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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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*/
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package eu.etaxonomy.cdm.persistence.dao.hibernate.name;
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import java.util.ArrayList;
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import java.util.Collection;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Optional;
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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.Query;
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import org.hibernate.SQLQuery;
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import org.hibernate.criterion.Criterion;
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import org.hibernate.criterion.LogicalExpression;
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import org.hibernate.criterion.Order;
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import org.hibernate.criterion.Projections;
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import org.hibernate.criterion.Restrictions;
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import org.hibernate.envers.query.AuditEntity;
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import org.hibernate.envers.query.AuditQuery;
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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.RelationshipBase;
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import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
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import eu.etaxonomy.cdm.model.name.HybridRelationship;
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import eu.etaxonomy.cdm.model.name.HybridRelationshipType;
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import eu.etaxonomy.cdm.model.name.INonViralName;
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import eu.etaxonomy.cdm.model.name.IZoologicalName;
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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.Rank;
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import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
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import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.name.TypeDesignationBase;
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import eu.etaxonomy.cdm.model.name.TypeDesignationStatusBase;
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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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.view.AuditEvent;
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import eu.etaxonomy.cdm.persistence.dao.common.Restriction;
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import eu.etaxonomy.cdm.persistence.dao.hibernate.common.IdentifiableDaoBase;
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import eu.etaxonomy.cdm.persistence.dao.name.IHomotypicalGroupDao;
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import eu.etaxonomy.cdm.persistence.dao.name.ITaxonNameDao;
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import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao;
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import eu.etaxonomy.cdm.persistence.dto.TaxonNameParts;
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import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;
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import eu.etaxonomy.cdm.persistence.query.MatchMode;
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import eu.etaxonomy.cdm.persistence.query.OrderHint;
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/**
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* @author a.mueller
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*
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*/
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@Repository
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@Qualifier("taxonNameDaoHibernateImpl")
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public class TaxonNameDaoHibernateImpl extends IdentifiableDaoBase<TaxonName> implements ITaxonNameDao {
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private static final Logger logger = Logger.getLogger(TaxonNameDaoHibernateImpl.class);
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@Autowired
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private ITaxonDao taxonDao;
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@Autowired
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private IHomotypicalGroupDao homotypicalGroupDao;
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public TaxonNameDaoHibernateImpl() {
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super(TaxonName.class);
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indexedClasses = new Class[1];
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indexedClasses[0] = TaxonName.class;
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}
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@Override
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public int countHybridNames(INonViralName name, HybridRelationshipType type) {
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AuditEvent auditEvent = getAuditEventFromContext();
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if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
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Query query = null;
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if(type == null) {
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query = getSession().createQuery("select count(relation) from HybridRelationship relation where relation.relatedFrom = :name");
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} else {
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query = getSession().createQuery("select count(relation) from HybridRelationship relation where relation.relatedFrom = :name and relation.type = :type");
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query.setParameter("type", type);
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}
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query.setParameter("name",name);
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return ((Long)query.uniqueResult()).intValue();
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} else {
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AuditQuery query = getAuditReader().createQuery().forEntitiesAtRevision(HybridRelationship.class,auditEvent.getRevisionNumber());
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query.add(AuditEntity.relatedId("relatedFrom").eq(name.getId()));
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query.addProjection(AuditEntity.id().count());
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if(type != null) {
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query.add(AuditEntity.relatedId("type").eq(type.getId()));
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}
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return ((Long)query.getSingleResult()).intValue();
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}
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}
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@Override
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public long countNames(String queryString) {
