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// $Id$
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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.pesi.out;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.HashSet;
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import java.util.Iterator;
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import java.util.List;
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import java.util.Set;
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import java.util.UUID;
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import org.apache.log4j.Logger;
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import eu.etaxonomy.cdm.api.service.pager.Pager;
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import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
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import eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer;
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import eu.etaxonomy.cdm.io.common.DbExportBase;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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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.RelationshipBase;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.TaxonNameDescription;
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import eu.etaxonomy.cdm.model.description.TextData;
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import eu.etaxonomy.cdm.model.name.BotanicalName;
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import eu.etaxonomy.cdm.model.name.HybridRelationship;
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import eu.etaxonomy.cdm.model.name.NameRelationship;
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import eu.etaxonomy.cdm.model.name.NameRelationshipType;
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import eu.etaxonomy.cdm.model.name.NonViralName;
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import eu.etaxonomy.cdm.model.name.TaxonNameBase;
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import eu.etaxonomy.cdm.model.name.ZoologicalName;
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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import eu.etaxonomy.cdm.model.taxon.SynonymRelationship;
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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.TaxonRelationship;
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
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import eu.etaxonomy.cdm.persistence.query.OrderHint;
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import eu.etaxonomy.cdm.strategy.cache.name.BotanicNameDefaultCacheStrategy;
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import eu.etaxonomy.cdm.strategy.cache.name.NonViralNameDefaultCacheStrategy;
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import eu.etaxonomy.cdm.strategy.cache.name.ZooNameNoMarkerCacheStrategy;
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/**
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* @author e.-m.lee
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* @date 12.02.2010
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*
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*/
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public abstract class PesiExportBase extends DbExportBase<PesiExportConfigurator, PesiExportState, PesiTransformer> {
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private static final Logger logger = Logger.getLogger(PesiExportBase.class);
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protected static final boolean IS_CACHE = true;
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private static Set<NameRelationshipType> excludedRelTypes = new HashSet<NameRelationshipType>();
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private static NonViralNameDefaultCacheStrategy<?> zooNameStrategy = ZooNameNoMarkerCacheStrategy.NewInstance();
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private static NonViralNameDefaultCacheStrategy<?> botanicalNameStrategy = BotanicNameDefaultCacheStrategy.NewInstance();
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public PesiExportBase() {
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super();
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}
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protected <CLASS extends TaxonBase> List<CLASS> getNextTaxonPartition(Class<CLASS> clazz, int limit, int partitionCount, List<String> propertyPath) {
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List<OrderHint> orderHints = new ArrayList<OrderHint>();
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orderHints.add(new OrderHint("id", OrderHint.SortOrder.ASCENDING ));
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List<CLASS> list = (List<CLASS>)getTaxonService().list(clazz, limit, partitionCount * limit, orderHints, propertyPath);
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if (list.isEmpty()){
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return null;
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}
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Iterator<CLASS> it = list.iterator();
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while (it.hasNext()){
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TaxonBase<?> taxonBase = it.next();
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if (! isPesiTaxon(taxonBase)){
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it.remove();
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}
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taxonBase = null;
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}
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it = null;
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return list;
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}
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protected List<TaxonNameDescription> getNextNameDescriptionPartition(int limit, int partitionCount, List<String> propertyPath) {
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List<OrderHint> orderHints = new ArrayList<OrderHint>();
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orderHints.add(new OrderHint("id", OrderHint.SortOrder.ASCENDING ));
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Pager<TaxonNameDescription> l = getDescriptionService().getTaxonNameDescriptions(null, limit, partitionCount, propertyPath);
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List<TaxonNameDescription> list = l.getRecords();
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if (list.isEmpty()){
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return null;
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}
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Iterator<TaxonNameDescription> it = list.iterator();
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while (it.hasNext()){
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TaxonNameDescription nameDescription = it.next();
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if (! isPesiNameDescriptionTaxon(nameDescription)){
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it.remove();
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}
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}
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return list;
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}
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private boolean isPesiNameDescriptionTaxon(TaxonNameDescription nameDescription) {
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TaxonNameBase<?,?> name = nameDescription.getTaxonName();
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if (isPurePesiName(name)){
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return true;
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}else{
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Set<TaxonBase> taxa = name.getTaxonBases();
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for (TaxonBase<?> taxonBase : taxa){
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if (isPesiTaxon(taxonBase)){
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return true;
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}
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}
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}
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return false;
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}
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/**
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* Returns the next list of pure names. If finished result will be null. If list is empty there may be result in further partitions.
