")){
|
|
1229
|
handleHomonym(state, element, name);
|
|
1230
|
}else{
|
|
1231
|
// child element is not "name"
|
|
1232
|
unhandledNomChildren.add(element.getName());
|
|
1233
|
}
|
|
1234
|
}
|
|
1235
|
|
|
1236
|
//handle key
|
|
1237
|
if (! isSynonym){
|
|
1238
|
String taxonString = name.getNameCache();
|
|
1239
|
//try to find matching lead nodes
|
|
1240
|
UnmatchedLeadsKey leadsKey = UnmatchedLeadsKey.NewInstance(num, taxonString);
|
|
1241
|
Set<PolytomousKeyNode> matchingNodes = handleMatchingNodes(state, taxon, leadsKey);
|
|
1242
|
//same without using the num
|
|
1243
|
if (num != null){
|
|
1244
|
UnmatchedLeadsKey noNumLeadsKey = UnmatchedLeadsKey.NewInstance("", taxonString);
|
|
1245
|
handleMatchingNodes(state, taxon, noNumLeadsKey);
|
|
1246
|
}
|
|
1247
|
if (matchingNodes.isEmpty() && num != null){
|
|
1248
|
logger.warn("Taxon has num but no matching nodes exist: " + num+ ", Key: " + leadsKey.toString());
|
|
1249
|
}
|
|
1250
|
}
|
|
1251
|
|
|
1252
|
//test nom element has no text
|
|
1253
|
if (StringUtils.isNotBlank(elNom.getTextNormalize().replace("—", "").replace("\u002d","").replace("\u2013", ""))){
|
|
1254
|
String strElNom = elNom.getTextNormalize();
|
|
1255
|
if ("?".equals(strElNom)){
|
|
1256
|
handleQuestionMark(name, taxon);
|
|
1257
|
}
|
|
1258
|
// Character c = strElNom.charAt(0);
|
|
1259
|
//System.out.println(CharUtils.unicodeEscaped(c));
|
|
1260
|
logger.warn("Nom tag has text: " + strElNom);
|
|
1261
|
}
|
|
1262
|
|
|
1263
|
return name.getHomotypicalGroup();
|
|
1264
|
}
|
|
1265
|
|
|
1266
|
|
|
1267
|
private void handleQuestionMark(INonViralName name, Taxon taxon) {
|
|
1268
|
int count = name.getTaxonBases().size();
|
|
1269
|
if (count != 1){
|
|
1270
|
logger.warn("Name has " + count + " taxa. This is not handled for question mark");
|
|
1271
|
}else{
|
|
1272
|
TaxonBase taxonBase = name.getTaxonBases().iterator().next();
|
|
1273
|
taxonBase.setDoubtful(true);
|
|
1274
|
}
|
|
1275
|
}
|
|
1276
|
|
|
1277
|
|
|
1278
|
//merge with handleNomTaxon
|
|
1279
|
private void handleHomonym(EfloraImportState state, Element elHomonym, TaxonNameBase upperName) {
|
|
1280
|
verifyNoAttribute(elHomonym);
|
|
1281
|
|
|
1282
|
//hommonym name
|
|
1283
|
TaxonNameBase<?,?> homonymName = TaxonNameFactory.NewBotanicalInstance(upperName.getRank());
|
|
1284
|
homonymName.setGenusOrUninomial(upperName.getGenusOrUninomial());
|
|
1285
|
homonymName.setInfraGenericEpithet(upperName.getInfraGenericEpithet());
|
|
1286
|
homonymName.setSpecificEpithet(upperName.getSpecificEpithet());
|
|
1287
|
homonymName.setInfraSpecificEpithet(upperName.getInfraSpecificEpithet());
|
|
1288
|
|
|
1289
|
for (Element elName : (List<Element>)elHomonym.getChildren("name")){
|
|
1290
|
String classValue = elName.getAttributeValue("class");
|
|
1291
|
String value = elName.getValue().trim();
|
|
1292
|
if (classValue.equalsIgnoreCase("genus") ){
|
|
1293
|
homonymName.setGenusOrUninomial(value);
|
|
1294
|
}else if (classValue.equalsIgnoreCase("epithet") ){
|
|
1295
|
homonymName.setSpecificEpithet(value);
|
|
1296
|
}else if (classValue.equalsIgnoreCase("author")){
|
|
1297
|
handleNameAuthors(elName, homonymName);
|
|
1298
|
}else if (classValue.equalsIgnoreCase("paraut")){
|
|
1299
|
handleBasionymAuthor(state, elName, homonymName, true);
|
|
1300
|
}else if (classValue.equalsIgnoreCase("pub")){
|
|
1301
|
handleNomenclaturalReference(homonymName, value);
|
|
1302
|
}else if (classValue.equalsIgnoreCase("note")){
|
|
1303
|
handleNameNote(homonymName, value);
|
|
1304
|
}else{
|
|
1305
|
logger.warn("Unhandled class value: " + classValue);
|
|
1306
|
}
|
|
1307
|
}
|
|
1308
|
//TODO verify other information
|
|
1309
|
|
|
1310
|
|
|
1311
|
//rel
|
|
1312
|
boolean homonymIsLater = false;
|
|
1313
|
NameRelationshipType relType = NameRelationshipType.LATER_HOMONYM();
|
|
1314
|
if (upperName.getNomenclaturalReference() != null && homonymName.getNomenclaturalReference() != null){
|
|
1315
|
TimePeriod homonymYear = homonymName.getNomenclaturalReference().getDatePublished();
|
|
1316
|
TimePeriod nameYear = upperName.getNomenclaturalReference().getDatePublished();
|
|
1317
|
homonymIsLater = homonymYear.getStart().compareTo(nameYear.getStart()) > 0;
|
|
1318
|
}else{
|
|
1319
|
if (upperName.getNomenclaturalReference() == null){
|
|
1320
|
logger.warn("Homonym parent does not have a nomenclatural reference or year: " + upperName.getTitleCache());
|
|
1321
|
}
|
|
1322
|
if (homonymName.getNomenclaturalReference() == null){
|
|
1323
|
logger.warn("Homonym does not have a nomenclatural reference or year: " + homonymName.getTitleCache());
|
|
1324
|
}
|
|
1325
|
}
|
|
1326
|
if (homonymIsLater){
|
|
1327
|
homonymName.addRelationshipToName(upperName, relType, null);
|
|
1328
|
}else{
|
|
1329
|
upperName.addRelationshipToName(homonymName, relType, null);
|
|
1330
|
}
|
|
1331
|
}
|
|
1332
|
|
|
1333
|
|
|
1334
|
/**
|
|
1335
|
* @param state
|
|
1336
|
* @param taxon
|
|
1337
|
* @param leadsKey
|
|
1338
|
* @return
|
|
1339
|
*/
|
|
1340
|
private Set<PolytomousKeyNode> handleMatchingNodes(EfloraImportState state, Taxon taxon, UnmatchedLeadsKey leadsKey) {
|
|
1341
|
Set<PolytomousKeyNode> matchingNodes = state.getUnmatchedLeads().getNodes(leadsKey);
|
|
1342
|
for (PolytomousKeyNode matchingNode : matchingNodes){
