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/**
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* Copyright (C) 2007 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.persistence.dao.hibernate.taxon;
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import java.math.BigInteger;
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import java.util.ArrayList;
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import java.util.Collection;
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import java.util.Collections;
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import java.util.HashMap;
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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.Map;
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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.Criteria;
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import org.hibernate.Hibernate;
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import org.hibernate.Query;
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import org.hibernate.criterion.Projections;
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import org.hibernate.criterion.Restrictions;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.beans.factory.annotation.Qualifier;
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import org.springframework.stereotype.Repository;
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import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
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import eu.etaxonomy.cdm.model.common.TreeIndex;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.taxon.Classification;
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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.model.taxon.TaxonNodeAgentRelation;
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import eu.etaxonomy.cdm.model.taxon.UuidAndTitleCacheTaxonComparator;
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import eu.etaxonomy.cdm.persistence.dao.hibernate.common.AnnotatableDaoImpl;
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import eu.etaxonomy.cdm.persistence.dao.taxon.IClassificationDao;
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import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao;
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import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonNodeDao;
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import eu.etaxonomy.cdm.persistence.dto.MergeResult;
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import eu.etaxonomy.cdm.persistence.dto.TaxonNodeDto;
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import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;
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/**
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* @author a.mueller
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* @created 16.06.2009
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*/
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@Repository
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@Qualifier("taxonNodeDaoHibernateImpl")
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public class TaxonNodeDaoHibernateImpl extends AnnotatableDaoImpl<TaxonNode>
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implements ITaxonNodeDao {
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@SuppressWarnings("unused")
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private static final Logger logger = Logger.getLogger(TaxonNodeDaoHibernateImpl.class);
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@Autowired
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private ITaxonDao taxonDao;
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@Autowired
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private IClassificationDao classificationDao;
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public TaxonNodeDaoHibernateImpl() {
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super(TaxonNode.class);
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}
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@Override
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public UUID delete(TaxonNode persistentObject, boolean deleteChildren){
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Taxon taxon = persistentObject.getTaxon();
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taxon = HibernateProxyHelper.deproxy(taxon, Taxon.class);
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/*Session session = this.getSession();
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Query query = session.createQuery("from TaxonNode t where t.taxon = :taxon");
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query.setParameter("taxon", taxon);
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List result = query.list();*/
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if (taxon != null){
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Hibernate.initialize(taxon);
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Hibernate.initialize(taxon.getTaxonNodes());
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Set<TaxonNode> nodes = taxon.getTaxonNodes();
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//Hibernate.initialize(taxon.getTaxonNodes());
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for (TaxonNode node:nodes) {
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node = HibernateProxyHelper.deproxy(node, TaxonNode.class);
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if (node.equals(persistentObject)){
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if (node.hasChildNodes()){
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Iterator<TaxonNode> childNodes = node.getChildNodes().iterator();
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TaxonNode childNode;
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List<TaxonNode> listForDeletion = new ArrayList<TaxonNode>();
