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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.HashMap;
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import java.util.List;
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import java.util.Set;
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import java.util.UUID;
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import org.apache.log4j.Logger;
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import org.hibernate.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.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.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.RelationshipBase;
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import eu.etaxonomy.cdm.model.name.BacterialName;
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import eu.etaxonomy.cdm.model.name.BotanicalName;
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import eu.etaxonomy.cdm.model.name.CultivarPlantName;
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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.NameRelationship;
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import eu.etaxonomy.cdm.model.name.NameRelationshipType;
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import eu.etaxonomy.cdm.model.name.NonViralName;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
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import eu.etaxonomy.cdm.model.name.TaxonNameBase;
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import eu.etaxonomy.cdm.model.name.TypeDesignationBase;
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import eu.etaxonomy.cdm.model.name.TypeDesignationStatusBase;
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import eu.etaxonomy.cdm.model.name.ViralName;
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import eu.etaxonomy.cdm.model.name.ZoologicalName;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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import eu.etaxonomy.cdm.model.view.AuditEvent;
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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.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<TaxonNameBase> 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(TaxonNameBase.class);
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indexedClasses = new Class[6];
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indexedClasses[0] = BacterialName.class;
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indexedClasses[1] = BotanicalName.class;
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indexedClasses[2] = CultivarPlantName.class;
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indexedClasses[3] = NonViralName.class;
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indexedClasses[4] = ViralName.class;
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indexedClasses[5] = ZoologicalName.class;
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}
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@Override
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public int countHybridNames(NonViralName 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 int countNames(String queryString) {
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checkNotInPriorView("TaxonNameDaoHibernateImpl.countNames(String queryString)");
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Criteria criteria = getSession().createCriteria(TaxonNameBase.class);
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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 ((Number)criteria.uniqueResult()).intValue();
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}
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@Override
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public int countNames(String queryString, MatchMode matchMode, List<Criterion> criteria) {
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Criteria crit = getSession().createCriteria(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 ((Number)crit.uniqueResult()).intValue();
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}
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@Override
