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eeef091f
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Patrick Plitzner
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/**
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* Copyright (C) 2008 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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package eu.etaxonomy.cdm.persistence.dao.hibernate.occurrence;
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import java.util.ArrayList;
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import java.util.Collection;
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import java.util.Collections;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Set;
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import java.util.UUID;
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import org.apache.log4j.Logger;
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import org.hibernate.Criteria;
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import org.hibernate.Hibernate;
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import org.hibernate.Query;
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import org.hibernate.Session;
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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.hibernate.search.FullTextSession;
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import org.hibernate.search.Search;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.stereotype.Repository;
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e4d66102
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Andreas Müller
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import eu.etaxonomy.cdm.model.common.CdmBase;
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eeef091f
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Patrick Plitzner
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import eu.etaxonomy.cdm.model.description.DescriptionBase;
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import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
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import eu.etaxonomy.cdm.model.media.Media;
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import eu.etaxonomy.cdm.model.molecular.DnaSample;
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import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
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import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
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9dc896c9
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Andreas Müller
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import eu.etaxonomy.cdm.model.name.TaxonName;
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eeef091f
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Patrick Plitzner
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import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;
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import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
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import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;
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import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
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cc1e6737
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Patrick Plitzner
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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eeef091f
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Patrick Plitzner
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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.view.AuditEvent;
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import eu.etaxonomy.cdm.persistence.dao.description.IDescriptionDao;
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import eu.etaxonomy.cdm.persistence.dao.hibernate.common.IdentifiableDaoBase;
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import eu.etaxonomy.cdm.persistence.dao.hibernate.taxon.TaxonDaoHibernateImpl;
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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.occurrence.IOccurrenceDao;
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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.babadshanjan
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* @created 01.09.2008
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*/
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@Repository
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public class OccurrenceDaoHibernateImpl extends IdentifiableDaoBase<SpecimenOrObservationBase> implements IOccurrenceDao {
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@SuppressWarnings("unused")
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private static final Logger logger = Logger.getLogger(TaxonDaoHibernateImpl.class);
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@Autowired
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private IDescriptionDao descriptionDao;
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@Autowired
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private ITaxonNameDao taxonNameDao;
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@Autowired
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private IHomotypicalGroupDao homotypicalGroupDao;
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public OccurrenceDaoHibernateImpl() {
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super(SpecimenOrObservationBase.class);
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indexedClasses = new Class[7];
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indexedClasses[0] = FieldUnit.class;
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indexedClasses[1] = DerivedUnit.class;
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indexedClasses[5] = DnaSample.class;
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}
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@Override
