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/**
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* Copyright (C) 2018 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.persistence.dao.hibernate.taxonGraph;
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import java.util.ArrayList;
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import java.util.EnumSet;
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import java.util.HashSet;
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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 org.hibernate.Query;
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import org.hibernate.Session;
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import eu.etaxonomy.cdm.model.common.RelationshipBase.Direction;
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import eu.etaxonomy.cdm.model.metadata.CdmPreference;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.reference.ReferenceType;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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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.dao.hibernate.common.CdmPreferenceLookup;
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import eu.etaxonomy.cdm.persistence.dao.taxonGraph.TaxonGraphException;
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/**
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* @author a.kohlbecker
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* @since Oct 4, 2018
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*
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*/
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public abstract class AbstractHibernateTaxonGraphProcessor {
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private static final Logger logger = Logger.getLogger(AbstractHibernateTaxonGraphProcessor.class);
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EnumSet<ReferenceType> referenceSectionTypes = EnumSet.of(ReferenceType.Section, ReferenceType.BookSection);
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private Reference secReference = null;
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private TaxonRelationshipType relType = TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN();
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protected TaxonRelationshipType relType() {
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if(relType == null){
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relType = TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN();
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}
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return relType;
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}
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/**
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* MUST ONLY BE USED IN TESTS
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*/
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@Deprecated
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protected UUID secReferenceUUID;
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/**
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* MUST ONLY BE USED IN TESTS
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*/
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@Deprecated
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protected void setSecReferenceUUID(UUID uuid){
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secReferenceUUID = uuid;
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}
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public UUID getSecReferenceUUID(){
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if(secReferenceUUID != null){
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return secReferenceUUID;
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} else {
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CdmPreference pref = CdmPreferenceLookup.instance().get(TaxonGraphDaoHibernateImpl.CDM_PREF_KEY_SEC_REF_UUID);
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UUID uuid = null;
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if(pref != null && pref.getValue() != null){
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try {
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uuid = UUID.fromString(pref.getValue());
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} catch (Exception e) {
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// TODO is logging only ok?
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logger.error(e);
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}
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}
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if(uuid == null){
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logger.error("missing cdm property: " + TaxonGraphDaoHibernateImpl.CDM_PREF_KEY_SEC_REF_UUID.getSubject() + TaxonGraphDaoHibernateImpl.CDM_PREF_KEY_SEC_REF_UUID.getPredicate());
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}
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return uuid;
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}
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}
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public Reference secReference(){
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if(secReference == null){
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Query q = getSession().createQuery("SELECT r FROM Reference r WHERE r.uuid = :uuid");
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q.setParameter("uuid", getSecReferenceUUID());
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secReference = (Reference) q.uniqueResult();
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} else {
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// make sure the entity is still in the current session
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secReference = getSession().load(Reference.class, secReference.getId());
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}
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return secReference;
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}
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/**
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* Create all missing edges from the <code>taxon</code>.