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public int 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 = getSession().createCriteria(TaxonNameBase.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 ((Number)criteria.uniqueResult()).intValue();
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} else {
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AuditQuery query = getAuditReader().createQuery().forEntitiesAtRevision(TaxonNameBase.class,auditEvent.getRevisionNumber());
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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()).intValue();
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}
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}
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@Override
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public int countNameRelationships(TaxonNameBase 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 int countTypeDesignations(TaxonNameBase name, SpecimenTypeDesignationStatus status) {
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checkNotInPriorView("countTypeDesignations(TaxonNameBase 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()).intValue();
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}
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@Override
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public List<HybridRelationship> getHybridNames(NonViralName name, HybridRelationshipType type, 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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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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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(TaxonNameBase 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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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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if(type != null) {
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query.add(AuditEntity.relatedId("type").eq(type.getId()));
|
|
345
|
}
|
|
346
|
|
|
347
|
if(pageSize != null) {
|
|
348
|
query.setMaxResults(pageSize);
|
|
349
|
if(pageNumber != null) {
|
|
350
|
query.setFirstResult(pageNumber * pageSize);
|
|
351
|
} else {
|
|
352
|
query.setFirstResult(0);
|
|
353
|
}
|
|
354
|
}
|
|
355
|
|
|
356
|
List<NameRelationship> results = query.getResultList();
|
|
357
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
|
358
|
return results;
|
|
359
|
}
|
|
360
|
}
|
|
361
|
|
|
362
|
@Override
|
|
363
|
public List<TypeDesignationBase> getTypeDesignations(TaxonNameBase name, TypeDesignationStatusBase status, Integer pageSize, Integer pageNumber, List<String> propertyPaths){
|
|
364
|
return getTypeDesignations(name, null, status, pageSize, pageNumber, propertyPaths);
|
|
365
|
}
|
|
366
|
|
|
367
|
@Override
|
|
368
|
public <T extends TypeDesignationBase> List<T> getTypeDesignations(TaxonNameBase name,
|
|
369
|
Class<T> type,
|
|
370
|
TypeDesignationStatusBase status, Integer pageSize, Integer pageNumber,
|
|
371
|
List<String> propertyPaths){
|
|
372
|
checkNotInPriorView("getTypeDesignations(TaxonNameBase name,TypeDesignationStatusBase status, Integer pageSize, Integer pageNumber, List<String> propertyPaths)");
|
|
373
|
Query query = null;
|
|
374
|
String queryString = "select designation from TypeDesignationBase designation join designation.typifiedNames name where name = :name";
|
|
375
|
|
|
376
|
if(status != null) {
|
|
377
|
queryString += " and designation.typeStatus = :status";
|
|
378
|
}
|
|
379
|
if(type != null){
|
|
380
|
queryString += " and designation.class = :type";
|
|
381
|
}
|
|
382
|
|
|
383
|
query = getSession().createQuery(queryString);
|
|
384
|
|
|
385
|
if(status != null) {
|
|
386
|
query.setParameter("status", status);
|
|
387
|
}
|
|
388
|
if(type != null){
|
|
389
|
query.setParameter("type", type.getSimpleName());
|
|
390
|
}
|
|
391
|
|
|
392
|
query.setParameter("name",name);
|
|
393
|
|
|
394
|
if(pageSize != null) {
|
|
395
|
query.setMaxResults(pageSize);
|
|
396
|
if(pageNumber != null) {
|
|
397
|
query.setFirstResult(pageNumber * pageSize);
|
|
398
|
} else {
|
|
399
|
query.setFirstResult(0);
|
|
400
|
}
|
|
401
|
}
|
|
402
|
return defaultBeanInitializer.initializeAll((List<T>)query.list(), propertyPaths);
|
|
403
|
}
|
|
404
|
|
|
405
|
|
|
406
|