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public int countDerivationEvents(SpecimenOrObservationBase occurence) {
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checkNotInPriorView("OccurrenceDaoHibernateImpl.countDerivationEvents(SpecimenOrObservationBase occurence)");
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Query query = getSession().createQuery("select count(distinct derivationEvent) from DerivationEvent derivationEvent join derivationEvent.originals occurence where occurence = :occurence");
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query.setParameter("occurence", occurence);
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return ((Long)query.uniqueResult()).intValue();
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}
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@Override
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public int countDeterminations(SpecimenOrObservationBase occurrence, TaxonBase taxonBase) {
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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(DeterminationEvent.class);
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if(occurrence != null) {
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criteria.add(Restrictions.eq("identifiedUnit",occurrence));
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}
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if(taxonBase != null) {
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criteria.add(Restrictions.eq("taxon",taxonBase));
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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(DeterminationEvent.class,auditEvent.getRevisionNumber());
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if(occurrence != null) {
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query.add(AuditEntity.relatedId("identifiedUnit").eq(occurrence.getId()));
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}
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if(taxonBase != null) {
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query.add(AuditEntity.relatedId("taxon").eq(taxonBase.getId()));
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}
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3dd6c00e
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Andreas Müller
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query.addProjection(AuditEntity.id().count());
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eeef091f
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Patrick Plitzner
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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 countMedia(SpecimenOrObservationBase occurence) {
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checkNotInPriorView("OccurrenceDaoHibernateImpl.countMedia(SpecimenOrObservationBase occurence)");
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Query query = getSession().createQuery("select count(media) from SpecimenOrObservationBase occurence join occurence.media media where occurence = :occurence");
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query.setParameter("occurence", occurence);
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return ((Long)query.uniqueResult()).intValue();
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}
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@Override
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public List<DerivationEvent> getDerivationEvents(SpecimenOrObservationBase occurence, Integer pageSize,Integer pageNumber, List<String> propertyPaths) {
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checkNotInPriorView("OccurrenceDaoHibernateImpl.getDerivationEvents(SpecimenOrObservationBase occurence, Integer pageSize,Integer pageNumber)");
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Query query = getSession().createQuery("select distinct derivationEvent from DerivationEvent derivationEvent join derivationEvent.originals occurence where occurence = :occurence");
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query.setParameter("occurence", occurence);
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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<DerivationEvent> result = query.list();
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defaultBeanInitializer.initializeAll(result, propertyPaths);
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return result;
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}
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@Override
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public List<DeterminationEvent> getDeterminations(SpecimenOrObservationBase occurrence, TaxonBase taxonBase, Integer pageSize, Integer pageNumber, 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(DeterminationEvent.class);
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if(occurrence != null) {
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criteria.add(Restrictions.eq("identifiedUnit",occurrence));
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}
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if(taxonBase != null) {
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criteria.add(Restrictions.eq("taxon",taxonBase));
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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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List<DeterminationEvent> result = criteria.list();
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defaultBeanInitializer.initializeAll(result, propertyPaths);
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return result;
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} else {
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AuditQuery query = getAuditReader().createQuery().forEntitiesAtRevision(DeterminationEvent.class,auditEvent.getRevisionNumber());
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if(occurrence != null) {
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query.add(AuditEntity.relatedId("identifiedUnit").eq(occurrence.getId()));