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*
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* @param taxonName
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*/
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public void updateEdges(Taxon taxon) throws TaxonGraphException {
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Reference conceptReference = conceptReference(taxon.getName().getNomenclaturalReference());
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if(conceptReference != null){
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// update edges to higher names
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List<TaxonName> relatedHigherNames = relatedHigherNames(taxon.getName());
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List<TaxonRelationship> relationsFrom = taxonGraphRelationsFrom(taxon, conceptReference);
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List<TaxonName> relatedHigherNamesWithoutRels = new ArrayList<>(relatedHigherNames);
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for(TaxonRelationship rel : relationsFrom){
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boolean isRelToHigherName = relatedHigherNames.contains(rel.getToTaxon().getName());
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if(isRelToHigherName){
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relatedHigherNamesWithoutRels.remove(rel.getToTaxon().getName());
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} else {
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taxon.removeTaxonRelation(rel);
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}
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}
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for(TaxonName name : relatedHigherNamesWithoutRels){
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Taxon toTaxon = assureSingleTaxon(name);
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taxon.addTaxonRelation(toTaxon, relType(), conceptReference, null);
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}
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// update edges from lower names
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List<TaxonName> relatedLowerNames = relatedLowerNames(taxon.getName());
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List<TaxonRelationship> relationsTo = taxonGraphRelationsTo(taxon, null);
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List<TaxonName> relatedLowerNamesWithoutRels = new ArrayList<>(relatedLowerNames);
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for(TaxonRelationship rel : relationsTo){
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boolean isRelFromLowerName = relatedLowerNames.contains(rel.getFromTaxon().getName());
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if(isRelFromLowerName){
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relatedLowerNamesWithoutRels.remove(rel.getFromTaxon().getName());
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} else {
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taxon.removeTaxonRelation(rel);
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}
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}
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for(TaxonName name : relatedLowerNamesWithoutRels){
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Taxon fromTaxon = assureSingleTaxon(name);
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fromTaxon.addTaxonRelation(taxon, relType(), conceptReference, null);
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}
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}
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}
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/**
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* Remove all edges from the <code>taxon</code> having the <code>conceptReference</code>
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*
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* @param taxon
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* @param oldConceptReference
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*/
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public void removeEdges(Taxon taxon, Reference conceptReference) {
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List<TaxonRelationship> relations = taxonGraphRelationsFrom(taxon, conceptReference);
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List<TaxonName> relatedHigherNames = relatedHigherNames(taxon.getName());
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for(TaxonRelationship rel : relations){
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boolean isRelToHigherName = relatedHigherNames.contains(rel.getToTaxon().getName());
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if(isRelToHigherName){
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taxon.removeTaxonRelation(rel);
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}
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}
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}
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/**
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* @param taxon
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*/
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public void updateConceptReferenceInEdges(Taxon taxon, Reference oldNomReference) throws TaxonGraphException {
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Reference conceptReference = conceptReference(taxon.getName().getNomenclaturalReference());
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Reference oldConceptReference = conceptReference(oldNomReference);
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if(conceptReference != null && oldConceptReference != null){
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// update old with new ref
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updateReferenceInEdges(taxon, conceptReference, oldConceptReference);
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} else if(conceptReference != null && oldConceptReference == null) {
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// create new relations for the name as there are none so far
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updateEdges(taxon);
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} else if(conceptReference == null && oldConceptReference != null){
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// remove all relations
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removeEdges(taxon, oldConceptReference);
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}
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}
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/**
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* @param taxon
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* @param conceptReference
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* @param oldConceptReference
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*/
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protected void updateReferenceInEdges(Taxon taxon, Reference conceptReference, Reference oldConceptReference) {
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List<TaxonRelationship> relations = taxonGraphRelationsFrom(taxon, oldConceptReference);