public List<TaxonNameBase<?,?>> searchNames(String queryString, MatchMode matchMode, Integer pageSize, Integer pageNumber) {
|
|
407
|
checkNotInPriorView("TaxonNameDaoHibernateImpl.searchNames(String queryString, Integer pageSize, Integer pageNumber)");
|
|
408
|
Criteria criteria = getSession().createCriteria(TaxonNameBase.class);
|
|
409
|
|
|
410
|
if (queryString != null) {
|
|
411
|
criteria.add(Restrictions.ilike("nameCache", queryString));
|
|
412
|
}
|
|
413
|
if(pageSize != null) {
|
|
414
|
criteria.setMaxResults(pageSize);
|
|
415
|
if(pageNumber != null) {
|
|
416
|
criteria.setFirstResult(pageNumber * pageSize);
|
|
417
|
} else {
|
|
418
|
criteria.setFirstResult(0);
|
|
419
|
}
|
|
420
|
}
|
|
421
|
List<TaxonNameBase<?,?>> results = criteria.list();
|
|
422
|
return results;
|
|
423
|
}
|
|
424
|
|
|
425
|
|
|
426
|
@Override
|
|
427
|
public List<TaxonNameBase<?,?>> searchNames(String queryString, Integer pageSize, Integer pageNumber) {
|
|
428
|
return searchNames(queryString, MatchMode.BEGINNING, pageSize, pageNumber);
|
|
429
|
}
|
|
430
|
|
|
431
|
|
|
432
|
@Override
|
|
433
|
public List<TaxonNameBase> searchNames(String genusOrUninomial,String infraGenericEpithet, String specificEpithet, String infraSpecificEpithet, Rank rank, Integer pageSize,Integer pageNumber, List<OrderHint> orderHints,
|
|
434
|
List<String> propertyPaths) {
|
|
435
|
AuditEvent auditEvent = getAuditEventFromContext();
|
|
436
|
if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
|
|
437
|
Criteria criteria = getSession().createCriteria(TaxonNameBase.class);
|
|
438
|
|
|
439
|
/**
|
|
440
|
* Given HHH-2951 - "Restrictions.eq when passed null, should create a NullRestriction"
|
|
441
|
* We need to convert nulls to NullRestrictions for now
|
|
442
|
*/
|
|
443
|
if(genusOrUninomial != null) {
|
|
444
|
criteria.add(Restrictions.eq("genusOrUninomial",genusOrUninomial));
|
|
445
|
} else {
|
|
446
|
criteria.add(Restrictions.isNull("genusOrUninomial"));
|
|
447
|
}
|
|
448
|
|
|
449
|
if(infraGenericEpithet != null) {
|
|
450
|
criteria.add(Restrictions.eq("infraGenericEpithet", infraGenericEpithet));
|
|
451
|
} else {
|
|
452
|
criteria.add(Restrictions.isNull("infraGenericEpithet"));
|
|
453
|
}
|
|
454
|
|
|
455
|
if(specificEpithet != null) {
|
|
456
|
criteria.add(Restrictions.eq("specificEpithet", specificEpithet));
|
|
457
|
} else {
|
|
458
|
criteria.add(Restrictions.isNull("specificEpithet"));
|
|
459
|
}
|
|
460
|
|
|
461
|
if(infraSpecificEpithet != null) {
|
|
462
|
criteria.add(Restrictions.eq("infraSpecificEpithet",infraSpecificEpithet));
|
|
463
|
} else {
|
|
464
|
criteria.add(Restrictions.isNull("infraSpecificEpithet"));
|
|
465
|
}
|
|
466
|
|
|
467
|
if(rank != null) {
|
|
468
|
criteria.add(Restrictions.eq("rank", rank));
|
|
469
|
}
|
|
470
|
|
|
471
|
if(pageSize != null) {
|
|
472
|
criteria.setMaxResults(pageSize);
|
|
473
|
if(pageNumber != null) {
|
|
474
|
criteria.setFirstResult(pageNumber * pageSize);
|
|
475
|
} else {
|
|
476
|
criteria.setFirstResult(0);
|
|
477
|
}
|
|
478
|
}
|
|
479
|
|
|
480
|
addOrder(criteria, orderHints);
|
|
481
|
|
|
482
|
List<TaxonNameBase> results = criteria.list();
|
|
483
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
|
484
|
return results;
|
|
485
|
} else {
|
|
486
|
AuditQuery query = getAuditReader().createQuery().forEntitiesAtRevision(TaxonNameBase.class,auditEvent.getRevisionNumber());
|
|
487
|
|
|
488
|
if(genusOrUninomial != null) {
|
|
489
|
query.add(AuditEntity.property("genusOrUninomial").eq(genusOrUninomial));
|
|
490
|
} else {
|
|
491
|
query.add(AuditEntity.property("genusOrUninomial").isNull());
|
|
492
|
}
|
|
493
|
|
|
494
|
if(infraGenericEpithet != null) {
|
|
495
|
query.add(AuditEntity.property("infraGenericEpithet").eq(infraGenericEpithet));
|
|
496
|
} else {
|
|
497
|
query.add(AuditEntity.property("infraGenericEpithet").isNull());
|
|
498
|
}
|
|
499
|
|
|
500
|
if(specificEpithet != null) {
|
|
501
|
query.add(AuditEntity.property("specificEpithet").eq(specificEpithet));
|
|
502
|
} else {
|
|
503
|
query.add(AuditEntity.property("specificEpithet").isNull());
|
|
504
|
}
|
|
505
|
|
|
506
|
if(infraSpecificEpithet != null) {
|
|
507
|
query.add(AuditEntity.property("infraSpecificEpithet").eq(infraSpecificEpithet));
|
|
508
|
} else {
|
|
509
|
query.add(AuditEntity.property("infraSpecificEpithet").isNull());
|
|
510
|
}
|
|
511
|
|