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}
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if(taxonBase != null) {
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query.add(AuditEntity.relatedId("taxon").eq(taxonBase.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<DeterminationEvent> result = query.getResultList();
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defaultBeanInitializer.initializeAll(result, propertyPaths);
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return result;
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}
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}
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@Override
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public List<Media> getMedia(SpecimenOrObservationBase occurence, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
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checkNotInPriorView("OccurrenceDaoHibernateImpl.getMedia(SpecimenOrObservationBase occurence, Integer pageSize, Integer pageNumber, List<String> propertyPaths)");
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Query query = getSession().createQuery("select media from SpecimenOrObservationBase occurence join occurence.media media where occurence = :occurence");
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query.setParameter("occurence", occurence);
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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<Media> results = query.list();
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defaultBeanInitializer.initializeAll(results, propertyPaths);
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return results;
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}
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@Override
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public void rebuildIndex() {
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FullTextSession fullTextSession = Search.getFullTextSession(getSession());
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e4d66102
|
Andreas Müller
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for(SpecimenOrObservationBase<?> occurrence : list(null,null)) { // re-index all taxon base
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eeef091f
|
Patrick Plitzner
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e4d66102
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Andreas Müller
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for(DeterminationEvent determination : occurrence.getDeterminations()) {
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eeef091f
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Patrick Plitzner
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Hibernate.initialize(determination.getActor());
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Hibernate.initialize(determination.getTaxon());
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}
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Hibernate.initialize(occurrence.getDefinition());
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if(occurrence instanceof DerivedUnit) {
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DerivedUnit derivedUnit = (DerivedUnit) occurrence;
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Hibernate.initialize(derivedUnit.getCollection());
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if(derivedUnit.getCollection() != null) {
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Hibernate.initialize(derivedUnit.getCollection().getSuperCollection());
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Hibernate.initialize(derivedUnit.getCollection().getInstitute());
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}
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Hibernate.initialize(derivedUnit.getStoredUnder());
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e4d66102
|
Andreas Müller
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SpecimenOrObservationBase<?> original = derivedUnit.getOriginalUnit();
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eeef091f
|
Patrick Plitzner
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if(original != null && original.isInstanceOf(FieldUnit.class)) {
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e4d66102
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Andreas Müller
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FieldUnit fieldUnit = CdmBase.deproxy(original, FieldUnit.class);
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eeef091f
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Patrick Plitzner
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Hibernate.initialize(fieldUnit.getGatheringEvent());
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if(fieldUnit.getGatheringEvent() != null) {
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Hibernate.initialize(fieldUnit.getGatheringEvent().getActor());
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}
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}
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}
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fullTextSession.index(occurrence);
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}
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fullTextSession.flushToIndexes();
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}
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e6e5ebdc
|
Patrick Plitzner
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@Override
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9dc896c9
|
Andreas Müller
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public int count(Class<? extends SpecimenOrObservationBase> clazz, TaxonName determinedAs) {
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e6e5ebdc
|
Patrick Plitzner
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Criteria criteria = null;
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if(clazz == null) {
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criteria = getSession().createCriteria(type);