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while (childNodes.hasNext()){
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childNode = childNodes.next();
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listForDeletion.add(childNode);
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childNodes.remove();
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}
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for (TaxonNode deleteNode:listForDeletion){
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delete(deleteNode, deleteChildren);
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}
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}
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taxon.removeTaxonNode(node, deleteChildren);
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taxonDao.saveOrUpdate(taxon);
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taxon = HibernateProxyHelper.deproxy(taxonDao.findByUuid(taxon.getUuid()), Taxon.class);
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taxonDao.delete(taxon);
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}
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}
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}
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UUID result = super.delete(persistentObject);
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return result;
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}
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@Override
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public List<TaxonNode> getTaxonOfAcceptedTaxaByClassification(Classification classification, Integer start, Integer end) {
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int classificationId = classification.getId();
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String limit = "";
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if(start !=null && end != null){
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limit = "LIMIT "+start+"," +end;
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}
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//FIXME write test
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String queryString = "SELECT DISTINCT nodes.*,taxa.titleCache FROM TaxonNode AS nodes LEFT JOIN TaxonBase AS taxa ON nodes.taxon_id = taxa.id WHERE taxa.DTYPE = 'Taxon' AND nodes.classification_id = " + classificationId + " ORDER BY taxa.titleCache " + limit;
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@SuppressWarnings("unchecked")
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List<TaxonNode> result = getSession().createSQLQuery(queryString).addEntity(TaxonNode.class).list();
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return result;
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}
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@Override
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public int countTaxonOfAcceptedTaxaByClassification(Classification classification){
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int classificationId = classification.getId();
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//FIXME write test
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String queryString = "SELECT DISTINCT COUNT('nodes.*') FROM TaxonNode AS nodes LEFT JOIN TaxonBase AS taxa ON nodes.taxon_id = taxa.id WHERE taxa.DTYPE = 'Taxon' AND nodes.classification_id = " + classificationId;
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@SuppressWarnings("unchecked")
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List<BigInteger> result = getSession().createSQLQuery(queryString).list();
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return result.get(0).intValue ();
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}
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@Override
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public List<TaxonNodeDto> listChildNodesAsUuidAndTitleCache(UuidAndTitleCache<TaxonNode> parent) {
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String queryString = "select tn from TaxonNode tn INNER JOIN tn.taxon as tx where tn.parent.uuid = :parentId";
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Query query = getSession().createQuery(queryString);
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query.setParameter("parentId", parent.getUuid());
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List<TaxonNodeDto> list = new ArrayList<>();
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@SuppressWarnings("unchecked")
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List<TaxonNode> result = query.list();
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for(TaxonNode object : result){
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list.add(new TaxonNodeDto(object));
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}
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return list;
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}
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@Override
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public List<UuidAndTitleCache<TaxonNode>> getUuidAndTitleCache(Integer limit, String pattern, UUID classificationUuid) {
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String queryString = "select tn.uuid, tn.id, tx.titleCache, tx.name.rank from TaxonNode tn "
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+ "INNER JOIN tn.taxon as tx "
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+ "INNER JOIN tn.classification as cls "
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+ "WHERE tx.titleCache like :pattern ";
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if(classificationUuid!=null){
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queryString += "AND cls.uuid = :classificationUuid";
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}
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Query query = getSession().createQuery(queryString);
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query.setParameter("pattern", pattern.toLowerCase()+"%");