|
|
1343
|
state.getUnmatchedLeads().removeNode(leadsKey, matchingNode);
|
|
1344
|
matchingNode.setTaxon(taxon);
|
|
1345
|
state.getPolytomousKeyNodesToSave().add(matchingNode);
|
|
1346
|
}
|
|
1347
|
return matchingNodes;
|
|
1348
|
}
|
|
1349
|
|
|
1350
|
|
|
1351
|
private void handleNameNote(INonViralName name, String value) {
|
|
1352
|
logger.warn("Name note: " + value + ". Available in portal?");
|
|
1353
|
Annotation annotation = Annotation.NewInstance(value, AnnotationType.EDITORIAL(), Language.DEFAULT());
|
|
1354
|
name.addAnnotation(annotation);
|
|
1355
|
}
|
|
1356
|
|
|
1357
|
|
|
1358
|
/**
|
|
1359
|
* @param taxon
|
|
1360
|
* @param name
|
|
1361
|
* @param value
|
|
1362
|
*/
|
|
1363
|
protected TeamOrPersonBase handleNameUsage(Taxon taxon, INonViralName name, String referenceTitle, TeamOrPersonBase lastTeam) {
|
|
1364
|
Reference ref = ReferenceFactory.newGeneric();
|
|
1365
|
referenceTitle = removeStartingSymbols(referenceTitle, ref);
|
|
1366
|
|
|
1367
|
ref.setTitleCache(referenceTitle, true);
|
|
1368
|
String microReference = parseReferenceYearAndDetail(ref);
|
|
1369
|
TeamOrPersonBase<?> team = getReferenceAuthor(ref);
|
|
1370
|
parseReferenceType(ref);
|
|
1371
|
if (team == null){
|
|
1372
|
team = lastTeam;
|
|
1373
|
}
|
|
1374
|
ref.setAuthorship(team);
|
|
1375
|
|
|
1376
|
TaxonDescription description = getDescription(taxon);
|
|
1377
|
TextData textData = TextData.NewInstance(Feature.CITATION());
|
|
1378
|
textData.addSource(OriginalSourceType.PrimaryTaxonomicSource, null, null, ref, microReference, (TaxonNameBase)name, null);
|
|
1379
|
description.addElement(textData);
|
|
1380
|
return team;
|
|
1381
|
}
|
|
1382
|
|
|
1383
|
|
|
1384
|
/**
|
|
1385
|
* @param referenceTitle
|
|
1386
|
* @param ref
|
|
1387
|
* @return
|
|
1388
|
*/
|
|
1389
|
private String removeStartingSymbols(String referenceTitle, Reference ref) {
|
|
1390
|
if (referenceTitle.startsWith(";") || referenceTitle.startsWith(",") || referenceTitle.startsWith(":")){
|
|
1391
|
referenceTitle = referenceTitle.substring(1).trim();
|
|
1392
|
ref.setTitleCache(referenceTitle);
|
|
1393
|
}
|
|
1394
|
return referenceTitle;
|
|
1395
|
}
|
|
1396
|
|
|
1397
|
|
|
1398
|
private void parseReferenceType(Reference ref) {
|
|
1399
|
String title = ref.getTitle();
|
|
1400
|
if (title == null){
|
|
1401
|
return;
|
|
1402
|
}
|
|
1403
|
title = title.trim();
|
|
1404
|
//no in reference
|
|
1405
|
if (! title.startsWith("in ")){
|
|
1406
|
ref.setType(ReferenceType.Book);
|
|
1407
|
return;
|
|
1408
|
}
|
|
1409
|
|
|
1410
|
title = title.substring(3);
|
|
1411
|
//in reference
|
|
1412
|
//no ,
|
|
1413
|
if (title.indexOf(",") == -1){
|
|
1414
|
ref.setType(ReferenceType.Article);
|
|
1415
|
IJournal journal = ReferenceFactory.newJournal();
|
|
1416
|
journal.setTitle(title);
|
|
1417
|
ref.setTitle(null);
|
|
1418
|
ref.setInJournal(journal);
|
|
1419
|
//return;
|
|
1420
|
}else{
|
|
1421
|
//,-references
|
|
1422
|
ref.setType(ReferenceType.BookSection);
|
|
1423
|
String[] split = (title).split(",\\s*[A-Z]");
|
|
1424
|
if (split.length <= 1){
|
|
1425
|
logger.warn("Can not fully decide what reference type. Guess it is a book section: " + title );
|
|
1426
|
}
|
|
1427
|
IBook book = ReferenceFactory.newBook();
|
|
1428
|
Team bookTeam = Team.NewTitledInstance(split[0].trim(), split[0].trim());
|
|
1429
|
try {
|
|
1430
|
title = title.substring(split[0].length() + 1).trim();
|
|
1431
|
} catch (Exception e) {
|
|
1432
|
logger.error("ERROR occurred when trying to split title: " + title + "; split[0]: + " + split[0]);
|
|
1433
|
}
|
|
1434
|
book.setTitle(title);
|
|
1435
|
book.setAuthorship(bookTeam);
|
|
1436
|
book.setDatePublished(ref.getDatePublished());
|
|
1437
|
ref.setTitle(null);
|
|
1438
|
ref.setInBook(book);
|
|
1439
|
}
|
|
1440
|
}
|
|
1441
|
|
|
1442
|
|
|
1443
|
protected Team getReferenceAuthor (Reference ref) {
|
|
1444
|
boolean isCache = false;
|
|
1445
|
String referenceTitle = ref.getTitle();
|
|
1446
|
if (referenceTitle == null){
|
|
1447
|
isCache = true;
|
|
1448
|
referenceTitle = ref.getTitleCache();
|
|
1449
|
}
|
|
1450
|
//in references
|
|
1451
|
String[] split = (" " + referenceTitle).split(" in ");
|
|
1452
|
if (split.length > 1){
|
|
1453
|
if (StringUtils.isNotBlank(split[0])){
|
|
1454
|
//' in ' is within the reference string, take the preceding string as the team
|
|
1455
|
Team team = Team.NewTitledInstance(split[0].trim(), split[0].trim());
|
|
1456
|
if (! isCache){
|
|
1457
|
ref.setTitle("in " + split[1]);
|
|
1458
|
}
|
|
1459
|
return team;
|
|
1460
|
}else{
|
|
1461
|
//string starts with in therefore no author is given
|
|
1462
|
return null;
|
|
1463
|
}
|
|
1464
|
}
|
|
1465
|
//no ,-reference
|
|
1466
|
split = referenceTitle.split(",");
|
|
1467
|
if (split.length < 2){
|
|
1468
|
//no author is given
|
|
1469
|
return null;
|
|
1470
|
}
|
|
1471
|
|
|
1472
|
//,-references
|
|
1473
|
split = (referenceTitle).split(",\\s*[A-Z]");
|
|
1474
|
if (split.length > 1){
|
|
1475
|
Team team = Team.NewTitledInstance(split[0].trim(), split[0].trim());
|
|
1476
|
if (! isCache){
|
|
1477
|
ref.setTitle(referenceTitle.substring(split[0].length()+1).trim());
|
|
1478
|
}
|
|
1479
|
return team;
|
|
1480
|
}else{
|
|
1481
|