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} else {
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criteria = getSession().createCriteria(clazz);
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}
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criteria.createCriteria("determinations").add(Restrictions.eq("taxonName", determinedAs));
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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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271 |
9dc896c9
|
Andreas Müller
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public List<SpecimenOrObservationBase> list(Class<? extends SpecimenOrObservationBase> clazz, TaxonName determinedAs, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
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272 |
e6e5ebdc
|
Patrick Plitzner
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Criteria criteria = null;
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if(clazz == null) {
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criteria = getSession().createCriteria(type);
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} else {
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criteria = getSession().createCriteria(clazz);
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}
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criteria.createCriteria("determinations").add(Restrictions.eq("taxonName", determinedAs));
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if(limit != null) {
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if(start != null) {
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criteria.setFirstResult(start);
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} else {
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criteria.setFirstResult(0);
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}
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criteria.setMaxResults(limit);
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}
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addOrder(criteria,orderHints);
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e4d66102
|
Andreas Müller
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@SuppressWarnings("unchecked")
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293 |
e6e5ebdc
|
Patrick Plitzner
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List<SpecimenOrObservationBase> results = criteria.list();
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defaultBeanInitializer.initializeAll(results, propertyPaths);
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return results;
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}
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eeef091f
|
Patrick Plitzner
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@Override
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public int count(Class<? extends SpecimenOrObservationBase> clazz, TaxonBase determinedAs) {
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Criteria criteria = null;
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if(clazz == null) {
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criteria = getSession().createCriteria(type);
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} else {
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criteria = getSession().createCriteria(clazz);
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}
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criteria.createCriteria("determinations").add(Restrictions.eq("taxon", determinedAs));
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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 List<SpecimenOrObservationBase> list(Class<? extends SpecimenOrObservationBase> clazz, TaxonBase determinedAs, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
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Criteria criteria = null;
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if(clazz == null) {
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criteria = getSession().createCriteria(type);
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} else {
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|
|
criteria = getSession().createCriteria(clazz);
|
320 |
|
|
}
|
321 |
|
|
|
322 |
|
|
criteria.createCriteria("determinations").add(Restrictions.eq("taxon", determinedAs));
|
323 |
|
|
|
324 |
|
|
if(limit != null) {
|
325 |
|
|
if(start != null) {
|
326 |
|
|
criteria.setFirstResult(start);
|
327 |
|
|
} else {
|
328 |
|
|
criteria.setFirstResult(0);
|
329 |
|
|
}
|
330 |
|
|
criteria.setMaxResults(limit);
|
331 |
|
|
}
|
332 |
|
|
|
333 |
|
|
addOrder(criteria,orderHints);
|
334 |
|
|
|
335 |
e4d66102
|
Andreas Müller
|
@SuppressWarnings("unchecked")
|
336 |
eeef091f
|
Patrick Plitzner
|
List<SpecimenOrObservationBase> results = criteria.list();
|
337 |
|
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
338 |
|
|
return results;
|
339 |
|
|
}
|
340 |
|
|
|
341 |
|
|
@Override
|
342 |
|
|
public <T extends SpecimenOrObservationBase> List<T> findOccurrences(Class<T> clazz, String queryString,
|
343 |
9dc896c9
|
Andreas Müller
|
String significantIdentifier, SpecimenOrObservationType recordBasis, Taxon associatedTaxon, TaxonName associatedTaxonName,
|
344 |
eeef091f
|
Patrick Plitzner
|
MatchMode matchmode, Integer limit,
|
345 |
|
|
Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
|
346 |
|
|
|
347 |
|
|
Criteria criteria = createFindOccurrenceCriteria(clazz, queryString, significantIdentifier, recordBasis,
|
348 |
e6e5ebdc
|
Patrick Plitzner
|
associatedTaxon, associatedTaxonName, matchmode, limit, start, orderHints, propertyPaths);
|
349 |
eeef091f
|
Patrick Plitzner
|
|
350 |
|
|
if(criteria!=null){
|
351 |
|
|
|
352 |
|
|
if(limit != null) {
|
353 |
|
|
if(start != null) {
|
354 |
|
|
criteria.setFirstResult(start);
|
355 |
|
|
} else {
|
356 |
|
|
criteria.setFirstResult(0);
|
357 |
|
|
}
|
358 |
|
|
criteria.setMaxResults(limit);
|
359 |
|
|
}
|
360 |
|
|
|
361 |
|
|
if(orderHints!=null){
|
362 |
|
|