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checkNotInPriorView("TaxonNameDaoHibernateImpl.countNames(String queryString)");
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Criteria criteria = getCriteria(null);
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if (queryString != null) {
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criteria.add(Restrictions.ilike("nameCache", queryString));
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}
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criteria.setProjection(Projections.projectionList().add(Projections.rowCount()));
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return (Long)criteria.uniqueResult();
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}
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@Override
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public long countNames(String queryString, MatchMode matchMode, List<Criterion> criteria) {
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Criteria crit = getCriteria(type);
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if (matchMode == MatchMode.EXACT) {
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crit.add(Restrictions.eq("nameCache", matchMode.queryStringFrom(queryString)));
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} else {
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crit.add(Restrictions.ilike("nameCache", matchMode.queryStringFrom(queryString)));
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}
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if(criteria != null) {
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for (Criterion criterion : criteria) {
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crit.add(criterion);
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}
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}
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crit.setProjection(Projections.projectionList().add(Projections.rowCount()));
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return (Long)crit.uniqueResult();
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}
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@Override
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public long countNames(String genusOrUninomial, String infraGenericEpithet, String specificEpithet, String infraSpecificEpithet, Rank rank) {
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AuditEvent auditEvent = getAuditEventFromContext();
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if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
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Criteria criteria = getCriteria(TaxonName.class);
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/**
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* Given HHH-2951 - "Restrictions.eq when passed null, should create a NullRestriction"
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* We need to convert nulls to NullRestrictions for now
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*/
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if(genusOrUninomial != null) {
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criteria.add(Restrictions.eq("genusOrUninomial",genusOrUninomial));
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} else {
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criteria.add(Restrictions.isNull("genusOrUninomial"));
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}
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if(infraGenericEpithet != null) {
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criteria.add(Restrictions.eq("infraGenericEpithet", infraGenericEpithet));
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} else {
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criteria.add(Restrictions.isNull("infraGenericEpithet"));
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}
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if(specificEpithet != null) {
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criteria.add(Restrictions.eq("specificEpithet", specificEpithet));
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} else {
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criteria.add(Restrictions.isNull("specificEpithet"));
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}
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if(infraSpecificEpithet != null) {
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criteria.add(Restrictions.eq("infraSpecificEpithet",infraSpecificEpithet));
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} else {
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criteria.add(Restrictions.isNull("infraSpecificEpithet"));
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}
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if(rank != null) {
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criteria.add(Restrictions.eq("rank", rank));
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}
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criteria.setProjection(Projections.rowCount());
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return (Long)criteria.uniqueResult();
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} else {
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AuditQuery query = makeAuditQuery(TaxonName.class, auditEvent);
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if(genusOrUninomial != null) {
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query.add(AuditEntity.property("genusOrUninomial").eq(genusOrUninomial));
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} else {
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query.add(AuditEntity.property("genusOrUninomial").isNull());
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}
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if(infraGenericEpithet != null) {
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query.add(AuditEntity.property("infraGenericEpithet").eq(infraGenericEpithet));
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} else {
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query.add(AuditEntity.property("infraGenericEpithet").isNull());
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}
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if(specificEpithet != null) {
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query.add(AuditEntity.property("specificEpithet").eq(specificEpithet));
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} else {
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query.add(AuditEntity.property("specificEpithet").isNull());
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}
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if(infraSpecificEpithet != null) {
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query.add(AuditEntity.property("infraSpecificEpithet").eq(infraSpecificEpithet));
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} else {
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query.add(AuditEntity.property("infraSpecificEpithet").isNull());
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}
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if(rank != null) {
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query.add(AuditEntity.relatedId("rank").eq(rank.getId()));
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}