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query.setParameter("classificationUuid", classificationUuid);
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List<UuidAndTitleCache<TaxonNode>> list = new ArrayList<>();
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@SuppressWarnings("unchecked")
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List<Object[]> result = query.list();
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if (result != null){
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Collections.sort(result, new UuidAndTitleCacheTaxonComparator());
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}
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for(Object[] object : result){
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list.add(new UuidAndTitleCache<TaxonNode>((UUID) object[0],(Integer) object[1], (String) object[2]));
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}
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return list;
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}
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/**
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* {@inheritDoc}
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*/
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@Override
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public UuidAndTitleCache<TaxonNode> getParentUuidAndTitleCache(UuidAndTitleCache<TaxonNode> child) {
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String queryString = "select tn.parent.uuid, tn.parent.id, tn.parent.taxon.titleCache, tn.parent.classification.titleCache "
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+ " from TaxonNode tn"
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+ " LEFT OUTER JOIN tn.parent.taxon"
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+ " where tn.id = :childId";
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Query query = getSession().createQuery(queryString);
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query.setParameter("childId", child.getId());
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List<UuidAndTitleCache<TaxonNode>> list = new ArrayList<>();
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@SuppressWarnings("unchecked")
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List<Object[]> result = query.list();
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for(Object[] object : result){
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UUID uuid = (UUID) object[0];
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Integer id = (Integer) object[1];
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String taxonTitleCache = (String) object[2];
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String classificationTitleCache = (String) object[3];
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if(taxonTitleCache!=null){
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list.add(new UuidAndTitleCache<TaxonNode>(uuid,id, taxonTitleCache));
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}
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else{
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list.add(new UuidAndTitleCache<TaxonNode>(uuid,id, classificationTitleCache));
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}
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}
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if(list.size()==1){
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return list.iterator().next();
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}
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return null;
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}
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@Override
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public List<TaxonNode> listChildrenOf(TaxonNode node, Integer pageSize, Integer pageIndex, List<String> propertyPaths, boolean recursive){
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if (recursive == true){
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Criteria crit = getSession().createCriteria(TaxonNode.class);
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crit.add( Restrictions.like("treeIndex", node.treeIndex()+ "%") );
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if(pageSize != null) {
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crit.setMaxResults(pageSize);
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if(pageIndex != null) {
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crit.setFirstResult(pageIndex * pageSize);
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} else {
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crit.setFirstResult(0);
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}
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}
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@SuppressWarnings("unchecked")
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List<TaxonNode> results = crit.list();
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results.remove(node);
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defaultBeanInitializer.initializeAll(results, propertyPaths);
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return results;
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}else{
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return classificationDao.listChildrenOf(node.getTaxon(), node.getClassification(), pageSize, pageIndex, propertyPaths);
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}
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}
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@Override
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public Long countChildrenOf(TaxonNode node, Classification classification,
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boolean recursive) {
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if (recursive == true){
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Criteria crit = getSession().createCriteria(TaxonNode.class);