addOrder(criteria,orderHints);
|
363 |
|
|
}
|
364 |
|
|
|
365 |
e4d66102
|
Andreas Müller
|
@SuppressWarnings("unchecked")
|
366 |
eeef091f
|
Patrick Plitzner
|
List<T> results = criteria.list();
|
367 |
|
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
368 |
|
|
return results;
|
369 |
|
|
}
|
370 |
e4d66102
|
Andreas Müller
|
return Collections.emptyList();
|
371 |
eeef091f
|
Patrick Plitzner
|
}
|
372 |
|
|
|
373 |
|
|
private <T extends SpecimenOrObservationBase> Criteria createFindOccurrenceCriteria(Class<T> clazz, String queryString,
|
374 |
9dc896c9
|
Andreas Müller
|
String significantIdentifier, SpecimenOrObservationType recordBasis, Taxon associatedTaxon, TaxonName associatedTaxonName, MatchMode matchmode, Integer limit,
|
375 |
eeef091f
|
Patrick Plitzner
|
Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
|
376 |
|
|
Criteria criteria = null;
|
377 |
|
|
|
378 |
|
|
if(clazz == null) {
|
379 |
|
|
criteria = getSession().createCriteria(type);
|
380 |
|
|
} else {
|
381 |
|
|
criteria = getSession().createCriteria(clazz);
|
382 |
|
|
}
|
383 |
|
|
|
384 |
|
|
//queryString
|
385 |
|
|
if (queryString != null) {
|
386 |
|
|
if(matchmode == null) {
|
387 |
|
|
matchmode = MatchMode.ANYWHERE;
|
388 |
|
|
criteria.add(Restrictions.ilike("titleCache", matchmode.queryStringFrom(queryString)));
|
389 |
|
|
} else if(matchmode == MatchMode.BEGINNING) {
|
390 |
|
|
criteria.add(Restrictions.ilike("titleCache", matchmode.queryStringFrom(queryString), org.hibernate.criterion.MatchMode.START));
|
391 |
|
|
} else if(matchmode == MatchMode.END) {
|
392 |
|
|
criteria.add(Restrictions.ilike("titleCache", matchmode.queryStringFrom(queryString), org.hibernate.criterion.MatchMode.END));
|
393 |
|
|
} else if(matchmode == MatchMode.EXACT) {
|
394 |
|
|
criteria.add(Restrictions.ilike("titleCache", matchmode.queryStringFrom(queryString), org.hibernate.criterion.MatchMode.EXACT));
|
395 |
|
|
} else {
|
396 |
|
|
criteria.add(Restrictions.ilike("titleCache", matchmode.queryStringFrom(queryString), org.hibernate.criterion.MatchMode.ANYWHERE));
|
397 |
|
|
}
|
398 |
|
|
}
|
399 |
|
|
|
400 |
|
|
//significant identifier
|
401 |
|
|
if (significantIdentifier != null) {
|
402 |
|
|
criteria.add(Restrictions.or(Restrictions.ilike("accessionNumber", significantIdentifier),
|
403 |
|
|
Restrictions.ilike("catalogNumber", significantIdentifier), Restrictions.ilike("barcode", significantIdentifier)));
|
404 |
|
|
}
|
405 |
|
|
|
406 |
|
|
//recordBasis/SpecimenOrObservationType
|
407 |
df85b8bf
|
Patrick Plitzner
|
Set<SpecimenOrObservationType> typeAndSubtypes = new HashSet<SpecimenOrObservationType>();
|
408 |
|
|
if(recordBasis==null){
|
409 |
|
|
//add all types
|
410 |
|
|
SpecimenOrObservationType[] values = SpecimenOrObservationType.values();
|
411 |
|
|
for (SpecimenOrObservationType specimenOrObservationType : values) {
|
412 |
|
|
typeAndSubtypes.add(specimenOrObservationType);
|
413 |
|
|
}
|
414 |
|
|
}
|
415 |
|
|
else{
|
416 |
|
|
typeAndSubtypes = recordBasis.getGeneralizationOf(true);
|
417 |
eeef091f
|
Patrick Plitzner
|
typeAndSubtypes.add(recordBasis);
|
418 |
|
|
}
|
419 |
df85b8bf
|
Patrick Plitzner
|
criteria.add(Restrictions.in("recordBasis", typeAndSubtypes));
|
420 |
eeef091f
|
Patrick Plitzner
|
|
421 |
cc1e6737
|
Patrick Plitzner
|
Set<UUID> associationUuids = new HashSet<UUID>();
|
422 |
eeef091f
|
Patrick Plitzner
|
//taxon associations
|
423 |
|
|
if(associatedTaxon!=null){
|
424 |
df85b8bf
|
Patrick Plitzner
|
List<? extends SpecimenOrObservationBase> associatedTaxaList = listByAssociatedTaxon(clazz, associatedTaxon, limit, start, orderHints, propertyPaths);
|
425 |
eeef091f
|
Patrick Plitzner
|
if(associatedTaxaList!=null){
|
426 |
|
|
for (SpecimenOrObservationBase specimenOrObservationBase : associatedTaxaList) {
|
427 |
cc1e6737
|
Patrick Plitzner
|
associationUuids.add(specimenOrObservationBase.getUuid());
|
428 |
eeef091f
|
Patrick Plitzner
|
}
|
429 |
|
|
}
|
430 |
|
|
}
|
431 |
e6e5ebdc
|
Patrick Plitzner
|
//taxon name associations
|
432 |
cc1e6737
|
Patrick Plitzner
|
else if(associatedTaxonName!=null){
|
433 |
e6e5ebdc
|
Patrick Plitzner
|
List<? extends SpecimenOrObservationBase> associatedTaxaList = listByAssociatedTaxonName(clazz, associatedTaxonName, limit, start, orderHints, propertyPaths);
|
434 |
|
|
if(associatedTaxaList!=null){
|
435 |
|
|
for (SpecimenOrObservationBase specimenOrObservationBase : associatedTaxaList) {
|
436 |
cc1e6737
|
Patrick Plitzner
|
associationUuids.add(specimenOrObservationBase.getUuid());
|
437 |
e6e5ebdc
|
Patrick Plitzner
|
}
|
438 |
|
|
}
|
439 |
42f8ab76
|
Patrick Plitzner
|
}
|
440 |
cc1e6737
|
Patrick Plitzner
|
if(associatedTaxon!=null || associatedTaxonName!=null){
|
441 |
|
|
if(!associationUuids.isEmpty()){
|
442 |
|
|
criteria.add(Restrictions.in("uuid", associationUuids));
|
443 |
|
|
}
|
444 |
|
|
else{
|
445 |
|
|
return null;
|
446 |
|
|
}
|
447 |
e6e5ebdc
|
Patrick Plitzner
|
}
|
448 |
|
|
|
449 |
eeef091f
|
Patrick Plitzner
|
return criteria;
|
450 |
|
|
}
|
451 |
|
|
|
452 |
|
|
|
453 |
|
|
@Override
|
454 |
|
|
public <T extends SpecimenOrObservationBase> int countOccurrences(Class<T> clazz, String queryString,
|
455 |
9dc896c9
|
Andreas Müller
|
String significantIdentifier, SpecimenOrObservationType recordBasis, Taxon associatedTaxon, TaxonName associatedTaxonName,
|
456 |
eeef091f
|
Patrick Plitzner
|
MatchMode matchmode, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
|
457 |
|
|
Criteria criteria = createFindOccurrenceCriteria(clazz, queryString, significantIdentifier, recordBasis,
|
458 |
e6e5ebdc
|
Patrick Plitzner
|
associatedTaxon, associatedTaxonName, matchmode, limit, start, orderHints, propertyPaths);
|
459 |
eeef091f
|
Patrick Plitzner
|
|
460 |
|
|
if(criteria!=null){
|
461 |
|
|
|
462 |
|
|
criteria.setProjection(Projections.rowCount());
|
463 |
|
|
|
464 |
|
|
return ((Number)criteria.uniqueResult()).intValue();
|
465 |
|
|
}
|
466 |
|
|
return 0;
|
467 |
|
|
}
|
468 |
|
|
|
469 |
|
|
@Override
|
470 |
|
|
public List<UuidAndTitleCache<DerivedUnit>> getDerivedUnitUuidAndTitleCache() {
|
471 |
|
|