logger.warn("Can't decide if a usage has an author: " + referenceTitle );
|
|
1482
|
return null;
|
|
1483
|
}
|
|
1484
|
}
|
|
1485
|
|
|
1486
|
|
|
1487
|
/**
|
|
1488
|
* Replaced by <homonym> tag but still in use for exceptions
|
|
1489
|
* @param detail
|
|
1490
|
* @param name
|
|
1491
|
* @return
|
|
1492
|
*/
|
|
1493
|
protected String parseHomonym(String detail, TaxonNameBase name) {
|
|
1494
|
String result;
|
|
1495
|
if (detail == null){
|
|
1496
|
return detail;
|
|
1497
|
}
|
|
1498
|
|
|
1499
|
|
|
1500
|
//non RE
|
|
1501
|
String reNon = "(\\s|,)non\\s";
|
|
1502
|
Pattern patReference = Pattern.compile(reNon);
|
|
1503
|
Matcher matcher = patReference.matcher(detail);
|
|
1504
|
if (matcher.find()){
|
|
1505
|
int start = matcher.start();
|
|
1506
|
int end = matcher.end();
|
|
1507
|
|
|
1508
|
if (detail != null){
|
|
1509
|
logger.warn("Unhandled non part: " + detail.substring(start));
|
|
1510
|
return detail;
|
|
1511
|
}
|
|
1512
|
|
|
1513
|
result = detail.substring(0, start);
|
|
1514
|
|
|
1515
|
//homonym string
|
|
1516
|
String homonymString = detail.substring(end);
|
|
1517
|
|
|
1518
|
//hommonym name
|
|
1519
|
TaxonNameBase<?,?> homonymName = TaxonNameFactory.NewBotanicalInstance(name.getRank());
|
|
1520
|
homonymName.setGenusOrUninomial(name.getGenusOrUninomial());
|
|
1521
|
homonymName.setInfraGenericEpithet(name.getInfraGenericEpithet());
|
|
1522
|
homonymName.setSpecificEpithet(name.getSpecificEpithet());
|
|
1523
|
homonymName.setInfraSpecificEpithet(name.getInfraSpecificEpithet());
|
|
1524
|
Reference homonymNomRef = ReferenceFactory.newGeneric();
|
|
1525
|
homonymNomRef.setTitleCache(homonymString, true);
|
|
1526
|
String homonymNomRefDetail = parseReferenceYearAndDetail(homonymNomRef);
|
|
1527
|
homonymName.setNomenclaturalMicroReference(homonymNomRefDetail);
|
|
1528
|
String authorTitle = homonymNomRef.getTitleCache();
|
|
1529
|
Team team = Team.NewTitledInstance(authorTitle, authorTitle);
|
|
1530
|
homonymNomRef.setAuthorship(team);
|
|
1531
|
homonymNomRef.setTitle("");
|
|
1532
|
homonymNomRef.setProtectedTitleCache(false);
|
|
1533
|
|
|
1534
|
//rel
|
|
1535
|
boolean homonymIsLater = false;
|
|
1536
|
NameRelationshipType relType = NameRelationshipType.LATER_HOMONYM();
|
|
1537
|
TimePeriod homonymYear = homonymNomRef.getDatePublished();
|
|
1538
|
if (name.getNomenclaturalReference() != null){
|
|
1539
|
TimePeriod nameYear = name.getNomenclaturalReference().getDatePublished();
|
|
1540
|
homonymIsLater = homonymYear.getStart().compareTo(nameYear.getStart()) > 0;
|
|
1541
|
}else{
|
|
1542
|
logger.warn("Classification name has no nomenclatural reference");
|
|
1543
|
}
|
|
1544
|
if (homonymIsLater){
|
|
1545
|
homonymName.addRelationshipToName(name, relType, null);
|
|
1546
|
}else{
|
|
1547
|
name.addRelationshipToName(homonymName, relType, null);
|
|
1548
|
}
|
|
1549
|
|
|
1550
|
}else{
|
|
1551
|
return detail;
|
|
1552
|
}
|
|
1553
|
return result;
|
|
1554
|
}
|
|
1555
|
|
|
1556
|
|
|
1557
|
/**
|
|
1558
|
* @Xpath body/taxon/nomenclature/homotypes/nom/name[@class="pub"]
|
|
1559
|
* @param name
|
|
1560
|
* @param value
|
|
1561
|
*/
|
|
1562
|
protected TeamOrPersonBase handleNomenclaturalReference(TaxonNameBase<?,?> name, String value) {
|
|
1563
|
Reference nomRef = ReferenceFactory.newGeneric();
|
|
1564
|
nomRef.setTitleCache(value, true);
|
|
1565
|
parseNomStatus(nomRef, name);
|
|
1566
|
String microReference = parseReferenceYearAndDetail(nomRef);
|
|
1567
|
name.setNomenclaturalReference(nomRef);
|
|
1568
|
microReference = parseHomonym(microReference, name);
|
|
1569
|
name.setNomenclaturalMicroReference(microReference);
|
|
1570
|
TeamOrPersonBase<?> team = name.getCombinationAuthorship();
|
|
1571
|
if (team == null){
|
|
1572
|
logger.warn("Name has nom. ref. but no author team. Name: " + name.getTitleCache() + ", Nom.Ref.: " + value);
|
|
1573
|
}else{
|
|
1574
|
nomRef.setAuthorship(team);
|
|
1575
|
}
|
|
1576
|
return team;
|
|
1577
|
}
|
|
1578
|
|
|
1579
|
private void handleInfrAuthor(EfloraImportState state, Element elAuthor, INonViralName name, boolean overwrite) {
|
|
1580
|
String strAuthor = elAuthor.getValue().trim();
|
|
1581
|
if (strAuthor.endsWith(",")){
|
|
1582
|
strAuthor = strAuthor.substring(0, strAuthor.length() -1);
|
|
1583
|
}
|
|
1584
|
TeamOrPersonBase[] team = getTeam(strAuthor);
|
|
1585
|
if (name.getCombinationAuthorship() != null && overwrite == false){
|
|
1586
|
logger.warn("Try to write combination author for a name that already has a combination author. Neglected.");
|
|
1587
|
}else{
|
|
1588
|
name.setCombinationAuthorship(team[0]);
|
|
1589
|
name.setExCombinationAuthorship(team[1]);
|
|
1590
|
}
|
|
1591
|
|
|
1592
|
|
|
1593
|
}
|
|
1594
|
|
|
1595
|
|
|
1596
|
/**
|
|
1597
|
* Sets the names rank according to the infrank value
|
|
1598
|
* @param name
|
|
1599
|
* @param elements
|
|
1600
|
* @param elInfraRank
|
|
1601
|
* @param infraRank
|
|
1602
|
* @return
|
|
1603
|
*/
|
|
1604
|
private Rank handleInfRank(INonViralName name, List<Element> elInfraRank, Rank infraRank) {
|
|
1605
|
if (elInfraRank.size() == 1){
|
|
1606
|
String strRank = elInfraRank.get(0).getTextNormalize();
|
|
1607
|
try {
|
|
1608
|
infraRank = Rank.getRankByNameOrIdInVoc(strRank);
|
|
1609
|
} catch (UnknownCdmTypeException e) {
|
|
1610
|
try{