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List<TaxonName> relatedHigherNames = relatedHigherNames(taxon.getName());
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for(TaxonRelationship rel : relations){
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boolean isRelToHigherName = relatedHigherNames.contains(rel.getToTaxon().getName());
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if(isRelToHigherName){
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rel.setCitation(conceptReference);
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getSession().saveOrUpdate(rel);
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}
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}
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}
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abstract public Session getSession();
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public Taxon assureSingleTaxon(TaxonName taxonName) throws TaxonGraphException {
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return assureSingleTaxon(taxonName, true);
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}
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public Taxon assureSingleTaxon(TaxonName taxonName, boolean createMissing) throws TaxonGraphException {
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UUID secRefUuid = getSecReferenceUUID();
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Session session = getSession();
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TaxonName taxonNamePersisted = session.load(TaxonName.class, taxonName.getId());
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// filter by secRefUuid
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Taxon taxon = null;
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Set<Taxon> taxa = new HashSet<>();
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for(Taxon t : taxonName.getTaxa()){
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if(t.getSec() != null && t.getSec().getUuid().equals(secRefUuid)){
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taxa.add(t);
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}
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}
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if(taxa.size() == 0){
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if(createMissing){
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if(taxonNamePersisted != null){
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Reference secRef = secReference();
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taxon = Taxon.NewInstance(taxonNamePersisted, secRef);
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session.saveOrUpdate(taxon);
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} else {
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throw new TaxonGraphException("Can't create taxon for deleted name: " + taxonName);
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}
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} else {
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if(logger.isDebugEnabled()){
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logger.debug("No taxon found for " + taxonName);
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}
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}
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} else if(taxa.size() == 1){
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taxon = taxa.iterator().next();
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} else {
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throw new TaxonGraphException("A name to be used in a taxon graph must only have one taxon with the default sec reference [secRef uuid: "+ secRefUuid.toString() +"]");
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}
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return taxon != null ? session.load(Taxon.class, taxon.getId()) : null;
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}
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protected Reference conceptReference(Reference nomenclaturalReference) {
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Reference conceptRef = nomenclaturalReference;
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if(conceptRef != null){
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while(referenceSectionTypes.contains(conceptRef.getType()) && conceptRef.getInReference() != null){
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conceptRef = conceptRef.getInReference();
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}
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}
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return conceptRef;
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}
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/**
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* @param name
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* @return
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*/
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protected List<TaxonName> relatedHigherNames(TaxonName name) {
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List<TaxonName> relatedNames = new ArrayList<>();
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if(name.getRank().isSpecies() || name.getRank().isInfraSpecific()){
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if(name.getGenusOrUninomial() != null){
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List<TaxonName> names = listNamesAtRank(Rank.GENUS(), name.getGenusOrUninomial(), null);
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if(names.size() == 0){
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logger.warn("Genus entity with \"" + name.getGenusOrUninomial() + "\" missing");
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} else {
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if(names.size() > 1){
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logger.warn("Duplicate genus entities found for \"" + name.getGenusOrUninomial() + "\", will create taxon graph relation to all of them!");
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}
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relatedNames.addAll(names);
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}
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}
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}
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if(name.getRank().isInfraSpecific()){
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if(name.getGenusOrUninomial() != null && name.getSpecificEpithet() != null){
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List<TaxonName> names = listNamesAtRank(Rank.SPECIES(), name.getGenusOrUninomial(), name.getSpecificEpithet());
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if(names.size() == 0){
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logger.warn("Species entity with \"" + name.getGenusOrUninomial() + " " + name.getSpecificEpithet() + "\" missing");
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} else {
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if(names.size() > 1){
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logger.warn("Duplicate species entities found for \"" + name.getGenusOrUninomial() + " " + name.getSpecificEpithet() + "\", will create taxon graph relation to all of them!");