|
512
|
if(rank != null) {
|
|
513
|
query.add(AuditEntity.relatedId("rank").eq(rank.getId()));
|
|
514
|
}
|
|
515
|
|
|
516
|
if(pageSize != null) {
|
|
517
|
query.setMaxResults(pageSize);
|
|
518
|
if(pageNumber != null) {
|
|
519
|
query.setFirstResult(pageNumber * pageSize);
|
|
520
|
} else {
|
|
521
|
query.setFirstResult(0);
|
|
522
|
}
|
|
523
|
}
|
|
524
|
|
|
525
|
List<TaxonNameBase> results = query.getResultList();
|
|
526
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
|
527
|
return results;
|
|
528
|
}
|
|
529
|
}
|
|
530
|
|
|
531
|
@Override
|
|
532
|
public List<? extends TaxonNameBase<?,?>> findByName(String queryString,
|
|
533
|
MatchMode matchmode, Integer pageSize, Integer pageNumber, List<Criterion> criteria, List<String> propertyPaths) {
|
|
534
|
|
|
535
|
Criteria crit = getSession().createCriteria(type);
|
|
536
|
if (matchmode == MatchMode.EXACT) {
|
|
537
|
crit.add(Restrictions.eq("nameCache", matchmode.queryStringFrom(queryString)));
|
|
538
|
} else {
|
|
539
|
crit.add(Restrictions.ilike("nameCache", matchmode.queryStringFrom(queryString)));
|
|
540
|
}
|
|
541
|
if(criteria != null){
|
|
542
|
for (Criterion criterion : criteria) {
|
|
543
|
crit.add(criterion);
|
|
544
|
}
|
|
545
|
}
|
|
546
|
crit.addOrder(Order.asc("nameCache"));
|
|
547
|
|
|
548
|
if(pageSize != null) {
|
|
549
|
crit.setMaxResults(pageSize);
|
|
550
|
if(pageNumber != null) {
|
|
551
|
crit.setFirstResult(pageNumber * pageSize);
|
|
552
|
}
|
|
553
|
}
|
|
554
|
|
|
555
|
List<? extends TaxonNameBase<?,?>> results = crit.list();
|
|
556
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
|
557
|
|
|
558
|
return results;
|
|
559
|
}
|
|
560
|
|
|
561
|
@Override
|
|
562
|
public List<? extends TaxonNameBase<?,?>> findByTitle(String queryString,
|
|
563
|
MatchMode matchmode, Integer pageSize, Integer pageNumber, List<Criterion> criteria, List<String> propertyPaths) {
|
|
564
|
|
|
565
|
Criteria crit = getSession().createCriteria(type);
|
|
566
|
if (matchmode == MatchMode.EXACT) {
|
|
567
|
crit.add(Restrictions.eq("titleCache", matchmode.queryStringFrom(queryString)));
|
|
568
|
} else {
|
|
569
|
crit.add(Restrictions.ilike("titleCache", matchmode.queryStringFrom(queryString)));
|
|
570
|
}
|
|
571
|
if(criteria != null){
|
|
572
|
for (Criterion criterion : criteria) {
|
|
573
|
crit.add(criterion);
|
|
574
|
}
|
|
575
|
}
|
|
576
|
crit.addOrder(Order.asc("titleCache"));
|
|
577
|
|
|
578
|
if(pageSize != null) {
|
|
579
|
crit.setMaxResults(pageSize);
|
|
580
|
if(pageNumber != null) {
|
|
581
|
crit.setFirstResult(pageNumber * pageSize);
|
|
582
|
}
|
|
583
|
}
|
|
584
|
|
|
585
|
List<? extends TaxonNameBase<?,?>> results = crit.list();
|
|
586
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
|
587
|
|
|
588
|
return results;
|
|
589
|
}
|
|
590
|
|
|
591
|
|
|
592
|
@Override
|
|
593
|
public TaxonNameBase<?,?> findByUuid(UUID uuid, List<Criterion> criteria, List<String> propertyPaths) {
|
|
594
|
|
|
595
|
Criteria crit = getSession().createCriteria(type);
|
|
596
|
|
|
597
|
if (uuid != null) {
|
|
598
|
crit.add(Restrictions.eq("uuid", uuid));
|
|
599
|
} else {
|
|
600
|
logger.warn("UUID is NULL");
|
|
601
|
return null;
|
|
602
|
}
|
|
603
|
if(criteria != null){
|
|
604
|
for (Criterion criterion : criteria) {
|
|
605
|
crit.add(criterion);
|
|
606
|
}
|
|
607
|
}
|
|
608
|
crit.addOrder(Order.asc("uuid"));
|
|
609
|
|
|
610
|
List<? extends TaxonNameBase<?,?>> results = crit.list();
|
|
611
|
if (results.size() == 1) {
|
|
612
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
|
613
|
TaxonNameBase<?, ?> taxonName = results.iterator().next();
|
|
614
|
return taxonName;
|
|
615
|
} else if (results.size() > 1) {
|
|
616
|
logger.error("Multiple results for UUID: " + uuid);
|
|
617
|
} else if (results.size() == 0) {
|
|
618
|
logger.info("No results for UUID: " + uuid);
|
|
619
|
}
|
|
620
|
|
|
621
|
return null;
|
|
622
|
}
|
|
623
|
|
|
624
|
@Override
|
|
625
|
public List<RelationshipBase> getAllRelationships(Integer limit, Integer start) {
|
|
626
|
AuditEvent auditEvent = getAuditEventFromContext();
|
|
627
|
if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {
|
|
628
|
// for some reason the HQL .class discriminator didn't work here so I created this preliminary
|
|
629
|
// implementation for now. Should be cleaned in future.