|
|
1611
|
infraRank = Rank.getRankByNameOrIdInVoc(strRank + ".");
|
|
1612
|
} catch (UnknownCdmTypeException e2) {
|
|
1613
|
logger.warn("Unknown infrank " + strRank + ". Set infraRank to (null).");
|
|
1614
|
}
|
|
1615
|
}
|
|
1616
|
}else if (elInfraRank.size() > 1){
|
|
1617
|
logger.warn ("There is more than 1 infrank");
|
|
1618
|
}
|
|
1619
|
if (infraRank != null){
|
|
1620
|
name.setRank(infraRank);
|
|
1621
|
}
|
|
1622
|
return infraRank;
|
|
1623
|
}
|
|
1624
|
|
|
1625
|
|
|
1626
|
private void handleInfrEpi(INonViralName name, Rank infraRank, String value) {
|
|
1627
|
if (infraRank != null && infraRank.isInfraSpecific()){
|
|
1628
|
name.setInfraSpecificEpithet(value);
|
|
1629
|
if (CdmUtils.isCapital(value)){
|
|
1630
|
logger.warn("Infraspecific epithet starts with a capital letter: " + value);
|
|
1631
|
}
|
|
1632
|
}else if (infraRank != null && infraRank.isInfraGeneric()){
|
|
1633
|
name.setInfraGenericEpithet(value);
|
|
1634
|
if (! CdmUtils.isCapital(value)){
|
|
1635
|
logger.warn("Infrageneric epithet does not start with a capital letter: " + value);
|
|
1636
|
}
|
|
1637
|
}else{
|
|
1638
|
logger.warn("Infrepi could not be handled: " + value);
|
|
1639
|
}
|
|
1640
|
}
|
|
1641
|
|
|
1642
|
|
|
1643
|
|
|
1644
|
/**
|
|
1645
|
* Returns the (empty) with the correct homotypical group depending on the taxon status
|
|
1646
|
* @param taxon
|
|
1647
|
* @param homotypicalGroup
|
|
1648
|
* @param isSynonym
|
|
1649
|
* @return
|
|
1650
|
*/
|
|
1651
|
private TaxonNameBase makeName(Taxon taxon,HomotypicalGroup homotypicalGroup, boolean isSynonym) {
|
|
1652
|
TaxonNameBase<?,?> name;
|
|
1653
|
if (isSynonym){
|
|
1654
|
name = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES(), homotypicalGroup);
|
|
1655
|
SynonymType synonymType = SynonymType.HETEROTYPIC_SYNONYM_OF();
|
|
1656
|
if (taxon.getHomotypicGroup().equals(homotypicalGroup)){
|
|
1657
|
synonymType = SynonymType.HOMOTYPIC_SYNONYM_OF();
|
|
1658
|
}
|
|
1659
|
taxon.addSynonymName(name, synonymType);
|
|
1660
|
}else{
|
|
1661
|
name = taxon.getName();
|
|
1662
|
}
|
|
1663
|
return name;
|
|
1664
|
}
|
|
1665
|
|
|
1666
|
|
|
1667
|
/**
|
|
1668
|
* @param element
|
|
1669
|
* @param taxon
|
|
1670
|
*/
|
|
1671
|
private void handleInfraspecificEpithet(Element element, String attrValue, INonViralName name) {
|
|
1672
|
String value = element.getTextNormalize();
|
|
1673
|
if (value.indexOf("subsp.") != -1){
|
|
1674
|
//TODO genus and species epi
|
|
1675
|
String infrEpi = value.substring(value.indexOf("subsp.") + 6).trim();
|
|
1676
|
name.setInfraSpecificEpithet(infrEpi);
|
|
1677
|
name.setRank(Rank.SUBSPECIES());
|
|
1678
|
}else if (value.indexOf("var.") != -1){
|
|
1679
|
//TODO genus and species epi
|
|
1680
|
String infrEpi = value.substring(value.indexOf("var.") + 4).trim();
|
|
1681
|
name.setInfraSpecificEpithet(infrEpi);
|
|
1682
|
name.setRank(Rank.VARIETY());
|
|
1683
|
}else{
|
|
1684
|
logger.warn("Unhandled infraspecific type: " + value);
|
|
1685
|
}
|
|
1686
|
}
|
|
1687
|
|
|
1688
|
|
|
1689
|
/**
|
|
1690
|
* @param state
|
|
1691
|
* @param element
|
|
1692
|
* @param name
|
|
1693
|
*/
|
|
1694
|
private void handleBasionymAuthor(EfloraImportState state, Element elBasionymAuthor, INonViralName name, boolean overwrite) {
|
|
1695
|
String strAuthor = elBasionymAuthor.getValue().trim();
|
|
1696
|
Pattern reBasionymAuthor = Pattern.compile("^\\(.*\\)$");
|
|
1697
|
if (reBasionymAuthor.matcher(strAuthor).matches()){
|
|
1698
|
strAuthor = strAuthor.substring(1, strAuthor.length()-1);
|
|
1699
|
}else{
|
|
1700
|
logger.warn("Brackets are missing for original combination author " + strAuthor);
|
|
1701
|
}
|
|
1702
|
TeamOrPersonBase[] basionymTeam = getTeam(strAuthor);
|
|
1703
|
if (name.getBasionymAuthorship() != null && overwrite == false){
|
|
1704
|
logger.warn("Try to write basionym author for a name that already has a basionym author. Neglected.");
|
|
1705
|
}else{
|
|
1706
|
name.setBasionymAuthorship(basionymTeam[0]);
|
|
1707
|
name.setExBasionymAuthorship(basionymTeam[1]);
|
|
1708
|
|
|
1709
|
}
|
|
1710
|
}
|
|
1711
|
|
|
1712
|
private final Map<String, UUID> teamMap = new HashMap<String, UUID>();
|
|
1713
|
/**
|
|
1714
|
* @param elAuthors
|
|
1715
|
* @param name
|
|
1716
|
* @param elNom
|
|
1717
|
*/
|
|
1718
|
private void handleNameAuthors(Element elAuthor, INonViralName name) {
|
|
1719
|
if (name.getCombinationAuthorship() != null){
|
|
1720
|
logger.warn("Name already has a combination author. Name: " + name.getTitleCache() + ", Author: " + elAuthor.getTextNormalize());
|
|
1721
|
}
|
|
1722
|
String strAuthor = elAuthor.getValue().trim();
|
|
1723
|
if (strAuthor.endsWith(",")){
|
|
1724
|
strAuthor = strAuthor.substring(0, strAuthor.length() -1);
|
|
1725
|
}
|
|
1726
|
if (strAuthor.indexOf("(") > -1 || strAuthor.indexOf(")") > -1){
|
|
1727
|
logger.warn("Author has brackets. Basionym authors should be handled in separate tags: " + strAuthor);
|
|
1728
|
}
|
|
1729
|
TeamOrPersonBase[] team = getTeam(strAuthor);
|
|
1730
|
name.setCombinationAuthorship(team[0]);
|
|
1731
|
name.setExCombinationAuthorship(team[1]);
|
|
1732
|
}
|
|
1733
|
|
|
1734
|
|
|
1735
|
/**
|
|
1736
|
* @param strAuthor
|
|
1737
|
* @return
|
|
1738
|
*/
|
|
1739
|
private TeamOrPersonBase[] getTeam(String strAuthor) {