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crit.add( Restrictions.like("treeIndex", node.treeIndex()+ "%") );
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crit.setProjection(Projections.rowCount());
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return ((Integer)crit.uniqueResult().hashCode()).longValue();
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}else{
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return classificationDao.countChildrenOf(node.getTaxon(), classification);
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}
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}
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/**
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* {@inheritDoc}
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*/
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@Override
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public List<TaxonNodeAgentRelation> listTaxonNodeAgentRelations(UUID taxonUuid, UUID classificationUuid,
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UUID agentUuid, UUID rankUuid, UUID relTypeUuid, Integer start, Integer limit, List<String> propertyPaths) {
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StringBuilder hql = prepareListTaxonNodeAgentRelations(taxonUuid, classificationUuid, agentUuid, rankUuid, relTypeUuid, false);
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Query query = getSession().createQuery(hql.toString());
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if(limit != null) {
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query.setMaxResults(limit);
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if(start != null) {
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query.setFirstResult(start);
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}
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}
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setParamsForListTaxonNodeAgentRelations(taxonUuid, classificationUuid, agentUuid, rankUuid, relTypeUuid, query);
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@SuppressWarnings("unchecked")
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List<TaxonNodeAgentRelation> records = query.list();
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if(propertyPaths != null) {
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defaultBeanInitializer.initializeAll(records, propertyPaths);
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}
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return records;
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}
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/**
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* {@inheritDoc}
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*/
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@Override
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public long countTaxonNodeAgentRelations(UUID taxonUuid, UUID classificationUuid, UUID agentUuid, UUID rankUuid, UUID relTypeUuid) {
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StringBuilder hql = prepareListTaxonNodeAgentRelations(taxonUuid, classificationUuid, agentUuid, rankUuid, relTypeUuid, true);
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Query query = getSession().createQuery(hql.toString());
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setParamsForListTaxonNodeAgentRelations(taxonUuid, classificationUuid, agentUuid, rankUuid, relTypeUuid, query);
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Long count = Long.parseLong(query.uniqueResult().toString());
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return count;
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}
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/**
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* @param taxonUuid
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* @param classificationUuid
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* @param agentUuid
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* @param relTypeUuid TODO
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* @param doCount TODO
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* @param rankId
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* limit to taxa having this rank, only applies if <code>taxonUuid = null</code>
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* @return
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*/
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private StringBuilder prepareListTaxonNodeAgentRelations(UUID taxonUuid, UUID classificationUuid, UUID agentUuid, UUID rankUuid, UUID relTypeUuid, boolean doCount) {
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StringBuilder hql = new StringBuilder();
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String join_fetch_mode = doCount ? "join" : "join fetch";
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if(doCount) {
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hql.append("select count(tnar)");
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} else {
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hql.append("select tnar");
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}
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hql.append(" from TaxonNodeAgentRelation as tnar ");
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if(taxonUuid != null) {
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// taxonUuid is search filter, do not fetch it
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hql.append(" join tnar.taxonNode as tn join tn.taxon as t ");
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} else {
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hql.append(join_fetch_mode).append(" tnar.taxonNode as tn ").append(join_fetch_mode).append(" tn.taxon as t ");
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if(rankUuid != null) {
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hql.append(" join t.name as n ");