List<UuidAndTitleCache<DerivedUnit>> list = new ArrayList<UuidAndTitleCache<DerivedUnit>>();
|
472 |
|
|
Session session = getSession();
|
473 |
|
|
|
474 |
|
|
Query query = session.createQuery("select uuid, id, titleCache from " + type.getSimpleName() + " where NOT dtype = " + FieldUnit.class.getSimpleName());
|
475 |
|
|
|
476 |
|
|
List<Object[]> result = query.list();
|
477 |
|
|
|
478 |
|
|
for(Object[] object : result){
|
479 |
|
|
list.add(new UuidAndTitleCache<DerivedUnit>(DerivedUnit.class, (UUID) object[0], (Integer)object[1], (String) object[2]));
|
480 |
|
|
}
|
481 |
|
|
|
482 |
|
|
return list;
|
483 |
|
|
}
|
484 |
|
|
|
485 |
|
|
@Override
|
486 |
|
|
public List<UuidAndTitleCache<FieldUnit>> getFieldUnitUuidAndTitleCache() {
|
487 |
|
|
List<UuidAndTitleCache<FieldUnit>> list = new ArrayList<UuidAndTitleCache<FieldUnit>>();
|
488 |
|
|
Session session = getSession();
|
489 |
|
|
|
490 |
|
|
Query query = session.createQuery("select uuid, id, titleCache from " + type.getSimpleName() + " where dtype = " + FieldUnit.class.getSimpleName());
|
491 |
|
|
|
492 |
|
|
List<Object[]> result = query.list();
|
493 |
|
|
|
494 |
|
|
for(Object[] object : result){
|
495 |
|
|
list.add(new UuidAndTitleCache<FieldUnit>(FieldUnit.class, (UUID) object[0], (Integer)object[1], (String) object[2]));
|
496 |
|
|
}
|
497 |
|
|
|
498 |
|
|
return list;
|
499 |
|
|
}
|
500 |
|
|
|
501 |
e6e5ebdc
|
Patrick Plitzner
|
@Override
|
502 |
|
|
public <T extends SpecimenOrObservationBase> List<T> listByAssociatedTaxonName(Class<T> type,
|
503 |
9dc896c9
|
Andreas Müller
|
TaxonName associatedTaxonName, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
|
504 |
e6e5ebdc
|
Patrick Plitzner
|
Set<SpecimenOrObservationBase> setOfAll = new HashSet<SpecimenOrObservationBase>();
|
505 |
|
|
|
506 |
|
|
// A Taxon name may be referenced by the DeterminationEvent of the SpecimenOrObservationBase
|
507 |
|
|
List<SpecimenOrObservationBase> byDetermination = list(type, associatedTaxonName, null, 0, null, null);
|
508 |
|
|
setOfAll.addAll(byDetermination);
|
509 |
|
|
|
510 |
|
|
if(setOfAll.size() == 0){
|
511 |
|
|
// no need querying the data base
|
512 |
|
|
return new ArrayList<T>();
|
513 |
|
|
}
|
514 |
|
|
|
515 |
|
|
String queryString =
|
516 |
|
|
"select sob " +
|
517 |
|
|
" from SpecimenOrObservationBase sob" +
|
518 |
|
|
" where sob in (:setOfAll)";
|
519 |
|
|
|
520 |
fd8e61f7
|
Patrick Plitzner
|
if(type != null && !type.equals(SpecimenOrObservationBase.class)){
|
521 |
e6e5ebdc
|
Patrick Plitzner
|
queryString += " and sob.class = :type";
|
522 |
|
|
}
|
523 |
|
|
|
524 |
|
|
if(orderHints != null && orderHints.size() > 0){
|
525 |
|
|
queryString += " order by ";
|
526 |
|
|
String orderStr = "";
|
527 |
|
|
for(OrderHint orderHint : orderHints){
|
528 |
|
|
if(orderStr.length() > 0){
|
529 |
|
|
orderStr += ", ";
|
530 |
|
|
}
|
531 |
|
|
queryString += "sob." + orderHint.getPropertyName() + " " + orderHint.getSortOrder().toHql();
|
532 |
|
|
}
|
533 |
|
|
queryString += orderStr;
|
534 |
|
|
}
|
535 |
|
|
|
536 |
|
|
Query query = getSession().createQuery(queryString);
|
537 |
|
|
query.setParameterList("setOfAll", setOfAll);
|
538 |
|
|
|
539 |
fd8e61f7
|
Patrick Plitzner
|
if(type != null && !type.equals(SpecimenOrObservationBase.class)){
|
540 |
e6e5ebdc
|
Patrick Plitzner
|
query.setParameter("type", type.getSimpleName());
|
541 |
|
|
}
|
542 |
|
|
|
543 |
|
|
if(limit != null) {
|
544 |
|
|
if(start != null) {
|
545 |
|
|
query.setFirstResult(start);
|
546 |
|
|
} else {
|
547 |
|
|
query.setFirstResult(0);
|
548 |
|
|
}
|
549 |
|
|
query.setMaxResults(limit);
|
550 |
|
|
}
|
551 |
|
|
|
552 |
|
|
|
553 |
|
|
List<T> results = query.list();
|
554 |
|
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
555 |
|
|
return results;
|
556 |
|
|
}
|
557 |
cc1e6737
|
Patrick Plitzner
|
|
558 |
eeef091f
|
Patrick Plitzner
|
@Override
|
559 |
|
|
public <T extends SpecimenOrObservationBase> List<T> listByAssociatedTaxon(Class<T> type,
|
560 |
|
|
Taxon associatedTaxon, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
|
561 |
|
|
|
562 |
|
|
Set<SpecimenOrObservationBase> setOfAll = new HashSet<SpecimenOrObservationBase>();
|
563 |
|
|
|
564 |
|
|
// A Taxon may be referenced by the DeterminationEvent of the SpecimenOrObservationBase
|
565 |
|
|
List<SpecimenOrObservationBase> byDetermination = list(type, associatedTaxon, null, 0, null, null);
|
566 |
|
|
setOfAll.addAll(byDetermination);
|
567 |
cc1e6737
|
Patrick Plitzner
|
//check also for synonyms
|
568 |
|
|
for (Synonym synonym : associatedTaxon.getSynonyms()) {
|
569 |
|
|
setOfAll.addAll(list(type, synonym, null, 0, null, null));
|
570 |
|
|
}
|
571 |
|
|
//check also for name determinations
|
572 |
|
|
setOfAll.addAll(list(type, associatedTaxon.getName(), null, 0, null, null));
|
573 |
9dc896c9
|
Andreas Müller
|
for (TaxonName synonymName : associatedTaxon.getSynonymNames()) {
|
574 |
cc1e6737
|
Patrick Plitzner
|
setOfAll.addAll(list(type, synonymName, null, 0, null, null));
|
575 |
|
|
}
|
576 |
|
|
|
577 |
eeef091f
|
Patrick Plitzner
|
|
578 |
|
|
// The IndividualsAssociation elements in a TaxonDescription contain DerivedUnits
|
579 |
|
|
List<IndividualsAssociation> byIndividualsAssociation = descriptionDao.getDescriptionElementForTaxon(
|
580 |
|
|
associatedTaxon.getUuid(), null, IndividualsAssociation.class, null, 0, null);
|
581 |
|
|
for(IndividualsAssociation individualsAssociation : byIndividualsAssociation){
|
582 |
|
|
setOfAll.add(individualsAssociation.getAssociatedSpecimenOrObservation());
|
583 |
|
|
}
|
584 |
|
|
|
585 |
|
|
// SpecimenTypeDesignations may be associated with the TaxonName.
|
586 |
|
|
List<SpecimenTypeDesignation> bySpecimenTypeDesignation = taxonNameDao.getTypeDesignations(associatedTaxon.getName(),
|
587 |
|
|
SpecimenTypeDesignation.class, null, null, 0, null);
|
588 |
|
|
for (SpecimenTypeDesignation specimenTypeDesignation : bySpecimenTypeDesignation) {
|
589 |
|
|
setOfAll.add(specimenTypeDesignation.getTypeSpecimen());
|
590 |
|
|
}
|
591 |
|
|
|
592 |
|
|
// SpecimenTypeDesignations may be associated with any HomotypicalGroup related to the specific Taxon.