|
|
1740
|
TeamOrPersonBase[] result = new TeamOrPersonBase[2];
|
|
1741
|
String[] split = strAuthor.split(" ex ");
|
|
1742
|
String strBaseAuthor = null;
|
|
1743
|
String strExAuthor = null;
|
|
1744
|
|
|
1745
|
if (split.length == 2){
|
|
1746
|
strBaseAuthor = split[1];
|
|
1747
|
strExAuthor = split[0];
|
|
1748
|
}else if (split.length == 1){
|
|
1749
|
strBaseAuthor = split[0];
|
|
1750
|
}else{
|
|
1751
|
logger.warn("Could not parse (ex) author: " + strAuthor);
|
|
1752
|
}
|
|
1753
|
result[0] = getUuidTeam(strBaseAuthor);
|
|
1754
|
if (result[0] == null){
|
|
1755
|
result[0] = parseSingleTeam(strBaseAuthor);
|
|
1756
|
teamMap.put(strBaseAuthor, result[0].getUuid());
|
|
1757
|
}
|
|
1758
|
if (strExAuthor != null){
|
|
1759
|
result[1] = getUuidTeam(strExAuthor);
|
|
1760
|
if (result[1] == null){
|
|
1761
|
result[1] = Team.NewInstance();
|
|
1762
|
result[1].setTitleCache(strExAuthor, true);
|
|
1763
|
teamMap.put(strExAuthor, result[1].getUuid());
|
|
1764
|
}
|
|
1765
|
|
|
1766
|
}
|
|
1767
|
return result;
|
|
1768
|
}
|
|
1769
|
|
|
1770
|
|
|
1771
|
protected TeamOrPersonBase parseSingleTeam(String strBaseAuthor) {
|
|
1772
|
TeamOrPersonBase result;
|
|
1773
|
String[] split = strBaseAuthor.split("&");
|
|
1774
|
if (split.length > 1){
|
|
1775
|
result = Team.NewInstance();
|
|
1776
|
for (String personString : split){
|
|
1777
|
Person person = makePerson(personString);
|
|
1778
|
((Team)result).addTeamMember(person);
|
|
1779
|
}
|
|
1780
|
}else{
|
|
1781
|
result = makePerson(strBaseAuthor.trim());
|
|
1782
|
}
|
|
1783
|
return result;
|
|
1784
|
}
|
|
1785
|
|
|
1786
|
|
|
1787
|
/**
|
|
1788
|
* @param personString
|
|
1789
|
* @return
|
|
1790
|
*/
|
|
1791
|
private Person makePerson(String personString) {
|
|
1792
|
personString = personString.trim();
|
|
1793
|
Person person = Person.NewTitledInstance(personString);
|
|
1794
|
person.setNomenclaturalTitle(personString);
|
|
1795
|
return person;
|
|
1796
|
}
|
|
1797
|
|
|
1798
|
|
|
1799
|
/**
|
|
1800
|
* @param result
|
|
1801
|
* @param strBaseAuthor
|
|
1802
|
*/
|
|
1803
|
private TeamOrPersonBase getUuidTeam(String strBaseAuthor) {
|
|
1804
|
UUID uuidTeam = teamMap.get(strBaseAuthor);
|
|
1805
|
return CdmBase.deproxy(getAgentService().find(uuidTeam), TeamOrPersonBase.class);
|
|
1806
|
}
|
|
1807
|
|
|
1808
|
|
|
1809
|
private void handleDescription(EfloraImportState state, Element elDescription, Taxon taxon, Set<String> unhandledChildren) {
|
|
1810
|
verifyNoAttribute(elDescription);
|
|
1811
|
|
|
1812
|
List<Element> elements = elDescription.getChildren();
|
|
1813
|
for (Element element : elements){
|
|
1814
|
if (element.getName().equalsIgnoreCase("char")){
|
|
1815
|
handleChar(state, element, taxon);
|
|
1816
|
}else{
|
|
1817
|
logger.warn("Unhandled description child: " + element.getName());
|
|
1818
|
}
|
|
1819
|
}
|
|
1820
|
|
|
1821
|
}
|
|
1822
|
|
|
1823
|
|
|
1824
|
/**
|
|
1825
|
* @param state
|
|
1826
|
* @param element
|
|
1827
|
* @param taxon
|
|
1828
|
*/
|
|
1829
|
private void handleChar(EfloraImportState state, Element element, Taxon taxon) {
|
|
1830
|
List<Attribute> attributes = element.getAttributes();
|
|
1831
|
for (Attribute attribute : attributes){
|
|
1832
|
if (! attribute.getName().equalsIgnoreCase("class")){
|
|
1833
|
logger.warn("Char has unhandled attribute " + attribute.getName());
|
|
1834
|
}else{
|
|
1835
|
String classValue = attribute.getValue();
|
|
1836
|
Feature feature = getFeature(classValue, state);
|
|
1837
|
if (feature == null){
|
|
1838
|
logger.warn("Unhandled feature: " + classValue);
|
|
1839
|
}else{
|
|
1840
|
String value = element.getValue();
|
|
1841
|
addDescriptionElement(state, taxon, value, feature, null);
|
|
1842
|
}
|
|
1843
|
|
|
1844
|
}
|
|
1845
|
}
|
|
1846
|
|
|
1847
|
List<Element> elements = element.getChildren();
|
|
1848
|
if (! elements.isEmpty()){
|
|
1849
|
logger.warn("Char has unhandled children");
|
|
1850
|
}
|
|
1851
|
}
|
|
1852
|
|
|
1853
|
|
|
1854
|
/**
|
|
1855
|
* @param taxon
|
|
1856
|
* @return
|
|
1857
|
*/
|
|
1858
|
protected TaxonDescription getDescription(Taxon taxon) {
|
|
1859
|
for (TaxonDescription description : taxon.getDescriptions()){
|
|
1860
|
if (! description.isImageGallery()){
|
|
1861
|
return description;
|
|
1862
|
}
|
|
1863
|
}
|
|
1864
|
TaxonDescription newDescription = TaxonDescription.NewInstance(taxon);
|
|
1865
|
return newDescription;
|
|
1866
|
}
|
|
1867
|
|
|
1868
|
|
|
1869
|
/**
|
|
1870
|
* @param classValue
|
|
1871
|
* @param state
|
|
1872
|
* @return
|
|
1873
|
* @throws UndefinedTransformerMethodException
|
|
1874
|
*/
|
|
1875
|
private Feature getFeature(String classValue, EfloraImportState state) {
|
|
1876
|
UUID uuid;
|
|
1877
|
try {
|
|
1878
|
uuid = state.getTransformer().getFeatureUuid(classValue);
|
|
1879
|
if (uuid == null){
|
|
1880
|
logger.info("Uuid is null for " + classValue);
|
|
1881
|
}
|
|
1882
|
String featureText = StringUtils.capitalize(classValue);
|
|
1883
|
//TODO eFlora feature vocabulary
|
|
1884
|
Feature feature = getFeature(state, uuid, featureText, featureText, classValue, null);
|
|
1885
|
if (feature == null){
|
|
1886
|
throw new NullPointerException(classValue + " not recognized as a feature");
|
|
1887
|
}
|
|
1888
|