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}
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relatedNames.addAll(names);
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}
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}
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}
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return relatedNames;
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}
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/**
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* @param name
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* @return
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*/
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protected List<TaxonName> relatedLowerNames(TaxonName name) {
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List<TaxonName> relatedNames = new ArrayList<>();
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if(name.getRank().isGenus()){
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if(name.getGenusOrUninomial() != null){
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List<TaxonName> names = listNamesAtRank(Rank.SPECIES(), name.getGenusOrUninomial(), null);
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if(names.size() == 0){
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logger.debug("No species entity with \"" + name.getGenusOrUninomial() + " *\" found");
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} else {
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logger.debug(names.size() + " species entities found with \"" + name.getGenusOrUninomial() + " *\"");
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relatedNames.addAll(names);
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}
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}
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}
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if(name.getRank().isSpecies()){
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if(name.getGenusOrUninomial() != null && name.getSpecificEpithet() != null){
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List<TaxonName> names = listNamesBelowRank(Rank.SPECIES(), name.getGenusOrUninomial(), name.getSpecificEpithet());
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if(names.size() == 0){
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logger.warn("No infraspecific entity with \"" + name.getGenusOrUninomial() + " " + name.getSpecificEpithet() + "*\" found");
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} else {
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if(names.size() > 1){
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logger.warn(names.size() + " infraspecific entities found with \"" + name.getGenusOrUninomial() + " " + name.getSpecificEpithet() + "*\"found");
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}
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relatedNames.addAll(names);
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}
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}
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}
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return relatedNames;
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}
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/**
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* @param taxon
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*/
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protected List<TaxonRelationship> taxonGraphRelationsFrom(Taxon taxon, Reference citation) {
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List<TaxonRelationship> relations = getTaxonRelationships(taxon, relType(), citation, TaxonRelationship.Direction.relatedFrom);
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return relations;
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}
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/**
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* @param taxon
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*/
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protected List<TaxonRelationship> taxonGraphRelationsTo(Taxon taxon, Reference citation) {
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List<TaxonRelationship> relations = getTaxonRelationships(taxon, relType(), citation, TaxonRelationship.Direction.relatedTo);
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return relations;
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}
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protected List<TaxonName> listNamesAtRank(Rank rank, String genusOrUninomial, String specificEpithet){
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String hql = "SELECT n FROM TaxonName n WHERE n.rank = :rank AND n.genusOrUninomial = :genusOrUninomial";
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if(specificEpithet != null){
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hql += " AND n.specificEpithet = :specificEpithet";
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}
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356
|
Query q = getSession().createQuery(hql);
|
|
357
|
|
|
358
|
q.setParameter("rank", rank);
|
|
359
|
q.setParameter("genusOrUninomial", genusOrUninomial);
|
|
360
|
if(specificEpithet != null){
|
|
361
|
q.setParameter("specificEpithet", specificEpithet);
|
|
362
|
}
|
|
363
|
|
|
364
|
List<TaxonName> result = q.list();
|
|
365
|
return result;
|
|
366
|
}
|
|
367
|
|
|
368
|
protected List<TaxonName> listNamesBelowRank(Rank rank, String genusOrUninomial, String specificEpithet){
|
|
369
|
String hql = "SELECT n FROM TaxonName n WHERE n.rank.orderIndex > :rankOrderIndex AND n.genusOrUninomial = :genusOrUninomial";
|
|
370
|
if(specificEpithet != null){
|
|
371
|
hql += " AND n.specificEpithet = :specificEpithet";
|
|
372
|
}
|
|
373
|
Query q = getSession().createQuery(hql);
|
|
374
|
|
|
375
|
q.setParameter("rankOrderIndex", rank.getOrderIndex());
|
|
376
|
q.setParameter("genusOrUninomial", genusOrUninomial);
|
|
377
|
if(specificEpithet != null){
|
|
378
|
q.setParameter("specificEpithet", specificEpithet);
|
|
379
|
}
|
|
380
|
|
|
381
|
@SuppressWarnings("unchecked")
|
|
382
|
List<TaxonName> result = q.list();
|
|
383
|
return result;
|
|
384
|
}
|
|
385
|
|
|
386
|
/**
|
|
387
|
*
|
|
388
|
* @param relatedTaxon required
|
|
389
|
* @param type required
|
|
390
|
* @param citation can be null
|
|
391
|
* @param direction required
|
|
392
|
* @return
|
|
393
|
*/
|
|
394
|
protected List<TaxonRelationship> getTaxonRelationships(Taxon relatedTaxon, TaxonRelationshipType type, Reference citation, Direction direction){
|
|
395
|
|
|
396
|
String hql = "SELECT rel FROM TaxonRelationship rel WHERE rel." + direction + " = :relatedTaxon AND rel.type = :type";
|
|
397
|
if(citation != null){
|
|
398
|
hql += " AND rel.citation = :citation";
|
|
399
|
}
|
|
400
|
Query q = getSession().createQuery(hql);
|
|
401
|
q.setParameter("relatedTaxon", relatedTaxon);
|
|
402
|
q.setParameter("type", type);
|
|
403
|
if(citation != null){
|
|
404
|
q.setParameter("citation", citation);
|
|
405
|
}
|
|
406
|
@SuppressWarnings("unchecked")
|
|
407
|
List<TaxonRelationship> rels = q.list();
|
|
408
|
return rels;
|
|
409
|
}
|
|
410
|
|
|
411
|
|
|
412
|
}
|