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* @param clazz
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* @param limit
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* @param partitionCount
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* @return
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*/
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protected List<NonViralName<?>> getNextPureNamePartition(Class<? extends NonViralName> clazz,int limit, int partitionCount) {
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List<OrderHint> orderHints = new ArrayList<OrderHint>();
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orderHints.add(new OrderHint("id", OrderHint.SortOrder.ASCENDING ));
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List<String> propPath = Arrays.asList(new String[]{"taxonBases"});
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List<NonViralName<?>> list = (List)getNameService().list(clazz, limit, partitionCount * limit, orderHints, null);
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if (list.isEmpty()){
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return null;
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}
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Iterator<NonViralName<?>> it = list.iterator();
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while (it.hasNext()){
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NonViralName<?> taxonName = HibernateProxyHelper.deproxy(it.next(), NonViralName.class);
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if (! isPurePesiName(taxonName)){
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it.remove();
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}
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}
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return list;
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}
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protected <CLASS extends RelationshipBase> List<CLASS> getNextNameRelationshipPartition(Class<CLASS> clazz, int limit, int partitionCount, List<String> propertyPath) {
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List<CLASS> result = new ArrayList<CLASS>();
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String[] propertyPaths = null;
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String orderHints = null;
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List<CLASS> list = (List<CLASS>)getNameService().getAllRelationships(limit, partitionCount * limit);
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if (list.isEmpty()){
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return null;
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}
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for (CLASS rel : list){
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if (isPesiNameRelationship(rel)){
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result.add(rel);
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}
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}
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return result;
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}
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protected <CLASS extends RelationshipBase> List<CLASS> getNextTaxonRelationshipPartition( int limit, int partitionCount, List<String> propertyPath) {
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List<CLASS> result = new ArrayList<CLASS>();
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String[] propertyPaths = null;
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String orderHints = null;
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List<CLASS> list = (List<CLASS>)getTaxonService().getAllRelationships(limit, partitionCount * limit);
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if (list.isEmpty()){
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return null;
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}
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for (CLASS rel : list){
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if (isPesiTaxonOrSynonymRelationship(rel)){
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result.add(rel);
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}
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}
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return result;
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}
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protected boolean isPesiNameRelationship(RelationshipBase rel){
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TaxonNameBase<?,?> name1;
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TaxonNameBase<?,?> name2;
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if (rel.isInstanceOf(HybridRelationship.class)){
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HybridRelationship hybridRel = CdmBase.deproxy(rel, HybridRelationship.class);
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name1 = hybridRel.getParentName();
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name2 = hybridRel.getHybridName();
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}else if (rel.isInstanceOf(NameRelationship.class)){
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NameRelationship nameRel = CdmBase.deproxy(rel, NameRelationship.class);
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name1 = nameRel.getFromName();
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name2 = nameRel.getToName();
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}else{
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logger.warn ("Only hybrid- and name-relationships alowed here");
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return false;
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}
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return (isPesiName(name1) && isPesiName(name2));
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}
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private boolean isPesiName(TaxonNameBase<?,?> name) {
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return hasPesiTaxon(name) || isPurePesiName(name);
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}
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protected boolean isPesiTaxonOrSynonymRelationship(RelationshipBase rel){
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TaxonBase<?> fromTaxon;
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Taxon toTaxon;
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if (rel.isInstanceOf(SynonymRelationship.class)){
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SynonymRelationship synRel = CdmBase.deproxy(rel, SynonymRelationship.class);
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fromTaxon = synRel.getSynonym();
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toTaxon = synRel.getAcceptedTaxon();
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synRel = null;
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}else if (rel.isInstanceOf(TaxonRelationship.class)){
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TaxonRelationship taxRel = CdmBase.deproxy(rel, TaxonRelationship.class);
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fromTaxon = taxRel.getFromTaxon();
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toTaxon = taxRel.getToTaxon();
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taxRel = null;
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}else{
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logger.warn ("Only synonym - and taxon-relationships allowed here");
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return false;
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}
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return (isPesiTaxon(fromTaxon, false) && isPesiTaxon(toTaxon, true));
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}
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/**
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* Decides if a name is not used as the name part of a PESI taxon (and therefore is
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* exported to PESI as taxon already) but is related to a name used as a PESI taxon
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* (e.g. as basionym, orthographic variant, etc.) and therefore should be exported
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* to PESI as part of the name relationship.