return feature;
|
|
1889
|
} catch (Exception e) {
|
|
1890
|
logger.warn("Could not create feature for " + classValue + ": " + e.getMessage()) ;
|
|
1891
|
return Feature.UNKNOWN();
|
|
1892
|
}
|
|
1893
|
}
|
|
1894
|
|
|
1895
|
|
|
1896
|
/**
|
|
1897
|
* @param state
|
|
1898
|
* @param element
|
|
1899
|
* @param taxon
|
|
1900
|
* @param unhandledTitleClassess
|
|
1901
|
*/
|
|
1902
|
private void handleTitle(EfloraImportState state, Element element, Taxon taxon, Set<String> unhandledTitleClassess) {
|
|
1903
|
// attributes
|
|
1904
|
List<Attribute> attributes = element.getAttributes();
|
|
1905
|
for (Attribute attribute : attributes){
|
|
1906
|
if (! attribute.getName().equalsIgnoreCase("class") ){
|
|
1907
|
if (! attribute.getName().equalsIgnoreCase("num")){
|
|
1908
|
logger.warn("Title has unhandled attribute " + attribute.getName());
|
|
1909
|
}else{
|
|
1910
|
//TODO num attribute in taxon
|
|
1911
|
}
|
|
1912
|
}else{
|
|
1913
|
String classValue = attribute.getValue();
|
|
1914
|
try {
|
|
1915
|
Rank rank;
|
|
1916
|
try {
|
|
1917
|
rank = Rank.getRankByNameOrIdInVoc(classValue);
|
|
1918
|
} catch (Exception e) {
|
|
1919
|
//TODO nc
|
|
1920
|
rank = Rank.getRankByEnglishName(classValue, NomenclaturalCode.ICNAFP, false);
|
|
1921
|
}
|
|
1922
|
taxon.getName().setRank(rank);
|
|
1923
|
if (rank.equals(Rank.FAMILY()) || rank.equals(Rank.GENUS())){
|
|
1924
|
handleGenus(element.getValue(), taxon.getName());
|
|
1925
|
}else if (rank.equals(Rank.SUBGENUS())){
|
|
1926
|
handleSubGenus(element.getValue(), taxon.getName());
|
|
1927
|
}else if (rank.equals(Rank.SECTION_BOTANY())){
|
|
1928
|
handleSection(element.getValue(), taxon.getName());
|
|
1929
|
}else if (rank.equals(Rank.SPECIES())){
|
|
1930
|
handleSpecies(element.getValue(), taxon.getName());
|
|
1931
|
}else if (rank.equals(Rank.SUBSPECIES())){
|
|
1932
|
handleSubSpecies(element.getValue(), taxon.getName());
|
|
1933
|
}else if (rank.equals(Rank.VARIETY())){
|
|
1934
|
handleVariety(element.getValue(), taxon.getName());
|
|
1935
|
}else{
|
|
1936
|
logger.warn("Unhandled rank: " + rank.getLabel());
|
|
1937
|
}
|
|
1938
|
} catch (UnknownCdmTypeException e) {
|
|
1939
|
logger.warn("Unknown rank " + classValue);
|
|
1940
|
unhandledTitleClassess.add(classValue);
|
|
1941
|
}
|
|
1942
|
}
|
|
1943
|
}
|
|
1944
|
List<Element> elements = element.getChildren();
|
|
1945
|
if (! elements.isEmpty()){
|
|
1946
|
logger.warn("Title has unexpected children");
|
|
1947
|
}
|
|
1948
|
UUID uuidTitle = EfloraTransformer.uuidTitle;
|
|
1949
|
ExtensionType titleExtension = this.getExtensionType(state, uuidTitle, "title", "title", "title");
|
|
1950
|
taxon.addExtension(element.getTextNormalize(), titleExtension);
|
|
1951
|
|
|
1952
|
}
|
|
1953
|
|
|
1954
|
|
|
1955
|
/**
|
|
1956
|
* @param value
|
|
1957
|
* @param taxonNameBase
|
|
1958
|
*/
|
|
1959
|
private void handleSubGenus(String value, INonViralName taxonNameBase) {
|
|
1960
|
String name = value.replace("Subgenus", "").trim();
|
|
1961
|
taxonNameBase.setInfraGenericEpithet(name);
|
|
1962
|
}
|
|
1963
|
|
|
1964
|
/**
|
|
1965
|
* @param value
|
|
1966
|
* @param taxonNameBase
|
|
1967
|
*/
|
|
1968
|
private void handleSection(String value, INonViralName taxonNameBase) {
|
|
1969
|
String name = value.replace("Section", "").trim();
|
|
1970
|
taxonNameBase.setInfraGenericEpithet(name);
|
|
1971
|
}
|
|
1972
|
|
|
1973
|
/**
|
|
1974
|
* @param value
|
|
1975
|
* @param taxonNameBase
|
|
1976
|
*/
|
|
1977
|
private void handleSpecies(String value, TaxonNameBase taxonNameBase) {
|
|
1978
|
//do nothing
|
|
1979
|
}
|
|
1980
|
|
|
1981
|
/**
|
|
1982
|
* @param value
|
|
1983
|
* @param taxonNameBase
|
|
1984
|
*/
|
|
1985
|
private void handleVariety(String value, TaxonNameBase taxonNameBase) {
|
|
1986
|
//do nothing
|
|
1987
|
}
|
|
1988
|
|
|
1989
|
/**
|
|
1990
|
* @param value
|
|
1991
|
* @param taxonNameBase
|
|
1992
|
*/
|
|
1993
|
private void handleSubSpecies(String value, TaxonNameBase taxonNameBase) {
|
|
1994
|
//do nothing
|
|
1995
|
}
|
|
1996
|
|
|
1997
|
|
|
1998
|
private final Pattern rexGenusAuthor = Pattern.compile("(\\[|\\().*(\\]|\\))");
|
|
1999
|
|
|
2000
|
/**
|
|
2001
|
* @param value
|
|
2002
|
* @param taxonNameBase
|
|
2003
|
*/
|
|
2004
|
protected void handleGenus(String value, INonViralName taxonName) {
|
|
2005
|
Matcher matcher = rexGenusAuthor.matcher(value);
|
|
2006
|
if (matcher.find()){
|
|
2007
|
String author = matcher.group();
|
|
2008
|
// String genus = value.replace(author, "");
|
|
2009
|
author = author.substring(1, author.length() - 1);
|
|
2010
|
Team team = Team.NewInstance();
|
|
2011
|
team.setTitleCache(author, true);
|
|
2012
|
Credit credit = Credit.NewInstance(team, null);
|
|
2013
|
taxonName.addCredit(credit);
|
|
2014
|
// taxonName.setCombinationAuthorship(team);
|
|
2015
|
// taxonName.setGenusOrUninomial(genus);
|
|
2016
|
}else{
|
|
2017
|
logger.info("No Author match for " + value);
|
|
2018
|
}
|
|
2019
|
}
|
|
2020
|
|
|
2021
|
|
|
2022
|
/**
|
|
2023
|
* @param taxon
|
|
2024
|
* @param lastTaxon
|
|
2025
|
*/
|
|
2026
|
private void handleTaxonRelation(EfloraImportState state, Taxon taxon, Taxon lastTaxon) {
|
|
2027
|
|
|
2028
|
Classification tree = getTree(state);
|
|
2029
|
if (lastTaxon == null){
|
|
2030
|