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query.addProjection(AuditEntity.id().count());
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return (Long)query.getSingleResult();
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}
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}
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@Override
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public int countNameRelationships(TaxonName name, NameRelationship.Direction direction, NameRelationshipType type) {
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AuditEvent auditEvent = getAuditEventFromContext();
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if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
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Query query = null;
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if(type == null) {
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query = getSession().createQuery("select count(relation) from NameRelationship relation where relation." + direction +" = :name");
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} else {
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query = getSession().createQuery("select count(relation) from NameRelationship relation where relation." + direction +" = :name and relation.type = :type");
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query.setParameter("type", type);
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}
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query.setParameter("name",name);
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return ((Long)query.uniqueResult()).intValue();
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} else {
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AuditQuery query = getAuditReader().createQuery().forEntitiesAtRevision(NameRelationship.class,auditEvent.getRevisionNumber());
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query.add(AuditEntity.relatedId(direction.toString()).eq(name.getId()));
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query.addProjection(AuditEntity.id().count());
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if(type != null) {
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query.add(AuditEntity.relatedId("type").eq(type.getId()));
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}
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return ((Long)query.getSingleResult()).intValue();
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}
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}
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@Override
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public long countTypeDesignations(TaxonName name, SpecimenTypeDesignationStatus status) {
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checkNotInPriorView("countTypeDesignations(TaxonName name, SpecimenTypeDesignationStatus status)");
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Query query = null;
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if(status == null) {
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query = getSession().createQuery("select count(designation) from TypeDesignationBase designation join designation.typifiedNames name where name = :name");
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} else {
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query = getSession().createQuery("select count(designation) from TypeDesignationBase designation join designation.typifiedNames name where name = :name and designation.typeStatus = :status");
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query.setParameter("status", status);
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}
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query.setParameter("name",name);
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return (Long)query.uniqueResult();
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}
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@Override
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public List<HybridRelationship> getHybridNames(INonViralName name, HybridRelationshipType type,
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Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
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AuditEvent auditEvent = getAuditEventFromContext();
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if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
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Criteria criteria = getSession().createCriteria(HybridRelationship.class);
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criteria.add(Restrictions.eq("relatedFrom", name));
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if(type != null) {
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criteria.add(Restrictions.eq("type", type));
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}
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if(pageSize != null) {
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criteria.setMaxResults(pageSize);
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if(pageNumber != null) {
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criteria.setFirstResult(pageNumber * pageSize);
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} else {
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criteria.setFirstResult(0);
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}
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}
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addOrder(criteria, orderHints);
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@SuppressWarnings("unchecked")
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List<HybridRelationship> results = criteria.list();
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defaultBeanInitializer.initializeAll(results, propertyPaths);
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return results;
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} else {
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AuditQuery query = getAuditReader().createQuery().forEntitiesAtRevision(HybridRelationship.class,auditEvent.getRevisionNumber());
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query.add(AuditEntity.relatedId("relatedFrom").eq(name.getId()));
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if(type != null) {
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query.add(AuditEntity.relatedId("type").eq(type.getId()));
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}
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if(pageSize != null) {
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query.setMaxResults(pageSize);
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if(pageNumber != null) {
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query.setFirstResult(pageNumber * pageSize);
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} else {
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query.setFirstResult(0);
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}
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}
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@SuppressWarnings("unchecked")
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List<HybridRelationship> results = query.getResultList();
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defaultBeanInitializer.initializeAll(results, propertyPaths);