|
|
630
|
|
|
631
|
List<RelationshipBase> result = new ArrayList<RelationshipBase>();
|
|
632
|
|
|
633
|
int nameRelSize = countAllRelationships(NameRelationship.class);
|
|
634
|
if (nameRelSize > start){
|
|
635
|
|
|
636
|
String hql = " FROM %s as rb ORDER BY rb.id ";
|
|
637
|
hql = String.format(hql, NameRelationship.class.getSimpleName());
|
|
638
|
Query query = getSession().createQuery(hql);
|
|
639
|
query.setFirstResult(start);
|
|
640
|
if (limit != null){
|
|
641
|
query.setMaxResults(limit);
|
|
642
|
}
|
|
643
|
result = query.list();
|
|
644
|
}
|
|
645
|
limit = limit - result.size();
|
|
646
|
if (limit > 0){
|
|
647
|
String hql = " FROM HybridRelationship as rb ORDER BY rb.id ";
|
|
648
|
hql = String.format(hql, HybridRelationship.class.getSimpleName());
|
|
649
|
Query query = getSession().createQuery(hql);
|
|
650
|
start = (nameRelSize > start) ? 0 : (start - nameRelSize);
|
|
651
|
query.setFirstResult(start);
|
|
652
|
if (limit != null){
|
|
653
|
query.setMaxResults(limit);
|
|
654
|
}
|
|
655
|
result.addAll( query.list());
|
|
656
|
}
|
|
657
|
return result;
|
|
658
|
} else {
|
|
659
|
AuditQuery query = getAuditReader().createQuery().forEntitiesAtRevision(RelationshipBase.class,auditEvent.getRevisionNumber());
|
|
660
|
return query.getResultList();
|
|
661
|
}
|
|
662
|
}
|
|
663
|
|
|
664
|
|
|
665
|
/**
|
|
666
|
* TODO not yet in interface
|
|
667
|
* @param clazz
|
|
668
|
* @return
|
|
669
|
*/
|
|
670
|
public int countAllRelationships(Class<? extends RelationshipBase> clazz) {
|
|
671
|
if (clazz != null && ! NameRelationship.class.isAssignableFrom(clazz) && ! HybridRelationship.class.isAssignableFrom(clazz) ){
|
|
672
|
throw new RuntimeException("Class must be assignable by a taxon or snonym relation");
|
|
673
|
}
|
|
674
|
int size = 0;
|
|
675
|
|
|
676
|
if (clazz == null || NameRelationship.class.isAssignableFrom(clazz)){
|
|
677
|
String hql = " SELECT count(rel) FROM NameRelationship rel";
|
|
678
|
size += (Long)getSession().createQuery(hql).list().get(0);
|
|
679
|
}
|
|
680
|
if (clazz == null || HybridRelationship.class.isAssignableFrom(clazz)){
|
|
681
|
String hql = " SELECT count(rel) FROM HybridRelationship rel";
|
|
682
|
size += (Long)getSession().createQuery(hql).list().get(0);
|
|
683
|
}
|
|
684
|
return size;
|
|
685
|
}
|
|
686
|
|
|
687
|
|
|
688
|
@Override
|
|
689
|
public Integer countByName(String queryString, MatchMode matchmode, List<Criterion> criteria) {
|
|
690
|
//TODO improve performance
|
|
691
|
List<? extends TaxonNameBase<?,?>> results = findByName(queryString, matchmode, null, null, criteria, null);
|
|
692
|
return results.size();
|
|
693
|
|
|
694
|
}
|
|
695
|
|
|
696
|
@Override
|
|
697
|
public List<UuidAndTitleCache> getUuidAndTitleCacheOfNames() {
|
|
698
|