tree.addChildTaxon(taxon, null, null);
|
|
2031
|
return;
|
|
2032
|
}
|
|
2033
|
Rank thisRank = taxon.getName().getRank();
|
|
2034
|
Rank lastRank = lastTaxon.getName().getRank();
|
|
2035
|
if (lastTaxon.getTaxonNodes().size() > 0){
|
|
2036
|
TaxonNode lastNode = lastTaxon.getTaxonNodes().iterator().next();
|
|
2037
|
if (thisRank.isLower(lastRank ) ){
|
|
2038
|
lastNode.addChildTaxon(taxon, null, null);
|
|
2039
|
fillMissingEpithetsForTaxa(lastTaxon, taxon);
|
|
2040
|
}else if (thisRank.equals(lastRank)){
|
|
2041
|
TaxonNode parent = lastNode.getParent();
|
|
2042
|
if (parent != null){
|
|
2043
|
parent.addChildTaxon(taxon, null, null);
|
|
2044
|
fillMissingEpithetsForTaxa(parent.getTaxon(), taxon);
|
|
2045
|
}else{
|
|
2046
|
tree.addChildTaxon(taxon, null, null);
|
|
2047
|
}
|
|
2048
|
}else if (thisRank.isHigher(lastRank)){
|
|
2049
|
handleTaxonRelation(state, taxon, lastNode.getParent().getTaxon());
|
|
2050
|
// TaxonNode parentNode = handleTaxonRelation(state, taxon, lastNode.getParent().getTaxon());
|
|
2051
|
// parentNode.addChildTaxon(taxon, null, null, null);
|
|
2052
|
}
|
|
2053
|
}else{
|
|
2054
|
logger.warn("Last taxon has no node");
|
|
2055
|
}
|
|
2056
|
}
|
|
2057
|
|
|
2058
|
|
|
2059
|
|
|
2060
|
/**
|
|
2061
|
* @param state
|
|
2062
|
* @return
|
|
2063
|
*/
|
|
2064
|
private Classification getTree(EfloraImportState state) {
|
|
2065
|
Classification result = state.getTree(null);
|
|
2066
|
if (result == null){
|
|
2067
|
UUID uuid = state.getConfig().getClassificationUuid();
|
|
2068
|
if (uuid == null){
|
|
2069
|
logger.warn("No classification uuid is defined");
|
|
2070
|
result = getNewClassification(state);
|
|
2071
|
}else{
|
|
2072
|
result = getClassificationService().find(uuid);
|
|
2073
|
if (result == null){
|
|
2074
|
result = getNewClassification(state);
|
|
2075
|
result.setUuid(uuid);
|
|
2076
|
}
|
|
2077
|
}
|
|
2078
|
state.putTree(null, result);
|
|
2079
|
}
|
|
2080
|
return result;
|
|
2081
|
}
|
|
2082
|
|
|
2083
|
|
|
2084
|
private Classification getNewClassification(EfloraImportState state) {
|
|
2085
|
Classification result;
|
|
2086
|
result = Classification.NewInstance(state.getConfig().getClassificationTitle());
|
|
2087
|
state.putTree(null, result);
|
|
2088
|
return result;
|
|
2089
|
}
|
|
2090
|
|
|
2091
|
|
|
2092
|
/**
|
|
2093
|
* @param state
|
|
2094
|
* @param taxon
|
|
2095
|
* @param value
|
|
2096
|
* @param feature
|
|
2097
|
* @return
|
|
2098
|
*/
|
|
2099
|
private TextData addDescriptionElement(EfloraImportState state, Taxon taxon, String value, Feature feature, String references) {
|
|
2100
|
TextData textData = TextData.NewInstance(feature);
|
|
2101
|
Language textLanguage = getDefaultLanguage(state);
|
|
2102
|
textData.putText(textLanguage, value);
|
|
2103
|
TaxonDescription description = getDescription(taxon);
|
|
2104
|
description.addElement(textData);
|
|
2105
|
if (references != null){
|
|
2106
|
makeOriginalSourceReferences(textData, ";", references);
|
|
2107
|
}
|
|
2108
|
return textData;
|
|
2109
|
}
|
|
2110
|
|
|
2111
|
private Language getDefaultLanguage(EfloraImportState state) {
|
|
2112
|
UUID defaultLanguageUuid = state.getConfig().getDefaultLanguageUuid();
|
|
2113
|
if (defaultLanguageUuid != null){
|
|
2114
|
Language result = state.getDefaultLanguage();
|
|
2115
|
if (result == null || ! result.getUuid().equals(defaultLanguageUuid)){
|
|
2116
|
result = (Language)getTermService().find(defaultLanguageUuid);
|
|
2117
|
state.setDefaultLanguage(result);
|
|
2118
|
if (result == null){
|
|
2119
|
logger.warn("Default language for " + defaultLanguageUuid + " does not exist.");
|
|
2120
|
}
|
|
2121
|
}
|
|
2122
|
return result;
|
|
2123
|
}else{
|
|
2124
|
return Language.DEFAULT();
|
|
2125
|
}
|
|
2126
|
}
|
|
2127
|
|
|
2128
|
|
|
2129
|
/**
|
|
2130
|
* @param elNomenclature
|
|
2131
|
*/
|
|
2132
|
private void verifyNoAttribute(Element element) {
|
|
2133
|
List<Attribute> attributes = element.getAttributes();
|
|
2134
|
if (! attributes.isEmpty()){
|
|
2135
|
logger.warn(element.getName() + " has unhandled attributes: " + attributes.get(0).getValue() + "..." );
|
|
2136
|
}
|
|
2137
|
}
|
|
2138
|
|
|
2139
|
/**
|
|
2140
|
* @param elNomenclature
|
|
2141
|
*/
|
|
2142
|
protected void verifyNoChildren(Element element) {
|
|
2143
|
verifyNoChildren(element, false);
|
|
2144
|
}
|
|
2145
|
|
|
2146
|
/**
|
|
2147
|
* @param elNomenclature
|
|
2148
|
*/
|
|
2149
|
private void verifyNoChildren(Element element, boolean ignoreLineBreak) {
|
|
2150
|
List<Element> children = element.getChildren();
|
|
2151
|
if (! children.isEmpty()){
|
|
2152
|
if (ignoreLineBreak == true){
|
|
2153
|
for (Element child : children){
|
|
2154
|
if (! child.getName().equalsIgnoreCase("BR")){
|
|
2155
|
logger.warn(element.getName() + " has unhandled child: " + child.getName());
|
|
2156
|
}
|
|
2157
|
}
|
|
2158
|
}else{
|
|
2159
|
logger.warn(element.getName() + " has unhandled children");
|
|
2160
|
}
|
|
2161
|
}
|
|
2162
|
}
|
|
2163
|
|
|
2164
|
|
|
2165
|
|
|
2166
|
/**
|
|
2167
|
* Parses the nomenclatural status from the references titleCache. If a nomenclatural status
|
|
2168
|
* exists it is added to the name and the nom. status part of the references title cache is
|
|
2169
|
* removed. Requires protected title cache.