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return results;
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}
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}
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@Override
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public List<NameRelationship> getNameRelationships(TaxonName name, NameRelationship.Direction direction,
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NameRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints,
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List<String> propertyPaths) {
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AuditEvent auditEvent = getAuditEventFromContext();
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if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
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Criteria criteria = getSession().createCriteria(NameRelationship.class);
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if (name != null || direction != null){
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criteria.add(Restrictions.eq(direction.toString(), name));
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}
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if(type != null) {
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criteria.add(Restrictions.eq("type", type));
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}
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if(pageSize != null) {
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criteria.setMaxResults(pageSize);
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if(pageNumber != null) {
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criteria.setFirstResult(pageNumber * pageSize);
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} else {
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criteria.setFirstResult(0);
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}
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}
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addOrder(criteria, orderHints);
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@SuppressWarnings("unchecked")
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List<NameRelationship> results = criteria.list();
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defaultBeanInitializer.initializeAll(results, propertyPaths);
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return results;
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} else {
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AuditQuery query = getAuditReader().createQuery().forEntitiesAtRevision(NameRelationship.class,auditEvent.getRevisionNumber());
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query.add(AuditEntity.relatedId(direction.toString()).eq(name.getId()));
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347
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if(type != null) {
|
|
348
|
query.add(AuditEntity.relatedId("type").eq(type.getId()));
|
|
349
|
}
|
|
350
|
|
|
351
|
if(pageSize != null) {
|
|
352
|
query.setMaxResults(pageSize);
|
|
353
|
if(pageNumber != null) {
|
|
354
|
query.setFirstResult(pageNumber * pageSize);
|
|
355
|
} else {
|
|
356
|
query.setFirstResult(0);
|
|
357
|
}
|
|
358
|
}
|
|
359
|
|
|
360
|
@SuppressWarnings("unchecked")
|
|
361
|
List<NameRelationship> results = query.getResultList();
|
|
362
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
|
363
|
return results;
|
|
364
|
}
|
|
365
|
}
|
|
366
|
|
|
367
|
@Override
|
|
368
|
public List<TypeDesignationBase> getTypeDesignations(TaxonName name, TypeDesignationStatusBase status, Integer pageSize, Integer pageNumber, List<String> propertyPaths){
|
|
369
|
return getTypeDesignations(name, null, status, pageSize, pageNumber, propertyPaths);
|
|
370
|
}
|
|
371
|
|
|
372
|
@Override
|
|
373
|
public List<Integer> getTypeSpecimenIdsForTaxonName(TaxonName name,
|
|
374
|
TypeDesignationStatusBase status, Integer pageSize, Integer pageNumber){
|
|
375
|
Query query = getTypeDesignationQuery("designation.typeSpecimen.id", name, SpecimenTypeDesignation.class, status);
|
|
376
|
|
|
377
|
if(pageSize != null) {
|
|
378
|
query.setMaxResults(pageSize);
|
|
379
|
if(pageNumber != null) {
|
|
380
|
query.setFirstResult(pageNumber * pageSize);
|
|
381
|
} else {
|
|
382
|
query.setFirstResult(0);
|
|
383
|
}
|
|
384
|
}
|
|
385
|
@SuppressWarnings("unchecked")
|
|
386
|
List<Integer> result = query.list();
|
|
387
|
return result;
|
|
388
|
}
|
|
389
|
|
|
390
|
@Override
|
|
391
|
public <T extends TypeDesignationBase> List<T> getTypeDesignations(TaxonName name,
|
|
392
|
Class<T> type,
|
|
393
|
TypeDesignationStatusBase status, Integer pageSize, Integer pageNumber,
|
|
394
|
List<String> propertyPaths){
|
|
395
|
checkNotInPriorView("getTypeDesignations(TaxonName name,TypeDesignationStatusBase status, Integer pageSize, Integer pageNumber, List<String> propertyPaths)");
|
|
396
|
|
|
397
|
Query query = getTypeDesignationQuery("designation", name, type, status);
|
|
398
|
|
|
399
|
if(pageSize != null) {
|
|
400
|
query.setMaxResults(pageSize);
|
|
401
|
if(pageNumber != null) {
|
|
402
|
query.setFirstResult(pageNumber * pageSize);
|
|
403
|
} else {
|
|
404
|
query.setFirstResult(0);
|
|
405
|
}
|
|
406
|
}
|
|
407
|
@SuppressWarnings("unchecked")
|
|
408
|
List<T> result = defaultBeanInitializer.initializeAll((List<T>)query.list(), propertyPaths);
|
|
409
|
return result;
|
|
410
|
}
|
|
411
|
|
|
412
|
private <T extends TypeDesignationBase> Query getTypeDesignationQuery(String select, TaxonName name,
|
|
413
|
Class<T> type, TypeDesignationStatusBase status){
|
|
414
|
Query query = null;
|
|
415
|
String queryString = "select "+select+" from TypeDesignationBase designation join designation.typifiedNames name where name = :name";
|
|
416
|
|
|
417
|
if(status != null) {
|
|
418
|
queryString += " and designation.typeStatus = :status";
|
|
419
|
}
|
|
420
|
if(type != null){
|
|
421
|
queryString += " and designation.class = :type";
|
|
422
|
}
|
|
423
|
|
|
424
|
query = getSession().createQuery(queryString);
|
|
425
|
|
|
426
|
if(status != null) {
|
|
427
|
query.setParameter("status", status);
|
|
428
|
}
|
|
429
|
if(type != null){
|
|
430
|
query.setParameter("type", type.getSimpleName());
|
|
431
|
}
|
|
432
|
|
|
433
|
query.setParameter("name",name);
|
|
434
|
return query;
|
|
435
|
}
|
|
436
|
|
|
437
|
public List<TaxonName> searchNames(String queryString, MatchMode matchMode, Integer pageSize, Integer pageNumber) {
|
|
438
|
checkNotInPriorView("TaxonNameDaoHibernateImpl.searchNames(String queryString, Integer pageSize, Integer pageNumber)");
|
|
439
|
Criteria criteria = getSession().createCriteria(TaxonName.class);
|
|
440
|
|
|
441
|
if (queryString != null) {
|
|
442
|
criteria.add(Restrictions.ilike("nameCache", queryString));
|
|
443
|
}
|
|
444
|
if(pageSize != null) {
|
|
445
|
criteria.setMaxResults(pageSize);
|
|
446
|
if(pageNumber != null) {
|
|
447
|
criteria.setFirstResult(pageNumber * pageSize);
|
|
448
|
} else {
|
|
449
|
criteria.setFirstResult(0);
|
|
450
|
}
|
|
451
|
}
|
|
452
|
@SuppressWarnings("unchecked")
|
|
453
|
List<TaxonName> results = criteria.list();
|
|
454
|
return results;
|
|
455
|
}
|
|
456
|
|
|
457
|
|
|
458
|
@Override
|
|
459
|
public List<TaxonName> searchNames(String queryString, Integer pageSize, Integer pageNumber) {
|
|
460
|
return searchNames(queryString, MatchMode.BEGINNING, pageSize, pageNumber);