String queryString = "SELECT uuid, id, fullTitleCache FROM TaxonNameBase";
|
|
699
|
|
|
700
|
@SuppressWarnings("unchecked")
|
|
701
|
List<Object[]> result = getSession().createSQLQuery(queryString).list();
|
|
702
|
|
|
703
|
if(result.size() == 0){
|
|
704
|
return null;
|
|
705
|
}else{
|
|
706
|
List<UuidAndTitleCache> list = new ArrayList<UuidAndTitleCache>(result.size());
|
|
707
|
|
|
708
|
for (Object object : result){
|
|
709
|
|
|
710
|
Object[] objectArray = (Object[]) object;
|
|
711
|
|
|
712
|
UUID uuid = UUID.fromString((String) objectArray[0]);
|
|
713
|
Integer id = (Integer) objectArray[1];
|
|
714
|
String titleCache = (String) objectArray[2];
|
|
715
|
|
|
716
|
list.add(new UuidAndTitleCache(type, uuid, id, titleCache));
|
|
717
|
}
|
|
718
|
|
|
719
|
return list;
|
|
720
|
}
|
|
721
|
}
|
|
722
|
|
|
723
|
@Override
|
|
724
|
public Integer countByName(Class<? extends TaxonNameBase> clazz,String queryString, MatchMode matchmode, List<Criterion> criteria) {
|
|
725
|
return super.countByParam(clazz, "nameCache", queryString, matchmode, criteria);
|
|
726
|
}
|
|
727
|
|
|
728
|
@Override
|
|
729
|
public List<TaxonNameBase> findByName(Class<? extends TaxonNameBase> clazz, String queryString, MatchMode matchmode, List<Criterion> criteria,Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
|
|
730
|
return super.findByParam(clazz, "nameCache", queryString, matchmode, criteria, pageSize, pageNumber, orderHints, propertyPaths);
|
|
731
|
}
|
|
732
|
|
|
733
|
@Override
|
|
734
|
public UUID delete (TaxonNameBase persistentObject){
|
|
735
|
Set<TaxonBase> taxonBases = persistentObject.getTaxonBases();
|
|
736
|
|
|
737
|
if (persistentObject == null){
|
|
738
|
logger.warn(type.getName() + " was 'null'");
|
|
739
|
return null;
|
|
740
|
}
|
|
741
|
getSession().saveOrUpdate(persistentObject);
|
|
742
|
UUID persUuid = persistentObject.getUuid();
|
|
743
|
persistentObject = this.load(persUuid);
|
|
744
|
UUID homotypicalGroupUUID = persistentObject.getHomotypicalGroup().getUuid();
|
|
745
|
|
|
746
|
|
|
747
|
for (TaxonBase taxonBase: taxonBases){
|
|
748
|
taxonDao.delete(taxonBase);
|
|
749
|
}
|
|
750
|
HomotypicalGroup homotypicalGroup = homotypicalGroupDao.load(homotypicalGroupUUID);
|
|
751
|
if (homotypicalGroup != null){
|
|
752
|
if (homotypicalGroup.getTypifiedNames().isEmpty()){
|
|
753
|
homotypicalGroupDao.delete(homotypicalGroup);
|
|
754
|
}
|
|
755
|
}
|
|
756
|
|
|
757
|
getSession().delete(persistentObject);
|
|
758
|
return persistentObject.getUuid();
|
|
759
|
}
|
|
760
|
|
|
761
|
|
|
762
|
@Override
|
|
763
|
public ZoologicalName findZoologicalNameByUUID(UUID uuid){
|
|
764
|
Criteria criteria = getSession().createCriteria(type);
|
|
765
|
if (uuid != null) {
|
|
766
|
criteria.add(Restrictions.eq("uuid", uuid));
|
|
767
|