|
|
2170
|
* @param ref
|
|
2171
|
* @param nonViralName
|
|
2172
|
*/
|
|
2173
|
protected void parseNomStatus(Reference ref, INonViralName nonViralName) {
|
|
2174
|
String titleToParse = ref.getTitleCache();
|
|
2175
|
|
|
2176
|
String noStatusTitle = parser.parseNomStatus(titleToParse, nonViralName, true);
|
|
2177
|
if (! noStatusTitle.equals(titleToParse)){
|
|
2178
|
ref.setTitleCache(noStatusTitle, true);
|
|
2179
|
}
|
|
2180
|
}
|
|
2181
|
|
|
2182
|
|
|
2183
|
/**
|
|
2184
|
* Extracts the date published part and returns micro reference
|
|
2185
|
* @param ref
|
|
2186
|
* @return
|
|
2187
|
*/
|
|
2188
|
private String parseReferenceYearAndDetail(Reference ref){
|
|
2189
|
String detailResult = null;
|
|
2190
|
String titleToParse = ref.getTitleCache();
|
|
2191
|
titleToParse = removeStartingSymbols(titleToParse, ref);
|
|
2192
|
String reReference = "^\\.{1,}";
|
|
2193
|
// String reYear = "\\([1-2]{1}[0-9]{3}\\)";
|
|
2194
|
String oneMonth = "(Feb.|Dec.|March|June|July)";
|
|
2195
|
String reYear = oneMonth + "?\\s?[1-2]\\s?[0-9]\\s?[0-9]\\s?[0-9]\\s?";
|
|
2196
|
String secondYear = "(\\s?[1-2]\\s?[0-9])?\\s?[0-9]\\s?[0-9]\\s?";
|
|
2197
|
|
|
2198
|
String reYearPeriod = "\\(" + reYear + "(\\-" + secondYear + ")?\\)";
|
|
2199
|
String reDetail = "\\.{1,10}$";
|
|
2200
|
|
|
2201
|
//pattern for the whole string
|
|
2202
|
Pattern patReference = Pattern.compile(/*reReference +*/ reYearPeriod /*+ reDetail */);
|
|
2203
|
Matcher matcher = patReference.matcher(titleToParse);
|
|
2204
|
if (matcher.find()){
|
|
2205
|
int start = matcher.start();
|
|
2206
|
int end = matcher.end();
|
|
2207
|
|
|
2208
|
//title and other information precedes the year part
|
|
2209
|
String title = titleToParse.substring(0, start).trim();
|
|
2210
|
//detail follows the year part
|
|
2211
|
String detail = titleToParse.substring(end).trim();
|
|
2212
|
|
|
2213
|
//time period
|
|
2214
|
String strPeriod = matcher.group().trim();
|
|
2215
|
strPeriod = strPeriod.substring(1, strPeriod.length()-1); //remove brackets
|
|
2216
|
Pattern patStartMonth = Pattern.compile("^" + oneMonth);
|
|
2217
|
matcher = patStartMonth.matcher(strPeriod);
|
|
2218
|
strPeriod = strPeriod.replace(" ", "");
|
|
2219
|
Integer startMonth = null;
|
|
2220
|
if (matcher.find()){
|
|
2221
|
end = matcher.end();
|
|
2222
|
strPeriod = strPeriod.substring(0, end) + " " + strPeriod.substring(end);
|
|
2223
|
startMonth = getMonth(strPeriod.substring(0, end));
|
|
2224
|
}
|
|
2225
|
|
|
2226
|
TimePeriod datePublished = TimePeriodParser.parseString(strPeriod);
|
|
2227
|
if (startMonth != null){
|
|
2228
|
datePublished.setStartMonth(startMonth);
|
|
2229
|
}
|
|
2230
|
ref.setDatePublished(datePublished);
|
|
2231
|
ref.setTitle(title);
|
|
2232
|
detailResult = CdmUtils.removeTrailingDot(detail);
|
|
2233
|
if (detailResult.endsWith(".") || detailResult.endsWith(";") || detailResult.endsWith(",") ){
|
|
2234
|
detailResult = detailResult.substring(0, detailResult.length() -1);
|
|
2235
|
}
|
|
2236
|
ref.setProtectedTitleCache(false);
|
|
2237
|
}else{
|
|
2238
|
logger.warn("Could not parse reference: " + titleToParse);
|
|
2239
|
}
|
|
2240
|
return detailResult;
|
|
2241
|
|
|
2242
|
}
|
|
2243
|
|
|
2244
|
|
|
2245
|
|
|
2246
|
private Integer getMonth(String month) {
|
|
2247
|
if (month.startsWith("Jan")){
|
|
2248
|
return 1;
|
|
2249
|
}else if (month.startsWith("Feb")){
|
|
2250
|
return 2;
|
|
2251
|
}else if (month.startsWith("Mar")){
|
|
2252
|
return 3;
|
|
2253
|
}else if (month.startsWith("Apr")){
|
|
2254
|
return 4;
|
|
2255
|
}else if (month.startsWith("May")){
|
|
2256
|
return 5;
|
|
2257
|
}else if (month.startsWith("Jun")){
|
|
2258
|
return 6;
|
|
2259
|
}else if (month.startsWith("Jul")){
|
|
2260
|
return 7;
|
|
2261
|
}else if (month.startsWith("Aug")){
|
|
2262
|
return 8;
|
|
2263
|
}else if (month.startsWith("Sep")){
|
|
2264
|
return 9;
|
|
2265
|
}else if (month.startsWith("Oct")){
|
|
2266
|
return 10;
|
|
2267
|
}else if (month.startsWith("Nov")){
|
|
2268
|
return 11;
|
|
2269
|
}else if (month.startsWith("Dec")){
|
|
2270
|
return 12;
|
|
2271
|
}else{
|
|
2272
|
logger.warn("Month not yet supported: " + month);
|
|
2273
|
return null;
|
|
2274
|
}
|
|
2275
|
}
|
|
2276
|
|
|
2277
|
|
|
2278
|
/* (non-Javadoc)
|
|
2279
|
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
|
|
2280
|
*/
|
|
2281
|
@Override
|
|
2282
|
protected boolean isIgnore(EfloraImportState state){
|
|
2283
|
return ! state.getConfig().isDoTaxa();
|
|
2284
|
}
|
|
2285
|
|
|
2286
|
}
|