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}
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}
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hql.append(" join tn.classification as c ");
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if(agentUuid != null) {
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// agentUuid is search filter, do not fetch it
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// hql.append(" join tnar.agent as a ");
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hql.append(join_fetch_mode).append(" tnar.agent as a ");
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} else {
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hql.append(join_fetch_mode).append(" tnar.agent as a ");
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}
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hql.append(" where 1 = 1 ");
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if(relTypeUuid != null) {
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hql.append(" and tnar.type.uuid = :relTypeUuid ");
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}
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if(taxonUuid != null) {
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hql.append(" and t.uuid = :taxonUuid ");
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} else {
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if(rankUuid != null) {
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hql.append(" and n.rank.uuid = :rankUuid ");
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}
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}
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if(classificationUuid != null) {
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hql.append(" and c.uuid = :classificationUuid ");
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}
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if(agentUuid != null) {
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hql.append(" and a.uuid = :agentUuid ");
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}
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hql.append(" order by a.titleCache");
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return hql;
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}
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/**
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* @param taxonUuid
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* @param classificationUuid
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* @param agentUuid
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* @param relTypeUuid TODO
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* @param query
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* @param rankId TODO
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*/
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private void setParamsForListTaxonNodeAgentRelations(UUID taxonUuid, UUID classificationUuid, UUID agentUuid,
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UUID rankUuid, UUID relTypeUuid, Query query) {
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if(taxonUuid != null) {
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query.setParameter("taxonUuid", taxonUuid);
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} else {
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if(rankUuid != null) {
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query.setParameter("rankUuid", rankUuid);
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}
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}
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if(classificationUuid != null) {
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query.setParameter("classificationUuid", classificationUuid);
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}
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if(agentUuid != null) {
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query.setParameter("agentUuid", agentUuid);
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}
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if(relTypeUuid != null) {
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query.setParameter("relTypeUuid", relTypeUuid);
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}
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}
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@Override
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public Map<TreeIndex, Integer> rankOrderIndexForTreeIndex(List<TreeIndex> treeIndexes,
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Integer minRankOrderIndex,
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Integer maxRankOrderIndex) {
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Map<TreeIndex, Integer> result = new HashMap<>();
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if (treeIndexes == null || treeIndexes.isEmpty()){
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return result;
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}
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String hql = " SELECT tn.treeIndex, r.orderIndex "
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+ " FROM TaxonNode tn JOIN tn.taxon t JOIN t.name n JOIN n.rank r "
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+ " WHERE tn.treeIndex IN (:treeIndexes) ";
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408
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if (minRankOrderIndex != null){
|
409
|
hql += " AND r.orderIndex <= :minOrderIndex";
|
410
|
}
|
411
|
if (maxRankOrderIndex != null){
|
412
|
hql += " AND r.orderIndex >= :maxOrderIndex";
|
413
|
}
|
414
|
|
415
|
Query query = getSession().createQuery(hql);
|
416
|
query.setParameterList("treeIndexes", TreeIndex.toString(treeIndexes));
|
417
|
if (minRankOrderIndex != null){
|
418
|
query.setParameter("minOrderIndex", minRankOrderIndex);
|
419
|
}
|
420
|
if (maxRankOrderIndex != null){
|
421
|
query.setParameter("maxOrderIndex", maxRankOrderIndex);