} else {
|
|
768
|
logger.warn("UUID is NULL");
|
|
769
|
return null;
|
|
770
|
}
|
|
771
|
|
|
772
|
List<? extends TaxonNameBase<?,?>> results = criteria.list();
|
|
773
|
if (results.size() == 1) {
|
|
774
|
defaultBeanInitializer.initializeAll(results, null);
|
|
775
|
TaxonNameBase<?, ?> taxonName = results.iterator().next();
|
|
776
|
if (taxonName.isInstanceOf(ZoologicalName.class)) {
|
|
777
|
ZoologicalName zoologicalName = CdmBase.deproxy(taxonName, ZoologicalName.class);
|
|
778
|
return zoologicalName;
|
|
779
|
} else {
|
|
780
|
logger.warn("This UUID (" + uuid + ") does not belong to a ZoologicalName. It belongs to: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");
|
|
781
|
}
|
|
782
|
} else if (results.size() > 1) {
|
|
783
|
logger.error("Multiple results for UUID: " + uuid);
|
|
784
|
} else if (results.size() == 0) {
|
|
785
|
logger.info("No results for UUID: " + uuid);
|
|
786
|
}
|
|
787
|
return null;
|
|
788
|
}
|
|
789
|
@Override
|
|
790
|
public List<HashMap<String,String>> getNameRecords(){
|
|
791
|
String sql= "SELECT"
|
|
792
|
+ " (SELECT famName.namecache FROM TaxonNode famNode"
|
|
793
|
+ " LEFT OUTER JOIN TaxonBase famTax ON famNode.taxon_id = famTax.id"
|
|
794
|
+ " LEFT OUTER JOIN TaxonNameBase famName ON famTax.name_id = famName.id"
|
|
795
|
+ " WHERE famName.rank_id = 795 AND famNode.treeIndex = SUBSTRING(tn.treeIndex, 1, length(famNode.treeIndex))"
|
|
796
|
+ " ) as famName, "
|
|
797
|
+ " (SELECT famName.namecache FROM TaxonNode famNode "
|
|
798
|
+ " LEFT OUTER JOIN TaxonBase famTax ON famNode.taxon_id = famTax.id "
|
|
799
|
+ " LEFT OUTER JOIN TaxonNameBase famName ON famTax.name_id = famName.id "
|
|
800
|
+ " WHERE famName.rank_id = 795 AND famNode.treeIndex = SUBSTRING(tnAcc.treeIndex, 1, length(famNode.treeIndex))"
|
|
801
|
+ " ) as accFamName,tb.DTYPE, tb.id as TaxonID ,tb.titleCache taxonTitle, tnb.rank_id as RankID, tnb.id as NameID,"
|
|
802
|
+ " tnb.namecache as name, tnb.titleCache as nameAuthor, tnb.fullTitleCache nameAndNomRef,"
|
|
803
|
+ " 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,"
|
|
804
|
+ " nameType.namecache nameType, nameType.titleCache nameTypeAuthor, nameType.fullTitleCache nameTypeFullTitle, nameTypeRef.titleCache nameTypeRef, inRef.seriespart as inRefSeries, inRef.datepublished_start inRefPublishedStart, inRef.datepublished_end inRefPublishedEnd, inRef.volume as inRefVolume"
|
|
805
|
+ " FROM TaxonBase tb"
|
|
806
|
+ " LEFT OUTER JOIN TaxonNameBase tnb ON tb.name_id = tnb.id"
|
|
807
|
+ " LEFT OUTER JOIN Reference r ON tnb.nomenclaturalreference_id = r.id"
|
|
808
|
+ " LEFT OUTER JOIN TaxonNode tn ON tn.taxon_id = tb.id"
|
|
809
|
+ " LEFT OUTER JOIN TaxonNameBase_TypeDesignationBase typeMN ON typeMN.TaxonNameBase_id = tnb.id"
|
|
810
|