|
593 |
|
|
for(HomotypicalGroup homotypicalGroup : associatedTaxon.getHomotypicSynonymyGroups()) {
|
594 |
|
|
List<SpecimenTypeDesignation> byHomotypicalGroup = homotypicalGroupDao.getTypeDesignations(homotypicalGroup, SpecimenTypeDesignation.class, null, null, 0, null);
|
595 |
|
|
for (SpecimenTypeDesignation specimenTypeDesignation : byHomotypicalGroup) {
|
596 |
|
|
setOfAll.add(specimenTypeDesignation.getTypeSpecimen());
|
597 |
|
|
}
|
598 |
|
|
}
|
599 |
|
|
|
600 |
|
|
if(setOfAll.size() == 0){
|
601 |
|
|
// no need querying the data base
|
602 |
|
|
return new ArrayList<T>();
|
603 |
|
|
}
|
604 |
|
|
|
605 |
|
|
String queryString =
|
606 |
|
|
"select sob " +
|
607 |
|
|
" from SpecimenOrObservationBase sob" +
|
608 |
|
|
" where sob in (:setOfAll)";
|
609 |
|
|
|
610 |
fd8e61f7
|
Patrick Plitzner
|
if(type != null && !type.equals(SpecimenOrObservationBase.class)){
|
611 |
eeef091f
|
Patrick Plitzner
|
queryString += " and sob.class = :type";
|
612 |
|
|
}
|
613 |
|
|
|
614 |
|
|
if(orderHints != null && orderHints.size() > 0){
|
615 |
|
|
queryString += " order by ";
|
616 |
|
|
String orderStr = "";
|
617 |
|
|
for(OrderHint orderHint : orderHints){
|
618 |
|
|
if(orderStr.length() > 0){
|
619 |
|
|
orderStr += ", ";
|
620 |
|
|
}
|
621 |
|
|
queryString += "sob." + orderHint.getPropertyName() + " " + orderHint.getSortOrder().toHql();
|
622 |
|
|
}
|
623 |
|
|
queryString += orderStr;
|
624 |
|
|
}
|
625 |
|
|
|
626 |
|
|
Query query = getSession().createQuery(queryString);
|
627 |
|
|
query.setParameterList("setOfAll", setOfAll);
|
628 |
|
|
|
629 |
fd8e61f7
|
Patrick Plitzner
|
if(type != null && !type.equals(SpecimenOrObservationBase.class)){
|
630 |
eeef091f
|
Patrick Plitzner
|
query.setParameter("type", type.getSimpleName());
|
631 |
|
|
}
|
632 |
|
|
|
633 |
|
|
if(limit != null) {
|
634 |
|
|
if(start != null) {
|
635 |
|
|
query.setFirstResult(start);
|
636 |
|
|
} else {
|
637 |
|
|
query.setFirstResult(0);
|
638 |
|
|
}
|
639 |
|
|
query.setMaxResults(limit);
|
640 |
|
|
}
|
641 |
|
|
|
642 |
|
|
|
643 |
|
|
List<T> results = query.list();
|
644 |
|
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
645 |
|
|
return results;
|
646 |
|
|
}
|
647 |
|
|
|
648 |
|
|
@Override
|
649 |
|
|
public Collection<SpecimenOrObservationBase> listBySpecimenOrObservationType(SpecimenOrObservationType type, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
|
650 |
|
|
String queryString = "FROM SpecimenOrObservationBase specimens WHERE specimens.recordBasis = :type";
|
651 |
|
|
|
652 |
|
|
if(orderHints != null && orderHints.size() > 0){
|
653 |
|
|
queryString += " order by ";
|
654 |
|
|
String orderStr = "";
|
655 |
|
|
for(OrderHint orderHint : orderHints){
|
656 |
|
|
if(orderStr.length() > 0){
|
657 |
|
|
orderStr += ", ";
|
658 |
|
|
}
|
659 |
|
|
queryString += "specimens." + orderHint.getPropertyName() + " " + orderHint.getSortOrder().toHql();
|
660 |
|
|
}
|
661 |
|
|
queryString += orderStr;
|
662 |
|
|
}
|
663 |
|
|
|
664 |
|
|
Query query = getSession().createQuery(queryString);
|
665 |
|
|
query.setParameter("type", type);
|
666 |
|
|
|
667 |
|
|
if(limit != null) {
|
668 |
|
|
if(start != null) {
|
669 |
|
|
query.setFirstResult(start);
|
670 |
|
|
} else {
|
671 |
|
|
query.setFirstResult(0);
|
672 |
|
|
}
|
673 |
|
|
query.setMaxResults(limit);
|
674 |
|
|
}
|
675 |
|
|
|
676 |
|
|
List results = query.list();
|
677 |
|
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
678 |
|
|
return results;
|
679 |
|
|
}
|
680 |
|
|
|
681 |
550eeb6f
|
Patrick Plitzner
|
@Override
|
682 |
|
|
public Collection<DeterminationEvent> listDeterminationEvents(SpecimenOrObservationBase<?> specimen, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
|
683 |
|
|
String queryString = "FROM DeterminationEvent determination WHERE determination.identifiedUnit = :specimen";
|
684 |
|
|
|
685 |
|
|
if(orderHints != null && orderHints.size() > 0){
|
686 |
|
|
queryString += " order by ";
|
687 |
|
|
String orderStr = "";
|
688 |
|
|
for(OrderHint orderHint : orderHints){
|
689 |
|
|
if(orderStr.length() > 0){
|
690 |
|
|
orderStr += ", ";
|
691 |
|
|
}
|
692 |
|
|
queryString += "determination." + orderHint.getPropertyName() + " " + orderHint.getSortOrder().toHql();
|
693 |
|
|
}
|
694 |
|
|
queryString += orderStr;
|
695 |
|
|
}
|
696 |
|
|
|
697 |
|
|
Query query = getSession().createQuery(queryString);
|
698 |
|
|
query.setParameter("specimen", specimen);
|
699 |
|
|
|
700 |
|
|
if(limit != null) {
|
701 |
|
|
if(start != null) {
|
702 |
|
|
query.setFirstResult(start);
|
703 |
|
|
} else {
|
704 |
|
|
query.setFirstResult(0);
|
705 |
|
|
}
|