|
|
461
|
}
|
|
462
|
|
|
463
|
|
|
464
|
@Override
|
|
465
|
public List<TaxonName> searchNames(String genusOrUninomial,String infraGenericEpithet, String specificEpithet, String infraSpecificEpithet, Rank rank, Integer pageSize,Integer pageNumber, List<OrderHint> orderHints,
|
|
466
|
List<String> propertyPaths) {
|
|
467
|
AuditEvent auditEvent = getAuditEventFromContext();
|
|
468
|
if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
|
|
469
|
Criteria criteria = getSession().createCriteria(TaxonName.class);
|
|
470
|
|
|
471
|
/**
|
|
472
|
* Given HHH-2951 - "Restrictions.eq when passed null, should create a NullRestriction"
|
|
473
|
* We need to convert nulls to NullRestrictions for now
|
|
474
|
*/
|
|
475
|
if(genusOrUninomial != null) {
|
|
476
|
criteria.add(Restrictions.eq("genusOrUninomial",genusOrUninomial));
|
|
477
|
} else {
|
|
478
|
criteria.add(Restrictions.isNull("genusOrUninomial"));
|
|
479
|
}
|
|
480
|
|
|
481
|
if(infraGenericEpithet != null) {
|
|
482
|
criteria.add(Restrictions.eq("infraGenericEpithet", infraGenericEpithet));
|
|
483
|
} else {
|
|
484
|
criteria.add(Restrictions.isNull("infraGenericEpithet"));
|
|
485
|
}
|
|
486
|
|
|
487
|
if(specificEpithet != null) {
|
|
488
|
criteria.add(Restrictions.eq("specificEpithet", specificEpithet));
|
|
489
|
} else {
|
|
490
|
criteria.add(Restrictions.isNull("specificEpithet"));
|
|
491
|
}
|
|
492
|
|
|
493
|
if(infraSpecificEpithet != null) {
|
|
494
|
criteria.add(Restrictions.eq("infraSpecificEpithet",infraSpecificEpithet));
|
|
495
|
} else {
|
|
496
|
criteria.add(Restrictions.isNull("infraSpecificEpithet"));
|
|
497
|
}
|
|
498
|
|
|
499
|
if(rank != null) {
|
|
500
|
criteria.add(Restrictions.eq("rank", rank));
|
|
501
|
}
|
|
502
|
|
|
503
|
if(pageSize != null) {
|
|
504
|
criteria.setMaxResults(pageSize);
|
|
505
|
if(pageNumber != null) {
|
|
506
|
criteria.setFirstResult(pageNumber * pageSize);
|
|
507
|
} else {
|
|
508
|
criteria.setFirstResult(0);
|
|
509
|
}
|
|
510
|
}
|
|
511
|
|
|
512
|
addOrder(criteria, orderHints);
|
|
513
|
|
|
514
|
@SuppressWarnings("unchecked")
|
|
515
|
List<TaxonName> results = criteria.list();
|
|
516
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
|
517
|
return results;
|
|
518
|
} else {
|
|
519
|
AuditQuery query = getAuditReader().createQuery().forEntitiesAtRevision(TaxonName.class,auditEvent.getRevisionNumber());
|
|
520
|
|
|
521
|
if(genusOrUninomial != null) {
|
|
522
|
query.add(AuditEntity.property("genusOrUninomial").eq(genusOrUninomial));
|
|
523
|
} else {
|
|
524
|
query.add(AuditEntity.property("genusOrUninomial").isNull());
|
|
525
|
}
|
|
526
|
|
|
527
|
if(infraGenericEpithet != null) {
|
|
528
|
query.add(AuditEntity.property("infraGenericEpithet").eq(infraGenericEpithet));
|
|
529
|
} else {
|
|
530
|
query.add(AuditEntity.property("infraGenericEpithet").isNull());
|
|
531
|
}
|
|
532
|
|
|
533
|
if(specificEpithet != null) {
|
|
534
|
query.add(AuditEntity.property("specificEpithet").eq(specificEpithet));
|
|
535
|
} else {
|
|
536
|
query.add(AuditEntity.property("specificEpithet").isNull());
|
|
537
|
}
|
|
538
|
|
|
539
|
if(infraSpecificEpithet != null) {
|
|
540
|
query.add(AuditEntity.property("infraSpecificEpithet").eq(infraSpecificEpithet));
|
|
541
|
} else {
|
|
542
|
query.add(AuditEntity.property("infraSpecificEpithet").isNull());
|
|
543
|
}
|
|
544
|
|
|
545
|
if(rank != null) {
|
|
546
|
query.add(AuditEntity.relatedId("rank").eq(rank.getId()));
|
|
547
|
}
|
|
548
|
|
|
549
|
if(pageSize != null) {
|
|
550
|
query.setMaxResults(pageSize);
|
|
551
|
if(pageNumber != null) {
|
|
552
|
query.setFirstResult(pageNumber * pageSize);
|
|
553
|
} else {
|
|
554
|
query.setFirstResult(0);
|
|
555
|
}
|
|
556
|
}
|
|
557
|
|
|
558
|
@SuppressWarnings("unchecked")
|
|
559
|
List<TaxonName> results = query.getResultList();
|
|
560
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
|
561
|
return results;
|
|
562
|
}
|
|
563
|
}
|
|
564
|
|
|
565
|
@Override
|
|
566
|
public List<TaxonName> findByName(boolean doIncludeAuthors,
|
|
567
|
String queryString, MatchMode matchmode, Integer pageSize,
|
|
568
|
Integer pageNumber, List<Criterion> criteria, List<String> propertyPaths) {
|
|
569
|
|
|
570
|
Criteria crit = getSession().createCriteria(type);
|
|
571
|
Criterion nameCacheLike;
|
|
572
|
if (matchmode == MatchMode.EXACT) {
|
|
573
|
nameCacheLike = Restrictions.eq("nameCache", matchmode.queryStringFrom(queryString));
|
|
574
|
} else {
|
|
575
|
nameCacheLike = Restrictions.ilike("nameCache", matchmode.queryStringFrom(queryString));
|
|
576
|
}
|
|
577
|
Criterion notNull = Restrictions.isNotNull("nameCache");
|
|
578
|
LogicalExpression nameCacheExpression = Restrictions.and(notNull, nameCacheLike);
|
|
579
|
|
|
580
|
Criterion titleCacheLike;
|
|
581
|
if (matchmode == MatchMode.EXACT) {
|
|
582
|
titleCacheLike = Restrictions.eq("titleCache", matchmode.queryStringFrom(queryString));
|
|
583
|
} else {
|
|
584
|
titleCacheLike =Restrictions.ilike("titleCache", matchmode.queryStringFrom(queryString));
|
|
585
|
}
|
|
586
|
Criterion isNull = Restrictions.isNull("nameCache");
|
|
587
|
LogicalExpression titleCacheExpression = Restrictions.and(isNull, titleCacheLike);
|
|
588
|
|
|
589
|
LogicalExpression orExpression = Restrictions.or(titleCacheExpression, nameCacheExpression);
|
|
590
|
|
|
591
|
Criterion finalCriterion = doIncludeAuthors ? titleCacheLike : orExpression;
|
|
592
|
|
|
593
|
crit.add(finalCriterion);
|
|
594
|
if(criteria != null){
|
|
595
|
for (Criterion criterion : criteria) {
|
|
596
|
crit.add(criterion);
|
|
597
|
}
|
|
598
|
}
|
|
599
|
crit.addOrder(Order.asc("nameCache"));
|
|
600
|
|
|
601
|
if(pageSize != null) {
|
|
602
|
crit.setMaxResults(pageSize);
|
|
603
|
if(pageNumber != null) {
|
|
604
|
crit.setFirstResult(pageNumber * pageSize);
|
|
605
|
}
|
|
606
|
}
|
|
607
|
|
|
608
|
@SuppressWarnings("unchecked")
|
|
609
|
List<TaxonName> results = crit.list();
|
|
610
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
|
611
|
|
|
612
|
return results;
|
|
613
|
}
|
|
614
|
|
|
615
|
@Override
|
|
616
|
public List<TaxonName> findByFullTitle(String queryString,
|
|
617
|
MatchMode matchmode, Integer pageSize, Integer pageNumber, List<Criterion> criteria, List<String> propertyPaths) {
|
|
618
|
|
|
619
|
Criteria crit = getSession().createCriteria(type);
|
|
620
|
if (matchmode == null){
|
|
621
|
matchmode = MatchMode.LIKE;
|
|
622
|
}
|
|
623
|
if (matchmode == MatchMode.EXACT) {
|
|
624
|
crit.add(Restrictions.eq("fullTitleCache", matchmode.queryStringFrom(queryString)));
|
|
625
|
} else {
|
|
626
|
crit.add(Restrictions.ilike("fullTitleCache", matchmode.queryStringFrom(queryString)));
|
|
627
|
}
|
|
628
|
if(criteria != null){
|
|
629
|
for (Criterion criterion : criteria) {
|
|
630
|
crit.add(criterion);
|
|
631
|
}
|
|
632
|
}
|
|
633
|
crit.addOrder(Order.asc("fullTitleCache"));
|
|
634
|
|
|
635
|
if(pageSize != null) {
|
|
636
|
crit.setMaxResults(pageSize);
|
|
637
|
if(pageNumber != null) {
|
|
638
|
crit.setFirstResult(pageNumber * pageSize);
|
|
639
|
}
|
|
640
|
}
|
|
641
|
|
|
642
|
@SuppressWarnings("unchecked")
|
|
643
|
List<TaxonName> results = crit.list();
|
|
644
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
|
645
|
|
|
646
|
return results;
|
|
647
|
}
|
|
648
|
|
|
649
|
@Override
|
|
650
|
public List<TaxonName> findByTitle(String queryString,
|
|
651
|