+ " LEFT OUTER JOIN TypeDesignationBase tdb ON tdb.id = typeMN.typedesignations_id"
|
|
811
|
+ " LEFT OUTER JOIN TaxonNameBase nameType ON tdb.typename_id = nameType.id"
|
|
812
|
+ " LEFT OUTER JOIN Reference nameTypeRef ON nameType.nomenclaturalreference_id = nameTypeRef.id"
|
|
813
|
+ " LEFT OUTER JOIN Reference inRef ON inRef.id = r.inreference_id"
|
|
814
|
+ " LEFT OUTER JOIN SynonymRelationship sr ON tb.id = sr.relatedfrom_id"
|
|
815
|
+ " LEFT OUTER JOIN TaxonBase accT ON accT.id = sr.relatedto_id"
|
|
816
|
+ " LEFT OUTER JOIN TaxonNode tnAcc ON tnAcc.taxon_id = accT.id"
|
|
817
|
+ " ORDER BY DTYPE, famName, accFamName, tnb.rank_id ,tb.titleCache";
|
|
818
|
|
|
819
|
|
|
820
|
SQLQuery query = getSession().createSQLQuery(sql);
|
|
821
|
List result = query.list();
|
|
822
|
//Delimiter used in CSV file
|
|
823
|
|
|
824
|
|
|
825
|
List<HashMap<String,String>> nameRecords = new ArrayList();
|
|
826
|
HashMap<String,String> nameRecord = new HashMap<String,String>();
|
|
827
|
for(Object object : result)
|
|
828
|
{
|
|
829
|
Object[] row = (Object[])object;
|
|
830
|
nameRecord = new HashMap<String,String>();
|
|
831
|
nameRecord.put("famName",(String)row[0]);
|
|
832
|
nameRecord.put("accFamName",(String)row[1]);
|
|
833
|
|
|
834
|
nameRecord.put("DTYPE",(String)row[2]);
|
|
835
|
nameRecord.put("TaxonID",String.valueOf(row[3]));
|
|
836
|
nameRecord.put("taxonTitle",(String)row[4]);
|
|
837
|
nameRecord.put("RankID",String.valueOf(row[5]));
|
|
838
|
nameRecord.put("NameID",String.valueOf(row[6]));
|
|
839
|
nameRecord.put("name",(String)row[7]);
|
|
840
|
nameRecord.put("nameAuthor",(String)row[8]);
|
|
841
|
nameRecord.put("nameAndNomRef",(String)row[9]);
|
|
842
|
nameRecord.put("nomRef",(String)row[10]);
|
|
843
|
nameRecord.put("nomRefAbbrevTitle",(String)row[11]);
|
|
844
|
nameRecord.put("nomRefTitle",(String)row[12]);
|
|
845
|
nameRecord.put("nomRefPublishedStart",(String)row[13]);
|
|
846
|
nameRecord.put("nomRefPublishedEnd",(String)row[14]);
|
|
847
|
nameRecord.put("nomRefPages",(String)row[15]);
|
|
848
|
nameRecord.put("inRefAbbrevTitle",(String)row[16]);
|
|
849
|
nameRecord.put("detail",(String)row[17]);
|
|
850
|
nameRecord.put("nameType",(String)row[18]);
|
|
851
|
nameRecord.put("nameTypeAuthor",(String)row[19]);
|
|
852
|
nameRecord.put("nameTypeFullTitle",(String)row[20]);
|
|
853
|
nameRecord.put("nameTypeRef",(String)row[21]);
|
|
854
|
nameRecord.put("inRefSeries",(String)row[22]);
|
|
855
|
nameRecord.put("inRefPublishedStart",(String)row[23]);
|
|
856
|
nameRecord.put("inRefPublishedEnd",(String)row[24]);
|
|
857
|
nameRecord.put("inRefVolume",(String)row[25]);
|
|
858
|
nameRecords.add(nameRecord);
|
|
859
|
}
|
|
860
|
|
|
861
|
return nameRecords;
|
|
862
|
|
|
863
|
|
|
864
|
|
|
865
|
}
|
|
866
|
|
|
867
|
|
|
868
|
|
|
869
|
|
|
870
|
}
|