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* @param taxonName
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* @return
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*/
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protected boolean isPurePesiName(TaxonNameBase<?,?> taxonName){
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if (hasPesiTaxon(taxonName)){
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return false;
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}
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//from names
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for (NameRelationship rel :taxonName.getRelationsFromThisName()){
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TaxonNameBase<?,?> relatedName = rel.getToName();
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if (hasPesiTaxon(relatedName)){
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return true;
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}
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}
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//excluded relationships on to-side
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initExcludedRelTypes();
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//to names
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for (NameRelationship rel :taxonName.getRelationsToThisName()){
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//exclude certain types
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if (excludedRelTypes.contains(rel.getType())){
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continue;
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}
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TaxonNameBase<?,?> relatedName = rel.getFromName();
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if (hasPesiTaxon(relatedName)){
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return true;
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}
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}
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//include hybrid parents, but no childs
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NonViralName nvn = CdmBase.deproxy(taxonName, NonViralName.class);
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for (HybridRelationship rel : (Set<HybridRelationship>)nvn.getHybridParentRelations()){
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NonViralName<?> child = rel.getHybridName();
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if (hasPesiTaxon(child)){
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return true;
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}
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}
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return false;
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}
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private void initExcludedRelTypes() {
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if (excludedRelTypes.isEmpty()){
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excludedRelTypes.add(NameRelationshipType.BASIONYM());
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excludedRelTypes.add(NameRelationshipType.REPLACED_SYNONYM());
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excludedRelTypes.add(NameRelationshipType.ORTHOGRAPHIC_VARIANT());
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}
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}
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/**
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* Decides if a given name has "PESI taxa" attached.
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*
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* @see #getPesiTaxa(TaxonNameBase)
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* @see #isPesiTaxon(TaxonBase)
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* @param taxonName
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* @return
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*/
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protected boolean hasPesiTaxon(TaxonNameBase<?,?> taxonName) {
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for (TaxonBase<?> taxon : taxonName.getTaxonBases()){
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if (isPesiTaxon(taxon)){
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return true;
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}
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}
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return false;
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}
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/**
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* Returns those concepts (taxon bases) for the given name that
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* are pesi taxa.