706 |
|
|
query.setMaxResults(limit);
|
707 |
|
|
}
|
708 |
|
|
|
709 |
|
|
List results = query.list();
|
710 |
|
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
711 |
|
|
return results;
|
712 |
|
|
}
|
713 |
|
|
|
714 |
eeef091f
|
Patrick Plitzner
|
@Override
|
715 |
|
|
public Collection<SpecimenTypeDesignation> listTypeDesignations(SpecimenOrObservationBase<?> specimen, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
|
716 |
|
|
String queryString = "FROM SpecimenTypeDesignation designations WHERE designations.typeSpecimen = :specimen";
|
717 |
|
|
|
718 |
|
|
if(orderHints != null && orderHints.size() > 0){
|
719 |
|
|
queryString += " order by ";
|
720 |
|
|
String orderStr = "";
|
721 |
|
|
for(OrderHint orderHint : orderHints){
|
722 |
|
|
if(orderStr.length() > 0){
|
723 |
|
|
orderStr += ", ";
|
724 |
|
|
}
|
725 |
|
|
queryString += "designations." + orderHint.getPropertyName() + " " + orderHint.getSortOrder().toHql();
|
726 |
|
|
}
|
727 |
|
|
queryString += orderStr;
|
728 |
|
|
}
|
729 |
|
|
|
730 |
|
|
Query query = getSession().createQuery(queryString);
|
731 |
|
|
query.setParameter("specimen", specimen);
|
732 |
|
|
|
733 |
|
|
if(limit != null) {
|
734 |
|
|
if(start != null) {
|
735 |
|
|
query.setFirstResult(start);
|
736 |
|
|
} else {
|
737 |
|
|
query.setFirstResult(0);
|
738 |
|
|
}
|
739 |
|
|
query.setMaxResults(limit);
|
740 |
|
|
}
|
741 |
|
|
|
742 |
|
|
List results = query.list();
|
743 |
|
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
744 |
|
|
return results;
|
745 |
|
|
}
|
746 |
|
|
|
747 |
|
|
@Override
|
748 |
|
|
public Collection<IndividualsAssociation> listIndividualsAssociations(SpecimenOrObservationBase<?> specimen, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
|
749 |
|
|
//DISTINCT is necessary if more than one description exists for a taxon because we create the cross product of all taxon descriptions and description elements
|
750 |
|
|
String queryString = "FROM IndividualsAssociation associations WHERE associations.associatedSpecimenOrObservation = :specimen";
|
751 |
|
|
|
752 |
|
|
if(orderHints != null && orderHints.size() > 0){
|
753 |
|
|
queryString += " order by ";
|
754 |
|
|
String orderStr = "";
|
755 |
|
|
for(OrderHint orderHint : orderHints){
|
756 |
|
|
if(orderStr.length() > 0){
|
757 |
|
|
orderStr += ", ";
|
758 |
|
|
}
|
759 |
|
|
queryString += "associations." + orderHint.getPropertyName() + " " + orderHint.getSortOrder().toHql();
|
760 |
|
|
}
|
761 |
|
|
queryString += orderStr;
|
762 |
|
|
}
|
763 |
|
|
|
764 |
|
|
Query query = getSession().createQuery(queryString);
|
765 |
|
|
query.setParameter("specimen", specimen);
|
766 |
|
|
|
767 |
|
|
if(limit != null) {
|
768 |
|
|
if(start != null) {
|
769 |
|
|
query.setFirstResult(start);
|
770 |
|
|
} else {
|
771 |
|
|
query.setFirstResult(0);
|
772 |
|
|
}
|
773 |
|
|
query.setMaxResults(limit);
|
774 |
|
|
}
|
775 |
|
|
|
776 |
|
|
List results = query.list();
|
777 |
|
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
778 |
|
|
return results;
|
779 |
|
|
}
|
780 |
|
|
|
781 |
|
|
@Override
|
782 |
|
|
public Collection<DescriptionBase<?>> listDescriptionsWithDescriptionSpecimen(SpecimenOrObservationBase<?> specimen, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {
|
783 |
|
|
//DISTINCT is necessary if more than one description exists for a taxon because we create the cross product of all taxon descriptions and description elements
|
784 |
|
|
String queryString = "FROM DescriptionBase descriptions WHERE descriptions.describedSpecimenOrObservation = :specimen";
|
785 |
|
|
|
786 |
|
|
if(orderHints != null && orderHints.size() > 0){
|
787 |
|
|
queryString += " order by ";
|
788 |
|
|
String orderStr = "";
|
789 |
|
|
for(OrderHint orderHint : orderHints){
|
790 |
|
|
if(orderStr.length() > 0){
|
791 |
|
|
orderStr += ", ";
|
792 |
|
|
}
|
793 |
|
|
queryString += "descriptions." + orderHint.getPropertyName() + " " + orderHint.getSortOrder().toHql();
|
794 |
|
|
}
|
795 |
|
|
queryString += orderStr;
|
796 |
|
|
}
|
797 |
|
|
|
798 |
|
|
Query query = getSession().createQuery(queryString);
|
799 |
|
|
query.setParameter("specimen", specimen);
|
800 |
|
|
|
801 |
|
|
if(limit != null) {
|
802 |
|
|
if(start != null) {
|
803 |
|
|
query.setFirstResult(start);
|
804 |
|
|
} else {
|
805 |
|
|
query.setFirstResult(0);
|
806 |
|
|
}
|
807 |
|
|
query.setMaxResults(limit);
|
808 |
|
|
}
|
809 |
|
|
|
810 |
|
|
List results = query.list();
|
811 |
|
|
defaultBeanInitializer.initializeAll(results, propertyPaths);
|
812 |
|
|
return results;
|
813 |
|
|
}
|
814 |
|
|
|
815 |
d45008d0
|
Andreas Kohlbecker
|
}
|