|
422
|
}
|
423
|
|
424
|
@SuppressWarnings("unchecked")
|
425
|
List<Object[]> list = query.list();
|
426
|
for (Object[] o : list){
|
427
|
result.put(TreeIndex.NewInstance((String)o[0]), (Integer)o[1]);
|
428
|
}
|
429
|
return result;
|
430
|
}
|
431
|
|
432
|
@Override
|
433
|
public Map<TreeIndex, UuidAndTitleCache<?>> taxonUuidsForTreeIndexes(Collection<TreeIndex> treeIndexes) {
|
434
|
Map<TreeIndex, UuidAndTitleCache<?>> result = new HashMap<>();
|
435
|
if (treeIndexes == null || treeIndexes.isEmpty()){
|
436
|
return result;
|
437
|
}
|
438
|
|
439
|
String hql = " SELECT tn.treeIndex, t.uuid, tnb.titleCache "
|
440
|
+ " FROM TaxonNode tn JOIN tn.taxon t Join t.name tnb "
|
441
|
+ " WHERE tn.treeIndex IN (:treeIndexes) ";
|
442
|
Query query = getSession().createQuery(hql);
|
443
|
query.setParameterList("treeIndexes", TreeIndex.toString(treeIndexes));
|
444
|
|
445
|
@SuppressWarnings("unchecked")
|
446
|
List<Object[]> list = query.list();
|
447
|
for (Object[] o : list){
|
448
|
result.put(TreeIndex.NewInstance((String)o[0]), new UuidAndTitleCache<>((UUID)o[1], null, (String)o[2]));
|
449
|
}
|
450
|
return result;
|
451
|
}
|
452
|
|
453
|
|
454
|
/**
|
455
|
* {@inheritDoc}
|
456
|
*/
|
457
|
//#3465
|
458
|
@Override
|
459
|
public Set<TaxonBase> setSecundumForSubtreeAcceptedTaxa(TreeIndex subTreeIndex, Reference newSec, boolean overwriteExisting, boolean includeSharedTaxa, boolean emptyDetail) {
|
460
|
//for some reason this does not work, maybe because the listeners are not activated,
|
461
|
//but also the first taxon for some reason does not get updated in terms of secundum, but only by the udpate listener
|
462
|
// String where = "SELECT t.id FROM TaxonNode tn JOIN tn.taxon t " +
|
463
|
// " WHERE tn.treeIndex like '%s%%' ORDER BY t.id";
|
464
|
// where = String.format(where, subTreeIndex.toString());
|
465
|
// Query query1 = getSession().createQuery(where);
|
466
|
// List l = query1.list();
|
467
|
//
|
468
|
// String hql = "UPDATE Taxon SET sec = :newSec, publish=false WHERE id IN (" + where + ")";
|
469
|
// Query query = getSession().createQuery(hql);
|
470
|
// query.setParameter("newSec", newSec);
|
471
|
// int n = query.executeUpdate();
|
472
|
|
473
|
String queryStr = acceptedForSubtreeQueryStr(includeSharedTaxa, subTreeIndex);
|
474
|
if (!overwriteExisting){
|
475
|
queryStr += " AND t.sec IS NULL ";
|
476
|
}
|
477
|
return setSecundum(newSec, emptyDetail, queryStr);
|
478
|
|
479
|
}
|
480
|
|
481
|
@Override
|
482
|
public Set<TaxonBase> setSecundumForSubtreeSynonyms(TreeIndex subTreeIndex, Reference newSec, boolean overwriteExisting, boolean includeSharedTaxa, boolean emptyDetail) {
|
483
|
|
484
|
String queryStr = synonymForSubtreeQueryStr(includeSharedTaxa, subTreeIndex);
|
485
|
if (!overwriteExisting){
|
486
|
queryStr += " AND syn.sec IS NULL ";
|
487
|
}
|
488
|
return setSecundum(newSec, emptyDetail, queryStr);
|
489
|
}
|
490
|
/**
|
491
|
* @param newSec
|
492
|
* @param emptyDetail
|
493
|
* @param queryStr
|
494
|
* @return
|
495
|
*/
|
496
|
@SuppressWarnings("unchecked")
|
497
|
private <T extends TaxonBase<?>> Set<T> setSecundum(Reference newSec, boolean emptyDetail, String queryStr) {
|
498
|
Query query = getSession().createQuery(queryStr);
|
499
|
@SuppressWarnings("unchecked")
|
500
|
List<T> synonymList = query.list();
|
501
|
MergeResult mergeResult;
|
502
|
Set<T> result = new HashSet<>();
|
503
|
for (T taxonBase : synonymList){
|
504
|
if (taxonBase != null){
|
505
|
taxonBase = (T) taxonDao.load(taxonBase.getUuid());
|
506
|
taxonBase.setSec(newSec);
|
507
|
if (emptyDetail){
|
508
|
taxonBase.setSecMicroReference(null);
|
509
|
}
|
510
|
result.add(taxonBase);
|
511
|
}
|
512
|
|
513
|
}
|
514
|
return result;
|
515
|
}
|
516
|
|
517
|
|
518
|
/**
|
519
|
* {@inheritDoc}
|
520
|
*/
|
521
|
@Override
|
522
|
public Set<TaxonBase> setPublishForSubtreeAcceptedTaxa(TreeIndex subTreeIndex, boolean publish,
|
523
|
boolean includeSharedTaxa) {
|
524
|
String queryStr = acceptedForSubtreeQueryStr(includeSharedTaxa, subTreeIndex);
|
525
|
return setPublish(publish, queryStr);
|
526
|
}
|
527
|
|
528
|
/**
|
529
|
* {@inheritDoc}
|
530
|
*/
|
531
|
@Override
|
532
|
public Set<TaxonBase> setPublishForSubtreeSynonyms(TreeIndex subTreeIndex, boolean publish,
|
533
|
boolean includeSharedTaxa) {
|
534
|
String queryStr = synonymForSubtreeQueryStr(includeSharedTaxa, subTreeIndex);
|
535
|
return setPublish(publish, queryStr);
|
536
|
}
|
537
|
|
538
|
/**
|
539
|
* @param publish
|
540
|
* @param queryStr
|
541
|
* @return
|
542
|
*/
|
543
|
private <T extends TaxonBase<?>> Set<T> setPublish(boolean publish, String queryStr) {
|
544
|
Query query = getSession().createQuery(queryStr);
|
545
|
@SuppressWarnings("unchecked")
|
546
|
List<T> taxonList = query.list();
|
547
|
Set<T> result = new HashSet<>();
|
548
|
for (T taxon : taxonList){
|
549
|
taxon = (T)taxonDao.load(taxon.getUuid());
|
550
|
taxon.setPublish(publish);
|
551
|
result.add(taxon);
|
552
|
}
|
553
|
return result;
|
554
|
}
|
555
|
|
556
|
|
557
|
/**
|
558
|
* @param includeSharedTaxa
|
559
|
* @param subTreeIndex
|
560
|
* @return
|
561
|
*/
|
562
|
private String synonymForSubtreeQueryStr(boolean includeSharedTaxa, TreeIndex subTreeIndex) {
|
563
|
String queryStr = "SELECT syn "
|
564
|
+ " FROM TaxonNode tn JOIN tn.taxon t JOIN t.synonyms syn"
|
565
|
+ " WHERE tn.treeIndex like '%s%%' ";
|
566
|
if (!includeSharedTaxa){
|
567
|
queryStr += " AND t.taxonNodes.size <= 1 ";
|
568
|
}
|
569
|
queryStr = String.format(queryStr, subTreeIndex.toString());
|
570
|
|
571
|
return queryStr;
|
572
|
}
|
573
|
|
574
|
private String acceptedForSubtreeQueryStr(boolean includeSharedTaxa, TreeIndex subTreeIndex) {
|
575
|
String queryStr = "SELECT t "
|
576
|
+ " FROM TaxonNode tn JOIN tn.taxon t "
|
577
|
+ " WHERE tn.treeIndex like '%s%%' ";
|
578
|
if (!includeSharedTaxa){
|
579
|
queryStr += " AND t.taxonNodes.size <= 1 ";
|
580
|
}
|
581
|
queryStr = String.format(queryStr, subTreeIndex.toString());
|
582
|
|
583
|
return queryStr;
|
584
|
}
|
585
|
|
586
|
|
587
|
}
|