MatchMode matchmode, Integer pageSize, Integer pageNumber, List<Criterion> criteria, List<String> propertyPaths) {
|
|
652
|
|
|
653
|
Criteria crit = getSession().createCriteria(type);
|
|
654
|
if (matchmode == MatchMode.EXACT) {
|
|
655
|
crit.add(Restrictions.eq("titleCache", matchmode.queryStringFrom(queryString)));
|
|
656
|
} else {
|
|
657
|
crit.add(Restrictions.ilike("titleCache", matchmode.queryStringFrom(queryString)));
|
|
658
|
}
|
|
659
|
if(criteria != null){
|
|
660
|
for (Criterion criterion : criteria) {
|
|
661
|
crit.add(criterion);
|
|
662
|
}
|
|
663
|
}
|
|
664
|
crit.addOrder(Order.asc("titleCache"));
|
|
665
|
|
|
666
|
if(pageSize != null) {
|
|
667
|
crit.setMaxResults(pageSize);
|
|
668
|
if(pageNumber != null) {
|
|
669
|
crit.setFirstResult(pageNumber * pageSize);
|
|
670
|
}
|
|
671
|
}
|
|
672
|
|
|
673
|
@SuppressWarnings("unchecked")
|
|
674
|
List<TaxonName> results = crit.list();
|
|
675
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
|
676
|
|
|
677
|
return results;
|
|
678
|
}
|
|
679
|
|
|
680
|
|
|
681
|
@Override
|
|
682
|
public TaxonName findByUuid(UUID uuid, List<Criterion> criteria, List<String> propertyPaths) {
|
|
683
|
|
|
684
|
Criteria crit = getSession().createCriteria(type);
|
|
685
|
|
|
686
|
if (uuid != null) {
|
|
687
|
crit.add(Restrictions.eq("uuid", uuid));
|
|
688
|
} else {
|
|
689
|
logger.warn("UUID is NULL");
|
|
690
|
return null;
|
|
691
|
}
|
|
692
|
if(criteria != null){
|
|
693
|
for (Criterion criterion : criteria) {
|
|
694
|
crit.add(criterion);
|
|
695
|
}
|
|
696
|
}
|
|
697
|
crit.addOrder(Order.asc("uuid"));
|
|
698
|
|
|
699
|
@SuppressWarnings("unchecked")
|
|
700
|
List<TaxonName> results = crit.list();
|
|
701
|
if (results.size() == 1) {
|
|
702
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
|
703
|
TaxonName taxonName = results.iterator().next();
|
|
704
|
return taxonName;
|
|
705
|
} else if (results.size() > 1) {
|
|
706
|
logger.error("Multiple results for UUID: " + uuid);
|
|
707
|
} else if (results.size() == 0) {
|
|
708
|
logger.info("No results for UUID: " + uuid);
|
|
709
|
}
|
|
710
|
|
|
711
|
return null;
|
|
712
|
}
|
|
713
|
|
|
714
|
|
|
715
|
@Override
|
|
716
|
public <S extends TaxonName> List<S> list(Class<S> type, List<Restriction<?>> restrictions, Integer limit,
|
|
717
|
Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
718
|
// TODO Auto-generated method stub
|
|
719
|
return list(type, restrictions, limit, start, orderHints, propertyPaths, INCLUDE_UNPUBLISHED);
|
|
720
|
}
|
|
721
|
|
|
722
|
@Override
|
|
723
|
public <S extends TaxonName> List<S> list(Class<S> type, List<Restriction<?>> restrictions, Integer limit,
|
|
724
|
Integer start, List<OrderHint> orderHints, List<String> propertyPaths, boolean includePublished) {
|
|
725
|
Criteria criteria = createCriteria(type, restrictions, false);
|
|
726
|
|
|
727
|
if(!includePublished){
|
|
728
|
criteria.add(Restrictions.eq("taxonBases.publish", true));
|
|
729
|
}
|
|
730
|
|
|
731
|
addLimitAndStart(criteria, limit, start);
|
|
732
|
addOrder(criteria, orderHints);
|
|
733
|
|
|
734
|
@SuppressWarnings("unchecked")
|
|
735
|
List<S> result = criteria.list();
|
|
736
|
defaultBeanInitializer.initializeAll(result, propertyPaths);
|
|
737
|
return result;
|
|
738
|
}
|
|
739
|
|
|
740
|
@Override
|
|
741
|
public long count(Class<? extends TaxonName> type, List<Restriction<?>> restrictions) {
|
|
742
|
return count(type, restrictions, INCLUDE_UNPUBLISHED);
|
|
743
|
}
|
|
744
|
|
|
745
|
|
|
746
|
@Override
|
|
747
|
public long count(Class<? extends TaxonName> type, List<Restriction<?>> restrictions, boolean includePublished) {
|
|
748
|
|
|
749
|
Criteria criteria = createCriteria(type, restrictions, false);
|
|
750
|
if(!includePublished){
|
|
751
|
criteria.add(Restrictions.eq("taxonBases.publish", true));
|
|
752
|
}
|
|
753
|
criteria.setProjection(Projections.projectionList().add(Projections.rowCount()));
|
|
754
|
return (Long) criteria.uniqueResult();
|
|
755
|
}
|
|
756
|
|
|
757
|
|
|
758
|
/**
|
|
759
|
* TODO not yet in interface
|
|
760
|
* @param clazz
|
|
761
|
* @return
|
|
762
|
*/
|
|
763
|
public int countAllRelationships(Class<? extends RelationshipBase> clazz) {
|
|
764
|
if (clazz != null && ! NameRelationship.class.isAssignableFrom(clazz) && ! HybridRelationship.class.isAssignableFrom(clazz) ){
|
|
765
|
throw new RuntimeException("Class must be assignable by a taxon or snonym relation");
|
|
766
|
}
|
|
767
|
int size = 0;
|
|
768
|
|
|
769
|
if (clazz == null || NameRelationship.class.isAssignableFrom(clazz)){
|
|
770
|
String hql = " SELECT count(rel) FROM NameRelationship rel";
|
|
771
|
size += (Long)getSession().createQuery(hql).list().get(0);
|
|
772
|
}
|
|
773
|
if (clazz == null || HybridRelationship.class.isAssignableFrom(clazz)){
|
|
774
|
String hql = " SELECT count(rel) FROM HybridRelationship rel";
|
|
775
|
size += (Long)getSession().createQuery(hql).list().get(0);
|
|
776
|
}
|
|
777
|
return size;
|
|
778
|
}
|
|
779
|
|
|
780
|
|
|
781
|
@Override
|
|
782
|
public Integer countByName(String queryString, MatchMode matchmode, List<Criterion> criteria) {
|
|
783
|
//TODO improve performance
|
|
784
|
boolean includeAuthors = false;
|
|
785
|
List<TaxonName> results = findByName(
|
|
786
|
includeAuthors,queryString, matchmode, null, null, criteria, null);
|
|
787
|
return results.size();
|
|
788
|
|
|
789
|
}
|
|
790
|
|
|
791
|
@Override
|
|
792
|
public List<UuidAndTitleCache> getUuidAndTitleCacheOfNames(Integer limit, String pattern) {
|
|
793
|
String queryString = "SELECT uuid, id, fullTitleCache FROM TaxonName LIMIT " + limit;
|
|
794
|
|
|
795
|
@SuppressWarnings("unchecked")
|
|
796
|
List<Object[]> result = getSession().createSQLQuery(queryString).list();
|
|
797
|
|
|
798
|
if(result.size() == 0){
|
|
799
|
return null;
|
|
800
|
}else{
|
|
801
|
List<UuidAndTitleCache> list = new ArrayList<>(result.size());
|
|
802
|
|
|
803
|
for (Object object : result){
|
|
804
|
|
|
805
|
Object[] objectArray = (Object[]) object;
|
|
806
|
|
|
807
|
UUID uuid = UUID.fromString((String) objectArray[0]);
|
|
808
|
Integer id = (Integer) objectArray[1];
|
|
809
|
String titleCache = (String) objectArray[2];
|
|
810
|
|
|
811
|
list.add(new UuidAndTitleCache(type, uuid, id, titleCache));
|
|
812
|
}
|
|
813
|
|
|
814
|
return list;
|
|
815
|
}
|
|
816
|
}
|
|
817
|
|
|
818
|
@Override
|
|
819
|
public long countByName(Class<TaxonName> clazz,String queryString, MatchMode matchmode, List<Criterion> criteria) {
|
|
820
|
return super.countByParam(clazz, "nameCache", queryString, matchmode, criteria);
|
|
821
|
}
|
|
822
|
|
|
823
|
@Override
|
|
824
|
public long countByFullTitle(Class<TaxonName> clazz,String queryString, MatchMode matchmode, List<Criterion> criteria) {
|
|
825
|
return super.countByParam(clazz, "fullTitleCache", queryString, matchmode, criteria);
|
|
826
|
}
|
|
827
|
|
|
828
|
@Override
|
|
829
|
public List<TaxonName> findByName(Class<TaxonName> clazz, String queryString, MatchMode matchmode, List<Criterion> criteria,Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
830
|
return super.findByParam(clazz, "nameCache", queryString, matchmode, criteria, pageSize, pageNumber, orderHints, propertyPaths);
|
|
831
|
}
|
|
832
|
|
|
833
|
@Override
|
|
834
|
public UUID delete (TaxonName persistentObject){
|
|
835
|
@SuppressWarnings("rawtypes")
|
|
836
|
Set<TaxonBase> taxonBases = persistentObject.getTaxonBases();
|
|
837
|
|
|
838
|
getSession().saveOrUpdate(persistentObject);
|
|
839
|