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*
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* @see #isPesiTaxon(TaxonBase)
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* @param name
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* @return
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*/
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protected Set<TaxonBase<?>> getPesiTaxa(TaxonNameBase<?,?> name){
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Set<TaxonBase<?>> result = new HashSet<TaxonBase<?>>();
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for (TaxonBase<?> taxonBase : name.getTaxonBases()){
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if (isPesiTaxon(taxonBase)){
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result.add(taxonBase);
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}
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}
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return result;
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}
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/**
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* @see #isPesiTaxon(TaxonBase, boolean)
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* @param taxonBase
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* @return
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*/
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protected static boolean isPesiTaxon(TaxonBase taxonBase) {
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return isPesiTaxon(taxonBase, false);
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}
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/**
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* Checks if this taxon base is a taxon that is to be exported to PESI. This is generally the case
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* but not for taxa that are marked as "unpublish". Synonyms and misapplied names are exported if they are
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* related at least to one accepted taxon that is also exported, except for those misapplied names
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* marked as misapplied names created by Euro+Med common names ({@linkplain http://dev.e-taxonomy.eu/trac/ticket/2786} ).
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* The list of conditions may change in future.
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* @param taxonBase
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* @return
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*/
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protected static boolean isPesiTaxon(TaxonBase taxonBase, boolean excludeMisappliedNames) {
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//handle accepted taxa
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if (taxonBase.isInstanceOf(Taxon.class)){
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Taxon taxon = CdmBase.deproxy(taxonBase, Taxon.class);
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if (! taxon.isPublish()){
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taxon = null;
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return false;
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}
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for (Marker marker : taxon.getMarkers()){
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//probably not needed anymore after #1780 was fixed, also #4046 interesting
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357
|
if (marker.getValue() == false && marker.getMarkerType().equals(MarkerType.PUBLISH())){
|
|
358
|
taxon = null;
|
|
359
|
return false;
|
|
360
|
//probably not needed any more after #2786 was fixed
|
|
361
|
}else if (marker.getValue() == true && marker.getMarkerType().getUuid().equals(BerlinModelTransformer.uuidMisappliedCommonName)){
|
|
362
|
logger.warn("Misapplied common name still exists");
|
|
363
|
taxon = null;
|
|
364
|
return false;
|
|
365
|
}
|
|
366
|
|
|
367
|
}
|
|
368
|
|
|
369
|
//handle PESI accepted taxa
|
|
370
|
if (! taxon.isMisapplication()){
|
|
371
|
for (Marker marker : taxon.getMarkers()){
|
|
372
|
if (marker.getValue() == false && marker.getMarkerType().equals(MarkerType.PUBLISH())){
|
|
373
|
taxon = null;
|
|
374
|
return false;
|
|
375
|
}
|
|
376
|
}
|
|
377
|
return true;
|
|
378
|
//handle misapplied names
|
|
379
|
}else{
|
|
380
|
if (excludeMisappliedNames){
|
|
381
|
taxon = null;
|
|
382
|
return false;
|
|
383
|
}
|
|
384
|
for (Marker marker : taxon.getMarkers()){
|
|
385
|
//probably not needed any more after #2786 was fixed
|
|
386
|
if (marker.getValue() == true && marker.getMarkerType().getUuid().equals(BerlinModelTransformer.uuidMisappliedCommonName)){
|
|
387
|
logger.warn("Misapplied common name still exists");
|
|
388
|
taxon = null;
|
|
389
|
return false;
|
|
390
|
}
|
|
391
|
}
|
|
392
|
for (TaxonRelationship taxRel : taxon.getRelationsFromThisTaxon()){
|
|
393
|
if (taxRel.getType().equals(TaxonRelationshipType.MISAPPLIED_NAME_FOR())){
|
|
394
|
// logger.warn(taxRel.getUuid() + "; " + taxRel.getToTaxon().getUuid() + " + " + taxRel.getToTaxon().getTitleCache());
|
|
395
|
if (isPesiTaxon(taxRel.getToTaxon(), true)){
|
|
396
|
taxon = null;
|
|
397
|
return true;
|
|
398
|
}
|
|
399
|
}
|
|
400
|
}
|
|
401
|
if (logger.isDebugEnabled()){ logger.debug("Misapplied name has no accepted PESI taxon: " + taxon.getUuid() + ", (" + taxon.getTitleCache() + ")");}
|
|
402
|
taxon = null;
|
|
403
|
return false;
|
|
404
|
}
|
|
405
|
//handle synonyms
|
|
406
|
}else if (taxonBase.isInstanceOf(Synonym.class)){
|
|
407
|
Synonym synonym = CdmBase.deproxy(taxonBase, Synonym.class);
|
|
408
|
boolean hasAcceptedPesiTaxon = false;
|
|
409
|
for (Taxon accTaxon : synonym.getAcceptedTaxa()){
|
|
410
|
if (isPesiTaxon(accTaxon)){
|
|
411
|
hasAcceptedPesiTaxon = true;
|
|
412
|
}
|
|
413
|
}
|
|
414
|
if (!hasAcceptedPesiTaxon) {if (logger.isDebugEnabled()){logger.debug("Synonym has no accepted PESI taxon: " + synonym.getUuid() + ", (" + synonym.getTitleCache() + ")");}}
|
|
415
|
synonym = null;
|
|
416
|
return hasAcceptedPesiTaxon;
|
|
417
|
}else {
|
|
418
|
throw new RuntimeException("Unknown taxon base type: " + taxonBase.getClass());
|
|
419
|
}
|
|
420
|
}
|
|
421
|
|
|
422
|
/* (non-Javadoc)
|
|
423
|
* @see eu.etaxonomy.cdm.io.common.DbExportBase#getDbIdCdmWithExceptions(eu.etaxonomy.cdm.model.common.CdmBase, eu.etaxonomy.cdm.io.common.ExportStateBase)
|
|
424
|
*/
|
|
425
|
protected Object getDbIdCdmWithExceptions(CdmBase cdmBase, PesiExportState state) {
|
|
426
|
if (cdmBase.isInstanceOf(TaxonNameBase.class)){
|
|
427
|
return ( cdmBase.getId() + state.getConfig().getNameIdStart() );
|
|
428
|
}if (isAdditionalSource(cdmBase) ){
|
|
429
|
return ( cdmBase.getId() + 2 * state.getConfig().getNameIdStart() ); //make it a separate variable if conflicts occur.
|
|
430
|
}else{
|
|
431
|
return super.getDbIdCdmWithExceptions(cdmBase, state);
|
|
432
|
}
|
|
433
|
}
|
|
434
|
|
|
435
|
|
|
436
|
|
|
437
|
private boolean isAdditionalSource(CdmBase cdmBase) {
|
|
438
|
if (cdmBase.isInstanceOf(TextData.class)){
|
|
439
|
TextData textData = CdmBase.deproxy(cdmBase, TextData.class);
|
|
440
|