UUID homotypicalGroupUUID = persistentObject.getHomotypicalGroup().getUuid();
|
|
840
|
|
|
841
|
|
|
842
|
for (TaxonBase<?> taxonBase: taxonBases){
|
|
843
|
taxonDao.delete(taxonBase);
|
|
844
|
}
|
|
845
|
HomotypicalGroup homotypicalGroup = homotypicalGroupDao.load(homotypicalGroupUUID);
|
|
846
|
homotypicalGroup = HibernateProxyHelper.deproxy(homotypicalGroup);
|
|
847
|
|
|
848
|
if (homotypicalGroup != null){
|
|
849
|
if (homotypicalGroup.getTypifiedNames().contains(persistentObject)){
|
|
850
|
homotypicalGroup.getTypifiedNames().remove(persistentObject);
|
|
851
|
homotypicalGroupDao.saveOrUpdate(homotypicalGroup);
|
|
852
|
}
|
|
853
|
}
|
|
854
|
|
|
855
|
getSession().delete(persistentObject);
|
|
856
|
if (homotypicalGroup.getTypifiedNames().isEmpty()){
|
|
857
|
homotypicalGroupDao.delete(homotypicalGroup);
|
|
858
|
}
|
|
859
|
return persistentObject.getUuid();
|
|
860
|
}
|
|
861
|
|
|
862
|
|
|
863
|
@Override
|
|
864
|
public IZoologicalName findZoologicalNameByUUID(UUID uuid){
|
|
865
|
Criteria criteria = getSession().createCriteria(type);
|
|
866
|
if (uuid != null) {
|
|
867
|
criteria.add(Restrictions.eq("uuid", uuid));
|
|
868
|
} else {
|
|
869
|
logger.warn("UUID is NULL");
|
|
870
|
return null;
|
|
871
|
}
|
|
872
|
|
|
873
|
@SuppressWarnings("unchecked")
|
|
874
|
List<TaxonName> results = criteria.list();
|
|
875
|
if (results.size() == 1) {
|
|
876
|
defaultBeanInitializer.initializeAll(results, null);
|
|
877
|
TaxonName taxonName = results.iterator().next();
|
|
878
|
if (taxonName.isZoological()) {
|
|
879
|
IZoologicalName zoologicalName = taxonName;
|
|
880
|
return zoologicalName;
|
|
881
|
} else {
|
|
882
|
logger.warn("This UUID (" + uuid + ") does not belong to a ZoologicalName. It belongs to: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");
|
|
883
|
}
|
|
884
|
} else if (results.size() > 1) {
|
|
885
|
logger.error("Multiple results for UUID: " + uuid);
|
|
886
|
} else if (results.size() == 0) {
|
|
887
|
logger.info("No results for UUID: " + uuid);
|
|
888
|
}
|
|
889
|
return null;
|
|
890
|
}
|
|
891
|
|
|
892
|
@Override
|
|
893
|
public List<HashMap<String,String>> getNameRecords(){
|
|
894
|
String sql= "SELECT"
|
|
895
|
+ " (SELECT famName.namecache FROM TaxonNode famNode"
|
|
896
|
+ " LEFT OUTER JOIN TaxonBase famTax ON famNode.taxon_id = famTax.id"
|
|
897
|
+ " LEFT OUTER JOIN TaxonName famName ON famTax.name_id = famName.id"
|
|
898
|
+ " WHERE famName.rank_id = 795 AND famNode.treeIndex = SUBSTRING(tn.treeIndex, 1, length(famNode.treeIndex))"
|
|
899
|
+ " ) as famName, "
|
|
900
|
+ " (SELECT famName.namecache FROM TaxonNode famNode "
|
|
901
|
+ " LEFT OUTER JOIN TaxonBase famTax ON famNode.taxon_id = famTax.id "
|
|
902
|
+ " LEFT OUTER JOIN TaxonName famName ON famTax.name_id = famName.id "
|
|
903
|
+ " WHERE famName.rank_id = 795 AND famNode.treeIndex = SUBSTRING(tnAcc.treeIndex, 1, length(famNode.treeIndex))"
|
|
904
|
+ " ) as accFamName,tb.DTYPE, tb.id as TaxonID ,tb.titleCache taxonTitle, tnb.rank_id as RankID, tnb.id as NameID,"
|
|
905
|
+ " tnb.namecache as name, tnb.titleCache as nameAuthor, tnb.fullTitleCache nameAndNomRef,"
|
|
906
|
+ " r.titleCache as nomRef, r.abbrevTitle nomRefAbbrevTitle, r.title nomRefTitle, r.datepublished_start nomRefPublishedStart, r.datepublished_end nomRefPublishedEnd, r.pages nomRefPages, inRef.abbrevTitle inRefAbbrevTitle,tnb.nomenclaturalmicroreference as detail,"
|
|
907
|
+ " nameType.namecache nameType, nameType.titleCache nameTypeAuthor, nameType.fullTitleCache nameTypeFullTitle, nameTypeRef.titleCache nameTypeRef, "
|
|
908
|
+ " inRef.seriespart as inRefSeries, inRef.datepublished_start inRefPublishedStart, inRef.datepublished_end inRefPublishedEnd, inRef.volume as inRefVolume"
|
|
909
|
+ " FROM TaxonBase tb"
|
|
910
|
+ " LEFT OUTER JOIN TaxonName tnb ON tb.name_id = tnb.id"
|
|
911
|
+ " LEFT OUTER JOIN OriginalSourceBase nosb ON tnb.nomenclaturalSource_id = nosb.id"
|
|
912
|
+ " LEFT OUTER JOIN Reference r ON nosb.citation_id = r.id"
|
|
913
|
+ " LEFT OUTER JOIN TaxonNode tn ON tn.taxon_id = tb.id"
|
|
914
|
+ " LEFT OUTER JOIN TaxonName_TypeDesignationBase typeMN ON typeMN.TaxonName_id = tnb.id"
|
|
915
|
+ " LEFT OUTER JOIN TypeDesignationBase tdb ON tdb.id = typeMN.typedesignations_id"
|
|
916
|
+ " LEFT OUTER JOIN TaxonName nameType ON tdb.typename_id = nameType.id"
|
|
917
|
+ " LEFT OUTER JOIN OriginalSourceBase nameTypeOsb ON nameType.nomenclaturalSource_id = nameTypeOsb.id"
|
|
918
|
+ " LEFT OUTER JOIN Reference nameTypeRef ON nameTypeOsb.citation_id = nameTypeRef.id"
|
|
919
|
+ " LEFT OUTER JOIN Reference inRef ON inRef.id = r.inreference_id"
|
|
920
|
+ " LEFT OUTER JOIN TaxonBase accT ON accT.id = tb.acceptedTaxon_id"
|
|
921
|
+ " LEFT OUTER JOIN TaxonNode tnAcc ON tnAcc.taxon_id = accT.id"
|
|
922
|
+ " ORDER BY DTYPE, famName, accFamName, tnb.rank_id ,tb.titleCache";
|
|
923
|
|
|
924
|
String hqlQueryStringFrom = "FROM TaxonBase taxonBase "
|
|
925
|
+ " LEFT OUTER JOIN taxonBase.name as tnb "
|
|
926
|
+ " LEFT OUTER JOIN tnb.nomenclaturalSource as nomSource "
|
|
927
|
+ " LEFT OUTER JOIN nomSource.citation as nomRef "
|
|
928
|
+ " LEFT OUTER JOIN taxonBase.taxonNodes as node "
|
|
929
|
+ " LEFT OUTER JOIN tnb.typeDesignations as type "
|
|
930
|
+ " LEFT OUTER JOIN type.typifiedNames as nameType "
|
|
931
|
+ " LEFT OUTER JOIN nameType.nomenclaturalSource as nameTypeSource "
|
|
932
|
+ " LEFT OUTER JOIN nameTypeSource.citation as nameTypeRef "
|
|
933
|
+ " LEFT OUTER JOIN nomRef.inReference as inRef "
|
|
934
|
+ " LEFT OUTER JOIN taxonBase.acceptedTaxon as accTaxon "
|
|
935
|
+ " LEFT OUTER JOIN accTaxon.taxonNodes as accTaxonNodes";
|
|
936
|
|
|
937
|
|
|
938
|
Query hqlQuery = getSession().createQuery(hqlQueryStringFrom);
|
|
939
|
List<?> hqlResult = hqlQuery.list();
|
|
940
|
|
|
941
|
|
|
942
|
List<HashMap<String,String>> nameRecords = new ArrayList<>();
|
|
943
|
HashMap<String,String> nameRecord = new HashMap<>();
|
|
944
|
TaxonNode familyNode = null;
|
|
945
|
for(Object object : hqlResult){
|
|
946
|
Object[] row = (Object[])object;
|
|
947
|
nameRecord = new HashMap<>();
|
|
948
|
TaxonBase<?> taxonBase = (TaxonBase<?>)row[0];
|
|
949
|
Taxon accTaxon = null;
|
|
950
|
if (taxonBase instanceof Taxon){
|
|
951
|
accTaxon = HibernateProxyHelper.deproxy(taxonBase, Taxon.class);
|
|
952
|
} else{
|
|
953
|
nameRecord.put("famName", "");
|
|
954
|
Synonym syn = HibernateProxyHelper.deproxy(taxonBase, Synonym.class);
|
|
955
|
accTaxon = syn.getAcceptedTaxon();
|
|
956
|
}
|
|
957
|
Set<TaxonNode> nodes = accTaxon.getTaxonNodes();
|
|
958
|
if (nodes.size() == 1){
|
|
959
|
TaxonNode node = nodes.iterator().next();
|
|
960
|
familyNode = node.getAncestorOfRank(Rank.FAMILY());
|
|
961
|
}
|
|
962
|
|
|
963
|
nameRecord.put("famName",familyNode.getTaxon().getName().getNameCache());
|
|
964
|
nameRecord.put("accFamName","");
|
|
965
|
|
|
966
|
|
|
967
|
//nameRecord.put("famName",(String)row[0]);
|
|
968
|
|
|
969
|
nameRecord.put("accFamName",(String)row[1]);
|
|
970
|
|
|
971
|
nameRecord.put("DTYPE",(String)row[2]);
|
|
972
|
nameRecord.put("TaxonID",String.valueOf(row[3]));
|
|
973
|
nameRecord.put("taxonTitle",(String)row[4]);
|
|
974
|
nameRecord.put("RankID",String.valueOf(row[5]));
|
|
975
|
nameRecord.put("NameID",String.valueOf(row[6]));
|
|
976
|
nameRecord.put("name",(String)row[7]);
|
|
977
|
nameRecord.put("nameAuthor",(String)row[8]);
|
|
978
|
nameRecord.put("nameAndNomRef",(String)row[9]);
|
|
979
|