if (textData.getFeature().equals(Feature.ADDITIONAL_PUBLICATION()) ||
|
|
441
|
textData.getFeature().equals(Feature.CITATION())){
|
|
442
|
return true;
|
|
443
|
}
|
|
444
|
}
|
|
445
|
return false;
|
|
446
|
}
|
|
447
|
|
|
448
|
|
|
449
|
protected MarkerType getUuidMarkerType(UUID uuid, PesiExportState state){
|
|
450
|
if (uuid == null){
|
|
451
|
uuid = UUID.randomUUID();
|
|
452
|
}
|
|
453
|
|
|
454
|
MarkerType markerType = state.getMarkerType(uuid);
|
|
455
|
if (markerType == null){
|
|
456
|
if (uuid.equals(PesiTransformer.uuidMarkerGuidIsMissing)){
|
|
457
|
markerType = MarkerType.NewInstance("Uuid is Missing", "Uuid is missing", null);
|
|
458
|
markerType.setUuid(uuid);
|
|
459
|
} else if (uuid.equals(PesiTransformer.uuidMarkerTypeHasNoLastAction)){
|
|
460
|
markerType = MarkerType.NewInstance("Has no last Action", "Has no last action", null);
|
|
461
|
markerType.setUuid(uuid);
|
|
462
|
}
|
|
463
|
}
|
|
464
|
|
|
465
|
state.putMarkerType(markerType);
|
|
466
|
return markerType;
|
|
467
|
}
|
|
468
|
|
|
469
|
|
|
470
|
|
|
471
|
protected static NonViralNameDefaultCacheStrategy getCacheStrategy(TaxonNameBase<?, ?> taxonName) {
|
|
472
|
NonViralNameDefaultCacheStrategy cacheStrategy;
|
|
473
|
if (taxonName.isInstanceOf(ZoologicalName.class)){
|
|
474
|
cacheStrategy = zooNameStrategy;
|
|
475
|
}else if (taxonName.isInstanceOf(BotanicalName.class)) {
|
|
476
|
cacheStrategy = botanicalNameStrategy;
|
|
477
|
}else{
|
|
478
|
logger.error("Unhandled taxon name type. Can't define strategy class");
|
|
479
|
cacheStrategy = botanicalNameStrategy;
|
|
480
|
}
|
|
481
|
return cacheStrategy;
|
|
482
|
}
|
|
483
|
|
|
484
|
|
|
485
|
|
|
486
|
|
|
487
|
/**
|
|
488
|
* Checks whether a given taxon is a misapplied name.
|
|
489
|
* @param taxon The {@link TaxonBase Taxon}.
|
|
490
|
* @return Whether the given TaxonName is a misapplied name or not.
|
|
491
|
*/
|
|
492
|
protected static boolean isMisappliedName(TaxonBase<?> taxon) {
|
|
493
|
return getAcceptedTaxonForMisappliedName(taxon) != null;
|
|
494
|
|
|
495
|
}
|
|
496
|
|
|
497
|
|
|
498
|
/**
|
|
499
|
* Returns the first accepted taxon for this misapplied name.
|
|
500
|
* If this misapplied name is not a misapplied name, <code>null</code> is returned.
|
|
501
|
* @param taxon The {@link TaxonBase Taxon}.
|
|
502
|
*/
|
|
503
|
private static Taxon getAcceptedTaxonForMisappliedName(TaxonBase<?> taxon) {
|
|
504
|
if (! taxon.isInstanceOf(Taxon.class)){
|
|
505
|
return null;
|
|
506
|
}
|
|
507
|
Set<TaxonRelationship> taxonRelations = CdmBase.deproxy(taxon, Taxon.class).getRelationsFromThisTaxon();
|
|
508
|
for (TaxonRelationship taxonRelationship : taxonRelations) {
|
|
509
|
TaxonRelationshipType taxonRelationshipType = taxonRelationship.getType();
|
|
510
|
if (taxonRelationshipType.equals(TaxonRelationshipType.MISAPPLIED_NAME_FOR())) {
|
|
511
|
return taxonRelationship.getToTaxon();
|
|
512
|
}
|
|
513
|
}
|
|
514
|
return null;
|
|
515
|
}
|
|
516
|
|
|
517
|
|
|
518
|
|
|
519
|
|
|
520
|
|
|
521
|
|
|
522
|
|
|
523
|
|
|
524
|
|
|
525
|
// protected List<TaxonBase> getNextDescriptionPartition(Class<? extends DescriptionElementBase> clazz,int limit, int partitionCount) {
|
|
526
|
// List<DescriptionElementBase> list = getDescriptionService().listDescriptionElements(null, null, pageSize, pageNumber, propPath);
|
|
527
|
//
|
|
528
|
// Iterator<TaxonBase> it = list.iterator();
|
|
529
|
// while (it.hasNext()){
|
|
530
|
// TaxonBase<?> taxonBase = it.next();
|
|
531
|
// if (! isPesiTaxon(taxonBase)){
|
|
532
|
// it.remove();
|
|
533
|
// }
|
|
534
|
// }
|
|
535
|
// return list;
|
|
536
|
// }
|
|
537
|
|
|
538
|
}
|