nameRecord.put("nomRef",(String)row[10]);
|
|
980
|
nameRecord.put("nomRefAbbrevTitle",(String)row[11]);
|
|
981
|
nameRecord.put("nomRefTitle",(String)row[12]);
|
|
982
|
nameRecord.put("nomRefPublishedStart",(String)row[13]);
|
|
983
|
nameRecord.put("nomRefPublishedEnd",(String)row[14]);
|
|
984
|
nameRecord.put("nomRefPages",(String)row[15]);
|
|
985
|
nameRecord.put("inRefAbbrevTitle",(String)row[16]);
|
|
986
|
nameRecord.put("detail",(String)row[17]);
|
|
987
|
nameRecord.put("nameType",(String)row[18]);
|
|
988
|
nameRecord.put("nameTypeAuthor",(String)row[19]);
|
|
989
|
nameRecord.put("nameTypeFullTitle",(String)row[20]);
|
|
990
|
nameRecord.put("nameTypeRef",(String)row[21]);
|
|
991
|
nameRecord.put("inRefSeries",(String)row[22]);
|
|
992
|
nameRecord.put("inRefPublishedStart",(String)row[23]);
|
|
993
|
nameRecord.put("inRefPublishedEnd",(String)row[24]);
|
|
994
|
nameRecord.put("inRefVolume",(String)row[25]);
|
|
995
|
nameRecords.add(nameRecord);
|
|
996
|
}
|
|
997
|
|
|
998
|
return nameRecords;
|
|
999
|
}
|
|
1000
|
|
|
1001
|
/**
|
|
1002
|
* {@inheritDoc}
|
|
1003
|
*/
|
|
1004
|
@Override
|
|
1005
|
public List<TaxonNameParts> findTaxonNameParts(Optional<String> genusOrUninomial,
|
|
1006
|
Optional<String> infraGenericEpithet, Optional<String> specificEpithet,
|
|
1007
|
Optional<String> infraSpecificEpithet, Rank rank, Collection<UUID> excludedNamesUuids, Integer pageSize, Integer pageIndex, List<OrderHint> orderHints) {
|
|
1008
|
|
|
1009
|
StringBuilder hql = prepareFindTaxonNameParts(false, genusOrUninomial, infraGenericEpithet,
|
|
1010
|
specificEpithet, infraSpecificEpithet, rank, excludedNamesUuids);
|
|
1011
|
addOrder(hql, "n", orderHints);
|
|
1012
|
Query query = getSession().createQuery(hql.toString());
|
|
1013
|
if(rank != null){
|
|
1014
|
query.setParameter("rank", rank);
|
|
1015
|
}
|
|
1016
|
if(excludedNamesUuids != null && excludedNamesUuids.size() > 0){
|
|
1017
|
query.setParameterList("excludedNamesUuids", excludedNamesUuids);
|
|
1018
|
}
|
|
1019
|
setPagingParameter(query, pageSize, pageIndex);
|
|
1020
|
@SuppressWarnings("unchecked")
|
|
1021
|
List<TaxonNameParts> result = query.list();
|
|
1022
|
return result;
|
|
1023
|
}
|
|
1024
|
|
|
1025
|
|
|
1026
|
|
|
1027
|
/**
|
|
1028
|
* {@inheritDoc}
|
|
1029
|
*/
|
|
1030
|
@Override
|
|
1031
|
public long countTaxonNameParts(Optional<String> genusOrUninomial, Optional<String> infraGenericEpithet,
|
|
1032
|
Optional<String> specificEpithet, Optional<String> infraSpecificEpithet, Rank rank, Collection<UUID> excludedNamesUUIDs) {
|
|
1033
|
|
|
1034
|
StringBuilder hql = prepareFindTaxonNameParts(true, genusOrUninomial, infraGenericEpithet, specificEpithet, infraSpecificEpithet, rank, excludedNamesUUIDs);
|
|
1035
|
Query query = getSession().createQuery(hql.toString());
|
|
1036
|
if(rank != null){
|
|
1037
|
query.setParameter("rank", rank);
|
|
1038
|
}
|
|
1039
|
if(excludedNamesUUIDs != null && excludedNamesUUIDs.size() > 0){
|
|
1040
|
query.setParameterList("excludedNamesUuids", excludedNamesUUIDs);
|
|
1041
|
}
|
|
1042
|
|
|
1043
|
Object count = query.uniqueResult();
|
|
1044
|
return (Long) count;
|
|
1045
|
}
|
|
1046
|
|
|
1047
|
/**
|
|
1048
|
* @return
|
|
1049
|
*/
|
|
1050
|
private StringBuilder prepareFindTaxonNameParts(boolean doCount, Optional<String> genusOrUninomial,
|
|
1051
|
Optional<String> infraGenericEpithet, Optional<String> specificEpithet,
|
|
1052
|
Optional<String> infraSpecificEpithet, Rank rank, Collection<UUID> excludedNamesUuids) {
|
|
1053
|
|
|
1054
|
StringBuilder hql = new StringBuilder();
|
|
1055
|
if(doCount){
|
|
1056
|
hql.append("select count(n.id) ");
|
|
1057
|
} else {
|
|
1058
|
hql.append("select new eu.etaxonomy.cdm.persistence.dto.TaxonNameParts(n.id, n.uuid, n.rank, n.genusOrUninomial, n.infraGenericEpithet, n.specificEpithet, n.infraSpecificEpithet) ");
|
|
1059
|
}
|
|
1060
|
hql.append("from TaxonName n where 1 = 1 ");
|
|
1061
|
|
|
1062
|
if(rank != null){
|
|
1063
|
hql.append("and n.rank = :rank ");
|
|
1064
|
}
|
|
1065
|
if(excludedNamesUuids != null && excludedNamesUuids.size() > 0){
|
|
1066
|
hql.append("and n.uuid not in ( :excludedNamesUuids ) ");
|
|
1067
|
}
|
|
1068
|
|
|
1069
|
addFieldPredicate(hql, "n.genusOrUninomial", genusOrUninomial);
|
|
1070
|
addFieldPredicate(hql, "n.infraGenericEpithet", infraGenericEpithet);
|
|
1071
|
addFieldPredicate(hql, "n.specificEpithet", specificEpithet);
|
|
1072
|
addFieldPredicate(hql, "n.infraSpecificEpithet", infraSpecificEpithet);
|
|
1073
|
|
|
1074
|
return hql;
|
|
1075
|
}
|
|
1076
|
|
|
1077
|
@Override
|
|
1078
|
public long countNameRelationships(Set<NameRelationshipType> types) {
|
|
1079
|
Criteria criteria = getSession().createCriteria(NameRelationship.class);
|
|
1080
|
|
|
1081
|
if (types != null) {
|
|
1082
|
if (types.isEmpty()){
|
|
1083
|
return 0l;
|
|
1084
|
}else{
|
|
1085
|
criteria.add(Restrictions.in("type", types) );
|
|
1086
|
}
|
|
1087
|
}
|
|
1088
|
//count
|
|
1089
|
criteria.setProjection(Projections.rowCount());
|
|
1090
|
long result = (Long)criteria.uniqueResult();
|
|
1091
|
|
|
1092
|
return result;
|
|
1093
|
}
|
|
1094
|
|
|
1095
|
@Override
|
|
1096
|
public List<NameRelationship> getNameRelationships(Set<NameRelationshipType> types,
|
|
1097
|
Integer pageSize, Integer pageNumber,
|
|
1098
|
List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
1099
|
|
|
1100
|
Criteria criteria = getCriteria(NameRelationship.class);
|
|
1101
|
if (types != null) {
|
|
1102
|
if (types.isEmpty()){
|
|
1103
|
return new ArrayList<>();
|
|
1104
|
}else{
|
|
1105
|
criteria.add(Restrictions.in("type", types) );
|
|
1106
|
}
|
|
1107
|
}
|
|
1108
|
addOrder(criteria,orderHints);
|
|
1109
|
addPageSizeAndNumber(criteria, pageSize, pageNumber);
|
|
1110
|
|
|
1111
|
@SuppressWarnings("unchecked")
|
|
1112
|
List<NameRelationship> results = criteria.list();
|
|
1113
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
|
1114
|
|
|
1115
|
return results;
|
|
1116
|
}
|
|
1117
|
|
|
1118
|
@Override
|
|
1119
|
public long countHybridRelationships(Set<HybridRelationshipType> types) {
|
|
1120
|
Criteria criteria = getSession().createCriteria(HybridRelationship.class);
|
|
1121
|
|
|
1122
|
if (types != null) {
|
|
1123
|
if (types.isEmpty()){
|
|
1124
|
return 0l;
|
|
1125
|
}else{
|
|
1126
|
criteria.add(Restrictions.in("type", types) );
|
|
1127
|
}
|
|
1128
|
}
|
|
1129
|
//count
|
|
1130
|
criteria.setProjection(Projections.rowCount());
|
|
1131
|
long result = (Long)criteria.uniqueResult();
|
|
1132
|
|
|
1133
|
return result;
|
|
1134
|
}
|
|
1135
|
|
|
1136
|
@Override
|
|
1137
|
public List<HybridRelationship> getHybridRelationships(Set<HybridRelationshipType> types,
|
|
1138
|
Integer pageSize, Integer pageNumber,
|
|
1139
|
List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
1140
|
|
|
1141
|
Criteria criteria = getCriteria(HybridRelationship.class);
|
|
1142
|
if (types != null) {
|
|
1143
|
if (types.isEmpty()){
|
|
1144
|
return new ArrayList<>();
|
|
1145
|
}else{
|
|
1146
|
criteria.add(Restrictions.in("type", types) );
|
|
1147
|
}
|
|
1148
|
}
|
|
1149
|
addOrder(criteria,orderHints);
|
|
1150
|
addPageSizeAndNumber(criteria, pageSize, pageNumber);
|
|
1151
|
|
|
1152
|
@SuppressWarnings("unchecked")
|
|
1153
|
List<HybridRelationship> results = criteria.list();
|
|
1154
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
|
1155
|
|
|
1156
|
return results;
|
|
1157
|
}
|
|
1158
|
|
|
1159
|
|
|
1160
|
}
|